From be3910c2f3b3d986726fc72f5f70a1bb64123da8 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Wed, 23 Aug 2023 15:07:09 -0400 Subject: [PATCH 01/10] update deepmd input to v2; format JSON files Signed-off-by: Jinzhe Zeng --- .pre-commit-config.yaml | 2 +- doc/simplify/simplify.md | 5 +- dpgen/data/jsons/al.diamond.111.json | 56 +- dpgen/data/jsons/al.diamond.222.json | 56 +- dpgen/data/jsons/al.fcc.111.json | 56 +- dpgen/data/jsons/al.fcc.222.json | 56 +- dpgen/data/jsons/al.hcp.111.json | 56 +- dpgen/data/jsons/al.hcp.222.json | 56 +- dpgen/data/jsons/al.hcp.332.json | 56 +- dpgen/data/jsons/al.sc.222.json | 56 +- dpgen/data/jsons/almg.diamond.111.json | 59 +- dpgen/data/jsons/almg.diamond.222.json | 59 +- dpgen/data/jsons/almg.fcc.111.json | 59 +- dpgen/data/jsons/almg.fcc.222.json | 59 +- dpgen/data/jsons/almg.hcp.111.json | 59 +- dpgen/data/jsons/almg.hcp.222.json | 59 +- dpgen/data/jsons/almg.hcp.332.json | 59 +- dpgen/data/jsons/almg.sc.222.json | 59 +- dpgen/data/jsons/almg.sc.333.json | 59 +- dpgen/data/jsons/mg.diamond.111.json | 56 +- dpgen/data/jsons/mg.diamond.222.json | 56 +- dpgen/data/jsons/mg.fcc.111.json | 56 +- dpgen/data/jsons/mg.fcc.222.json | 56 +- dpgen/data/jsons/mg.hcp.111.json | 56 +- dpgen/data/jsons/mg.hcp.222.json | 52 +- dpgen/data/jsons/mg.hcp.332.json | 52 +- dpgen/data/jsons/mg.sc.222.json | 56 +- dpgen/data/jsons/param.json | 60 +- dpgen/data/jsons/si.diamond.111.json | 56 +- dpgen/data/jsons/si.diamond.222.json | 56 +- dpgen/data/jsons/si.fcc.111.json | 56 +- dpgen/data/jsons/si.fcc.222.json | 56 +- dpgen/data/jsons/si.hcp.111.json | 56 +- dpgen/data/jsons/si.hcp.222.json | 56 +- dpgen/data/jsons/si.sc.222.json | 56 +- dpgen/data/jsons/surf.al.fcc.json | 64 +- dpgen/data/jsons/surf.al.hcp.json | 64 +- dpgen/data/jsons/surf.almg.fcc.json | 67 +- dpgen/data/jsons/surf.almg.hcp.json | 67 +- dpgen/data/jsons/surf.mg.fcc.json | 64 +- dpgen/data/jsons/surf.mg.hcp.json | 64 +- dpgen/data/jsons/surf.si.diamond.json | 84 +- dpgen/data/jsons/w.bcc.111.json | 60 +- dpgen/data/jsons/w.bcc.222.json | 60 +- dpgen/data/jsons/w.diamond.111.json | 60 +- dpgen/data/jsons/w.fcc.111.json | 60 +- dpgen/data/jsons/w.hcp.111.json | 60 +- dpgen/data/jsons/water.111.json | 64 +- .../machine-ali-ehpc.json | 163 +- .../machine-dpcloudserver.json | 231 +- .../param_CH4_deepmd-kit-1.1.0.json | 1 - .../param_CH4_deepmd-kit-2.x.json | 1 + examples/database/param_Ti.json | 117 +- examples/init/abacus/CuW/CuW.json | 93 +- examples/init/abacus/fcc-Al-lcao/init.json | 63 +- examples/init/abacus/fcc-Al-pw/init.json | 59 +- examples/init/al.json | 62 +- examples/init/ch4.json | 53 +- examples/init/cu.surf.hcp.111.json | 19 +- examples/init/reaction.json | 36 +- examples/init/surf.json | 6 +- .../DeePMD-kit-1.0/machine-local-4GPU.json | 172 +- .../machine/DeePMD-kit-1.x/machine-local.json | 124 +- .../machine-lsf-slurm-cp2k.json | 188 +- .../DeePMD-kit-1.x/machine-pbs-gaussian.json | 170 +- .../DeePMD-kit-1.x/machine-slurm-qe.json | 216 +- .../DeePMD-kit-2.x/lebesgue_v2_machine.json | 189 +- examples/run/ch4/machine.json | 150 +- examples/run/ch4/param.json | 299 +- .../dp0.12-lammps-cp2k/CH4/param_CH4.json | 136 - .../dp0.12-lammps-pwmat/param_CH4.json | 97 - .../dp-lammps-siesta/CH4/param_CH4.json | 134 - .../Al/param_al_all_gpu.json | 393 - .../dp0.12-lammps-vasp/CH4/param_CH4.json | 98 - .../param.json | 87 +- .../dp2.x-lammps-cp2k/CH4/param_CH4.json | 156 + .../CH4/param_CH4.yaml | 1 - .../machine-slurm-pwmat-single.json | 6 +- .../dp2.x-lammps-pwmat/param_CH4.json | 147 + .../dp-lammps-siesta/CH4/param_CH4.json | 148 + .../dp-lammps-siesta/CH4/param_CH4.yaml | 1 - .../Al/param_al_all_gpu.json | 450 + .../Al/param_al_all_gpu.yaml | 1 - .../dp2.x-lammps-vasp/CH4/param_CH4.json | 146 + .../CH4/param_CH4.yaml | 1 - .../run/deprecated/param-h2oscan-vasp.json | 897 +- .../run/deprecated/param-mg-vasp-ucloud.json | 608 +- examples/run/deprecated/param-mg-vasp.json | 621 +- .../run/deprecated/param-pyridine-pwscf.json | 431 +- examples/run/dp-calypso-vasp/machine.json | 66 +- examples/run/dp-calypso-vasp/param.json | 519 +- .../run/dp-lammps-enhance_sampling/param.json | 283 +- .../methane/machine.json | 75 - .../methane/param.json | 150 - .../methane/machine.json | 75 - .../dp1.x-lammps-ABACUS-pw/methane/param.json | 144 - .../dp1.x-lammps-cp2k/methane/param-ch4.json | 134 - .../run/dp1.x-lammps-vasp-et/param_elet.json | 99 - .../Al/param_al_all_gpu-deepmd-kit-1.1.0.json | 371 - .../CH4/param_CH4_deepmd-kit-1.1.0.json | 137 - .../dodecane/dodecane.json | 84 - .../run/dp2.x-gromacs-gaussian/param.json | 212 +- .../methane/machine.json | 85 + .../methane/param.json | 171 + .../fcc-al/machine.json | 184 +- .../fcc-al/run_param.json | 253 +- .../fcc-al/machine.json | 184 +- .../fcc-al/run_param.json | 249 +- .../methane/machine.json | 85 + .../dp2.x-lammps-ABACUS-pw/methane/param.json | 162 + .../dp2.x-lammps-cp2k/methane/param-ch4.json | 138 + .../methane/template.inp | 0 .../param_CH4_deepmd-kit-2.0.1.json | 281 +- .../run/dp2.x-lammps-gaussian/machine.json | 196 +- .../param_C4H16N4_deepmd-kit-2.0.1.json | 278 +- .../run/dp2.x-lammps-vasp-et/param_elet.json | 131 + .../Al/param_al_all_gpu-deepmd-kit-1.1.0.json | 430 + .../CH4/INCAR_methane | 0 .../CH4/POT_C | 0 .../CH4/POT_H | 0 .../CH4/param_CH4_deepmd-kit-2.x.json | 137 + .../param_CH4_deepmd-kit-2.0.1.json | 257 +- .../dodecane/dodecane.json | 152 + examples/run/dprc/generator.json | 708 +- .../simplify_example/machine.json | 216 +- .../simplify_example/simplify.json | 191 +- examples/simplify/qm7.json | 201 +- examples/test/deepmd_param.json | 121 +- examples/test/meam_param.json | 145 +- examples/test/vasp_param.json | 31 +- examples/test/vasp_param_from_incar.json | 94 +- tests/auto_test/equi/abacus/cell-relax.json | 9552 +++---- tests/auto_test/equi/vasp/Al-fcc.json | 530 +- tests/auto_test/equi/vasp/outcar.json | 9332 +++---- .../output/gamma_00/task.000000/inter.json | 12 +- .../output/gamma_00/task.000000/miller.json | 6 +- .../gamma_00/task.000000/result_task.json | 21356 ++++++++-------- .../output/gamma_00/task.000000/task.json | 64 +- .../output/gamma_00/task.000001/inter.json | 12 +- .../output/gamma_00/task.000001/miller.json | 6 +- .../gamma_00/task.000001/result_task.json | 21356 ++++++++-------- .../output/gamma_00/task.000001/task.json | 64 +- .../output/gamma_00/task.000002/inter.json | 12 +- .../output/gamma_00/task.000002/miller.json | 6 +- .../gamma_00/task.000002/result_task.json | 21356 ++++++++-------- .../output/gamma_00/task.000002/task.json | 64 +- .../output/relaxation/relax_task/result.json | 744 +- tests/data/CuW.json | 81 +- tests/data/al.json | 49 +- tests/data/alloy.json | 48 +- tests/data/ch4.json | 70 +- tests/data/surf.json | 6 +- tests/data/surf_poscar.json | 15 +- tests/database/param_Al.json | 117 +- tests/generator/cluster/cluster1.json | 424 +- .../gromacs/model_devi_case/input.json | 10 +- tests/generator/machine-local-v1.json | 99 +- tests/generator/machine-local.json | 105 +- .../02.fp/task.000.000000/job.json | 4 +- .../02.fp/task.000.000001/job.json | 4 +- .../02.fp/task.001.000000/job.json | 4 +- .../02.fp/task.001.000001/job.json | 4 +- tests/generator/param-amber.json | 112 +- tests/generator/param-custom-fp.json | 422 +- tests/generator/param-methane-abacus-diy.json | 174 +- tests/generator/param-methane-abacus.json | 190 +- tests/generator/param-mg-vasp-diy.json | 216 +- .../generator/param-mg-vasp-multi-trust.json | 266 +- tests/generator/param-mg-vasp-old.json | 244 +- tests/generator/param-mg-vasp-v1-et.json | 224 +- tests/generator/param-mg-vasp-v1.json | 222 +- tests/generator/param-mg-vasp.json | 254 +- tests/generator/param-mg-vasp_merge_traj.json | 254 +- tests/generator/param-mgo-cp2k-exinput.json | 414 +- tests/generator/param-pyridine-cp2k.json | 461 +- tests/generator/param-pyridine-gaussian.json | 418 +- tests/generator/param-pyridine-pwmat.json | 425 +- tests/generator/param-pyridine-pwscf-old.json | 432 +- tests/generator/param-pyridine-pwscf.json | 458 +- tests/generator/param-pyridine-siesta.json | 428 +- tests/sample.json | 4 +- tests/tools/machine_fp_single.json | 14 +- tests/tools/machine_fp_single2.json | 25 +- tests/tools/run_report_test_output/param.json | 213 +- 184 files changed, 57060 insertions(+), 51438 deletions(-) delete mode 120000 examples/CH4-refact-dpdispatcher/param_CH4_deepmd-kit-1.1.0.json create mode 120000 examples/CH4-refact-dpdispatcher/param_CH4_deepmd-kit-2.x.json delete mode 100644 examples/run/deprecated/dp0.12-lammps-cp2k/CH4/param_CH4.json delete mode 100644 examples/run/deprecated/dp0.12-lammps-pwmat/param_CH4.json delete mode 100644 examples/run/deprecated/dp0.12-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.json delete mode 100644 examples/run/deprecated/dp0.12-lammps-vasp/Al/param_al_all_gpu.json delete mode 100644 examples/run/deprecated/dp0.12-lammps-vasp/CH4/param_CH4.json rename examples/run/deprecated/{dp1.x-gromacs-gaussian => dp2.x-gromacs-gaussian}/param.json (73%) create mode 100644 examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.json rename examples/run/deprecated/{dp0.12-lammps-cp2k => dp2.x-lammps-cp2k}/CH4/param_CH4.yaml (98%) rename examples/run/deprecated/{dp0.12-lammps-pwmat => dp2.x-lammps-pwmat}/machine-slurm-pwmat-single.json (95%) create mode 100644 examples/run/deprecated/dp2.x-lammps-pwmat/param_CH4.json create mode 100644 examples/run/deprecated/dp2.x-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.json rename examples/run/deprecated/{dp0.12-lammps-siesta => dp2.x-lammps-siesta}/dp-lammps-siesta/CH4/param_CH4.yaml (98%) create mode 100644 examples/run/deprecated/dp2.x-lammps-vasp/Al/param_al_all_gpu.json rename examples/run/deprecated/{dp0.12-lammps-vasp => dp2.x-lammps-vasp}/Al/param_al_all_gpu.yaml (99%) create mode 100644 examples/run/deprecated/dp2.x-lammps-vasp/CH4/param_CH4.json rename examples/run/deprecated/{dp0.12-lammps-vasp => dp2.x-lammps-vasp}/CH4/param_CH4.yaml (98%) delete mode 100644 examples/run/dp1.x-lammps-ABACUS-lcao-dpks/methane/machine.json delete mode 100644 examples/run/dp1.x-lammps-ABACUS-lcao-dpks/methane/param.json delete mode 100644 examples/run/dp1.x-lammps-ABACUS-pw/methane/machine.json delete mode 100644 examples/run/dp1.x-lammps-ABACUS-pw/methane/param.json delete mode 100644 examples/run/dp1.x-lammps-cp2k/methane/param-ch4.json delete mode 100644 examples/run/dp1.x-lammps-vasp-et/param_elet.json delete mode 100644 examples/run/dp1.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-1.1.0.json delete mode 100644 examples/run/dp1.x-lammps-vasp/CH4/param_CH4_deepmd-kit-1.1.0.json delete mode 100644 examples/run/dp1.x_lammps_gaussian/dodecane/dodecane.json create mode 100644 examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/machine.json create mode 100644 examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/param.json create mode 100644 examples/run/dp2.x-lammps-ABACUS-pw/methane/machine.json create mode 100644 examples/run/dp2.x-lammps-ABACUS-pw/methane/param.json create mode 100644 examples/run/dp2.x-lammps-cp2k/methane/param-ch4.json rename examples/run/{dp1.x-lammps-cp2k => dp2.x-lammps-cp2k}/methane/template.inp (100%) create mode 100644 examples/run/dp2.x-lammps-vasp-et/param_elet.json create mode 100644 examples/run/dp2.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-1.1.0.json rename examples/run/{dp1.x-lammps-vasp => dp2.x-lammps-vasp}/CH4/INCAR_methane (100%) rename examples/run/{dp1.x-lammps-vasp => dp2.x-lammps-vasp}/CH4/POT_C (100%) rename examples/run/{dp1.x-lammps-vasp => dp2.x-lammps-vasp}/CH4/POT_H (100%) create mode 100644 examples/run/dp2.x-lammps-vasp/CH4/param_CH4_deepmd-kit-2.x.json create mode 100644 examples/run/dp2.x_lammps_gaussian/dodecane/dodecane.json diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 078492395..eab10454f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -12,7 +12,7 @@ repos: exclude: "^tests/.*$" - id: check-yaml exclude: "^conda/.*$" - #- id: check-json + - id: check-json - id: check-added-large-files - id: check-merge-conflict - id: check-symlinks diff --git a/doc/simplify/simplify.md b/doc/simplify/simplify.md index c462c85df..8a1fa6dec 100644 --- a/doc/simplify/simplify.md +++ b/doc/simplify/simplify.md @@ -70,7 +70,7 @@ Here is an example of `param.json` for QM7 dataset: "learning_rate": { "type": "exp", "start_lr": 0.001, - "decay_steps": 10, + "stop_lr": 5e-8, "decay_rate": 0.99 }, "loss": { @@ -85,12 +85,11 @@ Here is an example of `param.json` for QM7 dataset: }, "training": { "set_prefix": "set", - "stop_batch": 10000, + "numb_steps": 10000, "disp_file": "lcurve.out", "disp_freq": 1000, "numb_test": 1, "save_freq": 1000, - "save_ckpt": "model.ckpt", "disp_training": true, "time_training": true, "profiling": false, diff --git a/dpgen/data/jsons/al.diamond.111.json b/dpgen/data/jsons/al.diamond.111.json index ff015329f..85b9f9264 100644 --- a/dpgen/data/jsons/al.diamond.111.json +++ b/dpgen/data/jsons/al.diamond.111.json @@ -1,22 +1,36 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [1, 1, 1], - "elements": ["Al"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/al.diamond.222.json b/dpgen/data/jsons/al.diamond.222.json index 693390f4c..a3e25b2c3 100644 --- a/dpgen/data/jsons/al.diamond.222.json +++ b/dpgen/data/jsons/al.diamond.222.json @@ -1,22 +1,36 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [2, 2, 2], - "elements": ["Al"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/al.fcc.111.json b/dpgen/data/jsons/al.fcc.111.json index 4b0649d03..aaed5dafa 100644 --- a/dpgen/data/jsons/al.fcc.111.json +++ b/dpgen/data/jsons/al.fcc.111.json @@ -1,22 +1,36 @@ { - "cell_type": "fcc", - "latt": 4.04, - "super_cell": [1, 1, 1], - "elements": ["Al"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": true, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "fcc", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": true, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/al.fcc.222.json b/dpgen/data/jsons/al.fcc.222.json index c23f6ebe6..f8a244038 100644 --- a/dpgen/data/jsons/al.fcc.222.json +++ b/dpgen/data/jsons/al.fcc.222.json @@ -1,22 +1,36 @@ { - "cell_type": "fcc", - "latt": 4.04, - "super_cell": [2, 2, 2], - "elements": ["Al"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": true, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "fcc", + "latt": 4.04, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": true, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/al.hcp.111.json b/dpgen/data/jsons/al.hcp.111.json index 493fed54e..0a91fd0b4 100644 --- a/dpgen/data/jsons/al.hcp.111.json +++ b/dpgen/data/jsons/al.hcp.111.json @@ -1,22 +1,36 @@ { - "cell_type": "hcp", - "latt": 4.04, - "super_cell": [1, 1, 1], - "elements": ["Al"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "hcp", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/al.hcp.222.json b/dpgen/data/jsons/al.hcp.222.json index ce057c5ef..733baf1f5 100644 --- a/dpgen/data/jsons/al.hcp.222.json +++ b/dpgen/data/jsons/al.hcp.222.json @@ -1,22 +1,36 @@ { - "cell_type": "hcp", - "latt": 4.04, - "super_cell": [2, 2, 2], - "elements": ["Al"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "hcp", + "latt": 4.04, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/al.hcp.332.json b/dpgen/data/jsons/al.hcp.332.json index d16c2f1cc..20a208366 100644 --- a/dpgen/data/jsons/al.hcp.332.json +++ b/dpgen/data/jsons/al.hcp.332.json @@ -1,22 +1,36 @@ { - "cell_type": "hcp", - "latt": 4.04, - "super_cell": [3, 3, 2], - "elements": ["Al"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "hcp", + "latt": 4.04, + "super_cell": [ + 3, + 3, + 2 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/al.sc.222.json b/dpgen/data/jsons/al.sc.222.json index 6ab46dd98..7db2d21f6 100644 --- a/dpgen/data/jsons/al.sc.222.json +++ b/dpgen/data/jsons/al.sc.222.json @@ -1,22 +1,36 @@ { - "cell_type": "sc", - "latt": 2.5, - "super_cell": [2, 2, 2], - "elements": ["Al"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "sc", + "latt": 2.5, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/almg.diamond.111.json b/dpgen/data/jsons/almg.diamond.111.json index c41b905be..013c66aca 100644 --- a/dpgen/data/jsons/almg.diamond.111.json +++ b/dpgen/data/jsons/almg.diamond.111.json @@ -1,23 +1,38 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [1, 1, 1], - "elements": ["Al", "Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/almg.diamond.222.json b/dpgen/data/jsons/almg.diamond.222.json index b94c24b06..f8faefa11 100644 --- a/dpgen/data/jsons/almg.diamond.222.json +++ b/dpgen/data/jsons/almg.diamond.222.json @@ -1,23 +1,38 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [2, 2, 2], - "elements": ["Al", "Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/almg.fcc.111.json b/dpgen/data/jsons/almg.fcc.111.json index e6fb8d951..abd90eaaf 100644 --- a/dpgen/data/jsons/almg.fcc.111.json +++ b/dpgen/data/jsons/almg.fcc.111.json @@ -1,23 +1,38 @@ { - "cell_type": "fcc", - "latt": 4.3, - "super_cell": [1, 1, 1], - "elements": ["Al", "Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "fcc", + "latt": 4.3, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/almg.fcc.222.json b/dpgen/data/jsons/almg.fcc.222.json index dab0caf8f..92f24981e 100644 --- a/dpgen/data/jsons/almg.fcc.222.json +++ b/dpgen/data/jsons/almg.fcc.222.json @@ -1,23 +1,38 @@ { - "cell_type": "fcc", - "latt": 4.3, - "super_cell": [2, 2, 2], - "elements": ["Al", "Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "fcc", + "latt": 4.3, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/almg.hcp.111.json b/dpgen/data/jsons/almg.hcp.111.json index 9ef72bd4c..063d9f42e 100644 --- a/dpgen/data/jsons/almg.hcp.111.json +++ b/dpgen/data/jsons/almg.hcp.111.json @@ -1,23 +1,38 @@ { - "cell_type": "hcp", - "latt": 4.3, - "super_cell": [1, 1, 1], - "elements": ["Al", "Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "hcp", + "latt": 4.3, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/almg.hcp.222.json b/dpgen/data/jsons/almg.hcp.222.json index 1abe49cc5..2a00e64d8 100644 --- a/dpgen/data/jsons/almg.hcp.222.json +++ b/dpgen/data/jsons/almg.hcp.222.json @@ -1,23 +1,38 @@ { - "cell_type": "hcp", - "latt": 4.3, - "super_cell": [2, 2, 2], - "elements": ["Al", "Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "hcp", + "latt": 4.3, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/almg.hcp.332.json b/dpgen/data/jsons/almg.hcp.332.json index 024c1eb21..fc1e2f052 100644 --- a/dpgen/data/jsons/almg.hcp.332.json +++ b/dpgen/data/jsons/almg.hcp.332.json @@ -1,23 +1,38 @@ { - "cell_type": "hcp", - "latt": 4.3, - "super_cell": [3, 3, 2], - "elements": ["Al", "Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "hcp", + "latt": 4.3, + "super_cell": [ + 3, + 3, + 2 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/almg.sc.222.json b/dpgen/data/jsons/almg.sc.222.json index c27f9fd82..99c5420cc 100644 --- a/dpgen/data/jsons/almg.sc.222.json +++ b/dpgen/data/jsons/almg.sc.222.json @@ -1,23 +1,38 @@ { - "cell_type": "sc", - "latt": 2.5, - "super_cell": [2, 2, 2], - "elements": ["Al", "Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "sc", + "latt": 2.5, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/almg.sc.333.json b/dpgen/data/jsons/almg.sc.333.json index 31bf2e42c..74e9418cf 100644 --- a/dpgen/data/jsons/almg.sc.333.json +++ b/dpgen/data/jsons/almg.sc.333.json @@ -1,23 +1,38 @@ { - "cell_type": "sc", - "latt": 2.5, - "super_cell": [3, 3, 3], - "elements": ["Al", "Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "sc", + "latt": 2.5, + "super_cell": [ + 3, + 3, + 3 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/mg.diamond.111.json b/dpgen/data/jsons/mg.diamond.111.json index 27e9cf944..08d532134 100644 --- a/dpgen/data/jsons/mg.diamond.111.json +++ b/dpgen/data/jsons/mg.diamond.111.json @@ -1,22 +1,36 @@ { - "cell_type": "diamond", - "latt": 3.3, - "super_cell": [1, 1, 1], - "elements": ["Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "diamond", + "latt": 3.3, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/mg.diamond.222.json b/dpgen/data/jsons/mg.diamond.222.json index 91e371b20..398051f21 100644 --- a/dpgen/data/jsons/mg.diamond.222.json +++ b/dpgen/data/jsons/mg.diamond.222.json @@ -1,22 +1,36 @@ { - "cell_type": "diamond", - "latt": 3.3, - "super_cell": [2, 2, 2], - "elements": ["Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "diamond", + "latt": 3.3, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/mg.fcc.111.json b/dpgen/data/jsons/mg.fcc.111.json index aee62759b..d4bccfb2e 100644 --- a/dpgen/data/jsons/mg.fcc.111.json +++ b/dpgen/data/jsons/mg.fcc.111.json @@ -1,22 +1,36 @@ { - "cell_type": "fcc", - "latt": 4.48, - "super_cell": [1, 1, 1], - "elements": ["Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": true, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "fcc", + "latt": 4.48, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": true, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/mg.fcc.222.json b/dpgen/data/jsons/mg.fcc.222.json index dd42387a1..9e88a5c97 100644 --- a/dpgen/data/jsons/mg.fcc.222.json +++ b/dpgen/data/jsons/mg.fcc.222.json @@ -1,22 +1,36 @@ { - "cell_type": "fcc", - "latt": 4.48, - "super_cell": [2, 2, 2], - "elements": ["Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": true, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "fcc", + "latt": 4.48, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": true, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/mg.hcp.111.json b/dpgen/data/jsons/mg.hcp.111.json index cc36f847f..428d79197 100644 --- a/dpgen/data/jsons/mg.hcp.111.json +++ b/dpgen/data/jsons/mg.hcp.111.json @@ -1,22 +1,36 @@ { - "cell_type": "hcp", - "latt": 4.48, - "super_cell": [1, 1, 1], - "elements": ["Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "hcp", + "latt": 4.48, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/mg.hcp.222.json b/dpgen/data/jsons/mg.hcp.222.json index 54b06974a..8da4061c3 100644 --- a/dpgen/data/jsons/mg.hcp.222.json +++ b/dpgen/data/jsons/mg.hcp.222.json @@ -1,20 +1,34 @@ { - "cell_type": "hcp", - "latt": 4.48, - "super_cell": [2, 2, 2], - "elements": ["Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "_comment": "that's all" -} + "cell_type": "hcp", + "latt": 4.48, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/mg.hcp.332.json b/dpgen/data/jsons/mg.hcp.332.json index d81ce2bfe..1106092cd 100644 --- a/dpgen/data/jsons/mg.hcp.332.json +++ b/dpgen/data/jsons/mg.hcp.332.json @@ -1,20 +1,34 @@ { - "cell_type": "hcp", - "latt": 4.48, - "super_cell": [3, 3, 2], - "elements": ["Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "_comment": "that's all" -} + "cell_type": "hcp", + "latt": 4.48, + "super_cell": [ + 3, + 3, + 2 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/mg.sc.222.json b/dpgen/data/jsons/mg.sc.222.json index 137b39104..8ee5444fa 100644 --- a/dpgen/data/jsons/mg.sc.222.json +++ b/dpgen/data/jsons/mg.sc.222.json @@ -1,22 +1,36 @@ { - "cell_type": "sc", - "latt": 2.7, - "super_cell": [2, 2, 2], - "elements": ["Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "sc", + "latt": 2.7, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/param.json b/dpgen/data/jsons/param.json index 70eb96ea1..1601d3251 100644 --- a/dpgen/data/jsons/param.json +++ b/dpgen/data/jsons/param.json @@ -1,22 +1,40 @@ { - "cell_type": "hcp", - "latt": 4.03, - "super_cell": [2, 1, 1], - "elements": ["Al", "Mg"], - "potcars": ["/gpfs/share/home/1600017784/start/data/POTCAR/Al/POTCAR", - "/gpfs/share/home/1600017784/start/data/POTCAR/Mg/POTCAR" - ], - "encut": 600, - "kspacing": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": true, - "relax_incar": "INCAR", - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 20, - "_comment": "that's all", - "stages":[1,2] -} + "cell_type": "hcp", + "latt": 4.03, + "super_cell": [ + 2, + 1, + 1 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/gpfs/share/home/1600017784/start/data/POTCAR/Al/POTCAR", + "/gpfs/share/home/1600017784/start/data/POTCAR/Mg/POTCAR" + ], + "encut": 600, + "kspacing": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": true, + "relax_incar": "INCAR", + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 20, + "_comment1": "that's all", + "stages": [ + 1, + 2 + ] +} \ No newline at end of file diff --git a/dpgen/data/jsons/si.diamond.111.json b/dpgen/data/jsons/si.diamond.111.json index b9c63547c..9ef9e6ffb 100644 --- a/dpgen/data/jsons/si.diamond.111.json +++ b/dpgen/data/jsons/si.diamond.111.json @@ -1,22 +1,36 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [1, 1, 1], - "elements": ["Si"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Si" + ], + "potcars": [ 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at end of file diff --git a/dpgen/data/jsons/surf.al.hcp.json b/dpgen/data/jsons/surf.al.hcp.json index 9bc1971ea..2f3679a43 100644 --- a/dpgen/data/jsons/surf.al.hcp.json +++ b/dpgen/data/jsons/surf.al.hcp.json @@ -1,26 +1,40 @@ { - "cell_type": "hcp", - "latt": 4.04, - "super_cell": [1, 1, 1], - "z_min": 12, - "vacuum_max": 9, - "vacuum_resol": 0.2, - "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", - "elements": ["Al"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "hcp", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "z_min": 12, + "vacuum_max": 9, + "vacuum_resol": 0.2, + 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a/dpgen/data/jsons/surf.mg.fcc.json b/dpgen/data/jsons/surf.mg.fcc.json index d6353e3e0..94c527234 100644 --- a/dpgen/data/jsons/surf.mg.fcc.json +++ b/dpgen/data/jsons/surf.mg.fcc.json @@ -1,26 +1,40 @@ { - "cell_type": "fcc", - "latt": 4.48, - "super_cell": [1, 1, 1], - "z_min": 12, - "vacuum_max": 9, - "vacuum_resol": 0.2, - "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", - "elements": ["Mg"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "fcc", + "latt": 4.48, + "super_cell": [ + 1, + 1, + 1 + ], + "z_min": 12, + "vacuum_max": 9, + "vacuum_resol": 0.2, + "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 5, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/surf.mg.hcp.json b/dpgen/data/jsons/surf.mg.hcp.json index b18e8c365..705cc7858 100644 --- a/dpgen/data/jsons/surf.mg.hcp.json +++ b/dpgen/data/jsons/surf.mg.hcp.json @@ -1,26 +1,40 @@ { - "cell_type": "hcp", - "latt": 4.48, - "super_cell": [1, 1, 1], - "z_min": 12, - "vacuum_max": 9, - "vacuum_resol": 0.2, - "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", - "elements": ["Mg"], - "potcars": 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"deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/surf.si.diamond.json b/dpgen/data/jsons/surf.si.diamond.json index fc374346d..c5dd90c93 100644 --- a/dpgen/data/jsons/surf.si.diamond.json +++ b/dpgen/data/jsons/surf.si.diamond.json @@ -1,28 +1,58 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [1, 1, 1], - "z_min": 12, - "vacuum_max": 9, - "vacuum_resol": 0.2, - "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", - "pymatgen_surf": true, - "millers": [[0,0,1], [1,1,0], [1,1,1]], - "elements": ["Si"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 1, + 1, + 1 + ], + "z_min": 12, + "vacuum_max": 9, + "vacuum_resol": 0.2, + "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", + "pymatgen_surf": true, + "millers": [ + [ + 0, + 0, + 1 + ], + [ + 1, + 1, + 0 + ], + [ + 1, + 1, + 1 + ] + ], + "elements": [ + "Si" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 5, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/w.bcc.111.json b/dpgen/data/jsons/w.bcc.111.json index 7d18285bd..a1a759245 100644 --- a/dpgen/data/jsons/w.bcc.111.json +++ b/dpgen/data/jsons/w.bcc.111.json @@ -1,24 +1,38 @@ { - "cell_type": "bcc", - "latt": 3.2, - "super_cell": [1, 1, 1], - "elements": ["W"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "ismear": 1, - "sigma": 0.2, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 30, - "pert_box": 0.005, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "bcc", + "latt": 3.2, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "W" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "ismear": 1, + "sigma": 0.2, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 30, + "pert_box": 0.005, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/w.bcc.222.json b/dpgen/data/jsons/w.bcc.222.json index 6a3b223e1..1bb155a55 100644 --- a/dpgen/data/jsons/w.bcc.222.json +++ b/dpgen/data/jsons/w.bcc.222.json @@ -1,24 +1,38 @@ { - "cell_type": "bcc", - "latt": 3.173, - "super_cell": [2, 2, 2], - "elements": ["W"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "ismear": 1, - "sigma": 0.2, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": true, - "pert_numb": 100, - "pert_box": 0.005, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "bcc", + "latt": 3.173, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "W" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "ismear": 1, + "sigma": 0.2, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": true, + "pert_numb": 100, + "pert_box": 0.005, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/w.diamond.111.json b/dpgen/data/jsons/w.diamond.111.json index a0d04fc83..e2f61b2ab 100644 --- a/dpgen/data/jsons/w.diamond.111.json +++ b/dpgen/data/jsons/w.diamond.111.json @@ -1,24 +1,38 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [1, 1, 1], - "elements": ["W"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "ismear": 1, - "sigma": 0.2, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 30, - "pert_box": 0.005, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "W" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "ismear": 1, + "sigma": 0.2, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 30, + "pert_box": 0.005, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/w.fcc.111.json b/dpgen/data/jsons/w.fcc.111.json index e94ecaa56..f8ca14f52 100644 --- a/dpgen/data/jsons/w.fcc.111.json +++ b/dpgen/data/jsons/w.fcc.111.json @@ -1,24 +1,38 @@ { - "cell_type": "fcc", - "latt": 4.04, - "super_cell": [1, 1, 1], - "elements": ["W"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "ismear": 1, - "sigma": 0.2, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 30, - "pert_box": 0.005, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "fcc", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "W" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "ismear": 1, + "sigma": 0.2, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 30, + "pert_box": 0.005, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/w.hcp.111.json b/dpgen/data/jsons/w.hcp.111.json index 033bd13b6..1bc6cae02 100644 --- a/dpgen/data/jsons/w.hcp.111.json +++ b/dpgen/data/jsons/w.hcp.111.json @@ -1,24 +1,38 @@ { - "cell_type": "hcp", - "latt": 4.04, - "super_cell": [1, 1, 1], - "elements": ["W"], - "potcars": ["/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "ismear": 1, - "sigma": 0.2, - "scale": [0.96, 0.98, 1.00, 1.02, 1.04, 1.06], - "skip_relax": false, - "pert_numb": 30, - "pert_box": 0.005, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "cell_type": "hcp", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "W" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "ismear": 1, + "sigma": 0.2, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 30, + "pert_box": 0.005, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/dpgen/data/jsons/water.111.json b/dpgen/data/jsons/water.111.json index 4f5733a90..7547bb216 100644 --- a/dpgen/data/jsons/water.111.json +++ b/dpgen/data/jsons/water.111.json @@ -1,29 +1,37 @@ { - "_comment": "init poscars form a crystal structure", - "cell_type": "diamond", - "latt": 2.5, - "elements": ["Si"], - "_comment": "if set from poscar, the options above will be ignored", - "from_poscar": true, - "from_poscar_path": "ice6.POSCAR", - - "_comment": "", - "super_cell": [1, 1, 1], - "potcars": [ "/home/wanghan/Soft/vasp/potcar.52/potpaw_PBE.52/O/POTCAR", - "/home/wanghan/Soft/vasp/potcar.52/potpaw_PBE.52/H/POTCAR" - ], - "encut": 900, - "kspacing_relax": 0.75, - "kspacing_md": 0.75, - "kgamma": false, - "scale": [1.0], - "skip_relax": true, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "_comment1": "init poscars form a crystal structure", + "cell_type": "diamond", + "latt": 2.5, + "elements": [ + "Si" + ], + "_comment2": "if set from poscar, the options above will be ignored", + "from_poscar": true, + "from_poscar_path": "ice6.POSCAR", + "_comment3": "", + "super_cell": [ + 1, + 1, + 1 + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.52/potpaw_PBE.52/O/POTCAR", + "/home/wanghan/Soft/vasp/potcar.52/potpaw_PBE.52/H/POTCAR" + ], + "encut": 900, + "kspacing_relax": 0.75, + "kspacing_md": 0.75, + "kgamma": false, + "scale": [ + 1.0 + ], + "skip_relax": true, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment4": "that's all" +} \ No newline at end of file diff --git a/examples/CH4-refact-dpdispatcher/machine-ali-ehpc.json b/examples/CH4-refact-dpdispatcher/machine-ali-ehpc.json index 40bf56abe..bfefe10d5 100644 --- a/examples/CH4-refact-dpdispatcher/machine-ali-ehpc.json +++ b/examples/CH4-refact-dpdispatcher/machine-ali-ehpc.json @@ -1,83 +1,92 @@ { "api_version": "1.0", - "train": - { - "command": "dp", - "machine": { - "batch_type": "PBS", - "context_type": "SSHContext", - "local_root": "./", - "remote_root": "/home/fengbo/work_path_dpdispatcher_test", - "remote_profile": { - "hostname": "39.xxx.xx.xx", - "username": "fengbo" - } - }, - "resources": { - "batch_type": "PBS", - "number_node": 1, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "T4_4_15", - "group_size": 1, - "custom_flags":["#SBATCH --mem=32G"], - "strategy": {"if_cuda_multi_devices": true}, - "para_deg": 3, - "source_list": ["/home/fengbo/deepmd.1.2.4.env"] + "train": { + "command": "dp", + "machine": { + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/fengbo/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "fengbo" } }, - "model_devi": - { - "command": "lmp", - "machine":{ - "batch_type": "PBS", - "context_type": "SSHContext", - "local_root": "./", - "remote_root": "/home/fengbo/work_path_dpdispatcher_test", - "remote_profile": { - "hostname": "39.xxx.xx.xx", - "username": "fengbo" - } - }, - "resources": { - "batch_type": "PBS", - "number_node": 1, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "T4_4_15", - "group_size": 5, - "source_list": ["/home/fengbo/deepmd.1.2.4.env"] - }, - "_comments" : "In user_forward_files, define input files to be uploaded.", - "user_forward_files" : [], - "_comments" : "In user_backward_files, define output files to be collected.", - "user_backward_files" : ["HILLS"] - }, - "fp": - { - "command": "vasp_std", - "machine":{ - "batch_type": "PBS", - "context_type": "SSHContext", - "local_root": "./", - "remote_root": "/home/fengbo/work_path_dpdispatcher_test", - "remote_profile": { - "hostname": "39.xxx.xx.xx", - "username": "fengbo" - } - }, - "resources": { - "batch_type": "PBS", - "number_node": 1, - "cpu_per_node": 32, - "gpu_per_node": 0, - "queue_name": "G_32_128", - "group_size": 1, - "source_list": ["~/vasp.env"] + "resources": { + "batch_type": "PBS", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "T4_4_15", + "group_size": 1, + "custom_flags": [ + "#SBATCH --mem=32G" + ], + "strategy": { + "if_cuda_multi_devices": true }, - "_comments" : "In user_forward_files, define input files to be uploaded.", - "user_forward_files" : ["vdw_kernel.bindat"], - "_comments" : "In user_backward_files, define output files to be collected.", - "user_backward_files" : [] + "para_deg": 3, + "source_list": [ + "/home/fengbo/deepmd.1.2.4.env" + ] } -} + }, + "model_devi": { + "command": "lmp", + "machine": { + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/fengbo/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "fengbo" + } + }, + "resources": { + "batch_type": "PBS", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "T4_4_15", + "group_size": 5, + "source_list": [ + "/home/fengbo/deepmd.1.2.4.env" + ] + }, + "_comments": "In user_backward_files, define output files to be collected.", + "user_forward_files": [], + "user_backward_files": [ + "HILLS" + ] + }, + "fp": { + "command": "vasp_std", + "machine": { + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/fengbo/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "fengbo" + } + }, + "resources": { + "batch_type": "PBS", + "number_node": 1, + "cpu_per_node": 32, + "gpu_per_node": 0, + "queue_name": "G_32_128", + "group_size": 1, + "source_list": [ + "~/vasp.env" + ] + }, + "_comments": "In user_backward_files, define output files to be collected.", + "user_forward_files": [ + "vdw_kernel.bindat" + ], + "user_backward_files": [] + } +} \ No newline at end of file diff --git a/examples/CH4-refact-dpdispatcher/machine-dpcloudserver.json b/examples/CH4-refact-dpdispatcher/machine-dpcloudserver.json index b13293fe1..7fb68714b 100644 --- a/examples/CH4-refact-dpdispatcher/machine-dpcloudserver.json +++ b/examples/CH4-refact-dpdispatcher/machine-dpcloudserver.json @@ -1,131 +1,128 @@ { "api_version": "1.0", - "train" : - { - "command": "dp", - "machine": { - "batch_type": "DpCloudServer", - "context_type": "DpCloudServerContext", - "local_root" : "./", - "remote_profile":{ - "email": "yfb222333", - "password": "", - "program_id": 0, - "input_data":{ - "job_type": "indicate", - "log_file": "dp_cloud_server.log", - "command": null, - "backward_files": [], - "job_name": "dpgen_20210630_job", - "machine": { - "platform": "ali", - "resources": { - "gpu_type": "1 * NVIDIA P100", - "cpu_num": 4, - "mem_limit": 30, - "disk_size": 100, - "region": "cn-beijing", - "time_limit": "2:00:00", - "image_name": "yfb-deepmd-kit-1.2.4-cuda10" - } - }, - "job_resources": null + "train": { + "command": "dp", + "machine": { + "batch_type": "DpCloudServer", + "context_type": "DpCloudServerContext", + "local_root": "./", + "remote_profile": { + "email": "yfb222333", + "password": "", + "program_id": 0, + "input_data": { + "job_type": "indicate", + "log_file": "dp_cloud_server.log", + "command": null, + "backward_files": [], + "job_name": "dpgen_20210630_job", + "machine": { + "platform": "ali", + "resources": { + "gpu_type": "1 * NVIDIA P100", + "cpu_num": 4, + "mem_limit": 30, + "disk_size": 100, + "region": "cn-beijing", + "time_limit": "2:00:00", + "image_name": "yfb-deepmd-kit-1.2.4-cuda10" } + }, + "job_resources": null } - }, - "resources": { - "batch_type": "DpCloudServer", - "number_node": 1, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "GPU", - "group_size": 1 } }, - "model_devi": - { - "command": "lmp -i input.lammps -v restart 0", - "machine": { - "batch_type": "DpCloudServer", - "context_type": "DpCloudServerContext", - "local_root" : "./", - "remote_profile":{ - "email": "yfb222333", - "password": "", - "program_id": 0, - "input_data":{ - "job_type": "indicate", - "log_file": "dp_cloud_server.log", - "command": null, - "backward_files": [], - "job_name": "dpgen_20210630_job", - "machine": { - "platform": "ali", - "resources": { - "gpu_type": "1 * NVIDIA P100", - "cpu_num": 4, - "mem_limit": 30, - "disk_size": 100, - "region": "cn-beijing", - "time_limit": "2:00:00", - "image_name": "yfb-deepmd-kit-1.2.4-cuda10" - } - }, - "job_resources": null + "resources": { + "batch_type": "DpCloudServer", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "GPU", + "group_size": 1 + } + }, + "model_devi": { + "command": "lmp -i input.lammps -v restart 0", + "machine": { + "batch_type": "DpCloudServer", + "context_type": "DpCloudServerContext", + "local_root": "./", + "remote_profile": { + "email": "yfb222333", + "password": "", + "program_id": 0, + "input_data": { + "job_type": "indicate", + "log_file": "dp_cloud_server.log", + "command": null, + "backward_files": [], + "job_name": "dpgen_20210630_job", + "machine": { + "platform": "ali", + "resources": { + "gpu_type": "1 * NVIDIA P100", + "cpu_num": 4, + "mem_limit": 30, + "disk_size": 100, + "region": "cn-beijing", + "time_limit": "2:00:00", + "image_name": "yfb-deepmd-kit-1.2.4-cuda10" } + }, + "job_resources": null } - }, - "resources": { - "batch_type": "DpCloudServer", - "number_node": 1, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "GPU", - "group_size": 5 } }, - "fp": - { - "command": "mpirun -n 16 vasp_std", - "machine": { - "batch_type": "DpCloudServer", - "context_type": "DpCloudServerContext", - "local_root" : "./", - "remote_profile":{ - "email": "yfb222333", - "password": "", - "program_id": 0, - "input_data":{ - "job_type": "indicate", - "log_file": "dp_cloud_server.log", - "command": null, - "backward_files": [], - "job_name": "dpgen_20210630_job", - "machine": { - "platform": "ali", - "resources": { - "cpu_num": 32, - "mem_limit": 64, - "disk_size": 200, - "region": "cn-beijing", - "time_limit": "2:00:00", - "image_name": "deepmd-vasp-cloudserver-v8" - } - }, - "job_resources": null + "resources": { + "batch_type": "DpCloudServer", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "GPU", + "group_size": 5 + } + }, + "fp": { + "command": "mpirun -n 16 vasp_std", + "machine": { + "batch_type": "DpCloudServer", + "context_type": "DpCloudServerContext", + "local_root": "./", + "remote_profile": { + "email": "yfb222333", + "password": "", + "program_id": 0, + "input_data": { + "job_type": "indicate", + "log_file": "dp_cloud_server.log", + "command": null, + "backward_files": [], + "job_name": "dpgen_20210630_job", + "machine": { + "platform": "ali", + "resources": { + "cpu_num": 32, + "mem_limit": 64, + "disk_size": 200, + "region": "cn-beijing", + "time_limit": "2:00:00", + "image_name": "deepmd-vasp-cloudserver-v8" } + }, + "job_resources": null } - }, - "resources": { - "batch_type": "DpCloudServer", - "number_node": 1, - "cpu_per_node": 32, - "gpu_per_node": 0, - "queue_name": "CPU", - "group_size": 5, - "source_list": [ - "/opt/intel/oneapi/setvars.sh" - ] } + }, + "resources": { + "batch_type": "DpCloudServer", + "number_node": 1, + "cpu_per_node": 32, + "gpu_per_node": 0, + "queue_name": "CPU", + "group_size": 5, + "source_list": [ + "/opt/intel/oneapi/setvars.sh" + ] } -} + } +} \ No newline at end of file diff --git a/examples/CH4-refact-dpdispatcher/param_CH4_deepmd-kit-1.1.0.json b/examples/CH4-refact-dpdispatcher/param_CH4_deepmd-kit-1.1.0.json deleted file mode 120000 index 2916f7885..000000000 --- a/examples/CH4-refact-dpdispatcher/param_CH4_deepmd-kit-1.1.0.json +++ /dev/null @@ -1 +0,0 @@ -../run/dp1.x-lammps-vasp/CH4/param_CH4_deepmd-kit-1.1.0.json \ No newline at end of file diff --git a/examples/CH4-refact-dpdispatcher/param_CH4_deepmd-kit-2.x.json b/examples/CH4-refact-dpdispatcher/param_CH4_deepmd-kit-2.x.json new file mode 120000 index 000000000..3f11d42a7 --- /dev/null +++ b/examples/CH4-refact-dpdispatcher/param_CH4_deepmd-kit-2.x.json @@ -0,0 +1 @@ +../run/dp2.x-lammps-vasp/CH4/param_CH4_deepmd-kit-2.x.json \ No newline at end of file diff --git a/examples/database/param_Ti.json b/examples/database/param_Ti.json index be78af113..fbfccf773 100644 --- a/examples/database/param_Ti.json +++ b/examples/database/param_Ti.json @@ -1,19 +1,100 @@ { - "path" : "/path/to/Ti", - "calculator" : "vasp", - "_comment" : "Current only support VASP", - "output" : "./db_Ti.json", - "id_prefix" : "", - "config_info_dict" : { - "fcc-bulk" : [0,1,2,3,4,5,6,7], - "hcp-bulk" : [8,9,10,11,12,13,14,15], - "bcc-bulk" : [16,17,18,19,20,21,22,23], - "fcc-surf-100" : [24,25,26,27,28,29,30,31], - "fcc-surf-111" : [32,33,34,35,36,37,38,39], - "fcc-surf-110" : [40,41,42,43,44,45,46,47], - "hcp-surf-001" : [48,49,50,51,52,53,54,55], - "hcp-surf-100" : [56,57,58,59,60,61,62,63], - "hcp-surf-110" : [64,65,66,67,68,69,70,71] - }, - "skip_init" : true -} + "path": "/path/to/Ti", + "calculator": "vasp", + "_comment1": "Current only support VASP", + "output": "./db_Ti.json", + "id_prefix": "", + "config_info_dict": { + "fcc-bulk": [ + 0, + 1, + 2, + 3, + 4, + 5, + 6, + 7 + ], + "hcp-bulk": [ + 8, + 9, + 10, + 11, + 12, + 13, + 14, + 15 + ], + "bcc-bulk": [ + 16, + 17, + 18, + 19, + 20, + 21, + 22, + 23 + ], + "fcc-surf-100": [ + 24, + 25, + 26, + 27, + 28, + 29, + 30, + 31 + ], + "fcc-surf-111": [ + 32, + 33, + 34, + 35, + 36, + 37, + 38, + 39 + ], + "fcc-surf-110": [ + 40, + 41, + 42, + 43, + 44, + 45, + 46, + 47 + ], + "hcp-surf-001": [ + 48, + 49, + 50, + 51, + 52, + 53, + 54, + 55 + ], + "hcp-surf-100": [ + 56, + 57, + 58, + 59, + 60, + 61, + 62, + 63 + ], + "hcp-surf-110": [ + 64, + 65, + 66, + 67, + 68, + 69, + 70, + 71 + ] + }, + "skip_init": true +} \ No newline at end of file diff --git a/examples/init/abacus/CuW/CuW.json b/examples/init/abacus/CuW/CuW.json index 9abd406ce..1738d8f34 100644 --- a/examples/init/abacus/CuW/CuW.json +++ b/examples/init/abacus/CuW/CuW.json @@ -1,43 +1,52 @@ { - "init_fp_style": "ABACUS", - "stages": [1, 2, 3, 4], - "cell_type": "fcc", - "latt": 3.76, - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "Cu", "W" - ], - "atom_masses": [63.55, 183.8], - "potcars": [ - "Cu_ONCV_PBE-1.0.upf", - "W_ONCV_PBE-1.0.upf" - ], - "orb_files":[ - "Cu_gga_9au_60Ry_4s2p2d1f.orb", - "W_gga_10au_60Ry_4s2p2d2f.orb" - ], - "relax_incar": "INPUT", - "relax_kpt": "KPT", - "md_kpt": "KPT", - "md_incar": "INPUT.md", - "dpks_descriptor": "jle.orb", - "dpks_model": "model.ptg", - "scale": [ - 0.99 - ], - "skip_relax": true, - "pert_numb": 2, - "md_nstep": 2, - "pert_box": 0.01, - "pert_atom": 0.01, - "coll_ndata": 12, - "type_map": [ - "Cu", - "W" - ], - "_comment": "that's all" -} + "init_fp_style": "ABACUS", + "stages": [ + 1, + 2, + 3, + 4 + ], + "cell_type": "fcc", + "latt": 3.76, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Cu", + "W" + ], + "atom_masses": [ + 63.55, + 183.8 + ], + "potcars": [ + "Cu_ONCV_PBE-1.0.upf", + "W_ONCV_PBE-1.0.upf" + ], + "orb_files": [ + "Cu_gga_9au_60Ry_4s2p2d1f.orb", + "W_gga_10au_60Ry_4s2p2d2f.orb" + ], + "relax_incar": "INPUT", + "relax_kpt": "KPT", + "md_kpt": "KPT", + "md_incar": "INPUT.md", + "dpks_descriptor": "jle.orb", + "dpks_model": "model.ptg", + "scale": [ + 0.99 + ], + "skip_relax": true, + "pert_numb": 2, + "md_nstep": 2, + "pert_box": 0.01, + "pert_atom": 0.01, + "coll_ndata": 12, + "type_map": [ + "Cu", + "W" + ], + "_comment1": "that's all" +} \ No newline at end of file diff --git a/examples/init/abacus/fcc-Al-lcao/init.json b/examples/init/abacus/fcc-Al-lcao/init.json index fccb79da7..5a509478a 100644 --- a/examples/init/abacus/fcc-Al-lcao/init.json +++ b/examples/init/abacus/fcc-Al-lcao/init.json @@ -1,24 +1,41 @@ { - "init_fp_style": "ABACUS", - "stages": [1,2,3,4], - "cell_type": "diamond", - "super_cell": [2, 1, 1], - "elements": ["Al"], - "from_poscar": true, - "from_poscar_path": "./Al.STRU", - "potcars": ["Al_ONCV_PBE-1.0.upf"], - "orb_files": ["Al_gga_9au_100Ry_4s4p1d.orb"], - "relax_incar": "./INPUT.rlx", - "md_incar" : "./INPUT.md", - "relax_kpt": "./KPT.rlx", - "md_kpt": "./KPT.md", - "md_nstep": 3, - "scale": [1.00], - "skip_relax": false, - "pert_numb": 2, - "pert_box": 0.03, - "pert_atom": 0.01, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment": "that's all" -} + "init_fp_style": "ABACUS", + "stages": [ + 1, + 2, + 3, + 4 + ], + "cell_type": "diamond", + "super_cell": [ + 2, + 1, + 1 + ], + "elements": [ + "Al" + ], + "from_poscar": true, + "from_poscar_path": "./Al.STRU", + "potcars": [ + "Al_ONCV_PBE-1.0.upf" + ], + "orb_files": [ + "Al_gga_9au_100Ry_4s4p1d.orb" + ], + "relax_incar": "./INPUT.rlx", + "md_incar": "./INPUT.md", + "relax_kpt": "./KPT.rlx", + "md_kpt": "./KPT.md", + "md_nstep": 3, + "scale": [ + 1.0 + ], + "skip_relax": false, + "pert_numb": 2, + "pert_box": 0.03, + "pert_atom": 0.01, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/examples/init/abacus/fcc-Al-pw/init.json b/examples/init/abacus/fcc-Al-pw/init.json index 0874040e4..aa6be838c 100644 --- a/examples/init/abacus/fcc-Al-pw/init.json +++ b/examples/init/abacus/fcc-Al-pw/init.json @@ -1,23 +1,38 @@ { - "init_fp_style": "ABACUS", - "stages": [1,2,3,4], - "cell_type": "fcc", - "super_cell": [2, 1, 1], - "elements": ["Al"], - "from_poscar": true, - "from_poscar_path": "./Al.STRU", - "potcars": ["Al_ONCV_PBE-1.0.upf"], - "relax_incar": "INPUT.rlx", - "relax_kpt": "KPT", - "md_incar" : "INPUT.md", - "md_kpt" : "KPT", - "skip_relax": false, - "scale": [1.00], - "pert_numb": 10, - "md_nstep" : 10, - "pert_box": 0.01, - "pert_atom": 0.01, - "deepgen_templ": "../generator/template/", - "coll_ndata": 10, - "_comment": "that's all" -} + "init_fp_style": "ABACUS", + "stages": [ + 1, + 2, + 3, + 4 + ], + "cell_type": "fcc", + "super_cell": [ + 2, + 1, + 1 + ], + "elements": [ + "Al" + ], + "from_poscar": true, + "from_poscar_path": "./Al.STRU", + "potcars": [ + "Al_ONCV_PBE-1.0.upf" + ], + "relax_incar": "INPUT.rlx", + "relax_kpt": "KPT", + "md_incar": "INPUT.md", + "md_kpt": "KPT", + "skip_relax": false, + "scale": [ + 1.0 + ], + "pert_numb": 10, + "md_nstep": 10, + "pert_box": 0.01, + "pert_atom": 0.01, + "deepgen_templ": "../generator/template/", + "coll_ndata": 10, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/examples/init/al.json b/examples/init/al.json index 41e365cad..956e9646c 100644 --- a/examples/init/al.json +++ b/examples/init/al.json @@ -1,32 +1,32 @@ { - "cell_type": "fcc", - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "Al" - ], - "from_poscar": true, - "from_poscar_path": "al.POSCAR", - "potcars": [ - "POTCAR" - ], - "relax_incar": "INCAR.rlx", - "md_incar": "INCAR.md", - "scale": [ - 1.0 - ], - "skip_relax": true, - "pert_numb": 30, - "md_nstep": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "coll_ndata": 10, - "type_map": [ - "Mg", - "Al" - ], - "_comment": "that's all" -} + "cell_type": "fcc", + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al" + ], + "from_poscar": true, + "from_poscar_path": "al.POSCAR", + "potcars": [ + "POTCAR" + ], + "relax_incar": "INCAR.rlx", + "md_incar": "INCAR.md", + "scale": [ + 1.0 + ], + "skip_relax": true, + "pert_numb": 30, + "md_nstep": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "coll_ndata": 10, + "type_map": [ + "Mg", + "Al" + ], + "_comment1": "that's all" +} \ No newline at end of file diff --git a/examples/init/ch4.json b/examples/init/ch4.json index 3902c24da..28ab1954d 100644 --- a/examples/init/ch4.json +++ b/examples/init/ch4.json @@ -1,19 +1,36 @@ { - "stages": [1,2,3,4], - "cell_type": "diamond", - "super_cell": [1, 1, 1], - "elements": ["H","C"], - "from_poscar": true, - "from_poscar_path": "./CH4.POSCAR", - "potcars": ["./POTCAR_H", "./POTCAR_C"], - "relax_incar": "./INCAR_methane.rlx", - "md_incar" : "./INCAR_methane.md", - "scale": [1.00], - "skip_relax": false, - "pert_numb": 30, - "md_nstep" : 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "coll_ndata": 5000, - "_comment": "that's all" -} + "stages": [ + 1, + 2, + 3, + 4 + ], + "cell_type": "diamond", + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "H", + "C" + ], + "from_poscar": true, + "from_poscar_path": "./CH4.POSCAR", + "potcars": [ + "./POTCAR_H", + "./POTCAR_C" + ], + "relax_incar": "./INCAR_methane.rlx", + "md_incar": "./INCAR_methane.md", + "scale": [ + 1.0 + ], + "skip_relax": false, + "pert_numb": 30, + "md_nstep": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "coll_ndata": 5000, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/examples/init/cu.surf.hcp.111.json b/examples/init/cu.surf.hcp.111.json index 00816e09d..a3e5ec154 100644 --- a/examples/init/cu.surf.hcp.111.json +++ b/examples/init/cu.surf.hcp.111.json @@ -1,7 +1,5 @@ { - "_comments": "This is an example to generate Cu-hcp surface configurations.", - "_comments": "This example is used in Computer Physics Communications, 2020, 107206.", - "_comments" : "Last modified on 2019.8.27 by Yuzhi Zhang.", + "_comments": "Last modified on 2019.8.27 by Yuzhi Zhang.", "stages": [ 1, 2 @@ -43,14 +41,19 @@ "potcars": [ "PATH/POTCAR" ], - "relax_incar" : "PATH/INCAR_surf_rlx", + "relax_incar": "PATH/INCAR_surf_rlx", "scale": [ - 0.96,0.98, 1.0,1.02, 1.04, 1.06 + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 ], "skip_relax": false, "pert_numb": 20, "pert_box": 0.03, "pert_atom": 0.01, - "lmp_cmd" : "PATH/lmp_serial", - "_comment": "that's all" -} + "lmp_cmd": "PATH/lmp_serial", + "_comment1": "that's all" +} \ No newline at end of file diff --git a/examples/init/reaction.json b/examples/init/reaction.json index 8bf070726..02d3df6dd 100644 --- a/examples/init/reaction.json +++ b/examples/init/reaction.json @@ -1,19 +1,19 @@ { - "type_map": [ - "H", - "O" - ], - "reaxff": { - "data": "data.hydrogen", - "ff": "ffield.reax.cho", - "control": "lmp_control", - "temp": 3000, - "tau_t": 100, - "dt": 0.1, - "nstep": 10000, - "dump_freq": 100 - }, - "cutoff": 3.5, - "dataset_size": 100, - "qmkeywords": "b3lyp/6-31g** force Geom=PrintInputOrient" -} + "type_map": [ + "H", + "O" + ], + "reaxff": { + "data": "data.hydrogen", + "ff": "ffield.reax.cho", + "control": "lmp_control", + "temp": 3000, + "tau_t": 100, + "dt": 0.1, + "nstep": 10000, + "dump_freq": 100 + }, + "cutoff": 3.5, + "dataset_size": 100, + "qmkeywords": "b3lyp/6-31g** force Geom=PrintInputOrient" +} \ No newline at end of file diff --git a/examples/init/surf.json b/examples/init/surf.json index 902fc8d0b..7ab79189a 100644 --- a/examples/init/surf.json +++ b/examples/init/surf.json @@ -42,7 +42,7 @@ "potcars": [ "./POTCAR" ], - "relax_incar" : "INCAR_metal_rlx_low", + "relax_incar": "INCAR_metal_rlx_low", "scale": [ 0.98, 1.0 @@ -52,5 +52,5 @@ "pert_box": 0.03, "pert_atom": 0.01, "coll_ndata": 5000, - "_comment": "that's all" -} + "_comment1": "that's all" +} \ No newline at end of file diff --git a/examples/machine/DeePMD-kit-1.0/machine-local-4GPU.json b/examples/machine/DeePMD-kit-1.0/machine-local-4GPU.json index e0e6bfca0..dd6559a46 100644 --- a/examples/machine/DeePMD-kit-1.0/machine-local-4GPU.json +++ b/examples/machine/DeePMD-kit-1.0/machine-local-4GPU.json @@ -1,90 +1,90 @@ { - "_comment" : "This is an example of DP-GEN on Local device running with 4 GPUs", - "_comment": "Last updated on 2021.5.9 for DP-GEN 0.9.2 by Ke XU", - "train": { - "_comment" : "Specify the installed path of DeePMD-kit", - "command": "/home/user/anaconda3/bin/dp", - "_comment" : "Specify machine settings", - "machine": { - "_comment": "Supported batches include slurm, pbs, shell, lsf.", - "batch_type": "shell", - "context_type": "local", - "remote_root": "/tmp/dpwork", - "local_root": "./" - }, - "resources": { - "module_list": [], - "_comment": "Environment to be activated. This will generate source xxx/psxevars.sh in scripts. ", - "source_list": [ - "/opt/intel/parallel_studio_xe_2020/psxevars.sh" - ], - "batch_type": "shell", - "_comment": "DP-GEN will put 4 tasks together in one submitting script.", - "group_size": 4, - "_comment" : "The number of nodes.", - "number_node": 1, - "_comment" : "The number of CPUs.", - "cpu_per_node": 4, - "_comment" : "If you choose to run with multiple GPUs simultaneously, just ignore numb_gpu.", - "gpu_per_node": 0, - "kwargs": {}, - "strategy": { - "_comment" : "Allow the multi-GPU task running.", - "if_cuda_multi_devices": true - }, - "para_deg": 4, - "queue_name": "" - } + "_comment1": "This is an example of DP-GEN on Local device running with 4 GPUs", + "_comment2": "Last updated on 2021.5.9 for DP-GEN 0.9.2 by Ke XU", + "train": { + "_comment3": "Specify the installed path of DeePMD-kit", + "command": "/home/user/anaconda3/bin/dp", + "_comment4": "Specify machine settings", + "machine": { + "_comment5": "Supported batches include slurm, pbs, shell, lsf.", + "batch_type": "shell", + "context_type": "local", + "remote_root": "/tmp/dpwork", + "local_root": "./" }, - "model_devi": { - "machine": { - "batch_type": "shell", - "context_type": "local", - "remote_root": "/tmp/dpwork", - "local_root": "./" - }, - "resources": { - "source_list": [], - "module_list": [], - "batch_type": "shell", - "group_size": 4, - "number_node": 1, - "cpu_per_node": 4, - "gpu_per_node": 0, - "kwargs": {}, - "strategy": { - "if_cuda_multi_devices": true - }, - "para_deg": 4, - "queue_name": "" - }, - "command": "/home/user/Soft/Deepmd/lammps-stable_29Oct2020/src/lmp_mpi" + "resources": { + "module_list": [], + "_comment6": "Environment to be activated. This will generate source xxx/psxevars.sh in scripts. ", + "source_list": [ + "/opt/intel/parallel_studio_xe_2020/psxevars.sh" + ], + "batch_type": "shell", + "_comment7": "DP-GEN will put 4 tasks together in one submitting script.", + "group_size": 4, + "_comment8": "The number of nodes.", + "number_node": 1, + "_comment9": "The number of CPUs.", + "cpu_per_node": 4, + "_comment10": "If you choose to run with multiple GPUs simultaneously, just ignore numb_gpu.", + "gpu_per_node": 0, + "kwargs": {}, + "strategy": { + "_comment11": "Allow the multi-GPU task running.", + "if_cuda_multi_devices": true + }, + "para_deg": 4, + "queue_name": "" + } + }, + "model_devi": { + "machine": { + "batch_type": "shell", + "context_type": "local", + "remote_root": "/tmp/dpwork", + "local_root": "./" }, - "fp": { - "machine": { - "batch_type": "shell", - "context_type": "local", - "remote_root": "/tmp/dpwork", - "local_root": "./" - }, - "resources": { - "_comment" : "Load the intel compiler.", - "source_list": [ - "/opt/intel/parallel_studio_xe_2020/psxevars.sh" - ], - "_comment": "This will generate export PATH=/home/user/Soft/VASP/vasp.5.4.4-allbak/bin:$PATH in scripts;", - "envs": { - "PATH": "/home/user/Soft/VASP/vasp.5.4.4-allbak/bin:$PATH" - }, - "batch_type": "shell", - "group_size": 1, - "cpu_per_node": 16, - "kwargs": {}, - "queue_name": "", - "number_node": 1, - "gpu_per_node": 1 - }, - "command": "mpirun -n 16 vasp_std || :" + "resources": { + "source_list": [], + "module_list": [], + "batch_type": "shell", + "group_size": 4, + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 0, + "kwargs": {}, + "strategy": { + "if_cuda_multi_devices": true + }, + "para_deg": 4, + "queue_name": "" }, - "api_version": "1.0" -} + "command": "/home/user/Soft/Deepmd/lammps-stable_29Oct2020/src/lmp_mpi" + }, + "fp": { + "machine": { + "batch_type": "shell", + "context_type": "local", + "remote_root": "/tmp/dpwork", + "local_root": "./" + }, + "resources": { + "_comment12": "Load the intel compiler.", + "source_list": [ + "/opt/intel/parallel_studio_xe_2020/psxevars.sh" + ], + "_comment13": "This will generate export PATH=/home/user/Soft/VASP/vasp.5.4.4-allbak/bin:$PATH in scripts;", + "envs": { + "PATH": "/home/user/Soft/VASP/vasp.5.4.4-allbak/bin:$PATH" + }, + "batch_type": "shell", + "group_size": 1, + "cpu_per_node": 16, + "kwargs": {}, + "queue_name": "", + "number_node": 1, + "gpu_per_node": 1 + }, + "command": "mpirun -n 16 vasp_std || :" + }, + "api_version": "1.0" +} \ No newline at end of file diff --git a/examples/machine/DeePMD-kit-1.x/machine-local.json b/examples/machine/DeePMD-kit-1.x/machine-local.json index 2eb999743..c46989343 100644 --- a/examples/machine/DeePMD-kit-1.x/machine-local.json +++ b/examples/machine/DeePMD-kit-1.x/machine-local.json @@ -1,65 +1,65 @@ { - "api_version": "1.0", - "train": { - "_comment": "training on localhost", - "machine": { - "batch_type": "shell", - "context_type": "local", - "remote_root": "/home/wanghan/tmp/subs/", - "local_root": "./" - }, - "resources": { - "envs": {}, - "batch_type": "shell", - "group_size": 1, - "kwargs": {}, - "queue_name": "", - "number_node": 1, - "cpu_per_node": 1, - "gpu_per_node": 1 - }, - "command": "/home/wanghan/local/deepmd/1.*/dp" + "api_version": "1.0", + "train": { + "_comment1": "training on localhost", + "machine": { + "batch_type": "shell", + "context_type": "local", + "remote_root": "/home/wanghan/tmp/subs/", + "local_root": "./" }, - "model_devi": { - "_comment": "model devi on localhost", - "machine": { - "_comment": "If lazy_local, calculations are done directly in current folders.", - "batch_type": "shell", - "context_type": "lazylocal", - "local_root": "./" - }, - "resources": { - "batch_type": "shell", - "group_size": 5, - "kwargs": {}, - "queue_name": "", - "number_node": 1, - "cpu_per_node": 1, - "gpu_per_node": 1 - }, - "command": "/home/wanghan/local/bin/lmp_mpi_010" + "resources": { + "envs": {}, + "batch_type": "shell", + "group_size": 1, + "kwargs": {}, + "queue_name": "", + "number_node": 1, + "cpu_per_node": 1, + "gpu_per_node": 1 }, - "fp": { - "_comment": "fp on localhost", - "machine": { - "batch_type": "shell", - "context_type": "local", - "remote_root": "/home/wanghan/tmp/subs/", - "local_root": "./" - }, - "resources": { - "module_list": [ - "mpi" - ], - "_comment": "that's all", - "batch_type": "shell", - "group_size": 2, - "cpu_per_node": 4, - "kwargs": {}, - "queue_name": "", - "number_node": 1, - "gpu_per_node": 1 - }, - "command": "mpirun -n 4 /home/wanghan/local/bin/vasp_std" - } -} + "command": "/home/wanghan/local/deepmd/1.*/dp" + }, + "model_devi": { + "_comment2": "model devi on localhost", + "machine": { + "_comment3": "If lazy_local, calculations are done directly in current folders.", + "batch_type": "shell", + "context_type": "lazylocal", + "local_root": "./" + }, + "resources": { + "batch_type": "shell", + "group_size": 5, + "kwargs": {}, + "queue_name": "", + "number_node": 1, + "cpu_per_node": 1, + "gpu_per_node": 1 + }, + "command": "/home/wanghan/local/bin/lmp_mpi_010" + }, + "fp": { + "_comment4": "fp on localhost", + "machine": { + "batch_type": "shell", + "context_type": "local", + "remote_root": "/home/wanghan/tmp/subs/", + "local_root": "./" + }, + "resources": { + "module_list": [ + "mpi" + ], + "_comment5": "that's all", + "batch_type": "shell", + "group_size": 2, + "cpu_per_node": 4, + "kwargs": {}, + "queue_name": "", + "number_node": 1, + "gpu_per_node": 1 + }, + "command": "mpirun -n 4 /home/wanghan/local/bin/vasp_std" + } +} \ No newline at end of file diff --git a/examples/machine/DeePMD-kit-1.x/machine-lsf-slurm-cp2k.json b/examples/machine/DeePMD-kit-1.x/machine-lsf-slurm-cp2k.json index 0fab6e8b9..c044c1c77 100644 --- a/examples/machine/DeePMD-kit-1.x/machine-lsf-slurm-cp2k.json +++ b/examples/machine/DeePMD-kit-1.x/machine-lsf-slurm-cp2k.json @@ -1,98 +1,98 @@ { - "train": { - "machine": { - "batch_type": "slurm", - "context_type": "ssh", - "remote_profile": { - "hostname": "210.34.15.205", - "port": 22, - "username": "ybzhuang" - }, - "remote_root": "/home/ybzhuang/workdir", - "local_root": "./" - }, - "resources": { - "source_list": [], - "module_list": [ - "deepmd/1.2" - ], - "batch_type": "slurm", - "number_node": 1, - "cpu_per_node": 1, - "gpu_per_node": 1, - "queue_name": "emergency", - "custom_flags": [ - "#SBATCH -t 96:0:0" - ], - "kwargs": {}, - "wait_time": 60, - "group_size": 1 - }, - "command": "/share/apps/deepmd/compress/bin/python3.8-m deepmd" + "train": { + "machine": { + "batch_type": "slurm", + "context_type": "ssh", + "remote_profile": { + "hostname": "210.34.15.205", + "port": 22, + "username": "ybzhuang" + }, + "remote_root": "/home/ybzhuang/workdir", + "local_root": "./" }, - "model_devi": { - "machine": { - "batch_type": "slurm", - "context_type": "ssh", - "remote_profile": { - "hostname": "210.34.15.205", - "port": 22, - "username": "ybzhuang" - }, - "remote_root": "/home/ybzhuang/workdir", - "local_root": "./" - }, - "resources": { - "source_list": [], - "module_list": [ - "deepmd/1.2" - ], - "batch_type": "slurm", - "group_size": 5, - "number_node": 1, - "cpu_per_node": 1, - "gpu_per_node": 1, - "queue_name": "emergency", - "custom_flags": [ - "#SBATCH -t 96:0:0" - ], - "kwargs": {}, - "wait_time": 60 - }, - "command": "lmp_mpi" + "resources": { + "source_list": [], + "module_list": [ + "deepmd/1.2" + ], + "batch_type": "slurm", + "number_node": 1, + "cpu_per_node": 1, + "gpu_per_node": 1, + "queue_name": "emergency", + "custom_flags": [ + "#SBATCH -t 96:0:0" + ], + "kwargs": {}, + "wait_time": 60, + "group_size": 1 }, - "fp": { - "machine": { - "batch_type": "lsf", - "context_type": "ssh", - "remote_profile": { - "hostname": "localhost", - "port": 6666, - "username": "ybzhuang" - }, - "remote_root": "/data/ybzhuang/methane-dpgen/dpgen-tutorial-2020-08-23/dpgen-tutorial-mathane/workpath", - "local_root": "./" - }, - "resources": { - "source_list": [], - "module_list": [ - "intel/17.5.239", - "mpi/intel/2017.5.239", - "gcc/5.5.0", - "cp2k/7.1" - ], - "batch_type": "lsf", - "group_size": 50, - "number_node": 1, - "cpu_per_node": 32, - "queue_name": "53-medium", - "custom_flags": [ - "#BSUB -W 12:00:00" - ], - "kwargs": {}, - "gpu_per_node": 1 - }, - "command": "mpirun -n 32 cp2k.popt -i input.inp" + "command": "/share/apps/deepmd/compress/bin/python3.8-m deepmd" + }, + "model_devi": { + "machine": { + "batch_type": "slurm", + "context_type": "ssh", + "remote_profile": { + "hostname": "210.34.15.205", + "port": 22, + "username": "ybzhuang" + }, + "remote_root": "/home/ybzhuang/workdir", + "local_root": "./" }, - "api_version": "1.0" -} + "resources": { + "source_list": [], + "module_list": [ + "deepmd/1.2" + ], + "batch_type": "slurm", + "group_size": 5, + "number_node": 1, + "cpu_per_node": 1, + "gpu_per_node": 1, + "queue_name": "emergency", + "custom_flags": [ + "#SBATCH -t 96:0:0" + ], + "kwargs": {}, + "wait_time": 60 + }, + "command": "lmp_mpi" + }, + "fp": { + "machine": { + "batch_type": "lsf", + "context_type": "ssh", + "remote_profile": { + "hostname": "localhost", + "port": 6666, + "username": "ybzhuang" + }, + "remote_root": "/data/ybzhuang/methane-dpgen/dpgen-tutorial-2020-08-23/dpgen-tutorial-mathane/workpath", + "local_root": "./" + }, + "resources": { + "source_list": [], + "module_list": [ + "intel/17.5.239", + "mpi/intel/2017.5.239", + "gcc/5.5.0", + "cp2k/7.1" + ], + "batch_type": "lsf", + "group_size": 50, + "number_node": 1, + "cpu_per_node": 32, + "queue_name": "53-medium", + "custom_flags": [ + "#BSUB -W 12:00:00" + ], + "kwargs": {}, + "gpu_per_node": 1 + }, + "command": "mpirun -n 32 cp2k.popt -i input.inp" + }, + "api_version": "1.0" +} \ No newline at end of file diff --git a/examples/machine/DeePMD-kit-1.x/machine-pbs-gaussian.json b/examples/machine/DeePMD-kit-1.x/machine-pbs-gaussian.json index cc8eca816..876fee7b1 100644 --- a/examples/machine/DeePMD-kit-1.x/machine-pbs-gaussian.json +++ b/examples/machine/DeePMD-kit-1.x/machine-pbs-gaussian.json @@ -1,88 +1,88 @@ { - "api_version": "1.0", - "train": { - "machine": { - "batch_type": "lsf", - "context_type": "ssh", - "remote_profile": { - "hostname": "xxx.xxx.xxx.xxx", - "port": 22, - "username": "tzhu" - }, - "remote_root": "/gpfs/home/tzhu/jzzeng/dpgen_workdir", - "local_root": "./" - }, - "resources": { - "source_list": [ - "activate deepmd" - ], - "envs": { - "KMP_BLOCKTIME": 0, - "KMP_AFFINITY": "granularity=fine,verbose,compact,1,0" - }, - "batch_type": "lsf", - "group_size": 1, - "number_node": 1, - "cpu_per_node": 0, - "gpu_per_node": 1, - "queue_name": "newgpu", - "kwargs": {} - }, - "command": "/gpfs/home/tzhu/anaconda3/envs/python3.6/bin/dp" + "api_version": "1.0", + "train": { + "machine": { + "batch_type": "lsf", + "context_type": "ssh", + "remote_profile": { + "hostname": "xxx.xxx.xxx.xxx", + "port": 22, + "username": "tzhu" + }, + "remote_root": "/gpfs/home/tzhu/jzzeng/dpgen_workdir", + "local_root": "./" }, - "model_devi": { - "machine": { - "batch_type": "lsf", - "context_type": "ssh", - "remote_profile": { - "hostname": "xxx.xxx.xxx.xxx", - "port": 22, - "username": "tzhu" - }, - "remote_root": "/gpfs/home/tzhu/jzzeng/dpgen_workdir", - "local_root": "./" - }, - "resources": { - "envs": { - "KMP_BLOCKTIME": 0 - }, - "source_list": [ - "activate deepmd" - ], - "batch_type": "lsf", - "group_size": 1, - "number_node": 1, - "cpu_per_node": 0, - "gpu_per_node": 1, - "queue_name": "newgpu", - "kwargs": {} - }, - "command": "mpirun -n 0 /gpfs/home/tzhu/lammps-stable_5Jun2019/src/lmp_intel_cpu_intelmpi -pk intel 0 omp 2" + "resources": { + "source_list": [ + "activate deepmd" + ], + "envs": { + "KMP_BLOCKTIME": 0, + "KMP_AFFINITY": "granularity=fine,verbose,compact,1,0" + }, + "batch_type": "lsf", + "group_size": 1, + "number_node": 1, + "cpu_per_node": 0, + "gpu_per_node": 1, + "queue_name": "newgpu", + "kwargs": {} }, - "fp": { - "machine": { - "batch_type": "pbs", - "context_type": "ssh", - "remote_profile": { - "hostname": "xxx.xxx.xxx.xxx", - "port": 2323, - "username": "tzhu" - }, - "remote_root": "/public/home/tzhu/jzzeng/dpgen_workdir", - "local_root": "./" - }, - "resources": { - "batch_type": "pbs", - "group_size": 1, - "number_node": 1, - "cpu_per_node": 28, - "queue_name": "small", - "custom_flags": [ - "#PBS -l walltime=10:00:00" - ], - "kwargs": {}, - "gpu_per_node": 1 - }, - "command": "/public/home/tzhu/g16/g16 < input || :" - } -} + "command": "/gpfs/home/tzhu/anaconda3/envs/python3.6/bin/dp" + }, + "model_devi": { + "machine": { + "batch_type": "lsf", + "context_type": "ssh", + "remote_profile": { + "hostname": "xxx.xxx.xxx.xxx", + "port": 22, + "username": "tzhu" + }, + "remote_root": "/gpfs/home/tzhu/jzzeng/dpgen_workdir", + "local_root": "./" + }, + "resources": { + "envs": { + "KMP_BLOCKTIME": 0 + }, + "source_list": [ + "activate deepmd" + ], + "batch_type": "lsf", + "group_size": 1, + "number_node": 1, + "cpu_per_node": 0, + "gpu_per_node": 1, + "queue_name": "newgpu", + "kwargs": {} + }, + "command": "mpirun -n 0 /gpfs/home/tzhu/lammps-stable_5Jun2019/src/lmp_intel_cpu_intelmpi -pk intel 0 omp 2" + }, + "fp": { + "machine": { + "batch_type": "pbs", + "context_type": "ssh", + "remote_profile": { + "hostname": "xxx.xxx.xxx.xxx", + "port": 2323, + "username": "tzhu" + }, + "remote_root": "/public/home/tzhu/jzzeng/dpgen_workdir", + "local_root": "./" + }, + "resources": { + "batch_type": "pbs", + "group_size": 1, + "number_node": 1, + "cpu_per_node": 28, + "queue_name": "small", + "custom_flags": [ + "#PBS -l walltime=10:00:00" + ], + "kwargs": {}, + "gpu_per_node": 1 + }, + "command": "/public/home/tzhu/g16/g16 < input || :" + } +} \ No newline at end of file diff --git a/examples/machine/DeePMD-kit-1.x/machine-slurm-qe.json b/examples/machine/DeePMD-kit-1.x/machine-slurm-qe.json index 6f96d397d..cdff8d5f8 100644 --- a/examples/machine/DeePMD-kit-1.x/machine-slurm-qe.json +++ b/examples/machine/DeePMD-kit-1.x/machine-slurm-qe.json @@ -1,112 +1,112 @@ { - "_comment": "Last updated on 2021.4.30 for DP-GEN 0.9.2 by Yuzhi Zhang", - "train": { - "_comment" : "Specify the installed path of DeePMD-kit", - "command": "PATH_TO_DEEPMD/dp", - "_comment" : "Specify machine settings", - "machine": { - "batch_type": "slurm", - "context_type": "ssh", - "remote_profile": { - "hostname": "localhost", - "_comment" : "The port for connection, most common settings is 22", - "port": 22, - "_comment" : "Specify your username.", - "username": "USERNAME" - }, - "_comment" : "You should alwasy make sure that directory of work_path exits. ", - "remote_root": "PATH_TO_WORK", - "local_root": "./" - }, - "resources": { - "_comment" : "Environment to be activated. This will generate source PATH/train_new.env . ", - "source_list": [ - "PATH/train_new.env" - ], - "_comment" : " Module is a common tools on HPC clustes to manage softwares for multiple users.", - "_comment" : "Modules to be loaded. This will generate module load intel", - "module_list": [ - "intel" - ], - "batch_type": "slurm", - "_comment" : "The number of nodes. This will generate #SBATCH -N 1 in your script. ", - "number_node": 1, - "_comment" : "The number of CPUs. #SBATCH -n 4", - "cpu_per_node": 4, - "_comment" : "The number of GPU cards. #SBATCH --gres=gpu:1", - "gpu_per_node": 1, - "queue_name": "all", - "custom_flags": [ - "#SBATCH -t 23:0:0", - "#SBATCH --mem=16G", - "#SBATCH --exclude=gpu06,gpu07" - ], - "kwargs": {}, - "group_size": 1 - } + "_comment1": "Last updated on 2021.4.30 for DP-GEN 0.9.2 by Yuzhi Zhang", + "train": { + "_comment2": "Specify the installed path of DeePMD-kit", + "command": "PATH_TO_DEEPMD/dp", + "_comment3": "Specify machine settings", + "machine": { + "batch_type": "slurm", + "context_type": "ssh", + "remote_profile": { + "hostname": "localhost", + "_comment4": "The port for connection, most common settings is 22", + "port": 22, + "_comment5": "Specify your username.", + "username": "USERNAME" + }, + "_comment6": "You should alwasy make sure that directory of work_path exits. ", + "remote_root": "PATH_TO_WORK", + "local_root": "./" }, - "model_devi": { - "machine": { - "batch_type": "slurm", - "context_type": "ssh", - "remote_profile": { - "hostname": "localhost", - "port": 22, - "username": "USERNAME" - }, - "remote_root": "PATH_TO_WORK", - "local_root": "./" - }, - "resources": { - "source_list": [ - "PATH/lmp_new.env" - ], - "module_list": [], - "batch_type": "slurm", - "_comment": "DP-GEN will put 5 tasks together in one submitting script.", - "group_size": 5, - "number_node": 1, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "all", - "custom_flags": [ - "#SBATCH -t 23:0:0", - "#SBATCH --mem=16G", - "#SBATCH --exclude=" - ], - "kwargs": {} - }, - "command": "lmp_serial" + "resources": { + "_comment7": "Environment to be activated. This will generate source PATH/train_new.env . ", + "source_list": [ + "PATH/train_new.env" + ], + "_comment8": " Module is a common tools on HPC clustes to manage softwares for multiple users.", + "_comment9": "Modules to be loaded. This will generate module load intel", + "module_list": [ + "intel" + ], + "batch_type": "slurm", + "_comment10": "The number of nodes. This will generate #SBATCH -N 1 in your script. ", + "number_node": 1, + "_comment11": "The number of CPUs. #SBATCH -n 4", + "cpu_per_node": 4, + "_comment12": "The number of GPU cards. #SBATCH --gres=gpu:1", + "gpu_per_node": 1, + "queue_name": "all", + "custom_flags": [ + "#SBATCH -t 23:0:0", + "#SBATCH --mem=16G", + "#SBATCH --exclude=gpu06,gpu07" + ], + "kwargs": {}, + "group_size": 1 + } + }, + "model_devi": { + "machine": { + "batch_type": "slurm", + "context_type": "ssh", + "remote_profile": { + "hostname": "localhost", + "port": 22, + "username": "USERNAME" + }, + "remote_root": "PATH_TO_WORK", + "local_root": "./" }, - "fp": { - "machine": { - "batch_type": "slurm", - "context_type": "ssh", - "remote_profile": { - "hostname": "xxx.xxx.xxx.xxx", - "port": 22, - "username": "USERNAME" - }, - "remote_root": "PATH_TO_WORK", - "local_root": "./" - }, - "resources": { - "source_list": [], - "module_list": [ - "mpich/3.2.1-intel-2017.1" - ], - "batch_type": "slurm", - "group_size": 1, - "cpu_per_node": 8, - "gpu_per_node": 0, - "queue_name": "C032M0128G", - "custom_flags": [ - "#SBATCH -t 120:0:0" - ], - "kwargs": {}, - "number_node": 1 - }, - "command": "mpirun -n 8 /gpfs/share/home/1600017784/yuzhi/soft/QE-mpi/PW/src/pw.x < input" + "resources": { + "source_list": [ + "PATH/lmp_new.env" + ], + "module_list": [], + "batch_type": "slurm", + "_comment13": "DP-GEN will put 5 tasks together in one submitting script.", + "group_size": 5, + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "all", + "custom_flags": [ + "#SBATCH -t 23:0:0", + "#SBATCH --mem=16G", + "#SBATCH --exclude=" + ], + "kwargs": {} }, - "api_version": "1.0" -} + "command": "lmp_serial" + }, + "fp": { + "machine": { + "batch_type": "slurm", + "context_type": "ssh", + "remote_profile": { + "hostname": "xxx.xxx.xxx.xxx", + "port": 22, + "username": "USERNAME" + }, + "remote_root": "PATH_TO_WORK", + "local_root": "./" + }, + "resources": { + "source_list": [], + "module_list": [ + "mpich/3.2.1-intel-2017.1" + ], + "batch_type": "slurm", + "group_size": 1, + "cpu_per_node": 8, + "gpu_per_node": 0, + "queue_name": "C032M0128G", + "custom_flags": [ + "#SBATCH -t 120:0:0" + ], + "kwargs": {}, + "number_node": 1 + }, + "command": "mpirun -n 8 /gpfs/share/home/1600017784/yuzhi/soft/QE-mpi/PW/src/pw.x < input" + }, + "api_version": "1.0" +} \ No newline at end of file diff --git a/examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine.json b/examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine.json index ae6ac31ab..a31142677 100644 --- a/examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine.json +++ b/examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine.json @@ -1,107 +1,106 @@ { "api_version": "1.0", "deepmd_version": "2.0.1", - "train" : - { - "command": "dp", - "machine": { - "batch_type": "DpCloudServer", - "context_type": "DpCloudServerContext", - "local_root" : "./", - "remote_profile":{ - "email": "your lebesgue register email", - "password": "your lebesgue password", - "program_id": 0, - "input_data":{ - "api_version":2, - "job_type": "indicate", - "log_file": "00*/train.log", - "grouped":true, - "job_name": "dpgen_train_job", - "disk_size": 100, - "scass_type":"c8_m60_1 * NVIDIA P100", - "platform": "ali", - "image_name":"deepmd-kit:2.0.1", - "on_demand":0 - } + "train": { + "command": "dp", + "machine": { + "batch_type": "DpCloudServer", + "context_type": "DpCloudServerContext", + "local_root": "./", + "remote_profile": { + "email": "your lebesgue register email", + "password": "your lebesgue password", + "program_id": 0, + "input_data": { + "api_version": 2, + "job_type": "indicate", + "log_file": "00*/train.log", + "grouped": true, + "job_name": "dpgen_train_job", + "disk_size": 100, + "scass_type": "c8_m60_1 * NVIDIA P100", + "platform": "ali", + "image_name": "deepmd-kit:2.0.1", + "on_demand": 0 } - }, - "resources": { - "batch_type": "DpCloudServer", - "number_node": 1, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "GPU", - "group_size": 1 } }, - "model_devi": - { - "command": "lmp -i input.lammps -v restart 0", - "machine": { - "batch_type": "DpCloudServer", - "context_type": "DpCloudServerContext", - "local_root" : "./", - "remote_profile":{ - "email": "your lebesgue register email", - "password": "your lebesgue password", - "program_id": 0, - "input_data":{ - "api_version":2, - "job_type": "indicate", - "log_file": "*/model_devi.log", - "grouped":true, - "job_name": "dpgen_model_devi_job", - "disk_size": 200, - "scass_type":"c8_m60_1 * NVIDIA P100", - "platform": "ali", - "image_name":"deepmd-kit:2.0.1", - "on_demand":0 - } + "resources": { + "batch_type": "DpCloudServer", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "GPU", + "group_size": 1 + } + }, + "model_devi": { + "command": "lmp -i input.lammps -v restart 0", + "machine": { + "batch_type": "DpCloudServer", + "context_type": "DpCloudServerContext", + "local_root": "./", + "remote_profile": { + "email": "your lebesgue register email", + "password": "your lebesgue password", + "program_id": 0, + "input_data": { + "api_version": 2, + "job_type": "indicate", + "log_file": "*/model_devi.log", + "grouped": true, + "job_name": "dpgen_model_devi_job", + "disk_size": 200, + "scass_type": "c8_m60_1 * NVIDIA P100", + "platform": "ali", + "image_name": "deepmd-kit:2.0.1", + "on_demand": 0 } - }, - "resources": { - "batch_type": "DpCloudServer", - "number_node": 1, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "GPU", - "group_size": 5 } }, - "fp": - { - "command": "mpirun -n 16 vasp_std", - "machine": { - "batch_type": "DpCloudServer", - "context_type": "DpCloudServerContext", - "local_root" : "./", - "remote_profile":{ - "email": "your lebesgue register email", - "password": "your lebesgue password", - "program_id": 0, - "input_data":{ - "api_version":2, - "job_type": "indicate", - "log_file": "task*/fp.log", - "grouped":true, - "job_name": "dpgen_fp_job", - "disk_size": 100, - "scass_type":"c8_m8_cpu", - "platform": "ali", - "image_name":"vasp:5.4.4", - "on_demand":0 - } + "resources": { + "batch_type": "DpCloudServer", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "GPU", + "group_size": 5 + } + }, + "fp": { + "command": "mpirun -n 16 vasp_std", + "machine": { + "batch_type": "DpCloudServer", + "context_type": "DpCloudServerContext", + "local_root": "./", + "remote_profile": { + "email": "your lebesgue register email", + "password": "your lebesgue password", + "program_id": 0, + "input_data": { + "api_version": 2, + "job_type": "indicate", + "log_file": "task*/fp.log", + "grouped": true, + "job_name": "dpgen_fp_job", + "disk_size": 100, + "scass_type": "c8_m8_cpu", + "platform": "ali", + "image_name": "vasp:5.4.4", + "on_demand": 0 } - }, - "resources": { - "batch_type": "DpCloudServer", - "number_node": 1, - "cpu_per_node": 32, - "gpu_per_node": 0, - "queue_name": "CPU", - "group_size": 5, - "source_list": ["/opt/intel/oneapi/setvars.sh"] } + }, + "resources": { + "batch_type": "DpCloudServer", + "number_node": 1, + "cpu_per_node": 32, + "gpu_per_node": 0, + "queue_name": "CPU", + "group_size": 5, + "source_list": [ + "/opt/intel/oneapi/setvars.sh" + ] } -} + } +} \ No newline at end of file diff --git a/examples/run/ch4/machine.json b/examples/run/ch4/machine.json index 653f613d6..dcad44e9e 100644 --- a/examples/run/ch4/machine.json +++ b/examples/run/ch4/machine.json @@ -1,75 +1,77 @@ { - "deepmd_path": "/sharedext4/local/deepmd-kit-0.12.4/", - "train_machine": { - "machine_type": "slurm", - "hostname" : "localhost", - "port" : 22, - "username": "root", - "work_path" : "/sharedext4/generator/example/deep.gen/generator/ch4/", - "_comment" : "that's all" - }, - "train_resources": { - "numb_node": 1, - "numb_gpu": 1, - "task_per_node":8, - "partition" : "GPU-H", - "exclude_list" : [], - "source_list": [ "/sharedext4/local/deepmd-kit-0.12.4/bin/activate" ], - "module_list": [ ], - "time_limit": "23:0:0", - "mem_limit": 32, - "_comment": "that's all" - }, - - "model_devi_command": "/sharedext4/softwares/lammps/bin/lmp_serial", - "model_devi_group_size": 1, - "_comment": "model_devi on localhost", - "model_devi_machine": { - "machine_type": "slurm", - "hostname" : "localhost", - "port" : 22, - "username": "root", - "work_path" : "/sharedext4/generator/example/deep.gen/generator/ch4/", - "_comment" : "that's all" - }, - "_comment": " if use GPU, numb_nodes(nn) should always be 1 ", - "_comment": " if numb_nodes(nn) = 1 multi-threading rather than mpi is assumed", - "model_devi_resources": { - "numb_node": 1, - "numb_gpu": 0, - "task_per_node":1, - "source_list": ["/sharedext4/local/deepmd-kit-0.12.4/bin/lammps.activate" ], - "module_list": [ ], - "time_limit": "19:0:0", - "mem_limit": 32, - "partition" : "GPU-All", - "_comment": "that's all" - }, - - "_comment": "fp on localhost ", - "fp_command": "/sharedext4/vasp/vasp.5.4.4/bin/vasp_std", - "fp_group_size": 1, - "fp_machine": { - "machine_type": "slurm", - "hostname" : "localhost", - "port" : 22, - "username": "root", - "work_path" : "/sharedext4/generator/example/deep.gen/generator/ch4/", - "_comment" : "that's all" - }, - "fp_resources": { - "numb_node": 1, - "task_per_node":1, - "numb_gpu": 0, - "exclude_list" : [], - "source_list": ["/sharedext4/softwares/source/vasp_cpu.activate" ], - "module_list": [], - "with_mpi" : 1, - "time_limit": "1:0:0", - "partition" : "GPU-All", - "_comment": "that's all" - }, - - - "_comment": " that's all " -} + "deepmd_path": "/sharedext4/local/deepmd-kit-0.12.4/", + "train_machine": { + "machine_type": "slurm", + "hostname": "localhost", + "port": 22, + "username": "root", + "work_path": "/sharedext4/generator/example/deep.gen/generator/ch4/", + "_comment1": "that's all" + }, + "train_resources": { + "numb_node": 1, + "numb_gpu": 1, + "task_per_node": 8, + "partition": "GPU-H", + "exclude_list": [], + "source_list": [ + "/sharedext4/local/deepmd-kit-0.12.4/bin/activate" + ], + "module_list": [], + "time_limit": "23:0:0", + "mem_limit": 32, + "_comment2": "that's all" + }, + "model_devi_command": "/sharedext4/softwares/lammps/bin/lmp_serial", + "model_devi_group_size": 1, + "_comment3": "model_devi on localhost", + "model_devi_machine": { + "machine_type": "slurm", + "hostname": "localhost", + "port": 22, + "username": "root", + "work_path": "/sharedext4/generator/example/deep.gen/generator/ch4/", + "_comment4": "that's all" + }, + "_comment5": " if use GPU, numb_nodes(nn) should always be 1 ", + "_comment6": " if numb_nodes(nn) = 1 multi-threading rather than mpi is assumed", + "model_devi_resources": { + "numb_node": 1, + "numb_gpu": 0, + "task_per_node": 1, + "source_list": [ + "/sharedext4/local/deepmd-kit-0.12.4/bin/lammps.activate" + ], + "module_list": [], + "time_limit": "19:0:0", + "mem_limit": 32, + "partition": "GPU-All", + "_comment7": "that's all" + }, + "_comment8": "fp on localhost ", + "fp_command": "/sharedext4/vasp/vasp.5.4.4/bin/vasp_std", + "fp_group_size": 1, + "fp_machine": { + "machine_type": "slurm", + "hostname": "localhost", + "port": 22, + "username": "root", + "work_path": "/sharedext4/generator/example/deep.gen/generator/ch4/", + "_comment9": "that's all" + }, + "fp_resources": { + "numb_node": 1, + "task_per_node": 1, + "numb_gpu": 0, + "exclude_list": [], + "source_list": [ + "/sharedext4/softwares/source/vasp_cpu.activate" + ], + "module_list": [], + "with_mpi": 1, + "time_limit": "1:0:0", + "partition": "GPU-All", + "_comment10": "that's all" + }, + "_comment11": " that's all " +} \ No newline at end of file diff --git a/examples/run/ch4/param.json b/examples/run/ch4/param.json index 2a996e5fe..843530863 100644 --- a/examples/run/ch4/param.json +++ b/examples/run/ch4/param.json @@ -1,114 +1,193 @@ { - "type_map": ["H","C"], - "mass_map": [1, 12], - - "init_data_prefix": "/sharedext4/generator/example/deep.gen/data/", - - "init_data_sys": [ - "/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd" - ], - "init_batch_size": [ - 8 - ], - "sys_configs": [ - ["/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000[0-4]/POSCAR"], - ["/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000[5-9]/POSCAR"], - ["/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00001*/POSCAR"], - ["/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00002*/POSCAR"] - ], - "_comment": "0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25", - "sys_batch_size": [ - 8, 8, 8, 8 + "type_map": [ + "H", + "C" + ], + "mass_map": [ + 1, + 12 + ], + "init_data_prefix": "/sharedext4/generator/example/deep.gen/data/", + "init_data_sys": [ + "/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd" + ], + "init_batch_size": [ + 8 + ], + "sys_configs": [ + [ + "/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000[0-4]/POSCAR" ], - - - "_comment": " 00.train ", - "numb_models": 4, - "default_training_param" : { - "_comment": " model parameters", - "use_smooth": true, - "sel_a": [16,4], - "rcut_smth": 0.50, - "rcut": 5, - "filter_neuron": [10, 20, 40], - "filter_resnet_dt": false, - "n_axis_neuron": 12, - "n_neuron": [120,120,120], - "resnet_dt": true, - "coord_norm": true, - "type_fitting_net": false, - - "_comment": " traing controls", - "systems": [], - "set_prefix": "set", - "stop_batch": 30000, - "batch_size": 1, - "start_lr": 0.001, - "decay_steps": 150, - "decay_rate": 0.95, - "seed": 0, - - "start_pref_e": 0.02, - "limit_pref_e": 2, - "start_pref_f": 1000, - "limit_pref_f": 1, - "start_pref_v": 0.0, - "limit_pref_v": 0.0, - - "_comment": " display and restart", - "_comment": " frequencies counted in batch", - "disp_file": "lcurve.out", - "disp_freq": 1000, - "numb_test": 4, - "save_freq": 1000, - "save_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json", - - "_comment": "that's all" + [ + "/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000[5-9]/POSCAR" + ], + [ + "/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00001*/POSCAR" + ], + [ + "/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00002*/POSCAR" + ] + ], + "_comment1": "0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25", + "sys_batch_size": [ + 8, + 8, + 8, + 8 + ], + "_comment2": " 00.train ", + "numb_models": 4, + "default_training_param": { + "model": { + "descriptor": { + "seed": 0, + "type": "se_a", + "sel": [ + 16, + 4 + ], + "rcut": 5, + "rcut_smth": 0.5, + "neuron": [ + 10, + 20, + 40 + ], + "axis_neuron": 12, + "resnet_dt": false + }, + "fitting_net": { + "seed": 0, + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true + } + }, + "learning_rate": { + "type": "exp", + "decay_steps": 150, + "start_lr": 0.001, + "stop_lr": 3.505266624882874e-08 + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0.0, + "limit_pref_v": 0.0 + }, + "training": { + "seed": 0, + "stop_batch": 30000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "training_data": { + "systems": [], + "set_prefix": "set", + "batch_size": 1 + } + } + }, + "_comment8": " 01.model_devi ", + "_comment9": "model_devi_skip: the first x of the recorded frames", + "model_devi_dt": 0.002, + "model_devi_skip": 0, + "model_devi_f_trust_lo": 0.05, + "model_devi_f_trust_hi": 0.15, + "model_devi_clean_traj": true, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 100 + ], + "press": [ + 1.0 + ], + "trj_freq": 10, + "nsteps": 300, + "ensemble": "npt", + "_idx": "00" + }, + { + "sys_idx": [ + 1 + ], + "temps": [ + 100 + ], + "press": [ + 1.0 + ], + "trj_freq": 10, + "nsteps": 1000, + "ensemble": "npt", + "_idx": "01" }, - - "_comment": " 01.model_devi ", - "_comment": "model_devi_skip: the first x of the recorded frames", - "model_devi_dt": 0.002, - "model_devi_skip": 0, - "model_devi_f_trust_lo": 0.05, - "model_devi_f_trust_hi": 0.15, - "model_devi_clean_traj": true, - "model_devi_jobs": [ - {"sys_idx": [0], - "temps": [ 100], "press": [1.0], "trj_freq": 10, "nsteps": 300, "ensemble": "npt", "_idx": "00"}, - {"sys_idx": [1], - "temps": [ 100], "press": [1.0], "trj_freq": 10, "nsteps": 1000, "ensemble": "npt", "_idx": "01"}, - {"sys_idx": [2], - "temps": [ 100], "press": [1.0], "trj_freq": 10, "nsteps": 3000, "ensemble": "npt", "_idx": "02"}, - {"sys_idx": [3], - "temps": [ 100], "press": [1.0], "trj_freq": 10, "nsteps": 3000, "ensemble": "npt", "_idx": "03"} - ], - - - "_comment": " 02.fp ", - "fp_style": "vasp", - "shuffle_poscar": false, - "fp_task_max": 30, - "fp_task_min": 5, - "fp_pp_path": "/sharedext4/generator/example/deep.gen/data/ch4/", - "fp_pp_files": ["POTCAR"], - "fp_params": { - "_comment": "given in unit depending on the fp method", - "ecut": 400, - "ediff": 1e-6, - "kspacing": 2, - "_comment": "gauss, mp:N(methfessel-paxton:order by default order=1), fd(Fermi-Dirac)", - "smearing": "gauss", - "sigma": 0.05, - "_comment": "only for vasp, can be NONE, SCAN, TPSS, RTPSS, M06L or MBJ", - "metagga": "NONE", - "npar": 4, - "kpar": 1, - "_comment": " that's all " + { + "sys_idx": [ + 2 + ], + "temps": [ + 100 + ], + "press": [ + 1.0 + ], + "trj_freq": 10, + "nsteps": 3000, + "ensemble": "npt", + "_idx": "02" }, - "_comment": " that's all " -} + { + "sys_idx": [ + 3 + ], + "temps": [ + 100 + ], + "press": [ + 1.0 + ], + "trj_freq": 10, + "nsteps": 3000, + "ensemble": "npt", + "_idx": "03" + } + ], + "_comment10": " 02.fp ", + "fp_style": "vasp", + "shuffle_poscar": false, + "fp_task_max": 30, + "fp_task_min": 5, + "fp_pp_path": "/sharedext4/generator/example/deep.gen/data/ch4/", + "fp_pp_files": [ + "POTCAR" + ], + "fp_params": { + "_comment11": "given in unit depending on the fp method", + "ecut": 400, + "ediff": 1e-06, + "kspacing": 2, + "_comment12": "gauss, mp:N(methfessel-paxton:order by default order=1), fd(Fermi-Dirac)", + "smearing": "gauss", + "sigma": 0.05, + "_comment13": "only for vasp, can be NONE, SCAN, TPSS, RTPSS, M06L or MBJ", + "metagga": "NONE", + "npar": 4, + "kpar": 1, + "_comment14": " that's all " + }, + "_comment15": " that's all " +} \ No newline at end of file diff --git a/examples/run/deprecated/dp0.12-lammps-cp2k/CH4/param_CH4.json b/examples/run/deprecated/dp0.12-lammps-cp2k/CH4/param_CH4.json deleted file mode 100644 index b8163e785..000000000 --- a/examples/run/deprecated/dp0.12-lammps-cp2k/CH4/param_CH4.json +++ /dev/null @@ -1,136 +0,0 @@ -{ - "type_map": [ - "H", - "C" - ], - "mass_map": [ - 1, - 12 - ], - "init_data_prefix": "/public/data/deepmd-tutorial/data/", - "init_data_sys": [ - "deepmd" - ], - "init_batch_size": [ - 8 - ], - "sys_configs": [ - [ - "/public/data/deepmd-tutorial/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00000*/POSCAR" - ], - [ - "/public/data/deepmd-tutorial/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00001*/POSCAR" - ] - ], - "sys_batch_size": [ - 8, - 8, - 8, - 8 - ], - "_comment": " that's all ", - "numb_models": 4, - "default_training_param": { - "_comment": "that's all", - "use_smooth": true, - "sel_a": [ - 16, - 4 - ], - "rcut_smth": 0.5, - "rcut": 5, - "filter_neuron": [ - 10, - 20, - 40 - ], - "filter_resnet_dt": false, - "n_axis_neuron": 12, - "n_neuron": [ - 120, - 120, - 120 - ], - "resnet_dt": true, 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- "trj_freq": 10, - "nsteps": 5000, - "ensemble": "nvt", - "_idx": "01" - } - ], - "fp_style": "cp2k", - "shuffle_poscar": false, - "fp_task_max": 20, - "fp_task_min": 5, - "fp_params": { - "cutoff": "400", - "rel_cutoff": "50", - "functional": "PBE", - "pair_potential_path": "dftd3.dat", - "pair_ref_functional": "PBE", - "basis_path": "BASIS_MOLOPT", - "pp_path": "GTH_POTENTIALS", - "element_list": ["H", "C"], - "basis_list": ["DZVP-MOLOPT-GTH", "DZVP-MOLOPT-GTH"], - "_comment": "elment_list, basis_list, pp_list should be one to one correspondance", - "pp_list": ["GTH-PBE-q1", "GTH-PBE-q4"] - } -} diff --git a/examples/run/deprecated/dp0.12-lammps-pwmat/param_CH4.json b/examples/run/deprecated/dp0.12-lammps-pwmat/param_CH4.json deleted file mode 100644 index b1b3756ad..000000000 --- a/examples/run/deprecated/dp0.12-lammps-pwmat/param_CH4.json +++ /dev/null @@ -1,97 +0,0 @@ -{ - "type_map": ["H","C"], - "mass_map": [1, 12], - - "init_data_prefix": "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/", - - "init_data_sys": [ - "ch4/00.data" - ], - "init_batch_size": [ - 8 - ], - "sys_configs_prefix": - "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/", - "sys_configs": [ - ["/home/test/software/dpgen/examples/run/dp-lammps-pwmat/scale-1.000/00000*/POSCAR"], - ["/home/test/software/dpgen/examples/run/dp-lammps-pwmat/scale-1.000/00001*/POSCAR"] - ], - - "sys_batch_size": [ - 8, 8, 8, 8 - ], - - - "_comment": " 00.train ", - "numb_models": 4, - "default_training_param" : { - "_comment": " model parameters", - "use_smooth": true, - "sel_a": [16,4], - "rcut_smth": 0.50, - "rcut": 5, - "filter_neuron": [10, 20, 40], - "filter_resnet_dt": false, - "n_axis_neuron": 12, - "n_neuron": [120,120,120], - "resnet_dt": true, - "coord_norm": true, - "type_fitting_net": false, - - "_comment": " traing controls", - "systems": ["./00.data/"], - "set_prefix": "set", - "stop_batch": 2000, - "batch_size": 1, - "start_lr": 0.001, - 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300], "press": [0.0], "trj_freq": 10, "nsteps": 3000, "ensemble": "nvt", "_idx": "01"} - ], - - "_comment": " 02.fp ", - "fp_style": "pwmat", - "shuffle_poscar": false, - "fp_task_max": 20, - "fp_task_min": 8, - "fp_pp_path": ".", - "fp_pp_files": ["C.SG15.PBE.UPF", "H.SG15.PBE.UPF"], - "fp_incar" : "etot.input", - "_comment": " that's all " -} diff --git a/examples/run/deprecated/dp0.12-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.json b/examples/run/deprecated/dp0.12-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.json deleted file mode 100644 index 44ebced0e..000000000 --- a/examples/run/deprecated/dp0.12-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "type_map": [ - "H", - "C" - ], - "mass_map": [ - 1, - 12 - ], - "init_data_prefix": "/public/data/deepmd-tutorial/data/", - "init_data_sys": [ - "deepmd" - ], - "init_batch_size": [ - 8 - ], - "sys_configs": [ - [ - 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that's all " - }, - "_comment": " that's all " -} diff --git a/examples/run/deprecated/dp0.12-lammps-vasp/Al/param_al_all_gpu.json b/examples/run/deprecated/dp0.12-lammps-vasp/Al/param_al_all_gpu.json deleted file mode 100644 index f8950dca1..000000000 --- a/examples/run/deprecated/dp0.12-lammps-vasp/Al/param_al_all_gpu.json +++ /dev/null @@ -1,393 +0,0 @@ -{ - "type_map": ["Al"], - "mass_map": [27], - - "init_data_prefix": "/gpfs/share/home/1600017784/generator/Al/init/", - - "init_data_sys": [ - "al.fcc.02x02x02/02.md/sys-0032/deepmd", - "al.hcp.02x02x02/02.md/sys-0016/deepmd", - "al.bcc.02x02x02/02.md/sys-0016/deepmd" - ], - "init_batch_size": [ - 1, - 2, - 2 - ], - "sys_configs": [ - - ["/gpfs/share/home/1600017784/generator/Al/init/al.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00000[0-4]/POSCAR"], - ["/gpfs/share/home/1600017784/generator/Al/init/al.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00000[5-9]/POSCAR"], - 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], - "trj_freq": 10 - }, - { - "_idx": 4, - "ensemble": "npt", - "nsteps": 3000, - "press": [ - 1.0, - 10.0, - 100.0, - 1000.0, - 5000.0, - 10000.0, - 20000.0, - 50000.0 - ], - "sys_idx": [ - 4, - 12, - 20 - ], - "temps": [ - 50, - 132.0, - 198.0, - 264.0 - ], - "trj_freq": 10 - }, - { - "_idx": 5, - "ensemble": "npt", - "nsteps": 3000, - "press": [ - 1.0, - 10.0, - 100.0, - 1000.0, - 5000.0, - 10000.0, - 20000.0, - 50000.0 - ], - "sys_idx": [ - 5, - 13, - 21 - ], - "temps": [ - 50, - 132.0, - 198.0, - 264.0 - ], - "trj_freq": 10 - }, - { - "_idx": 6, - "ensemble": "npt", - "nsteps": 3000, - "press": [ - 1.0, - 10.0, - 100.0, - 1000.0, - 5000.0, - 10000.0, - 20000.0, - 50000.0 - ], - "sys_idx": [ - 6, - 14, - 22 - ], - "temps": [ - 50, - 132.0, - 198.0, - 264.0 - ], - "trj_freq": 10 - }, - { - "_idx": 7, - "ensemble": "npt", - "nsteps": 3000, - "press": [ - 1.0, - 10.0, - 100.0, - 1000.0, - 5000.0, - 10000.0, - 20000.0, - 50000.0 - ], - "sys_idx": [ - 7, - 15, - 23 - ], - "temps": [ - 50, - 132.0, - 198.0, - 264.0 - ], - "trj_freq": 10 - }, - { - "_idx": 8, - "ensemble": "npt", - "nsteps": 1000, - "press": [ - 1.0, - 10.0, - 100.0, - 1000.0, - 5000.0, - 10000.0, - 20000.0, - 50000.0 - ], - "sys_idx": [ - 0, - 8, - 16 - ], - "temps": [ - 330.0, - 396.0, - 462.0, - 528.0, - 594.0 - ], - "trj_freq": 10 - } -], - - - "_comment": " 02.fp ", - "fp_style": "vasp", - "shuffle_poscar": false, - "fp_task_max": 300, - "fp_task_min": 5, - "fp_pp_path": "/gpfs/share/home/1600017784/start/data/POTCAR/Al/", - "fp_pp_files": ["POTCAR"], - "fp_incar": "/gpfs/share/home/1600017784/start/pku_input_set/INCAR_metal_scf_gpu", - "_comment": " that's all " -} diff --git a/examples/run/deprecated/dp0.12-lammps-vasp/CH4/param_CH4.json b/examples/run/deprecated/dp0.12-lammps-vasp/CH4/param_CH4.json deleted file mode 100644 index 6af7ed649..000000000 --- a/examples/run/deprecated/dp0.12-lammps-vasp/CH4/param_CH4.json +++ /dev/null @@ -1,98 +0,0 @@ -{ - "type_map": ["H","C"], - "mass_map": [1, 12], - - "init_data_prefix": "/gpfs/share/home/1600017784/yuzhi/methane/init/", - - "init_data_sys": [ - "CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd" - ], - "init_batch_size": [ - 8 - ], - "sys_configs_prefix": - "/gpfs/share/home/1600017784/yuzhi/methane/init/", - "sys_configs": [ - ["CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000*/POSCAR"], - ["CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00001*/POSCAR"] - ], - - "sys_batch_size": [ - 8, 8, 8, 8 - ], - - - "_comment": " 00.train ", - "numb_models": 4, - "default_training_param" : { - "_comment": " model parameters", - "use_smooth": true, - "sel_a": [16,4], - "rcut_smth": 0.50, - "rcut": 5, - "filter_neuron": [10, 20, 40], - "filter_resnet_dt": false, - "n_axis_neuron": 12, - "n_neuron": [120,120,120], - "resnet_dt": true, - "coord_norm": true, - "type_fitting_net": false, - - "_comment": " traing controls", - "systems": [], - "set_prefix": "set", - "stop_batch": 2000, - "batch_size": 1, - "start_lr": 0.001, - "decay_steps": 100, - "decay_rate": 0.95, - "seed": 0, - - "start_pref_e": 0.02, - "limit_pref_e": 2, - "start_pref_f": 1000, - "limit_pref_f": 1, - "start_pref_v": 0.0, - "limit_pref_v": 0.0, - - "_comment": " display and restart", - "_comment": " frequencies counted in batch", - "disp_file": "lcurve.out", - "disp_freq": 1000, - "numb_test": 4, - "save_freq": 1000, - "save_ckpt": "model.ckpt", - "load_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json", - - "_comment": "that's all" - }, - - "_comment": " 01.model_devi ", - "_comment": "model_devi_skip: the first x of the recorded frames", - "model_devi_dt": 0.002, - "model_devi_skip": 0, - "model_devi_f_trust_lo": 0.05, - "model_devi_f_trust_hi": 0.15, - "model_devi_clean_traj": true, - "model_devi_jobs": [ - {"sys_idx": [0], - "temps": [ 100], "press": [1.0], "trj_freq": 10, "nsteps": 300, "ensemble": "nvt", "_idx": "00"}, - {"sys_idx": [1], - "temps": [ 100], "press": [1.0], "trj_freq": 10, "nsteps": 3000, "ensemble": "nvt", "_idx": "01"} - ], - - "_comment": " 02.fp ", - "cvasp": false, - "fp_style": "vasp", - "shuffle_poscar": false, - "fp_task_max": 20, - "fp_task_min": 5, - "fp_pp_path": "/gpfs/share/home/1600017784/yuzhi/methane/", - "fp_pp_files": ["POT_H","POT_C"], -"fp_incar" : "/gpfs/share/home/1600017784/yuzhi/methane/INCAR_methane", - "_comment": " that's all " -} diff --git a/examples/run/deprecated/dp1.x-gromacs-gaussian/param.json b/examples/run/deprecated/dp2.x-gromacs-gaussian/param.json similarity index 73% rename from examples/run/deprecated/dp1.x-gromacs-gaussian/param.json rename to examples/run/deprecated/dp2.x-gromacs-gaussian/param.json index 29065b3e4..4391640b2 100644 --- a/examples/run/deprecated/dp1.x-gromacs-gaussian/param.json +++ b/examples/run/deprecated/dp2.x-gromacs-gaussian/param.json @@ -14,24 +14,57 @@ 35 ], "init_data_prefix": "somplace/tyk2-dpgen", - "init_data_sys": ["init_data", "mdtraj_data"], + "init_data_sys": [ + "init_data", + "mdtraj_data" + ], "sys_configs_prefix": "somplace/tyk2-dpgen", "sys_configs": [ - ["model_devi/lig_ejm_31"], - ["model_devi/lig_ejm_42"], - ["model_devi/lig_ejm_43"], - ["model_devi/lig_ejm_44"], - ["model_devi/lig_ejm_45"], - ["model_devi/lig_ejm_46"], - ["model_devi/lig_ejm_47"], - ["model_devi/lig_ejm_48"], - ["model_devi/lig_ejm_49"], - ["model_devi/lig_ejm_50"], - ["model_devi/lig_ejm_54"], - ["model_devi/lig_ejm_55"], - ["model_devi/lig_jmc_27"], - ["model_devi/lig_jmc_28"], - ["model_devi/lig_jmc_30"] + [ + "model_devi/lig_ejm_31" + ], + [ + "model_devi/lig_ejm_42" + ], + [ + "model_devi/lig_ejm_43" + ], + [ + "model_devi/lig_ejm_44" + ], + [ + "model_devi/lig_ejm_45" + ], + [ + "model_devi/lig_ejm_46" + ], + [ + "model_devi/lig_ejm_47" + ], + [ + "model_devi/lig_ejm_48" + ], + [ + "model_devi/lig_ejm_49" + ], + [ + "model_devi/lig_ejm_50" + ], + [ + "model_devi/lig_ejm_54" + ], + [ + "model_devi/lig_ejm_55" + ], + [ + "model_devi/lig_jmc_27" + ], + [ + "model_devi/lig_jmc_28" + ], + [ + "model_devi/lig_jmc_30" + ] ], "sys_format": "gromacs/gro", "numb_models": 4, @@ -61,8 +94,8 @@ 48, 48 ], - "rcut_smth": 0.50, - "rcut": 6.00, + "rcut_smth": 0.5, + "rcut": 6.0, "neuron": [ 25, 50, @@ -85,7 +118,7 @@ "type": "exp", "start_lr": 0.001, "decay_steps": 2000, - "decay_rate": 0.95 + "stop_lr": 7.274491561439049e-15 }, "loss": { "start_pref_e": 0.02, @@ -98,18 +131,18 @@ "limit_pref_pf": 0 }, "training": { - "set_prefix": "set", "stop_batch": 1000000, "disp_file": "lcurve.out", "disp_freq": 1000, - "numb_test": 1, "save_freq": 1000, "save_ckpt": "model.ckpt", - "load_ckpt": "model.ckpt", "disp_training": true, "time_training": true, "profiling": false, - "profiling_file": "timeline.json" + "profiling_file": "timeline.json", + "training_data": { + "set_prefix": "set" + } } }, "model_devi_engine": "gromacs", @@ -123,8 +156,8 @@ "traj_filename": "deepmd_traj.gro" }, "model_devi_dt": 0.001, - "model_devi_f_trust_lo": 0.20, - "model_devi_f_trust_hi": 0.40, + "model_devi_f_trust_lo": 0.2, + "model_devi_f_trust_hi": 0.4, "model_devi_clean_traj": false, "model_devi_skip": 0, "model_devi_nopbc": true, @@ -159,7 +192,7 @@ ], "temps": [], "trj_freq": 10, - "_comment": "trj_freq should be consistent with nstxout in mdp" + "_comment1": "trj_freq should be consistent with nstxout in mdp" } ], "fp_style": "gaussian", @@ -173,4 +206,4 @@ "nproc": 16, "multiplicity": "auto" } -} +} \ No newline at end of file diff --git a/examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.json b/examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.json new file mode 100644 index 000000000..098b4224f --- /dev/null +++ b/examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.json @@ -0,0 +1,156 @@ +{ + "type_map": [ + "H", + "C" + ], + "mass_map": [ + 1, + 12 + ], + "init_data_prefix": "/public/data/deepmd-tutorial/data/", + "init_data_sys": [ + "deepmd" + ], + "init_batch_size": [ + 8 + ], + "sys_configs": [ + [ + "/public/data/deepmd-tutorial/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00000*/POSCAR" + ], + [ + "/public/data/deepmd-tutorial/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00001*/POSCAR" + ] + ], + "sys_batch_size": [ + 8, + 8, + 8, + 8 + ], + "_comment1": " that's all ", + "numb_models": 4, + "default_training_param": { + "model": { + "descriptor": { + "seed": 0, + "type": "se_a", + "sel": [ + 16, + 4 + ], + "rcut": 5, + "rcut_smth": 0.5, + "neuron": [ + 10, + 20, + 40 + ], + "axis_neuron": 12, + "resnet_dt": false + }, + "fitting_net": { + "seed": 0, + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true + } + }, + "learning_rate": { + "type": "exp", + "decay_steps": 200, + "start_lr": 0.001, + "stop_lr": 3.505266624882874e-08 + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0, + "limit_pref_v": 0 + }, + "training": { + "seed": 0, + "stop_batch": 40000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "training_data": { + "systems": [], + "set_prefix": "set", + "batch_size": 1 + } + } + }, + "model_devi_dt": 0.002, + "model_devi_skip": 0, + "model_devi_f_trust_lo": 0.05, + "model_devi_f_trust_hi": 0.15, + "model_devi_clean_traj": true, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 100 + ], + "press": [ + 1 + ], + "trj_freq": 10, + "nsteps": 1000, + "ensemble": "nvt", + "_idx": "00" + }, + { + "sys_idx": [ + 1 + ], + "temps": [ + 100 + ], + "press": [ + 1 + ], + "trj_freq": 10, + "nsteps": 5000, + "ensemble": "nvt", + "_idx": "01" + } + ], + "fp_style": "cp2k", + "shuffle_poscar": false, + "fp_task_max": 20, + "fp_task_min": 5, + "fp_params": { + "cutoff": "400", + "rel_cutoff": "50", + "functional": "PBE", + "pair_potential_path": "dftd3.dat", + "pair_ref_functional": "PBE", + "basis_path": "BASIS_MOLOPT", + "pp_path": "GTH_POTENTIALS", + "element_list": [ + "H", + "C" + ], + "basis_list": [ + "DZVP-MOLOPT-GTH", + "DZVP-MOLOPT-GTH" + ], + "_comment3": "elment_list, basis_list, pp_list should be one to one correspondance", + "pp_list": [ + "GTH-PBE-q1", + "GTH-PBE-q4" + ] + } +} \ No newline at end of file diff --git a/examples/run/deprecated/dp0.12-lammps-cp2k/CH4/param_CH4.yaml b/examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.yaml similarity index 98% rename from examples/run/deprecated/dp0.12-lammps-cp2k/CH4/param_CH4.yaml rename to examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.yaml index 8a7b83baf..358648077 100644 --- a/examples/run/deprecated/dp0.12-lammps-cp2k/CH4/param_CH4.yaml +++ b/examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.yaml @@ -61,7 +61,6 @@ default_training_param: numb_test: 4 save_freq: 1000 save_ckpt: model.ckpt - load_ckpt: model.ckpt disp_training: true time_training: true profiling: false diff --git a/examples/run/deprecated/dp0.12-lammps-pwmat/machine-slurm-pwmat-single.json b/examples/run/deprecated/dp2.x-lammps-pwmat/machine-slurm-pwmat-single.json similarity index 95% rename from examples/run/deprecated/dp0.12-lammps-pwmat/machine-slurm-pwmat-single.json rename to examples/run/deprecated/dp2.x-lammps-pwmat/machine-slurm-pwmat-single.json index 9138f0cbf..d245dbd2d 100644 --- a/examples/run/deprecated/dp0.12-lammps-pwmat/machine-slurm-pwmat-single.json +++ b/examples/run/deprecated/dp2.x-lammps-pwmat/machine-slurm-pwmat-single.json @@ -21,7 +21,7 @@ "module_list": [], "time_limit": "23:0:0" }, - "deepmd_path" : "/home/test/anaconda2/envs/python3/" + "deepmd_path": "/home/test/anaconda2/envs/python3/" } ], "model_devi": [ @@ -71,10 +71,10 @@ ], "time_limit": "120:0:0", "partition": "control", - "_comment": "that's All" + "_comment1": "that's All" }, "command": "mpirun -np 4 PWmat", "group_size": 5 } ] -} +} \ No newline at end of file diff --git a/examples/run/deprecated/dp2.x-lammps-pwmat/param_CH4.json b/examples/run/deprecated/dp2.x-lammps-pwmat/param_CH4.json new file mode 100644 index 000000000..beacfe0f3 --- /dev/null +++ b/examples/run/deprecated/dp2.x-lammps-pwmat/param_CH4.json @@ -0,0 +1,147 @@ +{ + "type_map": [ + "H", + "C" + ], + "mass_map": [ + 1, + 12 + ], + "init_data_prefix": "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/", + "init_data_sys": [ + "ch4/00.data" + ], + "init_batch_size": [ + 8 + ], + "sys_configs_prefix": "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/", + "sys_configs": [ + [ + "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/scale-1.000/00000*/POSCAR" + ], + [ + "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/scale-1.000/00001*/POSCAR" + ] + ], + "sys_batch_size": [ + 8, + 8, + 8, + 8 + ], + "_comment1": " 00.train ", + "numb_models": 4, + "default_training_param": { + "model": { + "descriptor": { + "seed": 0, + "type": "se_a", + "sel": [ + 16, + 4 + ], + "rcut": 5, + "rcut_smth": 0.5, + "neuron": [ + 10, + 20, + 40 + ], + "axis_neuron": 12, + "resnet_dt": false + }, + "fitting_net": { + "seed": 0, + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true + } + }, + "learning_rate": { + "type": "exp", + "decay_steps": 100, + "start_lr": 0.001, + "stop_lr": 0.0003584859224085419 + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0.0, + "limit_pref_v": 0.0 + }, + "training": { + "seed": 0, + "stop_batch": 2000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "training_data": { + "systems": [ + "./00.data/" + ], + "set_prefix": "set", + "batch_size": 1 + } + } + }, + "_comment7": " 01.model_devi ", + "_comment8": "model_devi_skip: the first x of the recorded frames", + "model_devi_dt": 0.002, + "model_devi_skip": 0, + "model_devi_f_trust_lo": 0.05, + "model_devi_f_trust_hi": 0.15, + "model_devi_clean_traj": true, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 300 + ], + "press": [ + 0.0 + ], + "trj_freq": 10, + "nsteps": 300, + "ensemble": "nvt", + "_idx": "00" + }, + { + "sys_idx": [ + 1 + ], + "temps": [ + 300 + ], + "press": [ + 0.0 + ], + "trj_freq": 10, + "nsteps": 3000, + "ensemble": "nvt", + "_idx": "01" + } + ], + "_comment9": " 02.fp ", + "fp_style": "pwmat", + "shuffle_poscar": false, + "fp_task_max": 20, + "fp_task_min": 8, + "fp_pp_path": ".", + "fp_pp_files": [ + "C.SG15.PBE.UPF", + "H.SG15.PBE.UPF" + ], + "fp_incar": "etot.input", + "_comment10": " that's all " +} \ No newline at end of file diff --git a/examples/run/deprecated/dp2.x-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.json b/examples/run/deprecated/dp2.x-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.json new file mode 100644 index 000000000..b85cd815c --- /dev/null +++ b/examples/run/deprecated/dp2.x-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.json @@ -0,0 +1,148 @@ +{ + "type_map": [ + "H", + "C" + ], + "mass_map": [ + 1, + 12 + ], + "init_data_prefix": "/public/data/deepmd-tutorial/data/", + "init_data_sys": [ + "deepmd" + ], + "init_batch_size": [ + 8 + ], + "sys_configs": [ + [ + "/public/data/deepmd-tutorial/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00000*/POSCAR" + ], + [ + "/public/data/deepmd-tutorial/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00001*/POSCAR" + ] + ], + "sys_batch_size": [ + 8, + 8, + 8, + 8 + ], + "_comment1": " that's all ", + "numb_models": 4, + "default_training_param": { + "model": { + "descriptor": { + "seed": 0, + "type": "se_a", + "sel": [ + 16, + 4 + ], + "rcut": 5, + "rcut_smth": 0.5, + "neuron": [ + 10, + 20, + 40 + ], + "axis_neuron": 12, + "resnet_dt": false + }, + "fitting_net": { + "seed": 0, + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true + } + }, + "learning_rate": { + "type": "exp", + "decay_steps": 200, + "start_lr": 0.001, + "stop_lr": 3.505266624882874e-08 + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0, + "limit_pref_v": 0 + }, + "training": { + "seed": 0, + "stop_batch": 40000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "training_data": { + "systems": [], + "set_prefix": "set", + "batch_size": 1 + } + } + }, + "model_devi_dt": 0.002, + "model_devi_skip": 0, + "model_devi_f_trust_lo": 0.05, + "model_devi_f_trust_hi": 0.15, + "model_devi_clean_traj": true, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 100 + ], + "press": [ + 1 + ], + "trj_freq": 10, + "nsteps": 1000, + "ensemble": "nvt", + "_idx": "00" + }, + { + "sys_idx": [ + 1 + ], + "temps": [ + 100 + ], + "press": [ + 1 + ], + "trj_freq": 10, + "nsteps": 5000, + "ensemble": "nvt", + "_idx": "01" + } + ], + "fp_style": "siesta", + "shuffle_poscar": false, + "fp_task_max": 20, + "fp_task_min": 5, + "fp_pp_path": ".", + "fp_pp_files": [ + "C.psf", + "H.psf" + ], + "fp_params": { + "ecut": 300, + "ediff": 0.0001, + "kspacing": 1.0, + "mixingWeight": 0.05, + "NumberPulay": 5, + "_comment3": " that's all " + }, + "_comment4": " that's all " +} \ No newline at end of file diff --git a/examples/run/deprecated/dp0.12-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.yaml b/examples/run/deprecated/dp2.x-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.yaml similarity index 98% rename from examples/run/deprecated/dp0.12-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.yaml rename to examples/run/deprecated/dp2.x-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.yaml index 6a3ae9598..77b426760 100644 --- a/examples/run/deprecated/dp0.12-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.yaml +++ b/examples/run/deprecated/dp2.x-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.yaml @@ -60,7 +60,6 @@ default_training_param: numb_test: 4 save_freq: 1000 save_ckpt: model.ckpt - load_ckpt: model.ckpt disp_training: true time_training: true profiling: false diff --git a/examples/run/deprecated/dp2.x-lammps-vasp/Al/param_al_all_gpu.json b/examples/run/deprecated/dp2.x-lammps-vasp/Al/param_al_all_gpu.json new file mode 100644 index 000000000..467a24ea6 --- /dev/null +++ b/examples/run/deprecated/dp2.x-lammps-vasp/Al/param_al_all_gpu.json @@ -0,0 +1,450 @@ +{ + "type_map": [ + "Al" + ], + "mass_map": [ + 27 + ], + "init_data_prefix": "/gpfs/share/home/1600017784/generator/Al/init/", + "init_data_sys": [ + "al.fcc.02x02x02/02.md/sys-0032/deepmd", + "al.hcp.02x02x02/02.md/sys-0016/deepmd", + "al.bcc.02x02x02/02.md/sys-0016/deepmd" + ], + "init_batch_size": [ + 1, + 2, + 2 + ], + "sys_configs": [ + [ + 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0, + "model_devi_f_trust_lo": 0.05, + "model_devi_f_trust_hi": 0.2, + "model_devi_clean_traj": false, + "model_devi_jobs": [ + { + "_idx": 0, + "ensemble": "npt", + "nsteps": 1000, + "press": [ + 1.0, + 10.0, + 100.0, + 1000.0, + 5000.0, + 10000.0, + 20000.0, + 50000.0 + ], + "sys_idx": [ + 0, + 8, + 16 + ], + "temps": [ + 50, + 132.0, + 198.0, + 264.0 + ], + "trj_freq": 10 + }, + { + "_idx": 1, + "ensemble": "npt", + "nsteps": 1000, + "press": [ + 1.0, + 10.0, + 100.0, + 1000.0, + 5000.0, + 10000.0, + 20000.0, + 50000.0 + ], + "sys_idx": [ + 1, + 9, + 17 + ], + "temps": [ + 50, + 132.0, + 198.0, + 264.0 + ], + "trj_freq": 10 + }, + { + "_idx": 2, + "ensemble": "npt", + "nsteps": 3000, + "press": [ + 1.0, + 10.0, + 100.0, + 1000.0, + 5000.0, + 10000.0, + 20000.0, + 50000.0 + ], + "sys_idx": [ + 2, + 10, + 18 + ], + "temps": [ + 50, + 132.0, + 198.0, + 264.0 + ], + "trj_freq": 10 + }, + { + "_idx": 3, + "ensemble": "npt", + "nsteps": 3000, + "press": [ + 1.0, + 10.0, + 100.0, + 1000.0, 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rename from examples/run/deprecated/dp0.12-lammps-vasp/Al/param_al_all_gpu.yaml rename to examples/run/deprecated/dp2.x-lammps-vasp/Al/param_al_all_gpu.yaml index 37409d69a..0a8d362fb 100644 --- a/examples/run/deprecated/dp0.12-lammps-vasp/Al/param_al_all_gpu.yaml +++ b/examples/run/deprecated/dp2.x-lammps-vasp/Al/param_al_all_gpu.yaml @@ -109,7 +109,6 @@ default_training_param: numb_test: 4 save_freq: 2000 save_ckpt: model.ckpt - load_ckpt: model.ckpt disp_training: true time_training: true profiling: false diff --git a/examples/run/deprecated/dp2.x-lammps-vasp/CH4/param_CH4.json b/examples/run/deprecated/dp2.x-lammps-vasp/CH4/param_CH4.json new file mode 100644 index 000000000..68c5ae374 --- /dev/null +++ b/examples/run/deprecated/dp2.x-lammps-vasp/CH4/param_CH4.json @@ -0,0 +1,146 @@ +{ + "type_map": [ + "H", + "C" + ], + "mass_map": [ + 1, + 12 + ], + "init_data_prefix": "/gpfs/share/home/1600017784/yuzhi/methane/init/", + "init_data_sys": [ + "CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd" + ], + "init_batch_size": [ + 8 + ], + "sys_configs_prefix": "/gpfs/share/home/1600017784/yuzhi/methane/init/", + "sys_configs": [ + [ + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000*/POSCAR" + ], + [ + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00001*/POSCAR" + ] + ], + "sys_batch_size": [ + 8, + 8, + 8, + 8 + ], + "_comment1": " 00.train ", + "numb_models": 4, + "default_training_param": { + "model": { + "descriptor": { + "seed": 0, + "type": "se_a", + "sel": [ + 16, + 4 + ], + "rcut": 5, + "rcut_smth": 0.5, + "neuron": [ + 10, + 20, + 40 + ], + "axis_neuron": 12, + "resnet_dt": false + }, + "fitting_net": { + "seed": 0, + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true + } + }, + "learning_rate": { + "type": "exp", + "decay_steps": 100, + "start_lr": 0.001, + "stop_lr": 0.0003584859224085419 + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0.0, + "limit_pref_v": 0.0 + }, + "training": { + "seed": 0, + "stop_batch": 2000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "training_data": { + "systems": [], + "set_prefix": "set", + "batch_size": 1 + } + } + }, + "_comment7": " 01.model_devi ", + "_comment8": "model_devi_skip: the first x of the recorded frames", + "model_devi_dt": 0.002, + "model_devi_skip": 0, + "model_devi_f_trust_lo": 0.05, + "model_devi_f_trust_hi": 0.15, + "model_devi_clean_traj": true, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 100 + ], + "press": [ + 1.0 + ], + "trj_freq": 10, + "nsteps": 300, + "ensemble": "nvt", + "_idx": "00" + }, + { + "sys_idx": [ + 1 + ], + "temps": [ + 100 + ], + "press": [ + 1.0 + ], + "trj_freq": 10, + "nsteps": 3000, + "ensemble": "nvt", + "_idx": "01" + } + ], + "_comment9": " 02.fp ", + "cvasp": false, + "fp_style": "vasp", + "shuffle_poscar": false, + "fp_task_max": 20, + "fp_task_min": 5, + "fp_pp_path": "/gpfs/share/home/1600017784/yuzhi/methane/", + "fp_pp_files": [ + "POT_H", + "POT_C" + ], + "fp_incar": "/gpfs/share/home/1600017784/yuzhi/methane/INCAR_methane", + "_comment10": " that's all " +} \ No newline at end of file diff --git a/examples/run/deprecated/dp0.12-lammps-vasp/CH4/param_CH4.yaml b/examples/run/deprecated/dp2.x-lammps-vasp/CH4/param_CH4.yaml similarity index 98% rename from examples/run/deprecated/dp0.12-lammps-vasp/CH4/param_CH4.yaml rename to examples/run/deprecated/dp2.x-lammps-vasp/CH4/param_CH4.yaml index 2a77eddef..7a34e9ef9 100644 --- a/examples/run/deprecated/dp0.12-lammps-vasp/CH4/param_CH4.yaml +++ b/examples/run/deprecated/dp2.x-lammps-vasp/CH4/param_CH4.yaml @@ -61,7 +61,6 @@ default_training_param: numb_test: 4 save_freq: 1000 save_ckpt: model.ckpt - load_ckpt: model.ckpt disp_training: true time_training: true profiling: false diff --git a/examples/run/deprecated/param-h2oscan-vasp.json b/examples/run/deprecated/param-h2oscan-vasp.json index 1ccc592b7..0d13136fd 100644 --- a/examples/run/deprecated/param-h2oscan-vasp.json +++ b/examples/run/deprecated/param-h2oscan-vasp.json @@ -1,209 +1,694 @@ { - "type_map": ["O", "H"], - "mass_map": [16, 2], - - "init_data_prefix": "/home/yixiaoc/SCR/wanghan/data/water.all.phase/init.train", - "init_data_sys": ["ice01c", - "ice01h", - "ice02", - "ice03", - "ice04", - "ice05", - "ice06", - "ice07", - "ice08", - "ice09", - "ice10", - "ice11", - "ice12", - "ice13", - "ice14", - "ice15", - "waterliquid/nvt-330K", - "waterliquid/nvt-360K" - ], - "init_batch_size": [1, 3, 3, 3, 1, 2, 3, 2, 4, 3, 2, 2, 3, 2, 3, 3, 1, 1], - "sys_configs": [ - ["/home/yixiaoc/SCR/wanghan/data/water.all.phase/init.md/ice01c/00009?/POSCAR"], - ["/home/yixiaoc/SCR/wanghan/data/water.all.phase/init.md/ice01c/0000[7-8]?/POSCAR"], - 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1, + "kpar": 1, + "_comment13": " that's all " + }, + "_comment14": " that's all " +} \ No newline at end of file diff --git a/examples/run/dp-calypso-vasp/machine.json b/examples/run/dp-calypso-vasp/machine.json index f07f2dd87..7a156efec 100644 --- a/examples/run/dp-calypso-vasp/machine.json +++ b/examples/run/dp-calypso-vasp/machine.json @@ -1,59 +1,67 @@ { "api_version": "1.0", "deepmd_version": "2.0.1", - "train" :[ + "train": [ { "command": "dp", "machine": { "batch_type": "pbs", "context_type": "lazylocal", - "local_root" : "./" + "local_root": "./" }, "resources": { - "envs": {"LD_LIBRARY_PATH": "/opt/software/cuda/10.1/lib64:$LD_LIBRARY_PATH"}, - "custom_flags":["#PBS -l walltime=48:0:0"], + "envs": { + "LD_LIBRARY_PATH": "/opt/software/cuda/10.1/lib64:$LD_LIBRARY_PATH" + }, + "custom_flags": [ + "#PBS -l walltime=48:0:0" + ], "number_node": 1, - "local_root":"./", + "local_root": "./", "cpu_per_node": 16, "gpu_per_node": 1, "queue_name": "T4_16_62", "group_size": 1 } - }], - "model_devi": - [{ - "calypso_path":"/home/zhenyu/workplace/dpgen/AA-2400/debug/calypso_input", - "deepmdkit_python":"/home/zhenyu/soft/deepmd-kit/envs/debug/bin/python", - "_deepmdkit_python":"this python will be used to optimize structures generated by CALYPSO with ase", - "_deepmdkit_python":"and also will be used to calculate model deviation in iter.000001/01.model_devi/model_devi_results", - "_deepmdkit_python":"with calypso_run_model_devi.py script", + } + ], + "model_devi": [ + { + "calypso_path": "/home/zhenyu/workplace/dpgen/AA-2400/debug/calypso_input", + "deepmdkit_python": "/home/zhenyu/soft/deepmd-kit/envs/debug/bin/python", + "_deepmdkit_python": "with calypso_run_model_devi.py script", "command": "", "machine": { "_batch_type": "pbs", "batch_type": "shell", "context_type": "lazylocal", - "remote_root": "/home/zhenyu/workplace/dpgen/AA-2400/debug/temp", - "local_root" : "./" + "remote_root": "/home/zhenyu/workplace/dpgen/AA-2400/debug/temp", + "local_root": "./" }, "resources": { - "envs": {"LD_LIBRARY_PATH": "/opt/software/cuda/10.1/lib64:$LD_LIBRARY_PATH"}, - "custom_flags":["#PBS -l walltime=48:0:0"], + "envs": { + "LD_LIBRARY_PATH": "/opt/software/cuda/10.1/lib64:$LD_LIBRARY_PATH" + }, + "custom_flags": [ + "#PBS -l walltime=48:0:0" + ], "number_node": 1, - "local_root":"./", + "local_root": "./", "cpu_per_node": 16, "gpu_per_node": 1, "queue_name": "T4_16_62", "group_size": 50 } - }], - "fp": - [{ + } + ], + "fp": [ + { "command": "mpirun -n 32 /opt/vasp/vasp_std", "machine": { "batch_type": "shell", "context_type": "lazylocal", - "local_root" : "./", - "remote_root": "/home/zhenyu/workplace/dpgen/AA-2400/debug/temp" + "local_root": "./", + "remote_root": "/home/zhenyu/workplace/dpgen/AA-2400/debug/temp" }, "resources": { "number_node": 1, @@ -61,10 +69,14 @@ "gpu_per_node": 0, "queue_name": "C_32_64", "group_size": 10, - "local_root":"./", - "custom_flags":["#PBS -l walltime=200:0:0"], - "source_list": ["/opt/intel/oneapi/setvars.sh"] + "local_root": "./", + "custom_flags": [ + "#PBS -l walltime=200:0:0" + ], + "source_list": [ + "/opt/intel/oneapi/setvars.sh" + ] } } ] -} +} \ No newline at end of file diff --git a/examples/run/dp-calypso-vasp/param.json b/examples/run/dp-calypso-vasp/param.json index 96f566938..4dc25b420 100644 --- a/examples/run/dp-calypso-vasp/param.json +++ b/examples/run/dp-calypso-vasp/param.json @@ -1,127 +1,412 @@ { - "model_devi_engine":"calypso", - "_calypso_path":"/home/zhenyu/workplace/dpgen/AA-2400/debug", - "_calypso_input_path":"/home/zhenyu/workplace/dpgen/AA-2400/debug/calypso_input", - "_model_devi_max_iter": 50, - "vsc":false, - - "type_map": [ - "Mg", + "model_devi_engine": "calypso", + "_calypso_path": "/home/zhenyu/workplace/dpgen/AA-2400/debug", + "_calypso_input_path": "/home/zhenyu/workplace/dpgen/AA-2400/debug/calypso_input", + "_model_devi_max_iter": 50, + "vsc": false, + "type_map": [ + "Mg", + "Al", + "Cu" + ], + "mass_map": [ + 24, + 27, + 64 + ], + "init_data_prefix": 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"model.ckpt", - "disp_training":true, - "time_training":true, - "profiling": false, - "profiling_file": "timeline.json" - }, - "_comment": "that's all" - }, - - "_comment": " 01.model_devi ", - "_comment": "model_devi_skip: the first x of the recorded frames", - "model_devi_dt": 0.002, - "model_devi_skip": 0, - "model_devi_f_trust_lo": 0.05, - "model_devi_f_trust_hi": 0.20, - "model_devi_clean_traj": false, - "model_devi_jobs": [ - { "_idx": 0, "ensemble": "npt", "nsteps": 50, "press": [1.0,2.0], "sys_idx": [0, 1], "temps": [50,100], "trj_freq": 10 } - ], - "_comment": " 02.fp ", - "fp_style": "vasp", - "shuffle_poscar": false, - "fp_task_max": 8, - "fp_task_min": 2, - "fp_pp_path": "/home/wanghan/study/deep.md/dpgen/almg/vasp", - "fp_pp_files": ["POTCAR.Al", "POTCAR.Mg"], - "fp_incar": "/home/wanghan/study/deep.md/dpgen/almg/vasp/INCAR", - "_comment": " that's all " -} diff --git a/examples/run/dp1.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-1.1.0.json b/examples/run/dp1.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-1.1.0.json deleted file mode 100644 index 4b4d92ba2..000000000 --- a/examples/run/dp1.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-1.1.0.json +++ /dev/null @@ -1,371 +0,0 @@ -{ - "type_map": ["Al"], - "mass_map": [27], - - "init_data_prefix": "/data1/yfb222333/2_dpgen_gpu_multi/init/", - - "init_data_sys": [ - "al.fcc.02x02x02/02.md/sys-0032/deepmd", - "al.hcp.02x02x02/02.md/sys-0016/deepmd", - "al.bcc.02x02x02/02.md/sys-0016/deepmd" - ], - "sys_configs": [ - - ["/data1/yfb222333/2_dpgen_gpu_multi/init/al.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00000[0-4]/POSCAR"], - ["/data1/yfb222333/2_dpgen_gpu_multi/init/al.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00000[5-9]/POSCAR"], - ["/data1/yfb222333/2_dpgen_gpu_multi/init/al.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00001*/POSCAR"], - ["/data1/yfb222333/2_dpgen_gpu_multi/init/al.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00002*/POSCAR"], - ["/data1/yfb222333/2_dpgen_gpu_multi/init/al.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00003*/POSCAR"], - ["/data1/yfb222333/2_dpgen_gpu_multi/init/al.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00004*/POSCAR"], - ["/data1/yfb222333/2_dpgen_gpu_multi/init/al.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00005*/POSCAR", - "/data1/yfb222333/2_dpgen_gpu_multi/init/al.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00006*/POSCAR"], - ["/data1/yfb222333/2_dpgen_gpu_multi/init/al.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00007*/POSCAR", - "/data1/yfb222333/2_dpgen_gpu_multi/init/al.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00008*/POSCAR"], - - ["/data1/yfb222333/2_dpgen_gpu_multi/init/al.hcp.02x02x02/01.scale_pert/sys-0016/scale-1.000/00000[0-4]/POSCAR"], - ["/data1/yfb222333/2_dpgen_gpu_multi/init/al.hcp.02x02x02/01.scale_pert/sys-0016/scale-1.000/00000[5-9]/POSCAR"], - 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["/data1/yfb222333/2_dpgen_gpu_multi/init/al.bcc.02x02x02/01.scale_pert/sys-0016/scale-1.000/00000[0-4]/POSCAR"], - ["/data1/yfb222333/2_dpgen_gpu_multi/init/al.bcc.02x02x02/01.scale_pert/sys-0016/scale-1.000/00000[5-9]/POSCAR"], - ["/data1/yfb222333/2_dpgen_gpu_multi/init/al.bcc.02x02x02/01.scale_pert/sys-0016/scale-1.000/00001*/POSCAR"], - ["/data1/yfb222333/2_dpgen_gpu_multi/init/al.bcc.02x02x02/01.scale_pert/sys-0016/scale-1.000/00002*/POSCAR"], - ["/data1/yfb222333/2_dpgen_gpu_multi/init/al.bcc.02x02x02/01.scale_pert/sys-0016/scale-1.000/00003*/POSCAR"], - ["/data1/yfb222333/2_dpgen_gpu_multi/init/al.bcc.02x02x02/01.scale_pert/sys-0016/scale-1.000/00004*/POSCAR"], - ["/data1/yfb222333/2_dpgen_gpu_multi/init/al.bcc.02x02x02/01.scale_pert/sys-0016/scale-1.000/00005*/POSCAR", - "/data1/yfb222333/2_dpgen_gpu_multi/init/al.bcc.02x02x02/01.scale_pert/sys-0016/scale-1.000/00006*/POSCAR"], - ["/data1/yfb222333/2_dpgen_gpu_multi/init/al.bcc.02x02x02/01.scale_pert/sys-0016/scale-1.000/00007*/POSCAR", - "/data1/yfb222333/2_dpgen_gpu_multi/init/al.bcc.02x02x02/01.scale_pert/sys-0016/scale-1.000/00008*/POSCAR"] - ], - "_comment": " 00.train ", - "numb_models": 4, - "default_training_param" : { - "model":{ - "_comment": " model parameters", - "type_map":["Al"], - "descriptor":{ - "type": "se_a", - "sel": [300], - "rcut_smth": 2.00, - "rcut": 8.00, - "neuron": [240, 240, 240], - "resnet_dt": true, - "axis_neuron": 12, - "seed": 1 -}, - "fitting_net":{ - "neuron": [25, 50, 100], - "resnet_dt": false, - "sedd": 1 -}}, - "learning_rate":{ - "type": "exp", - "start_lr": 0.001, - "decay_steps": 2000, - "decay_rate": 0.95 -}, - "loss":{ - "start_pref_e": 0.02, - "limit_pref_e": 2, - "start_pref_f": 1000, - "limit_pref_f": 1, - "start_pref_v": 0.0, - "limit_pref_v": 0.0 -}, - "training":{ - "coord_norm": true, - "type_fitting_net": false, - "_comment": " traing controls", - "systems": [], - "set_prefix": "set", - "stop_batch": 20000, - "batch_size": 1, - "seed": 0, - "_comment": " display and restart", - "_comment": " frequencies counted in batch", - "disp_file": "lcurve.out", - "disp_freq": 2000, - "numb_test": 4, - "save_freq": 2000, - "save_ckpt": "model.ckpt", - "load_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json", - "_comment": "that's all"} - }, - - "_comment": " 01.model_devi ", - "_comment": "model_devi_skip: the first x of the recorded frames", - "model_devi_dt": 0.002, - "model_devi_skip": 0, - "model_devi_f_trust_lo": 0.05, - "model_devi_f_trust_hi": 0.20, - "model_devi_clean_traj": false, - "model_devi_jobs": -[ - { - "_idx": 0, - "ensemble": "npt", - "nsteps": 1000, - "press": [ - 1.0, - 10.0, - 100.0, - 1000.0, - 5000.0, - 10000.0, - 20000.0, - 50000.0 - ], - "sys_idx": [ - 0, - 8, - 16 - ], - "temps": [ - 50, - 132.0, - 198.0, - 264.0 - ], - "trj_freq": 10 - }, - { - 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], - "trj_freq": 10 - }, - { - "_idx": 5, - "ensemble": "npt", - "nsteps": 3000, - "press": [ - 1.0, - 10.0, - 100.0, - 1000.0, - 5000.0, - 10000.0, - 20000.0, - 50000.0 - ], - "sys_idx": [ - 5, - 13, - 21 - ], - "temps": [ - 50, - 132.0, - 198.0, - 264.0 - ], - "trj_freq": 10 - }, - { - "_idx": 6, - "ensemble": "npt", - "nsteps": 3000, - "press": [ - 1.0, - 10.0, - 100.0, - 1000.0, - 5000.0, - 10000.0, - 20000.0, - 50000.0 - ], - "sys_idx": [ - 6, - 14, - 22 - ], - "temps": [ - 50, - 132.0, - 198.0, - 264.0 - ], - "trj_freq": 10 - }, - { - "_idx": 7, - "ensemble": "npt", - "nsteps": 3000, - "press": [ - 1.0, - 10.0, - 100.0, - 1000.0, - 5000.0, - 10000.0, - 20000.0, - 50000.0 - ], - "sys_idx": [ - 7, - 15, - 23 - ], - "temps": [ - 50, - 132.0, - 198.0, - 264.0 - ], - "trj_freq": 10 - }, - { - "_idx": 8, - "ensemble": "npt", - "nsteps": 1000, - "press": [ - 1.0, - 10.0, - 100.0, - 1000.0, - 5000.0, - 10000.0, - 20000.0, - 50000.0 - ], - "sys_idx": [ - 0, - 8, - 16 - ], - "temps": [ - 330.0, - 396.0, - 462.0, - 528.0, - 594.0 - ], - "trj_freq": 10 - } -], - - - "_comment": " 02.fp ", - "fp_style": "vasp", - "shuffle_poscar": false, - "fp_task_max": 300, - "fp_task_min": 5, - "fp_pp_path": "/data1/yfb222333/2_dpgen_gpu_multi/POTCAR-Al", - "fp_pp_files": ["POTCAR"], - "fp_incar": "/data1/yfb222333/2_dpgen_gpu_multi/INCAR_metal_scf_gpu", - "_comment": " that's all " -} diff --git a/examples/run/dp1.x-lammps-vasp/CH4/param_CH4_deepmd-kit-1.1.0.json b/examples/run/dp1.x-lammps-vasp/CH4/param_CH4_deepmd-kit-1.1.0.json deleted file mode 100644 index 7925ce3ee..000000000 --- a/examples/run/dp1.x-lammps-vasp/CH4/param_CH4_deepmd-kit-1.1.0.json +++ /dev/null @@ -1,137 +0,0 @@ -{ - "type_map": [ - "H", - "C" - ], - "mass_map": [ - 1, - 12 - ], - "init_data_prefix": "/data1/yfb222333/2_dpgen_gpu_multi", - "init_data_sys": [ - "CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd" - ], - "sys_configs_prefix": "/data1/yfb222333/2_dpgen_gpu_multi", - "sys_configs": [ - [ - "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000*/POSCAR" - ], - [ - "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00001*/POSCAR" - ] - ], - "_comment": " that's all ", - "numb_models": 4, - "default_training_param": { - "model": { - "type_map": [ - "H", - "C" - ], - "descriptor": { - "type": "se_a", - "sel": [ - 16, - 4 - ], - "rcut_smth": 0.5, - "rcut": 5, - "neuron": [ - 120, - 120, - 120 - ], - "resnet_dt": true, - "axis_neuron": 12, - "seed": 1 - }, - "fitting_net": { - "neuron": [ - 25, - 50, - 100 - ], - "resnet_dt": false, - "seed": 1 - } - }, - "learning_rate": { - "type": "exp", - "start_lr": 0.001, - "decay_steps": 100, - "decay_rate": 0.95 - }, - "loss": { - "start_pref_e": 0.02, - "limit_pref_e": 2, - "start_pref_f": 1000, - "limit_pref_f": 1, - "start_pref_v": 0.0, - "limit_pref_v": 0.0 - }, - "training": { - "set_prefix": "set", - "stop_batch": 2000, - "batch_size": 1, - "disp_file": "lcurve.out", - "disp_freq": 1000, - "numb_test": 4, - "save_freq": 1000, - "save_ckpt": "model.ckpt", - "load_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json", - "_comment": "that's all" - } - }, - "model_devi_dt": 0.002, - "model_devi_skip": 0, - "model_devi_f_trust_lo": 0.05, - "model_devi_f_trust_hi": 0.15, - "model_devi_clean_traj": true, - "model_devi_jobs": [ - { - "sys_idx": [ - 0 - ], - "temps": [ - 100 - ], - "press": [ - 1.0 - ], - "trj_freq": 10, - "nsteps": 300, - "ensemble": "nvt", - "_idx": "00" - }, - { - "sys_idx": [ - 1 - ], - "temps": [ - 100 - ], - "press": [ - 1.0 - ], - "trj_freq": 10, - "nsteps": 3000, - "ensemble": "nvt", - "_idx": "01" - } - ], - "fp_style": "vasp", - "shuffle_poscar": false, - "fp_task_max": 20, - "fp_task_min": 5, - "fp_pp_path": "/data1/yfb222333/2_dpgen_gpu_multi", - "fp_pp_files": [ - "POTCAR_H", - "POTCAR_C" - ], - "_comments" : "We can only provide empty files in public, you should provide valid POTCARS yourself when running DP-GEN", - "fp_incar": "/data1/yfb222333/2_dpgen_gpu_multi/INCAR_methane" -} diff --git a/examples/run/dp1.x_lammps_gaussian/dodecane/dodecane.json b/examples/run/dp1.x_lammps_gaussian/dodecane/dodecane.json deleted file mode 100644 index b6f80d142..000000000 --- a/examples/run/dp1.x_lammps_gaussian/dodecane/dodecane.json +++ /dev/null @@ -1,84 +0,0 @@ -{ - "type_map": ["C", "H"], - "mass_map": [12.011, 1.008], - "init_data_prefix": "/home/jzzeng/0719dodecane/gen/", - "init_data_sys": ["init_data"], - "sys_configs": [ - ["/home/jzzeng/0719dodecane/gen/data.dodecane.atomic"] - ], - "sys_format":"lammps/lmp", - "numb_models": 4, - "default_training_param" : { - "model":{ - "type_map": ["C","H"], - "descriptor":{ - "type":"se_a", - "sel": [40, 80], - "rcut_smth": 1.00, - "rcut": 6.00, - "neuron": [25, 50, 100], - "resnet_dt": false, - "axis_neuron": 12 - }, - "fitting_net":{ - "neuron": [240, 240, 240], - "resnet_dt": true - } - }, - "learning_rate":{ - "type": "exp", - "start_lr": 0.001, - "decay_steps": 400, - "decay_rate": 0.99 - }, - "loss":{ - "start_pref_e": 0.02, - "limit_pref_e": 1, - "start_pref_f": 1000, - "limit_pref_f": 1, - "start_pref_v": 0, - "limit_pref_v": 0, - "start_pref_pf": 0, - "limit_pref_pf": 0 - }, - "training":{ - "set_prefix": "set", - "stop_batch": 400000, - "disp_file": "lcurve.out", - "disp_freq": 1000, - "numb_test": 1, - "save_freq": 1000, - "save_ckpt": "model.ckpt", - "load_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json" - } - }, - "use_clusters": true, - "cluster_cutoff": 3.5, - "cluster_minify": true, - "use_relative": true, - "epsilon": 1.0, - "model_devi_dt": 0.0001, - "model_devi_skip": 100, - "model_devi_f_trust_lo": 0.20, - "model_devi_f_trust_hi": 0.45, - "model_devi_clean_traj": false, - "model_devi_jobs": [ - {"sys_idx": [0], "temps": [ 3000], "trj_freq": 10, "nsteps": 2000, "ensemble": "nvt", "_idx": "00"}, - {"sys_idx": [0], "temps": [ 3000], "trj_freq": 10, "nsteps": 4000, "ensemble": "nvt", "_idx": "01"}, - {"sys_idx": [0], "temps": [ 3000], "trj_freq": 10, "nsteps": 8000, "ensemble": "nvt", "_idx": "02"}, - {"sys_idx": [0], "temps": [ 3000], "trj_freq": 10, "nsteps": 16000, "ensemble": "nvt", "_idx": "03"} - ], - "fp_style": "gaussian", - "shuffle_poscar": false, - "fp_task_max": 1000, - "fp_task_min": 10, - "fp_params": { - "keywords": "force mn15/6-31g**", - "nproc": 4, - "multiplicity": "auto" - } -} diff --git a/examples/run/dp2.x-gromacs-gaussian/param.json b/examples/run/dp2.x-gromacs-gaussian/param.json index 86561e34a..089ab67a4 100644 --- a/examples/run/dp2.x-gromacs-gaussian/param.json +++ b/examples/run/dp2.x-gromacs-gaussian/param.json @@ -1,34 +1,100 @@ { - "type_map": ["H", "C", "N", "O", "F", "S", "Cl"], - "mass_map": [2, 12, 14, 16, 17, 32, 35], + "type_map": [ + "H", + "C", + "N", + "O", + "F", + "S", + "Cl" + ], + "mass_map": [ + 2, + 12, + 14, + 16, + 17, + 32, + 35 + ], "init_data_prefix": "/path/to/init/data", - "init_data_sys": ["data.init"], + "init_data_sys": [ + "data.init" + ], "sys_configs_prefix": "/path/to/model/devi/data", "sys_configs": [ - ["model_devi/CHEMBL3402749_500"], - ["model_devi/CHEMBL3402741_400"], - ["model_devi/CHEMBL3402748_5300"], - ["model_devi/CHEMBL3402743_42"], - ["model_devi/CHEMBL3402761_1"], - ["model_devi/CHEMBL3402756_2.7"], - ["model_devi/CHEMBL3402750_400"], - ["model_devi/CHEMBL3402764_90"], - ["model_devi/CHEMBL3402758_10"], - ["model_devi/CHEMBL3402754_40"], - ["model_devi/CHEMBL3402747_3400"], - ["model_devi/CHEMBL3402762_1"], - ["model_devi/CHEMBL3402744_300"], - ["model_devi/CHEMBL3402752_30000"], - ["model_devi/CHEMBL3402742_23"], - ["model_devi/CHEMBL3402759_5.7"], - ["model_devi/CHEMBL3402745_200"], - ["model_devi/CHEMBL3402757_6.5"], - ["model_devi/CHEMBL3402755_4200"], - ["model_devi/CHEMBL3402751_2100"], - ["model_devi/CHEMBL3402753_200"], - ["model_devi/CHEMBL3402763_90"], - ["model_devi/CHEMBL3402765_11-charged-pKa-8.1"], - ["model_devi/CHEMBL3402760_1"] + [ + "model_devi/CHEMBL3402749_500" + ], + [ + "model_devi/CHEMBL3402741_400" + ], + [ + "model_devi/CHEMBL3402748_5300" + ], + [ + "model_devi/CHEMBL3402743_42" + ], + [ + "model_devi/CHEMBL3402761_1" + ], + [ + "model_devi/CHEMBL3402756_2.7" + ], + [ + "model_devi/CHEMBL3402750_400" + ], + [ + "model_devi/CHEMBL3402764_90" + ], + [ + "model_devi/CHEMBL3402758_10" + ], + [ + "model_devi/CHEMBL3402754_40" + ], + [ + "model_devi/CHEMBL3402747_3400" + ], + [ + "model_devi/CHEMBL3402762_1" + ], + [ + "model_devi/CHEMBL3402744_300" + ], + [ + "model_devi/CHEMBL3402752_30000" + ], + [ + "model_devi/CHEMBL3402742_23" + ], + [ + "model_devi/CHEMBL3402759_5.7" + ], + [ + "model_devi/CHEMBL3402745_200" + ], + [ + "model_devi/CHEMBL3402757_6.5" + ], + [ + "model_devi/CHEMBL3402755_4200" + ], + [ + "model_devi/CHEMBL3402751_2100" + ], + [ + "model_devi/CHEMBL3402753_200" + ], + [ + "model_devi/CHEMBL3402763_90" + ], + [ + "model_devi/CHEMBL3402765_11-charged-pKa-8.1" + ], + [ + "model_devi/CHEMBL3402760_1" + ] ], "sys_charges": [ 0, @@ -68,19 +134,43 @@ "train_param": "input.json", "default_training_param": { "model": { - "type_map": ["H", "C", "N", "O", "F", "S", "Cl"], + "type_map": [ + "H", + "C", + "N", + "O", + "F", + "S", + "Cl" + ], "descriptor": { "type": "se_e2_a", - "sel": [40, 48, 48, 48, 48, 48, 48], - "rcut_smth": 0.50, - "rcut": 6.00, - "neuron": [25, 50, 100], + "sel": [ + 40, + 48, + 48, + 48, + 48, + 48, + 48 + ], + "rcut_smth": 0.5, + "rcut": 6.0, + "neuron": [ + 25, + 50, + 100 + ], "resnet_dt": false, "axis_neuron": 16, "type_one_side": true }, "fitting_net": { - "neuron": [240, 240, 240], + "neuron": [ + 240, + 240, + 240 + ], "resnet_dt": true, "type": "ener" } @@ -102,7 +192,6 @@ "numb_steps": 1000000, "disp_file": "lcurve.out", "disp_freq": 1000, - "numb_test": 1, "save_freq": 1000, "save_ckpt": "model.ckpt" } @@ -119,16 +208,28 @@ "group_name": "Other" }, "model_devi_dt": 0.001, - "model_devi_f_trust_lo": 0.20, - "model_devi_f_trust_hi": 0.60, + "model_devi_f_trust_lo": 0.2, + "model_devi_f_trust_hi": 0.6, "model_devi_clean_traj": false, "model_devi_skip": 0, "model_devi_nopbc": true, "model_devi_activation_func": [ - ["tanh", "tanh"], - ["tanh", "tanh"], - ["tanh", "tanh"], - ["tanh", "tanh"] + [ + "tanh", + "tanh" + ], + [ + "tanh", + "tanh" + ], + [ + "tanh", + "tanh" + ], + [ + "tanh", + "tanh" + ] ], "model_devi_jobs": [ { @@ -136,9 +237,32 @@ "ensemble": "nvt", "nsteps": 100, "press": [], - "sys_idx": [ 0, 1, 2, 3, 4, 5, 6, 7, - 8, 9, 10, 11, 12, 13, 14, 15, - 16, 17, 18, 19, 20, 21, 22, 23], + "sys_idx": [ + 0, + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11, + 12, + 13, + 14, + 15, + 16, + 17, + 18, + 19, + 20, + 21, + 22, + 23 + ], "temps": [], "trj_freq": 1 } @@ -154,4 +278,4 @@ "nproc": 28, "multiplicity": 1 } -} +} \ No newline at end of file diff --git a/examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/machine.json b/examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/machine.json new file mode 100644 index 000000000..705ab5733 --- /dev/null +++ b/examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/machine.json @@ -0,0 +1,85 @@ +{ + "api_version": "1.0", + "train": [ + { + "command": "dp", + "machine": { + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/user1234/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "user1234" + } + }, + "resources": { + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "T4_4_15", + "group_size": 1, + "custom_flags": [ + "#SBATCH --mem=32G" + ], + "strategy": { + "if_cuda_multi_devices": true + }, + "para_deg": 3, + "source_list": [ + "/home/user1234/deepmd.1.2.4.env" + ] + } + } + ], + "model_devi": [ + { + "command": "lmp", + "machine": { + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/user1234/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "user1234" + } + }, + "resources": { + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "T4_4_15", + "group_size": 5, + "source_list": [ + "/home/user1234/deepmd.1.2.4.env" + ] + } + } + ], + "fp": [ + { + "command": "ABACUS.mpi", + "machine": { + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/user1234/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "user1234" + } + }, + "resources": { + "number_node": 1, + "cpu_per_node": 32, + "gpu_per_node": 0, + "queue_name": "G_32_128", + "group_size": 1, + "source_list": [ + "~/abacus.env" + ] + } + } + ] +} \ No newline at end of file diff --git a/examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/param.json b/examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/param.json new file mode 100644 index 000000000..61983b76b --- /dev/null +++ b/examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/param.json @@ -0,0 +1,171 @@ +{ + "type_map": [ + "H", + "C" + ], + "mass_map": [ + 1.0, + 12.0 + ], + "_comment1": "initial data set for Training and the number of frames in each training batch", + "init_data_prefix": "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/5_dpgen_examples/dpgen-example/run_abacus/", + "init_data_sys": [ + "abacus_init_data" + ], + "init_batch_size": [ + 8 + ], + "_comment2": "configurations for starting MD in Exploration and batch sizes when traning snapshots derived from these configs (if they were selected)", + "sys_configs_prefix": "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/5_dpgen_examples/dpgen-example/run", + "sys_configs": [ + [ + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/000000/POSCAR", + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/000001/POSCAR", + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00000[2-9]/POSCAR" + ], + [ + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00001*/POSCAR" + ] + ], + "sys_batch_size": [ + 8, + 8 + ], + "_comment3": " 00.train ", + "numb_models": 4, + "default_training_param": { + "model": { + "type_map": [ + "H", + "C" + ], + "descriptor": { + "type": "se_a", + "sel": [ + 16, + 4 + ], + "rcut_smth": 0.5, + "rcut": 5.0, + "neuron": [ + 10, + 20, + 40 + ], + "resnet_dt": false, + "axis_neuron": 12, + "seed": 0 + }, + "fitting_net": { + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true, + "coord_norm": true, + "type_fitting_net": false, + "seed": 0 + } + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0, + "limit_pref_v": 0 + }, + "learning_rate": { + "type": "exp", + "start_lr": 0.001, + "decay_steps": 180, + "stop_lr": 0.0005655675757628467 + }, + "training": { + "numb_steps": 2000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "_comment4": "that's all", + "training_data": { + "set_prefix": "set", + "batch_size": 1 + } + } + }, + "_comment5": " 01.model_devi ", + "model_devi_dt": 0.002, + "model_devi_skip": 0, + "model_devi_f_trust_lo": 0.05, + "model_devi_f_trust_hi": 0.15, + "model_devi_clean_traj": false, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 100 + ], + "press": [ + 1 + ], + "trj_freq": 10, + "nsteps": 3000, + "ensemble": "nvt", + "_idx": "00" + }, + { + "sys_idx": [ + 1 + ], + "temps": [ + 150 + ], + "press": [ + 1 + ], + "trj_freq": 10, + "nsteps": 9000, + "ensemble": "nvt", + "_idx": "01" + } + ], + "_comment6": " 02.fp ", + "fp_style": "abacus", + "shuffle_poscar": false, + "fp_task_max": 50, + "fp_task_min": 8, + "fp_pp_path": "./", + "fp_pp_files": [ + "H_ONCV_PBE-1.0.upf", + "C_ONCV_PBE-1.0.upf" + ], + "fp_orb_files": [ + "H_gga_8au_60Ry_2s1p.orb", + "C_gga_8au_60Ry_2s2p1d.orb" + ], + "fp_dpks_descriptor": "jle.orb", + "user_fp_params": { + "ntype": 2, + "cal_force": 1, + "cal_stress": 1, + "deepks_model": "model.ptg", + "deepks_out_labels": 1, + "basis_type": "lcao", + "gamma_only": 1, + "ecutwfc": 80, + "mixing_type": "pulay", + "mixing_beta": 0.4, + "symmetry": 1, + "nbands": 5, + "nspin": 1, + "smearing_method": "fixed" + } +} \ No newline at end of file diff --git a/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/machine.json b/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/machine.json index 21d234673..e9d690ca6 100644 --- a/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/machine.json +++ b/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/machine.json @@ -1,103 +1,105 @@ { "api_version": "1.0", "deepmd_version": "2.0.1", - "train" : - { - "command": "dp", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": 0, - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "00*/train.log", - "grouped":true, - "job_name": "dpgen_train_job", - "disk_size": 200, - "scass_type":"", - "checkpoint_files":["00*/checkpoint","00*/model.ckpt*"], - "checkpoint_time":30, - "platform": "", - "region":"", - "image_name":"", - "on_demand":0 - } + "train": { + "command": "dp", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "00*/train.log", + "grouped": true, + "job_name": "dpgen_train_job", + "disk_size": 200, + "scass_type": "", + "checkpoint_files": [ + "00*/checkpoint", + "00*/model.ckpt*" + ], + "checkpoint_time": 30, + "platform": "", + "region": "", + "image_name": "", + "on_demand": 0 } - }, - "resources": { - "batch_type": "Lebesgue", - "group_size": 1 } }, - "model_devi": - { - "command": "lmp -i input.lammps -v restart 0", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": 0, - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "*/model_devi.log", - "grouped":true, - "job_name": "dpgen_model_devi_job", - "disk_size": 200, - "scass_type":"", - "platform": "", - "region":"", - "image_name":"", - "checkpoint_files": "sync_files", - "checkpoint_time":30, - "on_demand":0 - } + "resources": { + "batch_type": "Lebesgue", + "group_size": 1 + } + }, + "model_devi": { + "command": "lmp -i input.lammps -v restart 0", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "*/model_devi.log", + "grouped": true, + "job_name": "dpgen_model_devi_job", + "disk_size": 200, + "scass_type": "", + "platform": "", + "region": "", + "image_name": "", + "checkpoint_files": "sync_files", + "checkpoint_time": 30, + "on_demand": 0 } - }, - "resources": { - "batch_type": "Lebesgue", - "group_size": 50 } }, - "fp": - { - "command": "OMP_NUM_THREADS=1 mpirun -n 8 abacus", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": 0, - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "task*/fp.log", - "grouped":true, - "job_name": "dpgen_fp_job", - "disk_size": 100, - "checkpoint_files": "sync_files", - "checkpoint_time":30, - "scass_type":"", - "platform": "", - "image_name":"", - "on_demand":0 - } + "resources": { + "batch_type": "Lebesgue", + "group_size": 50 + } + }, + "fp": { + "command": "OMP_NUM_THREADS=1 mpirun -n 8 abacus", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "task*/fp.log", + "grouped": true, + "job_name": "dpgen_fp_job", + "disk_size": 100, + "checkpoint_files": "sync_files", + "checkpoint_time": 30, + "scass_type": "", + "platform": "", + "image_name": "", + "on_demand": 0 } - }, - "resources": { - "batch_type": "Lebesgue", - "group_size": 50, - "source_list": [""] } + }, + "resources": { + "batch_type": "Lebesgue", + "group_size": 50, + "source_list": [ + "" + ] } -} + } +} \ No newline at end of file diff --git a/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/run_param.json b/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/run_param.json index cdfc177a7..80349d31d 100644 --- a/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/run_param.json +++ b/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/run_param.json @@ -1,110 +1,149 @@ { - "type_map": [ + "type_map": [ + "Al" + ], + "mass_map": [ + 26.9815 + ], + "init_data_prefix": "./", + "init_data_sys": [ + "Al.STRU.02x01x01/02.md/sys-0008/deepmd" + ], + "sys_format": "abacus/stru", + "sys_configs_prefix": "./", + "sys_configs": [ + [ + "Al.STRU.02x01x01/01.scale_pert/sys-0008/scale*/00000*/STRU" + ] + ], + "_comment1": " that's all ", + "numb_models": 4, + "default_training_param": { + "model": { + "type_map": [ "Al" - ], - "mass_map": [ - 26.9815 - ], - "init_data_prefix": "./", - "init_data_sys": [ - "Al.STRU.02x01x01/02.md/sys-0008/deepmd" - ], - "sys_format":"abacus/stru", - "sys_configs_prefix": "./", - "sys_configs": [ - [ - "Al.STRU.02x01x01/01.scale_pert/sys-0008/scale*/00000*/STRU" - ] - ], - "_comment": " that's all ", - "numb_models": 4, - "default_training_param": { - "model": { - "type_map": [ - "Al" - ], - "descriptor": { - "type": "se_e2_a", - "sel": [ - 16 - ], - "rcut_smth": 0.5, - "rcut": 5.0, - "neuron": [ - 10, - 20, - 40 - ], - "resnet_dt": true, - "axis_neuron": 12, - "seed": 1 - }, - "fitting_net": { - "neuron": [ - 25, - 50, - 100 - ], - "resnet_dt": false, - "seed": 1 - } - }, - "learning_rate": { - "type": "exp", - "start_lr": 0.001, - "decay_steps": 100 - }, - "loss": { - "start_pref_e": 0.02, - "limit_pref_e": 2, - "start_pref_f": 1000, - "limit_pref_f": 1, - "start_pref_v": 0.0, - "limit_pref_v": 0.0 - }, - "training": { - "stop_batch": 20000, - "disp_file": "lcurve.out", - "disp_freq": 1000, - "numb_test": 4, - "save_freq": 1000, - "save_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json", - "_comment": "that's all" - } + ], + "descriptor": { + "type": "se_e2_a", + "sel": [ + 16 + ], + "rcut_smth": 0.5, + "rcut": 5.0, + "neuron": [ + 10, + 20, + 40 + ], + "resnet_dt": true, + "axis_neuron": 12, + "seed": 1 + }, + "fitting_net": { + "neuron": [ + 25, + 50, + 100 + ], + "resnet_dt": false, + "seed": 1 + } }, - "model_devi_dt": 0.002, - "model_devi_skip": 0, - "model_devi_f_trust_lo": 0.05, - "model_devi_f_trust_hi": 0.15, - "model_devi_clean_traj": false, - "model_devi_jobs": [ - { "sys_idx": [0], "temps": [100], "press": [1.0], "trj_freq": 10,"nsteps": 300, "ensemble": "nvt", "_idx": "00"}, - { "sys_idx": [0], "temps": [100, 300], "press": [1.0, 100.0], "trj_freq": 10,"nsteps": 300, "ensemble": "nvt", "_idx": "01"} - - ], - "fp_style": "abacus", - "shuffle_poscar": false, - "fp_task_max": 20, - "fp_task_min": 5, - "fp_pp_path": "./", - "fp_pp_files": ["Al_ONCV_PBE-1.0.upf"], - "fp_orb_files": ["Al_gga_9au_100Ry_4s4p1d.orb"], - "k_points": [1,1,1,0,0,0], - "user_fp_params":{ - "ntype": 1, - "symmetry": 0, - "basis_type": "lcao", - "ecutwfc": 100, - "scf_thr": 1e-8, - "scf_nmax": 100, - "smearing_method": "gauss", - "smearing_sigma": 0.002, - "mixing_type": "pulay", - "mixing_beta": 0.3, - "cal_force": 1 - } -} + "learning_rate": { + "type": "exp", + "start_lr": 0.001, + "decay_steps": 100 + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0.0, + "limit_pref_v": 0.0 + }, + "training": { + "stop_batch": 20000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "_comment2": "that's all" + } + }, + "model_devi_dt": 0.002, + "model_devi_skip": 0, + "model_devi_f_trust_lo": 0.05, + "model_devi_f_trust_hi": 0.15, + "model_devi_clean_traj": false, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 100 + ], + "press": [ + 1.0 + ], + "trj_freq": 10, + "nsteps": 300, + "ensemble": "nvt", + "_idx": "00" + }, + { + "sys_idx": [ + 0 + ], + "temps": [ + 100, + 300 + ], + "press": [ + 1.0, + 100.0 + ], + 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"image_name":"LBG_Gaussian_09_v2", - "on_demand":0 - } + "resources": { + "batch_type": "Lebesgue", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "T4_4_15", + "group_size": 50 + } + }, + "fp": { + "command": "g09 < input > output ||:", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "xxx", + "password": "xxx", + "program_id": 123, + "input_data": { + "api_version": 2, + "job_type": "indicate", + "log_file": "task*/fp.log", + "grouped": true, + "job_name": "dpgen_fp_job", + "disk_size": 100, + "scass_type": "c16_m32_cpu", + "platform": "ali", + "image_name": "LBG_Gaussian_09_v2", + "on_demand": 0 } - }, - "resources": { - "batch_type": "Lebesgue", - "source_list": ["/root/g09.sh"], - "number_node": 1, - "cpu_per_node": 16, - "gpu_per_node": 0, - "queue_name": "CPU", - "group_size": 10 } + }, + "resources": { + "batch_type": "Lebesgue", + "source_list": [ + "/root/g09.sh" + ], + "number_node": 1, + "cpu_per_node": 16, + "gpu_per_node": 0, + "queue_name": "CPU", + "group_size": 10 } -} + } +} \ No newline at end of file diff --git a/examples/run/dp2.x-lammps-gaussian/param_C4H16N4_deepmd-kit-2.0.1.json b/examples/run/dp2.x-lammps-gaussian/param_C4H16N4_deepmd-kit-2.0.1.json index 4f422fe73..fbe260e9f 100644 --- a/examples/run/dp2.x-lammps-gaussian/param_C4H16N4_deepmd-kit-2.0.1.json +++ b/examples/run/dp2.x-lammps-gaussian/param_C4H16N4_deepmd-kit-2.0.1.json @@ -1,140 +1,150 @@ { - "type_map": [ + "type_map": [ + "H", + "C", + "N" + ], + "mass_map": [ + 1, + 12, + 14 + ], + "init_data_prefix": "./data/deepmd/", + "init_data_sys": [ + "data.000", + "data.001", + "data.002", + "data.003", + "data.004", + "data.005" + ], + "init_batch_size": [ + "auto", + "auto", + "auto", + "auto", + "auto", + "auto" + ], + "sys_configs": [ + [ + "./data/md_sys/data.ch4n2" + ] + ], + "_comment1": " that's all ", + "numb_models": 4, + "sys_format": 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} + ], + "_comment9": " 02.fp ", + "fp_style": "vasp", + "shuffle_poscar": false, + "fp_task_max": 300, + "fp_task_min": 5, + "fp_pp_path": "/data1/yfb222333/2_dpgen_gpu_multi/POTCAR-Al", + "fp_pp_files": [ + "POTCAR" + ], + "fp_incar": "/data1/yfb222333/2_dpgen_gpu_multi/INCAR_metal_scf_gpu", + "_comment10": " that's all " +} \ No newline at end of file diff --git a/examples/run/dp1.x-lammps-vasp/CH4/INCAR_methane b/examples/run/dp2.x-lammps-vasp/CH4/INCAR_methane similarity index 100% rename from examples/run/dp1.x-lammps-vasp/CH4/INCAR_methane rename to examples/run/dp2.x-lammps-vasp/CH4/INCAR_methane diff --git a/examples/run/dp1.x-lammps-vasp/CH4/POT_C b/examples/run/dp2.x-lammps-vasp/CH4/POT_C similarity index 100% rename from examples/run/dp1.x-lammps-vasp/CH4/POT_C rename to examples/run/dp2.x-lammps-vasp/CH4/POT_C diff --git a/examples/run/dp1.x-lammps-vasp/CH4/POT_H b/examples/run/dp2.x-lammps-vasp/CH4/POT_H similarity index 100% rename from examples/run/dp1.x-lammps-vasp/CH4/POT_H rename to examples/run/dp2.x-lammps-vasp/CH4/POT_H diff --git a/examples/run/dp2.x-lammps-vasp/CH4/param_CH4_deepmd-kit-2.x.json b/examples/run/dp2.x-lammps-vasp/CH4/param_CH4_deepmd-kit-2.x.json new file mode 100644 index 000000000..932d511b9 --- /dev/null +++ b/examples/run/dp2.x-lammps-vasp/CH4/param_CH4_deepmd-kit-2.x.json @@ -0,0 +1,137 @@ +{ + "type_map": [ + "H", + "C" + ], + "mass_map": [ + 1, + 12 + ], + "init_data_prefix": "/data1/yfb222333/2_dpgen_gpu_multi", + "init_data_sys": [ + "CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd" + ], + "sys_configs_prefix": "/data1/yfb222333/2_dpgen_gpu_multi", + "sys_configs": [ + [ + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000*/POSCAR" + ], + [ + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00001*/POSCAR" + ] + ], + "_comment1": " that's all ", + "numb_models": 4, + "default_training_param": { + "model": { + "type_map": [ + "H", + "C" + ], + "descriptor": { + "type": "se_a", + "sel": [ + 16, + 4 + ], + "rcut_smth": 0.5, + "rcut": 5, + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true, + "axis_neuron": 12, + "seed": 1 + }, + "fitting_net": { + "neuron": [ + 25, + 50, + 100 + ], + "resnet_dt": false, + "seed": 1 + } + }, + "learning_rate": { + "type": "exp", + "start_lr": 0.001, + "decay_steps": 100, + "stop_lr": 0.0003584859224085419 + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0.0, + "limit_pref_v": 0.0 + }, + "training": { + "stop_batch": 2000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "_comment2": "that's all", + "training_data": { + "set_prefix": "set", + "batch_size": 1 + } + } + }, + "model_devi_dt": 0.002, + "model_devi_skip": 0, + "model_devi_f_trust_lo": 0.05, + "model_devi_f_trust_hi": 0.15, + "model_devi_clean_traj": true, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 100 + ], + "press": [ + 1.0 + ], + "trj_freq": 10, + "nsteps": 300, + "ensemble": "nvt", + "_idx": "00" + }, + { + "sys_idx": [ + 1 + ], + "temps": [ + 100 + ], + "press": [ + 1.0 + ], + "trj_freq": 10, + "nsteps": 3000, + "ensemble": "nvt", + "_idx": "01" + } + ], + "fp_style": "vasp", + "shuffle_poscar": false, + "fp_task_max": 20, + "fp_task_min": 5, + "fp_pp_path": "/data1/yfb222333/2_dpgen_gpu_multi", + "fp_pp_files": [ + "POTCAR_H", + "POTCAR_C" + ], + "_comments": "We can only provide empty files in public, you should provide valid POTCARS yourself when running DP-GEN", + "fp_incar": "/data1/yfb222333/2_dpgen_gpu_multi/INCAR_methane" +} \ No newline at end of file diff --git a/examples/run/dp2.x-lammps-vasp/param_CH4_deepmd-kit-2.0.1.json b/examples/run/dp2.x-lammps-vasp/param_CH4_deepmd-kit-2.0.1.json index b732f34e9..c1a95190b 100644 --- a/examples/run/dp2.x-lammps-vasp/param_CH4_deepmd-kit-2.0.1.json +++ b/examples/run/dp2.x-lammps-vasp/param_CH4_deepmd-kit-2.0.1.json @@ -1,134 +1,133 @@ { - "type_map": [ + "type_map": [ + "H", + "C" + ], + "mass_map": [ + 1, + 12 + ], + "init_data_prefix": "./", + "init_data_sys": [ + "CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd" + ], + "sys_configs_prefix": "./", + "sys_configs": [ + [ + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000*/POSCAR" + ], + [ + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00001*/POSCAR" + ] + ], + "_comment1": " that's all ", + "numb_models": 4, + "default_training_param": { + "model": { + "type_map": [ "H", "C" - ], - "mass_map": [ - 1, - 12 - ], - "init_data_prefix": "./", - "init_data_sys": [ - "CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd" - ], - "sys_configs_prefix": "./", - "sys_configs": [ - [ - "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000*/POSCAR" + ], + "descriptor": { + "type": "se_a", + "sel": [ + 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"**/fp.log", + "grouped": true, + "job_name": "simplify_MAPbI3-scan_fp_job", + "disk_size": 100, + "scass_type": "c32_m64_cpu", + "platform": "ali", + "checkpoint_files": "sync_files", + "checkpoint_time": 15, + "image_name": "LBG_vasp-5-4-4_v1", + "on_demand": 0 } } + }, + "resources": { + "batch_type": "Lebesgue", + "number_node": 15, + "cpu_per_node": 32, + "gpu_per_node": 0, + "queue_name": "CPU", + "group_size": 10, + "source_list": [ + "/opt/intel/oneapi/setvars.sh" + ] + } } +} \ No newline at end of file diff --git a/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/simplify.json b/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/simplify.json index cb5420910..fdc7658ae 100644 --- a/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/simplify.json +++ b/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/simplify.json @@ -1,94 +1,147 @@ { - "type_map": ["I","Pb","C","N","H"], - "mass_map": [126.90447, 207.2, 12.0108, 14.0067, 1.00795], - - "pick_data": "../data", + "type_map": [ + "I", + "Pb", + "C", + "N", + "H" + ], + "mass_map": [ + 126.90447, + 207.2, + 12.0108, + 14.0067, + 1.00795 + ], + "pick_data": "../data", "init_data_prefix": "", - "init_data_sys": [], - "sys_configs": [null], - "sys_batch_size": [1], - - "_comment": " 00.train ", + "init_data_sys": [], + "sys_configs": [ + null + ], + "sys_batch_size": [ + 1 + ], + "_comment1": " 00.train ", "numb_models": 4, - "model_devi_activation_func":[["tanh","tanh"],["tanh","gelu"],["gelu","gelu"],["gelu","tanh"]], - + "model_devi_activation_func": [ + [ + "tanh", + "tanh" + ], + [ + "tanh", + "gelu" + ], + [ + "gelu", + "gelu" + ], + [ + "gelu", + "tanh" + ] + ], "default_training_param": { "model": { - "type_map": ["I","Pb","C","N","H"], + "type_map": [ + "I", + "Pb", + "C", + "N", + "H" + ], "descriptor": { - "type": "se_e2_a", - "sel": - [ + "type": "se_e2_a", + "sel": [ 20, 8, 8, 8, 48 ], - "rcut_smth": 2.00, - "rcut": 6.00, - "neuron": [25, 50, 100], - "resnet_dt": false, - "type_one_side": true, - "trainable": true, - "axis_neuron": 12, - "seed": 0 + "rcut_smth": 2.0, + "rcut": 6.0, + "neuron": [ + 25, + 50, + 100 + ], + "resnet_dt": false, + "type_one_side": true, + "trainable": true, + "axis_neuron": 12, + "seed": 0 }, "fitting_net": { - "neuron": [240, 240, 240], - "resnet_dt": true, - "trainable": [true, true, true, true], + "neuron": [ + 240, + 240, + 240 + ], + "resnet_dt": true, + "trainable": [ + true, + true, + true, + true + ], "seed": 0 } }, - "loss": { - "start_pref_e": 0.02, - "limit_pref_e": 2, - "start_pref_f": 1000, - "limit_pref_f": 2, - "start_pref_v": 0.01, - "limit_pref_v": 1 + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 2, + "start_pref_v": 0.01, + "limit_pref_v": 1 }, - "learning_rate": { - "type": "exp", - "start_lr": 0.001, - "decay_steps": 25, - "decay_rate": 0.95 + "learning_rate": { + "type": "exp", + "start_lr": 0.001, + "decay_steps": 25, + "stop_lr": 3.505266624882874e-08 }, - "training": { - "set_prefix": "set", - "stop_batch": 5000, - "batch_size": "auto", - "seed": 1, - "_comment": "frequencies counted in batch", - "disp_file": "lcurve.out", - "disp_freq": 1000, - "numb_test": 4, - "save_freq": 10000, - "save_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json" + "training": { + "stop_batch": 5000, + "seed": 1, + "_comment2": "frequencies counted in batch", + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 10000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "training_data": { + "set_prefix": "set", + "batch_size": "auto" + } } }, - - "_comment": "02.fp", - "fp_style": "vasp", - "fp_skip_bad_box": "length_ratio:5;height_ratio:5", - "fp_accurate_threshold": 0.10, - "fp_accurate_soft_threshold": 0.00, - "fp_task_max": 20, - "fp_task_min": 5, - "ratio_failed": 0.30, + "_comment3": "02.fp", + "fp_style": "vasp", + "fp_skip_bad_box": "length_ratio:5;height_ratio:5", + "fp_accurate_threshold": 0.1, + "fp_accurate_soft_threshold": 0.0, + "fp_task_max": 20, + "fp_task_min": 5, + "ratio_failed": 0.3, "fp_pp_path": "../vasp_inputs/", - "fp_pp_files": ["POTCAR_I","POTCAR_Pb_d","POTCAR_C","POTCAR_N","POTCAR_H"], + "fp_pp_files": [ + "POTCAR_I", + "POTCAR_Pb_d", + "POTCAR_C", + "POTCAR_N", + "POTCAR_H" + ], "fp_incar": "INCAR", - "labeled": false, - "init_pick_number":5, - "iter_pick_number":5, - "model_devi_f_trust_lo":0.30, - "model_devi_f_trust_hi":100.00, + "init_pick_number": 5, + "iter_pick_number": 5, + "model_devi_f_trust_lo": 0.3, + "model_devi_f_trust_hi": 100.0, "cvasp": false -} +} \ No newline at end of file diff --git a/examples/simplify/qm7.json b/examples/simplify/qm7.json index 38ba048c2..d00847568 100644 --- a/examples/simplify/qm7.json +++ b/examples/simplify/qm7.json @@ -1,107 +1,110 @@ { - "type_map": [ + "type_map": [ + "C", + "H", + "N", + "O", + "S" + ], + "mass_map": [ + 12.011, + 1.008, + 14.007, + 15.999, + 32.065 + ], + "pick_data": "/scratch/jz748/simplify/qm7", + "init_data_prefix": "", + "init_data_sys": [], + "sys_configs": [ + null + ], + "sys_batch_size": [ + "auto" + ], + "numb_models": 4, + "default_training_param": { + "model": { + "type_map": [ "C", "H", "N", "O", "S" - ], - "mass_map": [ - 12.011, - 1.008, - 14.007, - 15.999, - 32.065 - ], - "pick_data": "/scratch/jz748/simplify/qm7", - "init_data_prefix": "", - "init_data_sys": [], - "sys_configs": [null], - "sys_batch_size": [ - "auto" - ], - "numb_models": 4, - "default_training_param": { - "model": { - "type_map": [ - "C", - "H", - "N", - "O", - "S" - ], - "descriptor": { - "type": "se_a", - "sel": [ - 7, - 16, - 3, - 3, - 1 - ], - "rcut_smth": 1.00, - "rcut": 6.00, - "neuron": [ - 25, - 50, - 100 - ], - "resnet_dt": false, - "axis_neuron": 12 - }, - "fitting_net": { - "neuron": [ - 240, - 240, - 240 - ], - "resnet_dt": true - } - }, - "learning_rate": { - "type": "exp", - "start_lr": 0.001, - "decay_steps": 10, - "decay_rate": 0.99 - }, - "loss": { - "start_pref_e": 0.02, - "limit_pref_e": 1, - "start_pref_f": 1000, - "limit_pref_f": 1, - "start_pref_v": 0, - "limit_pref_v": 0, - "start_pref_pf": 0, - "limit_pref_pf": 0 - }, - "training": { - "set_prefix": "set", - "stop_batch": 10000, - "disp_file": "lcurve.out", - "disp_freq": 1000, - "numb_test": 1, - "save_freq": 1000, - "save_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json" - }, - "_comment": "that's all" + ], + "descriptor": { + "type": "se_a", + "sel": [ + 7, + 16, + 3, + 3, + 1 + ], + "rcut_smth": 1.0, + "rcut": 6.0, + "neuron": [ + 25, + 50, + 100 + ], + "resnet_dt": false, + "axis_neuron": 12 + }, + "fitting_net": { + "neuron": [ + 240, + 240, + 240 + ], + "resnet_dt": true + } }, - "use_clusters": true, - "fp_style": "gaussian", - "fp_task_max": 1000, - "fp_task_min": 10, - "fp_params": { - "keywords": "mn15/6-31g** force nosymm scf(maxcyc=512)", - "nproc": 28, - "multiplicity": 1, - "_comment": " that's all " + "learning_rate": { + "type": "exp", + "start_lr": 0.001, + "decay_steps": 10, + "stop_lr": 4.317124741065782e-08 }, - "init_pick_number":100, - "iter_pick_number":100, - "model_devi_f_trust_lo":0.10, - "model_devi_f_trust_hi":0.30, - "_comment": " that's all " -} + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 1, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0, + "limit_pref_v": 0, + "start_pref_pf": 0, + "limit_pref_pf": 0 + }, + "training": { + "stop_batch": 10000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "training_data": { + "set_prefix": "set" + } + }, + "_comment1": "that's all" + }, + "use_clusters": true, + "fp_style": "gaussian", + "fp_task_max": 1000, + "fp_task_min": 10, + "fp_params": { + "keywords": "mn15/6-31g** force nosymm scf(maxcyc=512)", + "nproc": 28, + "multiplicity": 1, + "_comment2": " that's all " + }, + "init_pick_number": 100, + "iter_pick_number": 100, + "model_devi_f_trust_lo": 0.1, + "model_devi_f_trust_hi": 0.3, + "_comment3": " that's all " +} \ No newline at end of file diff --git a/examples/test/deepmd_param.json b/examples/test/deepmd_param.json index ae920184d..08bf864d3 100644 --- a/examples/test/deepmd_param.json +++ b/examples/test/deepmd_param.json @@ -1,63 +1,62 @@ { - "_comment": "models", - "potcar_map": { - "Al": "/somewhere/example/POTCAR" - }, - "conf_dir": "confs/Al/std-fcc", - "key_id": "key id of Material project", - "task_type": "deepmd", - "task": "all", - - "vasp_params": { - "ecut": 650, - "ediff": 1e-6, - "kspacing": 0.1, - "kgamma": false, - "npar": 1, - "kpar": 1, - "_comment": " that's all " - }, - "lammps_params": { - "model_dir": "somewhere/example/Al_model", - "type_map": [ - "Al" - ], - "model_name": false, - "model_param_type": false - }, - "_comment": "00.equi", - "alloy_shift": false, - "_comment": "01.eos", - "vol_start": 12, - "vol_end": 22, - "vol_step": 0.5, - "_comment": "02.elastic", - "norm_deform": 2e-2, - "shear_deform": 5e-2, - "_comment": "03.vacancy", - "supercell": [ - 3, - 3, - 3 + "_comment1": "models", + "potcar_map": { + "Al": "/somewhere/example/POTCAR" + }, + "conf_dir": "confs/Al/std-fcc", + "key_id": "key id of Material project", + "task_type": "deepmd", + "task": "all", + "vasp_params": { + "ecut": 650, + "ediff": 1e-06, + "kspacing": 0.1, + "kgamma": false, + "npar": 1, + "kpar": 1, + "_comment2": " that's all " + }, + "lammps_params": { + "model_dir": "somewhere/example/Al_model", + "type_map": [ + "Al" ], - "_comment": "04.interstitial", - "insert_ele": [ - "Al" - ], - "reprod-opt": false, - "_comment": "05.surface", - "min_slab_size": 10, - "min_vacuum_size": 11, - "_comment": "pert xz to work around vasp bug...", - "pert_xz": 0.01, - "max_miller": 2, - "relax_box": false, - "_comment": "06.phonon", - "supercell_matrix": [ - 2, - 2, - 2 - ], - "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", - "_comment": "that's all" -} + "model_name": false, + "model_param_type": false + }, + "_comment3": "00.equi", + "alloy_shift": false, + "_comment4": "01.eos", + "vol_start": 12, + "vol_end": 22, + "vol_step": 0.5, + "_comment5": "02.elastic", + "norm_deform": 0.02, + "shear_deform": 0.05, + "_comment6": "03.vacancy", + "supercell": [ + 3, + 3, + 3 + ], + "_comment7": "04.interstitial", + "insert_ele": [ + "Al" + ], + "reprod-opt": false, + "_comment8": "05.surface", + "min_slab_size": 10, + "min_vacuum_size": 11, + "_comment9": "pert xz to work around vasp bug...", + "pert_xz": 0.01, + "max_miller": 2, + "relax_box": false, + "_comment10": "06.phonon", + "supercell_matrix": [ + 2, + 2, + 2 + ], + "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", + "_comment11": "that's all" +} \ No newline at end of file diff --git a/examples/test/meam_param.json b/examples/test/meam_param.json index 1790bb2a9..ece70d04c 100644 --- a/examples/test/meam_param.json +++ b/examples/test/meam_param.json @@ -1,76 +1,75 @@ { - "_comment": "models", - "potcar_map": { - "Al": "/somewhere/example/POTCAR" - }, - "conf_dir": "confs/Al/std-fcc", - "key_id": "key id of Material project", - "task_type": "meam", - "task": "all", - - "vasp_params": { - "ecut": 650, - "ediff": 1e-6, - "kspacing": 0.1, - "kgamma": false, - "npar": 1, - "kpar": 1, - "_comment": " that's all " - }, - "lammps_params": { - "model_dir": "somewhere/example/meam", - "type_map": [ - "Al", - "Si", - "Mg", - "Cu", - "Fe" - ], - "model_name": [ - "meam.AlSiMgCuFe", - "meam.library" - ], - "model_param_type": [ - "AlS", - "SiS", - "MgS", - "CuS", - "FeS" - ] - }, - "_comment": "00.equi", - "alloy_shift": false, - "_comment": "01.eos", - "vol_start": 12, - "vol_end": 22, - "vol_step": 0.5, - "_comment": "02.elastic", - "norm_deform": 2e-2, - "shear_deform": 5e-2, - "_comment": "03.vacancy", - "supercell": [ - 3, - 3, - 3 + "_comment1": "models", + "potcar_map": { + "Al": "/somewhere/example/POTCAR" + }, + "conf_dir": "confs/Al/std-fcc", + "key_id": "key id of Material project", + "task_type": "meam", + "task": "all", + "vasp_params": { + "ecut": 650, + "ediff": 1e-06, + "kspacing": 0.1, + "kgamma": false, + "npar": 1, + "kpar": 1, + "_comment2": " that's all " + }, + "lammps_params": { + "model_dir": "somewhere/example/meam", + "type_map": [ + "Al", + "Si", + "Mg", + "Cu", + "Fe" ], - "_comment": "04.interstitial", - "insert_ele": [ - "Al" + "model_name": [ + "meam.AlSiMgCuFe", + "meam.library" ], - "reprod-opt": false, - "_comment": "05.surface", - "min_slab_size": 10, - "min_vacuum_size": 11, - "_comment": "pert xz to work around vasp bug...", - "pert_xz": 0.01, - "max_miller": 2, - "relax_box": false, - "_comment": "06.phonon", - "supercell_matrix": [ - 2, - 2, - 2 - ], - "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", - "_comment": "that's all" -} + "model_param_type": [ + "AlS", + "SiS", + "MgS", + "CuS", + "FeS" + ] + }, + "_comment3": "00.equi", + "alloy_shift": false, + "_comment4": "01.eos", + "vol_start": 12, + "vol_end": 22, + "vol_step": 0.5, + "_comment5": "02.elastic", + "norm_deform": 0.02, + "shear_deform": 0.05, + "_comment6": "03.vacancy", + "supercell": [ + 3, + 3, + 3 + ], + "_comment7": "04.interstitial", + "insert_ele": [ + "Al" + ], + "reprod-opt": false, + "_comment8": "05.surface", + "min_slab_size": 10, + "min_vacuum_size": 11, + "_comment9": "pert xz to work around vasp bug...", + "pert_xz": 0.01, + "max_miller": 2, + "relax_box": false, + "_comment10": "06.phonon", + "supercell_matrix": [ + 2, + 2, + 2 + ], + "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", + "_comment11": "that's all" +} \ No newline at end of file diff --git a/examples/test/vasp_param.json b/examples/test/vasp_param.json index d1dfb9a1d..7284af83c 100644 --- a/examples/test/vasp_param.json +++ b/examples/test/vasp_param.json @@ -1,5 +1,5 @@ { - "_comment": "models", + "_comment1": "models", "potcar_map": { "Al": "/somewhere/example/POTCAR" }, @@ -7,49 +7,48 @@ "key_id": "key id of Material project", "task_type": "vasp", "task": "all", - "vasp_params": { "ecut": 650, - "ediff": 1e-6, + "ediff": 1e-06, "kspacing": 0.1, "kgamma": false, "npar": 1, "kpar": 1, - "_comment": " that's all " + "_comment2": " that's all " }, - "_comment": "00.equi", + "_comment3": "00.equi", "alloy_shift": false, - "_comment": "01.eos", + "_comment4": "01.eos", "vol_start": 12, "vol_end": 22, "vol_step": 0.5, - "_comment": "02.elastic", - "norm_deform": 2e-2, - "shear_deform": 5e-2, - "_comment": "03.vacancy", + "_comment5": "02.elastic", + "norm_deform": 0.02, + "shear_deform": 0.05, + "_comment6": "03.vacancy", "supercell": [ 3, 3, 3 ], - "_comment": "04.interstitial", + "_comment7": "04.interstitial", "insert_ele": [ "Al" ], "reprod-opt": false, - "_comment": "05.surface", + "_comment8": "05.surface", "min_slab_size": 10, "min_vacuum_size": 11, - "_comment": "pert xz to work around vasp bug...", + "_comment9": "pert xz to work around vasp bug...", "pert_xz": 0.01, "max_miller": 2, "relax_box": false, - "_comment": "06.phonon", + "_comment10": "06.phonon", "supercell_matrix": [ 2, 2, 2 ], "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", - "_comment": "that's all" -} + "_comment11": "that's all" +} \ No newline at end of file diff --git a/examples/test/vasp_param_from_incar.json b/examples/test/vasp_param_from_incar.json index c5cf91ba4..558860831 100644 --- a/examples/test/vasp_param_from_incar.json +++ b/examples/test/vasp_param_from_incar.json @@ -1,49 +1,47 @@ { - "_comment": "models", - "potcar_map": { - "Al": "/somewhere/example/POTCAR" - }, - "conf_dir": "confs/Al/std-fcc", - "key_id": "key id of Material project", - "task_type": "vasp", - "task": "all", - - "relax_incar": "somewhere/relax_incar", - "scf_incar": "somewhere/scf_incar", - - "_comment": "00.equi", - "alloy_shift": false, - "_comment": "01.eos", - "vol_start": 12, - "vol_end": 22, - "vol_step": 0.5, - "_comment": "02.elastic", - "norm_deform": 2e-2, - "shear_deform": 5e-2, - "_comment": "03.vacancy", - "supercell": [ - 3, - 3, - 3 - ], - "_comment": "04.interstitial", - "insert_ele": [ - "Al" - ], - "reprod-opt": false, - "_comment": "05.surface", - "min_slab_size": 10, - "min_vacuum_size": 11, - "_comment": "pert xz to work around vasp bug...", - "pert_xz": 0.01, - "max_miller": 2, - "relax_box": false, - "_comment": "06.phonon", - "supercell_matrix": [ - 2, - 2, - 2 - ], - "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", - "_comment": "that's all" -} + "_comment1": "models", + "potcar_map": { + "Al": "/somewhere/example/POTCAR" + }, + "conf_dir": "confs/Al/std-fcc", + "key_id": "key id of Material project", + "task_type": "vasp", + "task": "all", + "relax_incar": "somewhere/relax_incar", + "scf_incar": 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a/tests/auto_test/output/gamma_00/task.000000/inter.json +++ b/tests/auto_test/output/gamma_00/task.000000/inter.json @@ -1,8 +1,8 @@ { - "type": "deepmd", - "model": "frozen_model.pb", - "deepmd_version": "2.1.0", - "type_map": { - "Mo": 0 - } + "type": "deepmd", + "model": "frozen_model.pb", + "deepmd_version": "2.1.0", + "type_map": { + "Mo": 0 + } } \ No newline at end of file diff --git a/tests/auto_test/output/gamma_00/task.000000/miller.json b/tests/auto_test/output/gamma_00/task.000000/miller.json index 0a6e1ab11..351a2f095 100644 --- a/tests/auto_test/output/gamma_00/task.000000/miller.json +++ b/tests/auto_test/output/gamma_00/task.000000/miller.json @@ -1 +1,5 @@ -[1, 1, 0] \ No newline at end of file +[ + 1, + 1, + 0 +] \ No newline at end of file diff --git a/tests/auto_test/output/gamma_00/task.000000/result_task.json b/tests/auto_test/output/gamma_00/task.000000/result_task.json index 591103fc6..acfd6846e 100644 --- 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- "md_incar": "abacus.in/INPUT.md", - "scale": [ - 0.99 - ], - "skip_relax": true, - "pert_numb": 2, - "md_nstep": 2, - "pert_box": 0.01, - "pert_atom": 0.01, - "coll_ndata": 12, - "type_map": [ - "Cu", - "W" - ], - "_comment": "that's all" -} + "init_fp_style": "ABACUS", + "stages": [ + 1, + 2, + 3, + 4 + ], + "cell_type": "fcc", + "latt": 3.76, + "super_cell": [ + 1, + 2, + 2 + ], + "elements": [ + "Cu", + "W" + ], + "atom_masses": [ + 63.55, + 183.8 + ], + "potcars": [ + "abacus.in/Cu_ONCV_PBE-1.0.upf", + "abacus.in/W_ONCV_PBE-1.0.upf" + ], + "relax_incar": "abacus.in/INPUT", + "relax_kpt": "abacus.in/KPT", + "md_kpt": "abacus.in/KPT", + "md_incar": "abacus.in/INPUT.md", + "scale": [ + 0.99 + ], + "skip_relax": true, + "pert_numb": 2, + "md_nstep": 2, + "pert_box": 0.01, + "pert_atom": 0.01, + "coll_ndata": 12, + "type_map": [ + "Cu", + "W" + ], + "_comment1": "that's all" +} \ No newline at end of file diff --git a/tests/data/al.json b/tests/data/al.json index b19e7c884..c04b95ad9 100644 --- a/tests/data/al.json +++ b/tests/data/al.json @@ -1,19 +1,32 @@ { - "cell_type": "fcc", - "super_cell": [1, 1, 1], - "elements": ["Al"], - "from_poscar": false, - "from_poscar_path": "example/POSCAR", - "potcars": ["example/POTCAR"], - "relax_incar": "example/INCAR.rlx", - "md_incar" : "example/INCAR.md", - "scale": [1.00], - "skip_relax": false, - "pert_numb": 2, - "md_nstep" : 1, - "pert_box": 0.03, - "pert_atom": 0.01, - "coll_ndata": 10, - "type_map" : ["Mg", "Al"], - "_comment": "that's all" -} + "cell_type": "fcc", + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al" + ], + "from_poscar": false, + "from_poscar_path": "example/POSCAR", + "potcars": [ + "example/POTCAR" + ], + "relax_incar": "example/INCAR.rlx", + "md_incar": "example/INCAR.md", + "scale": [ + 1.0 + ], + "skip_relax": false, + "pert_numb": 2, + "md_nstep": 1, + "pert_box": 0.03, + "pert_atom": 0.01, + "coll_ndata": 10, + "type_map": [ + "Mg", + "Al" + ], + "_comment1": "that's all" +} \ No newline at end of file diff --git a/tests/data/alloy.json b/tests/data/alloy.json index 78cfa5e61..04b831215 100644 --- a/tests/data/alloy.json +++ b/tests/data/alloy.json @@ -1,19 +1,31 @@ { - "cell_type": "fcc", - "latt": 2.4, - "super_cell": [1, 1, 1], - "elements": ["Al","Mg"], - "from_poscar": false, - "from_poscar_path": "example/POSCAR", - "potcars": ["./POTCAR","./POTCAR"], - "relax_incar": "./INCAR_metal_rlx_low", - "md_incar" : "example/INCAR.md", - "scale": [1.00], - "skip_relax": true, - "pert_numb": 3, - "md_nstep" : 1, - "pert_box": 0.03, - "pert_atom": 0.01, - "coll_ndata": 3, - "_comment": "that's all" -} + "cell_type": "fcc", + "latt": 2.4, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al", + "Mg" + ], + "from_poscar": false, + "from_poscar_path": "example/POSCAR", + "potcars": [ + "./POTCAR", + "./POTCAR" + ], + "relax_incar": "./INCAR_metal_rlx_low", + "md_incar": "example/INCAR.md", + "scale": [ + 1.0 + ], + "skip_relax": true, + "pert_numb": 3, + "md_nstep": 1, + "pert_box": 0.03, + "pert_atom": 0.01, + "coll_ndata": 3, + "_comment1": "that's all" +} \ No newline at end of file diff --git a/tests/data/ch4.json b/tests/data/ch4.json index 7f3a74933..fe9762bdf 100644 --- a/tests/data/ch4.json +++ b/tests/data/ch4.json @@ -1,26 +1,46 @@ { - "init_fp_style": "ABACUS", - "stages": [1, 2, 3, 4], - "super_cell": [1, 1, 1], - "_comment": "if from_poscar = true, the cell_type and super_cell keys are actually useless", - "cell_type": "fcc", - "elements": ["H","C"], - "atom_masses": [1, 12], - "_comment": "if from_poscar = false, you have to set atom_masse.", - "out_dir": "./", - "from_poscar": true, - "from_poscar_path": "./STRU", - "potcars": ["./H_ONCV_PBE-1.0.upf", "./C_ONCV_PBE-1.0.upf"], - "relax_incar": "./INPUT", - "relax_kspacing": 10, - "md_incar" : "./INPUT.md", - "md_kspacing": 10, - "scale": [0.95], - "skip_relax": false, - "pert_numb": 2, - "md_nstep" : 3, - "pert_box": 0.03, - "pert_atom": 0.01, - "coll_ndata": 10, - "_comment": "that's all" -} + "init_fp_style": "ABACUS", + "stages": [ + 1, + 2, + 3, + 4 + ], + "super_cell": [ + 1, + 1, + 1 + ], + "_comment1": "if from_poscar = true, the cell_type and super_cell keys are actually useless", + "cell_type": "fcc", + "elements": [ + "H", + "C" + ], + "atom_masses": [ + 1, + 12 + ], + "_comment2": "if from_poscar = false, you have to set atom_masse.", + "out_dir": "./", + "from_poscar": true, + "from_poscar_path": "./STRU", + "potcars": [ + "./H_ONCV_PBE-1.0.upf", + "./C_ONCV_PBE-1.0.upf" + ], + "relax_incar": "./INPUT", + "relax_kspacing": 10, + "md_incar": "./INPUT.md", + "md_kspacing": 10, + "scale": [ + 0.95 + ], + "skip_relax": false, + "pert_numb": 2, + "md_nstep": 3, + "pert_box": 0.03, + "pert_atom": 0.01, + "coll_ndata": 10, + "_comment3": "that's all" +} \ No newline at end of file diff --git a/tests/data/surf.json b/tests/data/surf.json index f0bcc45b1..4131ecf3a 100644 --- a/tests/data/surf.json +++ b/tests/data/surf.json @@ -32,7 +32,7 @@ "potcars": [ "./POTCAR" ], - "relax_incar" : "INCAR_metal_rlx_low", + "relax_incar": "INCAR_metal_rlx_low", "scale": [ 0.98, 1.0 @@ -42,5 +42,5 @@ "pert_box": 0.03, "pert_atom": 0.01, "coll_ndata": 5000, - "_comment": "that's all" -} + "_comment1": "that's all" +} \ No newline at end of file diff --git a/tests/data/surf_poscar.json b/tests/data/surf_poscar.json index 3399b920f..7e825dda7 100644 --- a/tests/data/surf_poscar.json +++ b/tests/data/surf_poscar.json @@ -4,8 +4,8 @@ 2 ], "cell_type": "fcc", - "from_poscar": true, - "from_poscar_path": "POSCAR", + "from_poscar": true, + "from_poscar_path": "POSCAR", "super_cell": [ 1, 1, @@ -13,7 +13,10 @@ ], "layer_numb": 3, "vacuum_max": 5, - "vacuum_resol": [0.5,2], + "vacuum_resol": [ + 0.5, + 2 + ], "mid_point": 2.0, "_head_ratio": 0.6, "_vacuum_numb": 20, @@ -30,7 +33,7 @@ "potcars": [ "./POTCAR" ], - "relax_incar" : "INCAR_metal_rlx_low", + "relax_incar": "INCAR_metal_rlx_low", "scale": [ 1.0 ], @@ -39,5 +42,5 @@ "pert_box": 0.03, "pert_atom": 0.01, "coll_ndata": 5000, - "_comment": "that's all" -} + "_comment1": "that's all" +} \ No newline at end of file diff --git a/tests/database/param_Al.json b/tests/database/param_Al.json index 3295d8ce8..07f7bd305 100644 --- a/tests/database/param_Al.json +++ b/tests/database/param_Al.json @@ -1,19 +1,100 @@ { - "path" : "./", - "calculator" : "vasp", - "_comment" : "vasp/pwscf/gaussian", - "output" : "dpgen_db.json", - "id_prefix" : "", - "config_info_dict" : { - "fcc-bulk" : [0,1,2,3,4,5,6,7], - "hcp-bulk" : [8,9,10,11,12,13,14,15], - "bcc-bulk" : [16,17,18,19,20,21,22,23], - "fcc-surf-100" : [24,25,26,27,28,29,30,31], - "fcc-surf-111" : [32,33,34,35,36,37,38,39], - "fcc-surf-110" : [40,41,42,43,44,45,46,47], - "hcp-surf-001" : [48,49,50,51,52,53,54,55], - "hcp-surf-100" : [56,57,58,59,60,61,62,63], - "hcp-surf-110" : [64,65,66,67,68,69,70,71] - }, - "skip_init" : true -} + "path": "./", + "calculator": "vasp", + "_comment1": "vasp/pwscf/gaussian", + "output": "dpgen_db.json", + 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"/data1/anguse/yingze/fep/deepmd/input/box.raw", + "type_file": "/data1/anguse/yuzhi/fep/DP_FF/tyk2/init_data/lig_ejm_31/type.raw", + "index_file": "index.raw", + "lambda": 1.0 } \ No newline at end of file diff --git a/tests/generator/machine-local-v1.json b/tests/generator/machine-local-v1.json index 2218884f2..81f0ce0ea 100644 --- a/tests/generator/machine-local-v1.json +++ b/tests/generator/machine-local-v1.json @@ -1,49 +1,52 @@ { - "train_machine": { - "machine_type": "shell", - "lazy_local": true - }, - "train_resources": { - "numb_node": 1, - "numb_gpu": 0, - "task_per_node": 4, - "exclude_list": [], - "source_list": ["/home/wanghan/study/deep.md/venvs/py3.6-tf1.8/bin/active"], - "envs" : { - }, - "_comment": "that's All" - }, - "python_path": "/home/wanghan/study/deep.md/venvs/py3.6-tf1.8/bin/python", - - "model_devi_machine": { - "machine_type": "shell", - "work_path": "/home/wanghan/study/deep.md/dpgen/almg/tmp" - }, - "model_devi_resources": { - "numb_node": 1, - "task_per_node": 4, - "with_mpi": true, - "module_list" : ["mpi"], - "exclude_list": [], - "source_list": [], - "_comment": "that's All" - }, - "model_devi_command": "/home/wanghan/local/bin/lmp_mpi_1_1_0", - "model_devi_group_size": 10, - - "fp_machine": { - "machine_type": "shell", - "work_path": "/home/wanghan/study/deep.md/dpgen/almg/tmp" - }, - "fp_resources": { - "cvasp": false, - "task_per_node": 4, - "exclude_list": [], - "with_mpi": true, - "module_list" : ["mpi"], - "source_list": [], - "_comment": "that's All" - }, - "fp_command": "/home/wanghan/local/bin/vasp_std", - "fp_group_size": 5 -} + "train_machine": { + "machine_type": "shell", + "lazy_local": true + }, + "train_resources": { + "numb_node": 1, + "numb_gpu": 0, + "task_per_node": 4, + "exclude_list": [], + "source_list": [ + "/home/wanghan/study/deep.md/venvs/py3.6-tf1.8/bin/active" + ], + "envs": {}, + "_comment1": "that's All" + }, + "python_path": "/home/wanghan/study/deep.md/venvs/py3.6-tf1.8/bin/python", + "model_devi_machine": { + "machine_type": "shell", + "work_path": "/home/wanghan/study/deep.md/dpgen/almg/tmp" + }, + "model_devi_resources": { + "numb_node": 1, + "task_per_node": 4, + "with_mpi": true, + "module_list": [ + "mpi" + ], + "exclude_list": [], + "source_list": [], + "_comment2": "that's All" + }, + "model_devi_command": "/home/wanghan/local/bin/lmp_mpi_1_1_0", + "model_devi_group_size": 10, + "fp_machine": { + "machine_type": "shell", + "work_path": "/home/wanghan/study/deep.md/dpgen/almg/tmp" + }, + "fp_resources": { + "cvasp": false, + "task_per_node": 4, + "exclude_list": [], + "with_mpi": true, + "module_list": [ + "mpi" + ], + "source_list": [], + "_comment3": "that's All" + }, + "fp_command": "/home/wanghan/local/bin/vasp_std", + "fp_group_size": 5 +} \ No newline at end of file diff --git a/tests/generator/machine-local.json b/tests/generator/machine-local.json index a4743c964..8404bd2ab 100644 --- a/tests/generator/machine-local.json +++ b/tests/generator/machine-local.json @@ -1,54 +1,55 @@ { - "_comment": "training on localhost ", - "deepmd_path": "/home/wanghan/local/deepmd/0.10.1/", - "train_machine": { - "machine_type": "local", - "hostname" : "127.0.0.1", - "port" : 22, - "username": "wanghan", - "work_path" : "/home/wanghan/tmp/subs/", - "_comment" : "that's all" - }, - "train_resources": { - "envs": { - "PYTHONPATH" : "/home/wanghan/local/tensorflow/1.8.py/lib/python3.6/site-packages/" - }, - "_comment": "that's all" - }, - - - "_comment": "model_devi on localhost ", - "model_devi_command": "/home/wanghan/local/bin/lmp_mpi_010", - "model_devi_group_size": 5, - "model_devi_machine": { - "machine_type": "local", - "hostname" : "127.0.0.1", - "port" : 22, - "username": "wanghan", - "work_path" : "/home/wanghan/tmp/subs/", - "_comment" : "that's all" - }, - "model_devi_resources": { - "_comment": "that's all" - }, - - "_comment": "fp on localhost ", - "fp_command": "/home/wanghan/local/bin/vasp_std", - "fp_group_size": 2, - "fp_machine": { - "machine_type": "local", - "hostname" : "127.0.0.1", - "port" : 22, - "username": "wanghan", - "work_path" : "/home/wanghan/tmp/subs/", - "_comment" : "that's all" - }, - "fp_resources": { - "module_list": ["mpi"], - "task_per_node":4, - "with_mpi": true, - "_comment": "that's all" + "_comment1": "training on localhost ", + "deepmd_path": "/home/wanghan/local/deepmd/0.10.1/", + "train_machine": { + "machine_type": "local", + "hostname": "127.0.0.1", + "port": 22, + "username": "wanghan", + "work_path": "/home/wanghan/tmp/subs/", + "_comment2": "that's all" + }, + "train_resources": { + "envs": { + "PYTHONPATH": "/home/wanghan/local/tensorflow/1.8.py/lib/python3.6/site-packages/" }, - "fp_user_forward_files" : ["vdw_kernel.bindat"], - "_comment": " that's all " -} + "_comment3": "that's all" + }, + "_comment4": "model_devi on localhost ", + "model_devi_command": "/home/wanghan/local/bin/lmp_mpi_010", + "model_devi_group_size": 5, + "model_devi_machine": { + "machine_type": "local", + "hostname": "127.0.0.1", + "port": 22, + "username": "wanghan", + "work_path": "/home/wanghan/tmp/subs/", + "_comment5": "that's all" + }, + "model_devi_resources": { + "_comment6": "that's all" + }, + "_comment7": "fp on localhost ", + "fp_command": "/home/wanghan/local/bin/vasp_std", + "fp_group_size": 2, + "fp_machine": { + "machine_type": "local", + "hostname": "127.0.0.1", + "port": 22, + "username": "wanghan", + "work_path": "/home/wanghan/tmp/subs/", + "_comment8": "that's all" + }, + "fp_resources": { + "module_list": [ + "mpi" + ], + "task_per_node": 4, + "with_mpi": true, + "_comment9": "that's all" + }, + "fp_user_forward_files": [ + "vdw_kernel.bindat" + ], + "_comment10": " that's all " +} \ No newline at end of file diff --git a/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000000/job.json b/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000000/job.json index e2f74b65b..9047111dd 100644 --- a/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000000/job.json +++ b/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000000/job.json @@ -1 +1,3 @@ -{ "ele_temp": 0 } +{ + "ele_temp": 0 +} \ No newline at end of file diff --git a/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000001/job.json b/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000001/job.json index ec49f8a06..11836af6a 100644 --- a/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000001/job.json +++ b/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000001/job.json @@ -1 +1,3 @@ -{ "ele_temp": 1 } +{ + "ele_temp": 1 +} \ No newline at end of file diff --git a/tests/generator/out_data_post_fp_vasp/02.fp/task.001.000000/job.json b/tests/generator/out_data_post_fp_vasp/02.fp/task.001.000000/job.json index c4924f0bd..174650337 100644 --- a/tests/generator/out_data_post_fp_vasp/02.fp/task.001.000000/job.json +++ b/tests/generator/out_data_post_fp_vasp/02.fp/task.001.000000/job.json @@ -1 +1,3 @@ -{ "ele_temp": 100000 } +{ + "ele_temp": 100000 +} \ No newline at end of file diff --git a/tests/generator/out_data_post_fp_vasp/02.fp/task.001.000001/job.json b/tests/generator/out_data_post_fp_vasp/02.fp/task.001.000001/job.json index a393fb733..a4b142373 100644 --- a/tests/generator/out_data_post_fp_vasp/02.fp/task.001.000001/job.json +++ b/tests/generator/out_data_post_fp_vasp/02.fp/task.001.000001/job.json @@ -1 +1,3 @@ -{ "ele_temp": 110000 } +{ + "ele_temp": 110000 +} \ No newline at end of file diff --git a/tests/generator/param-amber.json b/tests/generator/param-amber.json index 69df44ed3..7ca2171fc 100644 --- a/tests/generator/param-amber.json +++ b/tests/generator/param-amber.json @@ -1,54 +1,66 @@ { - "model_devi_jobs": [ - { - "sys_idx": [0] - } - ], - "use_multi_systems": true, - "model_devi_engine": "amber", - "fp_style": "amber/diff", - "numb_models": 4, - "mdin_prefix": "amber", - "parm7_prefix": "amber", - "sys_prefix": "amber", - "disang_prefix": "amber", - 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"ml.mdin" + ], + "qm_region": [ + ":1" + ], + "qm_charge": [ + 0 + ], + "r": [ + [ + -1.2 + ] + ], + "nsteps": [ + 1000 + ], + "type_map": [ + "C", + "H", + "O", + "N", + "P", + "HW", + "OW" + ], + "shuffle_poscar": false, + "low_level": "DFTB2", + "high_level": "PBE0", + "cutoff": 6.0, + "fp_task_max": 1000, + "model_devi_skip": 0, + "model_devi_f_trust_lo": 0.1, + "model_devi_f_trust_hi": 0.25, + "fp_params": { + "low_level_mdin": "ml.mdin", + "high_level_mdin": "ml.mdin" + } } \ No newline at end of file diff --git a/tests/generator/param-custom-fp.json b/tests/generator/param-custom-fp.json index f66cad71f..df57ee241 100644 --- a/tests/generator/param-custom-fp.json +++ b/tests/generator/param-custom-fp.json @@ -1,107 +1,321 @@ -{ - "type_map": ["C", "H", "N"], - "mass_map": [16, 2, 14], - - "init_data_prefix": "/home/linfengz/SCR/wanghan/deepgen.pyridine/init", - "init_data_sys": ["Pyridine-I", - "Pyridine-II" - ], - "init_batch_size": [1, 1], - "sys_configs": [ - 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a/tests/generator/param-methane-abacus-diy.json b/tests/generator/param-methane-abacus-diy.json index f7dbbe3d3..e35a8d91b 100644 --- a/tests/generator/param-methane-abacus-diy.json +++ b/tests/generator/param-methane-abacus-diy.json @@ -1,23 +1,27 @@ { - "type_map": ["H", "C"], - "mass_map": [1.0, 12.0], - - "_comment": "initial data set for Training and the number of frames in each training batch", + "type_map": [ + "H", + "C" + ], + "mass_map": [ + 1.0, + 12.0 + ], + "_comment1": "initial data set for Training and the number of frames in each training batch", "init_data_prefix": "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/5_dpgen_examples/dpgen-example/run_abacus/", - "init_data_sys": [ + "init_data_sys": [ "abacus_init_data" ], "init_batch_size": [ 8 ], - - "_comment": "configurations for starting MD in Exploration and batch sizes when traning snapshots derived from these configs (if they were selected)", + "_comment2": "configurations for starting MD in Exploration and batch sizes when traning snapshots derived from these configs (if they were selected)", "sys_configs_prefix": "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/5_dpgen_examples/dpgen-example/run", - "sys_configs": [ + "sys_configs": [ [ "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/000000/POSCAR", "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/000001/POSCAR", - "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00000[2-9]/POSCAR" + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00000[2-9]/POSCAR" ], [ "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00001*/POSCAR" @@ -27,71 +31,82 @@ 8, 8 ], - - "_comment": " 00.train ", - "numb_models": 4, - + "_comment3": " 00.train ", + "numb_models": 4, "default_training_param": { "model": { - "type_map": ["H","C"], - "descriptor": { - "type": "se_a", - "sel": [16,4], - "rcut_smth": 0.5, - "rcut": 5.0, - "neuron": [10,20,40], - "resnet_dt": false, - "axis_neuron": 12, - "seed": 0 + "type_map": [ + "H", + "C" + ], + "descriptor": { + "type": "se_a", + "sel": [ + 16, + 4 + ], + "rcut_smth": 0.5, + "rcut": 5.0, + "neuron": [ + 10, + 20, + 40 + ], + "resnet_dt": false, + "axis_neuron": 12, + "seed": 0 }, "fitting_net": { - "neuron": [120,120,120], - "resnet_dt": true, + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true, "coord_norm": true, "type_fitting_net": false, "seed": 0 } }, - "loss": { - "start_pref_e": 0.02, - "limit_pref_e": 2, - "start_pref_f": 1000, - "limit_pref_f": 1, - "start_pref_v": 0, - "limit_pref_v": 0 + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0, + "limit_pref_v": 0 }, - "learning_rate": { - "type": "exp", - "start_lr": 0.001, - "decay_steps": 180, - "decay_rate": 0.95 + "learning_rate": { + "type": "exp", + "start_lr": 0.001, + "decay_steps": 180, + "stop_lr": 3.505266624882874e-08 }, - "training": { - "systems": [], - "set_prefix": "set", - "stop_batch": 36000, - "batch_size": 1, - "seed": 1, - "_comment": "frequencies counted in batch", - "disp_file": "lcurve.out", - "disp_freq": 1000, - "numb_test": 4, - "save_freq": 1000, - "save_ckpt": "model.ckpt", - "load_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json" + "training": { + "stop_batch": 36000, + "seed": 1, + "_comment4": "frequencies counted in batch", + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "training_data": { + "systems": [], + "set_prefix": "set", + "batch_size": 1 + } } }, - - "_comment": " 01.model_devi ", + "_comment5": " 01.model_devi ", "model_devi_dt": 0.002, "model_devi_skip": 0, - "model_devi_f_trust_lo": 0.05, - "model_devi_f_trust_hi": 0.15, - "model_devi_clean_traj": false, + "model_devi_f_trust_lo": 0.05, + "model_devi_f_trust_hi": 0.15, + "model_devi_clean_traj": false, "model_devi_jobs": [ { "sys_idx": [ @@ -104,9 +119,9 @@ 1 ], "trj_freq": 10, - "nsteps": 1000, + "nsteps": 1000, "ensemble": "nvt", - "_idx": "00" + "_idx": "00" }, { "sys_idx": [ @@ -119,20 +134,29 @@ 1 ], "trj_freq": 10, - "nsteps": 3000, + "nsteps": 3000, "ensemble": "nvt", - "_idx": "01" + "_idx": "01" } ], - - "_comment": " 02.fp ", - "fp_style": "abacus", - "shuffle_poscar": false, - "fp_task_max": 30, - "fp_task_min": 8, - "fp_pp_path": ".", - "fp_pp_files": [ "./H_HSCV_PBE-1.0.UPF","./C_HSCV_PBE-1.0.UPF"], - "fp_incar": "abacus/INPUT.diy", - "_k_points": [3, 3, 3, 0, 0, 0], - "_fp_kpt_file": "./abacus/KPT" -} + "_comment6": " 02.fp ", + "fp_style": "abacus", + "shuffle_poscar": false, + "fp_task_max": 30, + "fp_task_min": 8, + "fp_pp_path": ".", + "fp_pp_files": [ + "./H_HSCV_PBE-1.0.UPF", + "./C_HSCV_PBE-1.0.UPF" + ], + "fp_incar": "abacus/INPUT.diy", + "_k_points": [ + 3, + 3, + 3, + 0, + 0, + 0 + ], + "_fp_kpt_file": "./abacus/KPT" +} \ No newline at end of file diff --git a/tests/generator/param-methane-abacus.json b/tests/generator/param-methane-abacus.json index 2f9ff1b96..ab4299401 100644 --- a/tests/generator/param-methane-abacus.json +++ b/tests/generator/param-methane-abacus.json @@ -1,23 +1,27 @@ { - "type_map": ["H", "C"], - "mass_map": [1.0, 12.0], - - "_comment": "initial data set for Training and the number of frames in each training batch", + "type_map": [ + "H", + "C" + ], + "mass_map": [ + 1.0, + 12.0 + ], + "_comment1": "initial data set for Training and the number of frames in each training batch", "init_data_prefix": "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/5_dpgen_examples/dpgen-example/run_abacus/", - "init_data_sys": [ + "init_data_sys": [ "abacus_init_data" ], "init_batch_size": [ 8 ], - - "_comment": "configurations for starting MD in Exploration and batch sizes when traning snapshots derived from these configs (if they were selected)", + "_comment2": "configurations for starting MD in Exploration and batch sizes when traning snapshots derived from these configs (if they were selected)", "sys_configs_prefix": "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/5_dpgen_examples/dpgen-example/run", - "sys_configs": [ + "sys_configs": [ [ "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/000000/POSCAR", "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/000001/POSCAR", - "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00000[2-9]/POSCAR" + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00000[2-9]/POSCAR" ], [ "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00001*/POSCAR" @@ -27,71 +31,82 @@ 8, 8 ], - - "_comment": " 00.train ", - "numb_models": 4, - + "_comment3": " 00.train ", + "numb_models": 4, "default_training_param": { "model": { - "type_map": ["H","C"], - "descriptor": { - "type": "se_a", - "sel": [16,4], - "rcut_smth": 0.5, - "rcut": 5.0, - "neuron": [10,20,40], - "resnet_dt": false, - "axis_neuron": 12, - "seed": 0 + "type_map": [ + "H", + "C" + ], + "descriptor": { + "type": "se_a", + "sel": [ + 16, + 4 + ], + "rcut_smth": 0.5, + "rcut": 5.0, + "neuron": [ + 10, + 20, + 40 + ], + "resnet_dt": false, + "axis_neuron": 12, + "seed": 0 }, "fitting_net": { - "neuron": [120,120,120], - "resnet_dt": true, + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true, "coord_norm": true, "type_fitting_net": false, "seed": 0 } }, - "loss": { - "start_pref_e": 0.02, - "limit_pref_e": 2, - "start_pref_f": 1000, - "limit_pref_f": 1, - "start_pref_v": 0, - "limit_pref_v": 0 + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0, + "limit_pref_v": 0 }, - "learning_rate": { - "type": "exp", - "start_lr": 0.001, - "decay_steps": 180, - "decay_rate": 0.95 + "learning_rate": { + "type": "exp", + "start_lr": 0.001, + "decay_steps": 180, + "stop_lr": 3.505266624882874e-08 }, - "training": { - "systems": [], - "set_prefix": "set", - "stop_batch": 36000, - "batch_size": 1, - "seed": 1, - "_comment": "frequencies counted in batch", - "disp_file": "lcurve.out", - "disp_freq": 1000, - "numb_test": 4, - "save_freq": 1000, - "save_ckpt": "model.ckpt", - "load_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json" + "training": { + "stop_batch": 36000, + "seed": 1, + "_comment4": "frequencies counted in batch", + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "training_data": { + "systems": [], + "set_prefix": "set", + "batch_size": 1 + } } }, - - "_comment": " 01.model_devi ", + "_comment5": " 01.model_devi ", "model_devi_dt": 0.002, "model_devi_skip": 0, - "model_devi_f_trust_lo": 0.05, - "model_devi_f_trust_hi": 0.15, - "model_devi_clean_traj": false, + "model_devi_f_trust_lo": 0.05, + "model_devi_f_trust_hi": 0.15, + "model_devi_clean_traj": false, "model_devi_jobs": [ { "sys_idx": [ @@ -104,9 +119,9 @@ 1 ], "trj_freq": 10, - "nsteps": 1000, + "nsteps": 1000, "ensemble": "nvt", - "_idx": "00" + "_idx": "00" }, { "sys_idx": [ @@ -119,24 +134,33 @@ 1 ], "trj_freq": 10, - "nsteps": 3000, + "nsteps": 3000, "ensemble": "nvt", - "_idx": "01" + "_idx": "01" } ], - - "_comment": " 02.fp ", - "fp_style": "abacus", - "shuffle_poscar": false, - "fp_task_max": 30, - "fp_task_min": 8, - "fp_pp_path": ".", - "fp_pp_files": [ "./H_HSCV_PBE-1.0.UPF","./C_HSCV_PBE-1.0.UPF"], - "_fp_kpt_file": "./abacus/KPT", - "_k_points": [3,3,3,0,0,0], - "user_fp_params":{ + "_comment6": " 02.fp ", + "fp_style": "abacus", + "shuffle_poscar": false, + "fp_task_max": 30, + "fp_task_min": 8, + "fp_pp_path": ".", + "fp_pp_files": [ + "./H_HSCV_PBE-1.0.UPF", + "./C_HSCV_PBE-1.0.UPF" + ], + "_fp_kpt_file": "./abacus/KPT", + "_k_points": [ + 3, + 3, + 3, + 0, + 0, + 0 + ], + "user_fp_params": { "ecutwfc": 80, - "scf_thr": 1e-7, + "scf_thr": 1e-07, "scf_nmax": 50, "basis_type": "pw", "gamma_only": 1, @@ -150,11 +174,11 @@ "ks_solver": "cg", "smearing_method": "fixed", "smearing_sigma": 0.001, - "cal_force":1, - "cal_stress":1, - "deepks_out_labels":0, - "deepks_descriptor_lmax":0, - "deepks_scf":0, - "deepks_model":"model.ptg" - } -} + "cal_force": 1, + "cal_stress": 1, + "deepks_out_labels": 0, + "deepks_descriptor_lmax": 0, + "deepks_scf": 0, + "deepks_model": "model.ptg" + } +} \ No newline at end of file diff --git a/tests/generator/param-mg-vasp-diy.json b/tests/generator/param-mg-vasp-diy.json index f095f85f1..8f53d269c 100644 --- a/tests/generator/param-mg-vasp-diy.json +++ b/tests/generator/param-mg-vasp-diy.json @@ -1,89 +1,133 @@ { - "type_map": ["Mg", "Al"], - "mass_map": [24, 27], - - "init_data_prefix": "data", - "init_data_sys": 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["data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/000001/POSCAR"] +{ + "type_map": [ + "Mg", + "Al" + ], + "mass_map": [ + 24, + 27 + ], + "init_data_prefix": "data", + "init_data_sys": [ + "deepmd" + ], + "init_batch_size": [ + 16 + ], + "sys_configs": [ + [ + "data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/000000/POSCAR" ], - "_comment": "0 1 2 3", - "_comment": "4 5 6 7", - "sys_batch_size": [1, 1 - ], - - "_comment": " 00.train ", - "numb_models": 4, - "train_param": "input.json", - "default_training_param" : { - "_comment": " model parameters", - "use_smooth": true, - "sel_a": [90], - "rcut_smth": 2.00, - "rcut": 6.00, - "filter_neuron": [25, 50, 100], - "filter_resnet_dt": false, - "n_axis_neuron": 12, - "n_neuron": [240, 240, 240], - "resnet_dt": true, - "coord_norm": true, - "type_fitting_net": false, - - "_comment": " traing controls", - "systems": [], - "set_prefix": "set", - "stop_batch": 400000, - "batch_size": 1, - "start_lr": 0.002, - "decay_steps": 2000, - 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+ "resnet_dt": false + }, + "fitting_net": { + "seed": 0, + "neuron": [ + 240, + 240, + 240 + ], + "resnet_dt": true + } }, - - "_comment": " 01.model_devi ", - "_comment": "model_devi_skip: the first x of the recorded frames", - "model_devi_dt": 0.002, - "model_devi_skip": 0, - "model_devi_f_trust_lo": [0.000, 0.050], - "model_devi_f_trust_hi": {"1": 0.100, "0": 0.150}, - "model_devi_e_trust_lo": 1e10, - "model_devi_e_trust_hi": 1e10, - "model_devi_clean_traj": false, - "model_devi_jobs": [ - {"sys_idx": [0, 1], "temps": [50,100], "press": [1.0,2.0], "trj_freq": 10, "nsteps": 1000, "ensemble": "npt", "_idx": "00"} - ], - - "_comment": " 02.fp ", - "fp_style": "vasp", - "shuffle_poscar": false, - "fp_task_max": 100, - "fp_task_min": 10, - "fp_pp_path": ".", - "fp_pp_files": ["vasp/potcars/POTCAR.mg", "vasp/potcars/POTCAR.al"], - "_comment": " user provided vasp script ", - "user_fp_params": { - "PREC": "A", - "ENCUT": 600, - "ISYM": 0, - "ALGO": "fast", - "EDIFF": 1e-05, - "LREAL": 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"KGAMMA": false + }, + "_comment13": " that's all " +} \ No newline at end of file diff --git a/tests/generator/param-mg-vasp-old.json b/tests/generator/param-mg-vasp-old.json index 3926876c2..13fa5c3c6 100644 --- a/tests/generator/param-mg-vasp-old.json +++ b/tests/generator/param-mg-vasp-old.json @@ -1,103 +1,147 @@ -{ - "type_map": ["Mg", "Al"], - "mass_map": [24, 27], - - "init_data_prefix": "data", - "init_data_sys": ["deepmd" - ], - "init_batch_size": [16], - "sys_configs": [ - ["data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/000010/POSCAR"], - ["data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/00000[8-9]/POSCAR"] +{ + "type_map": [ + "Mg", + "Al" + ], + "mass_map": [ + 24, + 27 + ], + "init_data_prefix": "data", + "init_data_sys": [ + "deepmd" + ], + "init_batch_size": [ + 16 + ], + "sys_configs": [ + [ + "data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/000010/POSCAR" ], - "_comment": "0 1 2 3", - "_comment": "4 5 6 7", - "sys_batch_size": [1, 1 - ], - - "_comment": " 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false, - "profiling_file": "timeline.json", - - "_comment": "that's all" + [ + "data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/00000[8-9]/POSCAR" + ] + ], + "_comment1": "0 1 2 3", + "_comment2": "4 5 6 7", + "sys_batch_size": [ + 1, + 1 + ], + "_comment3": " 00.train ", + "numb_models": 4, + "default_training_param": { + "model": { + "descriptor": { + "seed": 0, + "type": "se_a", + "sel": [ + 90 + ], + "rcut": 6.0, + "rcut_smth": 2.0, + "neuron": [ + 25, + 50, + 100 + ], + "axis_neuron": 12, + "resnet_dt": false + }, + "fitting_net": { + "seed": 0, + "neuron": [ + 240, + 240, + 240 + ], + "resnet_dt": true + } }, - - "_comment": " 01.model_devi ", - "_comment": "model_devi_skip: the first x of the recorded frames", - "model_devi_dt": 0.002, - "model_devi_skip": 0, - "model_devi_f_trust_lo": 0.050, - "model_devi_f_trust_hi": 0.150, - "model_devi_clean_traj": false, - "model_devi_jobs": [ - {"sys_idx": [0,1], "temps": [50,100], "press": [1.0,2.0], "trj_freq": 10, "nsteps": 1000, "ensemble": "npt", "_idx": "00"} - ], - - "_comment": " 02.fp ", - "fp_style": "vasp", - "shuffle_poscar": false, - "fp_task_max": 100, - "fp_task_min": 10, - "fp_pp_path": ".", - "fp_pp_files": ["vasp/potcars/POTCAR.mg", "vasp/potcars/POTCAR.al"], - "fp_params": { - "_comment": "given in unit depending on the fp method", - "ecut": 600, - "ediff": 1e-6, - "kspacing": 0.16, - "_comment": "gauss, mp:N(methfessel-paxton:order by default order=1), fd(Fermi-Dirac)", - "smearing": "mp", - "sigma": 0.25, - "_comment": "only for vasp, can be NONE, SCAN, TPSS, RTPSS, M06L or MBJ", - "metagga": "NONE", - "npar": 1, - "kpar": 1, - "user_vasp_params": { - "EDIFF" : 1e-5 - }, - "_comment": " that's all " + "learning_rate": { + "type": "exp", + "decay_steps": 2000, + "start_lr": 0.002, + "stop_lr": 7.010533249765748e-08 + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0.0, + "limit_pref_v": 0.0 + }, + "training": { + "seed": 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"given in unit depending on the fp method", + "ecut": 600, + "ediff": 1e-06, + "kspacing": 0.16, + "_comment13": "gauss, mp:N(methfessel-paxton:order by default order=1), fd(Fermi-Dirac)", + "smearing": "mp", + "sigma": 0.25, + "_comment14": "only for vasp, can be NONE, SCAN, TPSS, RTPSS, M06L or MBJ", + "metagga": "NONE", + "npar": 1, + "kpar": 1, + "user_vasp_params": { + "EDIFF": 1e-05 }, - "_comment": " that's all " -} + "_comment15": " that's all " + }, + "_comment16": " that's all " +} \ No newline at end of file diff --git a/tests/generator/param-mg-vasp-v1-et.json b/tests/generator/param-mg-vasp-v1-et.json index cfa8071d1..abf636261 100644 --- a/tests/generator/param-mg-vasp-v1-et.json +++ b/tests/generator/param-mg-vasp-v1-et.json @@ -1,96 +1,134 @@ { - "type_map": ["Al", "Mg"], - "mass_map": [27, 24], - "use_ele_temp": 2, - - "init_data_prefix": "data", - "init_data_sys": ["deepmd" - ], - "init_batch_size": [16], - "sys_configs": [ - 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120, + 120 + ], + "resnet_dt": true, + "numb_fparam": 10, + "seed": 1 + } }, - - "_comment": " 01.model_devi ", - "_comment": "model_devi_skip: the first x of the recorded frames", - "model_devi_dt": 0.002, - "model_devi_skip": 0, - "model_devi_f_trust_lo": 0.05, - "model_devi_f_trust_hi": 0.20, - "model_devi_clean_traj": false, - "model_devi_jobs": [ - { "_idx": 0, "ensemble": "npt", "nsteps": 50, "press": [1.0,2.0], "sys_idx": [0, 1], "temps": [50,100], "trj_freq": 10 } - ], - "_comment": " 02.fp ", - "fp_style": "vasp", - "shuffle_poscar": false, - "fp_task_max": 8, - "fp_task_min": 2, - "fp_pp_path": "/home/wanghan/study/deep.md/dpgen/almg/vasp", - "fp_pp_files": ["POTCAR.Al", "POTCAR.Mg"], - "fp_incar": "/home/wanghan/study/deep.md/dpgen/almg/vasp/INCAR", - "_comment": " that's all " -} - + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 1, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0, + "limit_pref_v": 0 + }, + "learning_rate": { + "start_lr": 0.001, + 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"init_data_sys": [ + "deepmd" + ], + "init_batch_size": [ + 16 + ], + "sys_configs": [ + [ + "data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/000010/POSCAR" ], - "sys_batch_size": [1,1], - - "_comment": " 00.train ", - "numb_models": 4, - "default_training_param" : { - "model" : { - "descriptor": { - "type": "se_a", - "sel": [90, 90], - "rcut_smth": 1.80, - "rcut": 6.00, - "neuron": [10, 20, 40], - "resnet_dt": false, - "axis_neuron": 4, - "seed": 1 - }, - "fitting_net" : { - "neuron": [120, 120, 120], - "resnet_dt": true, - "seed": 1 - } - }, - - "loss" : { - "start_pref_e": 0.02, - "limit_pref_e": 1, - "start_pref_f": 1000, - "limit_pref_f": 1, - "start_pref_v": 0, - "limit_pref_v": 0 - }, - - "learning_rate" : { - "start_lr": 0.001, - "decay_steps": 5000, - "decay_rate": 0.95 - }, - - "training" : { - "systems": [], - "set_prefix": "set", - "stop_batch": 1000, - "batch_size": 1, - - "seed": 1, - - "_comment": " display and restart", - "_comment": " frequencies counted in batch", 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file diff --git a/tests/generator/param-mg-vasp.json b/tests/generator/param-mg-vasp.json index df2c86172..4c88e5e4b 100644 --- a/tests/generator/param-mg-vasp.json +++ b/tests/generator/param-mg-vasp.json @@ -1,108 +1,152 @@ -{ - "type_map": ["Mg", "Al"], - "mass_map": [24, 27], - - "init_data_prefix": "data", - "init_data_sys": ["deepmd" - ], - "init_batch_size": [16], - "sys_configs": [ - ["data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/000000/POSCAR"], - ["data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/000001/POSCAR"] +{ + "type_map": [ + "Mg", + "Al" + ], + "mass_map": [ + 24, + 27 + ], + "init_data_prefix": "data", + "init_data_sys": [ + "deepmd" + ], + "init_batch_size": [ + 16 + ], + "sys_configs": [ + [ + "data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/000000/POSCAR" ], - "_comment": "0 1 2 3", - "_comment": "4 5 6 7", - "sys_batch_size": [1, 1 - ], - - "_comment": " 00.train ", - "numb_models": 4, - "default_training_param" : { - "_comment": " model parameters", - 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a/tests/sample.json b/tests/sample.json index c068f91ac..1d24fd344 100644 --- a/tests/sample.json +++ b/tests/sample.json @@ -1 +1,3 @@ -{"aa": "bb"} \ No newline at end of file +{ + "aa": "bb" +} \ No newline at end of file diff --git a/tests/tools/machine_fp_single.json b/tests/tools/machine_fp_single.json index f998388eb..9169f709c 100644 --- a/tests/tools/machine_fp_single.json +++ b/tests/tools/machine_fp_single.json @@ -1,15 +1,17 @@ { - "fp":[ + "fp": [ { "command": "vasp_std", - "machine":{ + "machine": { "batch_type": "PBS" }, "resources": { - "group_size" : 8 + "group_size": 8 }, - "_comments" : "In user_forward_files, define input files to be uploaded.", - "user_forward_files" : ["vdw_kernel.bindat"] + "_comments": "In user_forward_files, define input files to be uploaded.", + "user_forward_files": [ + "vdw_kernel.bindat" + ] } - ] + ] } \ No newline at end of file diff --git a/tests/tools/machine_fp_single2.json b/tests/tools/machine_fp_single2.json index 8c2212927..302a02d74 100644 --- a/tests/tools/machine_fp_single2.json +++ b/tests/tools/machine_fp_single2.json @@ -1,14 +1,15 @@ { - "fp": - { - "command": "vasp_std", - "machine":{ - "batch_type": "PBS" - }, - "resources": { - "group_size" : 8 - }, - "_comments" : "In user_forward_files, define input files to be uploaded.", - "user_forward_files" : ["vdw_kernel.bindat"] - } + "fp": { + "command": "vasp_std", + "machine": { + "batch_type": "PBS" + }, + "resources": { + "group_size": 8 + }, + "_comments": "In user_forward_files, define input files to be uploaded.", + "user_forward_files": [ + "vdw_kernel.bindat" + ] + } } \ No newline at end of file diff --git a/tests/tools/run_report_test_output/param.json b/tests/tools/run_report_test_output/param.json index e8d11b9a8..ce637c424 100644 --- a/tests/tools/run_report_test_output/param.json +++ b/tests/tools/run_report_test_output/param.json @@ -1,87 +1,132 @@ { - "type_map": ["Al", "Mg"], - "mass_map": [27, 24], - - "init_data_prefix": 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information, see https://pre-commit.ci --- dpgen/data/jsons/al.diamond.111.json | 2 +- dpgen/data/jsons/al.diamond.222.json | 2 +- dpgen/data/jsons/al.fcc.111.json | 2 +- dpgen/data/jsons/al.fcc.222.json | 2 +- dpgen/data/jsons/al.hcp.111.json | 2 +- dpgen/data/jsons/al.hcp.222.json | 2 +- dpgen/data/jsons/al.hcp.332.json | 2 +- dpgen/data/jsons/al.sc.222.json | 2 +- dpgen/data/jsons/almg.diamond.111.json | 2 +- dpgen/data/jsons/almg.diamond.222.json | 2 +- dpgen/data/jsons/almg.fcc.111.json | 2 +- dpgen/data/jsons/almg.fcc.222.json | 2 +- dpgen/data/jsons/almg.hcp.111.json | 2 +- dpgen/data/jsons/almg.hcp.222.json | 2 +- dpgen/data/jsons/almg.hcp.332.json | 2 +- dpgen/data/jsons/almg.sc.222.json | 2 +- dpgen/data/jsons/almg.sc.333.json | 2 +- dpgen/data/jsons/mg.diamond.111.json | 2 +- dpgen/data/jsons/mg.diamond.222.json | 2 +- dpgen/data/jsons/mg.fcc.111.json | 2 +- dpgen/data/jsons/mg.fcc.222.json | 2 +- dpgen/data/jsons/mg.hcp.111.json | 2 +- dpgen/data/jsons/mg.hcp.222.json | 2 +- dpgen/data/jsons/mg.hcp.332.json | 2 +- dpgen/data/jsons/mg.sc.222.json | 2 +- dpgen/data/jsons/param.json | 2 +- dpgen/data/jsons/si.diamond.111.json | 2 +- dpgen/data/jsons/si.diamond.222.json | 2 +- dpgen/data/jsons/si.fcc.111.json | 2 +- dpgen/data/jsons/si.fcc.222.json | 2 +- dpgen/data/jsons/si.hcp.111.json | 2 +- dpgen/data/jsons/si.hcp.222.json | 2 +- dpgen/data/jsons/si.sc.222.json | 2 +- dpgen/data/jsons/surf.al.fcc.json | 2 +- dpgen/data/jsons/surf.al.hcp.json | 2 +- dpgen/data/jsons/surf.almg.fcc.json | 2 +- dpgen/data/jsons/surf.almg.hcp.json | 2 +- dpgen/data/jsons/surf.mg.fcc.json | 2 +- dpgen/data/jsons/surf.mg.hcp.json | 2 +- dpgen/data/jsons/surf.si.diamond.json | 2 +- dpgen/data/jsons/w.bcc.111.json | 2 +- dpgen/data/jsons/w.bcc.222.json | 2 +- dpgen/data/jsons/w.diamond.111.json | 2 +- dpgen/data/jsons/w.fcc.111.json | 2 +- dpgen/data/jsons/w.hcp.111.json | 2 +- dpgen/data/jsons/water.111.json | 2 +- examples/CH4-refact-dpdispatcher/machine-ali-ehpc.json | 2 +- examples/CH4-refact-dpdispatcher/machine-dpcloudserver.json | 2 +- examples/database/param_Ti.json | 2 +- examples/init/abacus/CuW/CuW.json | 2 +- examples/init/abacus/fcc-Al-lcao/init.json | 2 +- examples/init/abacus/fcc-Al-pw/init.json | 2 +- examples/init/al.json | 2 +- examples/init/ch4.json | 2 +- examples/init/cu.surf.hcp.111.json | 2 +- examples/init/reaction.json | 2 +- examples/init/surf.json | 2 +- examples/machine/DeePMD-kit-1.0/machine-local-4GPU.json | 2 +- examples/machine/DeePMD-kit-1.x/machine-local.json | 2 +- examples/machine/DeePMD-kit-1.x/machine-lsf-slurm-cp2k.json | 2 +- examples/machine/DeePMD-kit-1.x/machine-pbs-gaussian.json | 2 +- examples/machine/DeePMD-kit-1.x/machine-slurm-qe.json | 2 +- examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine.json | 2 +- examples/run/ch4/machine.json | 2 +- examples/run/ch4/param.json | 2 +- examples/run/deprecated/dp2.x-gromacs-gaussian/param.json | 2 +- examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.json | 2 +- .../dp2.x-lammps-pwmat/machine-slurm-pwmat-single.json | 2 +- examples/run/deprecated/dp2.x-lammps-pwmat/param_CH4.json | 2 +- .../dp2.x-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.json | 2 +- .../run/deprecated/dp2.x-lammps-vasp/Al/param_al_all_gpu.json | 2 +- examples/run/deprecated/dp2.x-lammps-vasp/CH4/param_CH4.json | 2 +- examples/run/deprecated/param-h2oscan-vasp.json | 2 +- examples/run/deprecated/param-mg-vasp-ucloud.json | 2 +- examples/run/deprecated/param-mg-vasp.json | 2 +- examples/run/deprecated/param-pyridine-pwscf.json | 2 +- examples/run/dp-calypso-vasp/machine.json | 2 +- examples/run/dp-calypso-vasp/param.json | 2 +- examples/run/dp-lammps-enhance_sampling/param.json | 2 +- examples/run/dp2.x-gromacs-gaussian/param.json | 2 +- examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/machine.json | 2 +- examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/param.json | 2 +- examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/machine.json | 2 +- examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/run_param.json | 2 +- examples/run/dp2.x-lammps-ABACUS-pw/fcc-al/machine.json | 2 +- examples/run/dp2.x-lammps-ABACUS-pw/fcc-al/run_param.json | 2 +- examples/run/dp2.x-lammps-ABACUS-pw/methane/machine.json | 2 +- examples/run/dp2.x-lammps-ABACUS-pw/methane/param.json | 2 +- examples/run/dp2.x-lammps-cp2k/methane/param-ch4.json | 2 +- examples/run/dp2.x-lammps-cp2k/param_CH4_deepmd-kit-2.0.1.json | 2 +- examples/run/dp2.x-lammps-gaussian/machine.json | 2 +- .../dp2.x-lammps-gaussian/param_C4H16N4_deepmd-kit-2.0.1.json | 2 +- examples/run/dp2.x-lammps-vasp-et/param_elet.json | 2 +- .../dp2.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-1.1.0.json | 2 +- .../run/dp2.x-lammps-vasp/CH4/param_CH4_deepmd-kit-2.x.json | 2 +- examples/run/dp2.x-lammps-vasp/param_CH4_deepmd-kit-2.0.1.json | 2 +- examples/run/dp2.x_lammps_gaussian/dodecane/dodecane.json | 2 +- examples/run/dprc/generator.json | 2 +- .../simplify-MAPbI3-scan-lebesgue/simplify_example/machine.json | 2 +- .../simplify_example/simplify.json | 2 +- examples/simplify/qm7.json | 2 +- examples/test/deepmd_param.json | 2 +- examples/test/meam_param.json | 2 +- examples/test/vasp_param.json | 2 +- examples/test/vasp_param_from_incar.json | 2 +- 105 files changed, 105 insertions(+), 105 deletions(-) diff --git a/dpgen/data/jsons/al.diamond.111.json b/dpgen/data/jsons/al.diamond.111.json index 85b9f9264..83ccf6753 100644 --- a/dpgen/data/jsons/al.diamond.111.json +++ b/dpgen/data/jsons/al.diamond.111.json @@ -33,4 +33,4 @@ "deepgen_templ": "../generator/template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/al.diamond.222.json b/dpgen/data/jsons/al.diamond.222.json index a3e25b2c3..3d15c40f8 100644 --- a/dpgen/data/jsons/al.diamond.222.json +++ b/dpgen/data/jsons/al.diamond.222.json @@ -33,4 +33,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/al.fcc.111.json b/dpgen/data/jsons/al.fcc.111.json index aaed5dafa..50866a722 100644 --- a/dpgen/data/jsons/al.fcc.111.json +++ b/dpgen/data/jsons/al.fcc.111.json @@ -33,4 +33,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/al.fcc.222.json b/dpgen/data/jsons/al.fcc.222.json index f8a244038..14790cdbd 100644 --- a/dpgen/data/jsons/al.fcc.222.json +++ b/dpgen/data/jsons/al.fcc.222.json @@ -33,4 +33,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/al.hcp.111.json b/dpgen/data/jsons/al.hcp.111.json index 0a91fd0b4..2b14badba 100644 --- a/dpgen/data/jsons/al.hcp.111.json +++ b/dpgen/data/jsons/al.hcp.111.json @@ -33,4 +33,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/al.hcp.222.json b/dpgen/data/jsons/al.hcp.222.json index 733baf1f5..aa1d06abc 100644 --- a/dpgen/data/jsons/al.hcp.222.json +++ b/dpgen/data/jsons/al.hcp.222.json @@ -33,4 +33,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/al.hcp.332.json b/dpgen/data/jsons/al.hcp.332.json index 20a208366..77b2bdedc 100644 --- a/dpgen/data/jsons/al.hcp.332.json +++ b/dpgen/data/jsons/al.hcp.332.json @@ -33,4 +33,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/al.sc.222.json b/dpgen/data/jsons/al.sc.222.json index 7db2d21f6..1c5a5f43c 100644 --- a/dpgen/data/jsons/al.sc.222.json +++ b/dpgen/data/jsons/al.sc.222.json @@ -33,4 +33,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/almg.diamond.111.json b/dpgen/data/jsons/almg.diamond.111.json index 013c66aca..251425fd9 100644 --- a/dpgen/data/jsons/almg.diamond.111.json +++ b/dpgen/data/jsons/almg.diamond.111.json @@ -35,4 +35,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/almg.diamond.222.json b/dpgen/data/jsons/almg.diamond.222.json index f8faefa11..7b968c24c 100644 --- a/dpgen/data/jsons/almg.diamond.222.json +++ b/dpgen/data/jsons/almg.diamond.222.json @@ -35,4 +35,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/almg.fcc.111.json b/dpgen/data/jsons/almg.fcc.111.json index abd90eaaf..9246b1b03 100644 --- a/dpgen/data/jsons/almg.fcc.111.json +++ b/dpgen/data/jsons/almg.fcc.111.json @@ -35,4 +35,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/almg.fcc.222.json b/dpgen/data/jsons/almg.fcc.222.json index 92f24981e..8370e2025 100644 --- a/dpgen/data/jsons/almg.fcc.222.json +++ b/dpgen/data/jsons/almg.fcc.222.json @@ -35,4 +35,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/almg.hcp.111.json b/dpgen/data/jsons/almg.hcp.111.json index 063d9f42e..31fce16f3 100644 --- a/dpgen/data/jsons/almg.hcp.111.json +++ b/dpgen/data/jsons/almg.hcp.111.json @@ -35,4 +35,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/almg.hcp.222.json b/dpgen/data/jsons/almg.hcp.222.json index 2a00e64d8..bbff1dec1 100644 --- a/dpgen/data/jsons/almg.hcp.222.json +++ b/dpgen/data/jsons/almg.hcp.222.json @@ -35,4 +35,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/almg.hcp.332.json b/dpgen/data/jsons/almg.hcp.332.json index fc1e2f052..b7477e75b 100644 --- a/dpgen/data/jsons/almg.hcp.332.json +++ b/dpgen/data/jsons/almg.hcp.332.json @@ -35,4 +35,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/almg.sc.222.json b/dpgen/data/jsons/almg.sc.222.json index 99c5420cc..df9d25f53 100644 --- a/dpgen/data/jsons/almg.sc.222.json +++ b/dpgen/data/jsons/almg.sc.222.json @@ -35,4 +35,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/almg.sc.333.json b/dpgen/data/jsons/almg.sc.333.json index 74e9418cf..621b3ca84 100644 --- a/dpgen/data/jsons/almg.sc.333.json +++ b/dpgen/data/jsons/almg.sc.333.json @@ -35,4 +35,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/mg.diamond.111.json b/dpgen/data/jsons/mg.diamond.111.json index 08d532134..419154c68 100644 --- a/dpgen/data/jsons/mg.diamond.111.json +++ b/dpgen/data/jsons/mg.diamond.111.json @@ -33,4 +33,4 @@ "deepgen_templ": "../generator/template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/mg.diamond.222.json b/dpgen/data/jsons/mg.diamond.222.json index 398051f21..d3e19bc32 100644 --- a/dpgen/data/jsons/mg.diamond.222.json +++ b/dpgen/data/jsons/mg.diamond.222.json @@ -33,4 +33,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/mg.fcc.111.json b/dpgen/data/jsons/mg.fcc.111.json index d4bccfb2e..42662508b 100644 --- a/dpgen/data/jsons/mg.fcc.111.json +++ b/dpgen/data/jsons/mg.fcc.111.json @@ -33,4 +33,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/mg.fcc.222.json b/dpgen/data/jsons/mg.fcc.222.json index 9e88a5c97..18fd5f789 100644 --- a/dpgen/data/jsons/mg.fcc.222.json +++ b/dpgen/data/jsons/mg.fcc.222.json @@ -33,4 +33,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/mg.hcp.111.json b/dpgen/data/jsons/mg.hcp.111.json index 428d79197..56b8b10ee 100644 --- a/dpgen/data/jsons/mg.hcp.111.json +++ b/dpgen/data/jsons/mg.hcp.111.json @@ -33,4 +33,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/mg.hcp.222.json b/dpgen/data/jsons/mg.hcp.222.json index 8da4061c3..9d1507ae1 100644 --- a/dpgen/data/jsons/mg.hcp.222.json +++ b/dpgen/data/jsons/mg.hcp.222.json @@ -31,4 +31,4 @@ "md_temp": 100, "md_nstep": 10, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/mg.hcp.332.json b/dpgen/data/jsons/mg.hcp.332.json index 1106092cd..e39c3c3bc 100644 --- a/dpgen/data/jsons/mg.hcp.332.json +++ b/dpgen/data/jsons/mg.hcp.332.json @@ -31,4 +31,4 @@ "md_temp": 100, "md_nstep": 10, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/mg.sc.222.json b/dpgen/data/jsons/mg.sc.222.json index 8ee5444fa..5c2098ad7 100644 --- a/dpgen/data/jsons/mg.sc.222.json +++ b/dpgen/data/jsons/mg.sc.222.json @@ -33,4 +33,4 @@ "deepgen_templ": "../generator/template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/param.json b/dpgen/data/jsons/param.json index 1601d3251..5581417b7 100644 --- a/dpgen/data/jsons/param.json +++ b/dpgen/data/jsons/param.json @@ -37,4 +37,4 @@ 1, 2 ] -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/si.diamond.111.json b/dpgen/data/jsons/si.diamond.111.json index 9ef9e6ffb..808ff33fe 100644 --- a/dpgen/data/jsons/si.diamond.111.json +++ b/dpgen/data/jsons/si.diamond.111.json @@ -33,4 +33,4 @@ "deepgen_templ": "../generator/template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/si.diamond.222.json b/dpgen/data/jsons/si.diamond.222.json index 2f5ab7786..14c147250 100644 --- a/dpgen/data/jsons/si.diamond.222.json +++ b/dpgen/data/jsons/si.diamond.222.json @@ -33,4 +33,4 @@ "deepgen_templ": "../generator/template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/si.fcc.111.json b/dpgen/data/jsons/si.fcc.111.json index 67caa847e..af33644d2 100644 --- a/dpgen/data/jsons/si.fcc.111.json +++ b/dpgen/data/jsons/si.fcc.111.json @@ -33,4 +33,4 @@ "deepgen_templ": "../generator/template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/si.fcc.222.json b/dpgen/data/jsons/si.fcc.222.json index b563f2d68..3c7f41bf6 100644 --- a/dpgen/data/jsons/si.fcc.222.json +++ b/dpgen/data/jsons/si.fcc.222.json @@ -33,4 +33,4 @@ "deepgen_templ": "../generator/template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/si.hcp.111.json b/dpgen/data/jsons/si.hcp.111.json index d366d2b82..127c769b0 100644 --- a/dpgen/data/jsons/si.hcp.111.json +++ b/dpgen/data/jsons/si.hcp.111.json @@ -33,4 +33,4 @@ "deepgen_templ": "../generator/template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/si.hcp.222.json b/dpgen/data/jsons/si.hcp.222.json index 7582afbf2..b92ec401a 100644 --- a/dpgen/data/jsons/si.hcp.222.json +++ b/dpgen/data/jsons/si.hcp.222.json @@ -33,4 +33,4 @@ "deepgen_templ": "../generator/template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/si.sc.222.json b/dpgen/data/jsons/si.sc.222.json index 734c7e9a9..f321c2c79 100644 --- a/dpgen/data/jsons/si.sc.222.json +++ b/dpgen/data/jsons/si.sc.222.json @@ -33,4 +33,4 @@ "deepgen_templ": "../generator/template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/surf.al.fcc.json b/dpgen/data/jsons/surf.al.fcc.json index 5730de615..bc8a84023 100644 --- a/dpgen/data/jsons/surf.al.fcc.json +++ b/dpgen/data/jsons/surf.al.fcc.json @@ -37,4 +37,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/surf.al.hcp.json b/dpgen/data/jsons/surf.al.hcp.json index 2f3679a43..9e78a2207 100644 --- a/dpgen/data/jsons/surf.al.hcp.json +++ b/dpgen/data/jsons/surf.al.hcp.json @@ -37,4 +37,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/surf.almg.fcc.json b/dpgen/data/jsons/surf.almg.fcc.json index 776f21c91..311d38058 100644 --- a/dpgen/data/jsons/surf.almg.fcc.json +++ b/dpgen/data/jsons/surf.almg.fcc.json @@ -39,4 +39,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/surf.almg.hcp.json b/dpgen/data/jsons/surf.almg.hcp.json index fd6a8d8a8..2b6b29bac 100644 --- a/dpgen/data/jsons/surf.almg.hcp.json +++ b/dpgen/data/jsons/surf.almg.hcp.json @@ -39,4 +39,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/surf.mg.fcc.json b/dpgen/data/jsons/surf.mg.fcc.json index 94c527234..75504a33a 100644 --- a/dpgen/data/jsons/surf.mg.fcc.json +++ b/dpgen/data/jsons/surf.mg.fcc.json @@ -37,4 +37,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/surf.mg.hcp.json b/dpgen/data/jsons/surf.mg.hcp.json index 705cc7858..2ee3c7d4e 100644 --- a/dpgen/data/jsons/surf.mg.hcp.json +++ b/dpgen/data/jsons/surf.mg.hcp.json @@ -37,4 +37,4 @@ "deepgen_templ": "../template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/surf.si.diamond.json b/dpgen/data/jsons/surf.si.diamond.json index c5dd90c93..c34c05e30 100644 --- a/dpgen/data/jsons/surf.si.diamond.json +++ b/dpgen/data/jsons/surf.si.diamond.json @@ -55,4 +55,4 @@ "deepgen_templ": "../generator/template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/w.bcc.111.json b/dpgen/data/jsons/w.bcc.111.json index a1a759245..35c696d23 100644 --- a/dpgen/data/jsons/w.bcc.111.json +++ b/dpgen/data/jsons/w.bcc.111.json @@ -35,4 +35,4 @@ "deepgen_templ": "../generator/template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/w.bcc.222.json b/dpgen/data/jsons/w.bcc.222.json index 1bb155a55..76731b97b 100644 --- a/dpgen/data/jsons/w.bcc.222.json +++ b/dpgen/data/jsons/w.bcc.222.json @@ -35,4 +35,4 @@ "deepgen_templ": "../generator/template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/w.diamond.111.json b/dpgen/data/jsons/w.diamond.111.json index e2f61b2ab..3e140a071 100644 --- a/dpgen/data/jsons/w.diamond.111.json +++ b/dpgen/data/jsons/w.diamond.111.json @@ -35,4 +35,4 @@ "deepgen_templ": "../generator/template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/w.fcc.111.json b/dpgen/data/jsons/w.fcc.111.json index f8ca14f52..1ad0c6cc4 100644 --- a/dpgen/data/jsons/w.fcc.111.json +++ b/dpgen/data/jsons/w.fcc.111.json @@ -35,4 +35,4 @@ "deepgen_templ": "../generator/template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/w.hcp.111.json b/dpgen/data/jsons/w.hcp.111.json index 1bc6cae02..097daf9d4 100644 --- a/dpgen/data/jsons/w.hcp.111.json +++ b/dpgen/data/jsons/w.hcp.111.json @@ -35,4 +35,4 @@ "deepgen_templ": "../generator/template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/dpgen/data/jsons/water.111.json b/dpgen/data/jsons/water.111.json index 7547bb216..261575b03 100644 --- a/dpgen/data/jsons/water.111.json +++ b/dpgen/data/jsons/water.111.json @@ -34,4 +34,4 @@ "deepgen_templ": "../generator/template/", "coll_ndata": 5000, "_comment4": "that's all" -} \ No newline at end of file +} diff --git a/examples/CH4-refact-dpdispatcher/machine-ali-ehpc.json b/examples/CH4-refact-dpdispatcher/machine-ali-ehpc.json index bfefe10d5..9222aed6f 100644 --- a/examples/CH4-refact-dpdispatcher/machine-ali-ehpc.json +++ b/examples/CH4-refact-dpdispatcher/machine-ali-ehpc.json @@ -89,4 +89,4 @@ ], "user_backward_files": [] } -} \ No newline at end of file +} diff --git a/examples/CH4-refact-dpdispatcher/machine-dpcloudserver.json b/examples/CH4-refact-dpdispatcher/machine-dpcloudserver.json index 7fb68714b..c27db8859 100644 --- a/examples/CH4-refact-dpdispatcher/machine-dpcloudserver.json +++ b/examples/CH4-refact-dpdispatcher/machine-dpcloudserver.json @@ -125,4 +125,4 @@ ] } } -} \ No newline at end of file +} diff --git a/examples/database/param_Ti.json b/examples/database/param_Ti.json index fbfccf773..5560b31f9 100644 --- a/examples/database/param_Ti.json +++ b/examples/database/param_Ti.json @@ -97,4 +97,4 @@ ] }, "skip_init": true -} \ No newline at end of file +} diff --git a/examples/init/abacus/CuW/CuW.json b/examples/init/abacus/CuW/CuW.json index 1738d8f34..b351af657 100644 --- a/examples/init/abacus/CuW/CuW.json +++ b/examples/init/abacus/CuW/CuW.json @@ -49,4 +49,4 @@ "W" ], "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/examples/init/abacus/fcc-Al-lcao/init.json b/examples/init/abacus/fcc-Al-lcao/init.json index 5a509478a..76507f0df 100644 --- a/examples/init/abacus/fcc-Al-lcao/init.json +++ b/examples/init/abacus/fcc-Al-lcao/init.json @@ -38,4 +38,4 @@ "deepgen_templ": "../generator/template/", "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/examples/init/abacus/fcc-Al-pw/init.json b/examples/init/abacus/fcc-Al-pw/init.json index aa6be838c..a20ca4c87 100644 --- a/examples/init/abacus/fcc-Al-pw/init.json +++ b/examples/init/abacus/fcc-Al-pw/init.json @@ -35,4 +35,4 @@ "deepgen_templ": "../generator/template/", "coll_ndata": 10, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/examples/init/al.json b/examples/init/al.json index 956e9646c..76506d76d 100644 --- a/examples/init/al.json +++ b/examples/init/al.json @@ -29,4 +29,4 @@ "Al" ], "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/examples/init/ch4.json b/examples/init/ch4.json index 28ab1954d..d28e7ac26 100644 --- a/examples/init/ch4.json +++ b/examples/init/ch4.json @@ -33,4 +33,4 @@ "pert_atom": 0.01, "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/examples/init/cu.surf.hcp.111.json b/examples/init/cu.surf.hcp.111.json index a3e5ec154..7d29774fc 100644 --- a/examples/init/cu.surf.hcp.111.json +++ b/examples/init/cu.surf.hcp.111.json @@ -56,4 +56,4 @@ "pert_atom": 0.01, "lmp_cmd": "PATH/lmp_serial", "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/examples/init/reaction.json b/examples/init/reaction.json index 02d3df6dd..0d163343e 100644 --- a/examples/init/reaction.json +++ b/examples/init/reaction.json @@ -16,4 +16,4 @@ "cutoff": 3.5, "dataset_size": 100, "qmkeywords": "b3lyp/6-31g** force Geom=PrintInputOrient" -} \ No newline at end of file +} diff --git a/examples/init/surf.json b/examples/init/surf.json index 7ab79189a..4bb00df97 100644 --- a/examples/init/surf.json +++ b/examples/init/surf.json @@ -53,4 +53,4 @@ "pert_atom": 0.01, "coll_ndata": 5000, "_comment1": "that's all" -} \ No newline at end of file +} diff --git a/examples/machine/DeePMD-kit-1.0/machine-local-4GPU.json b/examples/machine/DeePMD-kit-1.0/machine-local-4GPU.json index dd6559a46..37526ab2f 100644 --- a/examples/machine/DeePMD-kit-1.0/machine-local-4GPU.json +++ b/examples/machine/DeePMD-kit-1.0/machine-local-4GPU.json @@ -87,4 +87,4 @@ "command": "mpirun -n 16 vasp_std || :" }, "api_version": "1.0" -} \ No newline at end of file +} diff --git a/examples/machine/DeePMD-kit-1.x/machine-local.json b/examples/machine/DeePMD-kit-1.x/machine-local.json index c46989343..6da8a09cb 100644 --- a/examples/machine/DeePMD-kit-1.x/machine-local.json +++ b/examples/machine/DeePMD-kit-1.x/machine-local.json @@ -62,4 +62,4 @@ }, "command": "mpirun -n 4 /home/wanghan/local/bin/vasp_std" } -} \ No newline at end of file +} diff --git a/examples/machine/DeePMD-kit-1.x/machine-lsf-slurm-cp2k.json b/examples/machine/DeePMD-kit-1.x/machine-lsf-slurm-cp2k.json index c044c1c77..634df15f5 100644 --- a/examples/machine/DeePMD-kit-1.x/machine-lsf-slurm-cp2k.json +++ b/examples/machine/DeePMD-kit-1.x/machine-lsf-slurm-cp2k.json @@ -95,4 +95,4 @@ "command": "mpirun -n 32 cp2k.popt -i input.inp" }, "api_version": "1.0" -} \ No newline at end of file +} diff --git a/examples/machine/DeePMD-kit-1.x/machine-pbs-gaussian.json b/examples/machine/DeePMD-kit-1.x/machine-pbs-gaussian.json index 876fee7b1..d7c0836cb 100644 --- a/examples/machine/DeePMD-kit-1.x/machine-pbs-gaussian.json +++ b/examples/machine/DeePMD-kit-1.x/machine-pbs-gaussian.json @@ -85,4 +85,4 @@ }, "command": "/public/home/tzhu/g16/g16 < input || :" } -} \ No newline at end of file +} diff --git a/examples/machine/DeePMD-kit-1.x/machine-slurm-qe.json b/examples/machine/DeePMD-kit-1.x/machine-slurm-qe.json index cdff8d5f8..0c40266e1 100644 --- a/examples/machine/DeePMD-kit-1.x/machine-slurm-qe.json +++ b/examples/machine/DeePMD-kit-1.x/machine-slurm-qe.json @@ -109,4 +109,4 @@ "command": "mpirun -n 8 /gpfs/share/home/1600017784/yuzhi/soft/QE-mpi/PW/src/pw.x < input" }, "api_version": "1.0" -} \ No newline at end of file +} diff --git a/examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine.json b/examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine.json index a31142677..49d0d4338 100644 --- a/examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine.json +++ b/examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine.json @@ -103,4 +103,4 @@ ] } } -} \ No newline at end of file +} diff --git a/examples/run/ch4/machine.json b/examples/run/ch4/machine.json index dcad44e9e..9c2431024 100644 --- a/examples/run/ch4/machine.json +++ b/examples/run/ch4/machine.json @@ -74,4 +74,4 @@ "_comment10": "that's all" }, "_comment11": " that's all " -} \ No newline at end of file +} diff --git a/examples/run/ch4/param.json b/examples/run/ch4/param.json index 843530863..d015c8bd8 100644 --- a/examples/run/ch4/param.json +++ b/examples/run/ch4/param.json @@ -190,4 +190,4 @@ "_comment14": " that's all " }, "_comment15": " that's all " -} \ No newline at end of file +} diff --git a/examples/run/deprecated/dp2.x-gromacs-gaussian/param.json b/examples/run/deprecated/dp2.x-gromacs-gaussian/param.json index 4391640b2..639039a5a 100644 --- a/examples/run/deprecated/dp2.x-gromacs-gaussian/param.json +++ b/examples/run/deprecated/dp2.x-gromacs-gaussian/param.json @@ -206,4 +206,4 @@ "nproc": 16, "multiplicity": "auto" } -} \ No newline at end of file +} diff --git a/examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.json b/examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.json index 098b4224f..061914c8c 100644 --- a/examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.json +++ b/examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.json @@ -153,4 +153,4 @@ "GTH-PBE-q4" ] } -} \ No newline at end of file +} diff --git a/examples/run/deprecated/dp2.x-lammps-pwmat/machine-slurm-pwmat-single.json b/examples/run/deprecated/dp2.x-lammps-pwmat/machine-slurm-pwmat-single.json index d245dbd2d..c63ac9613 100644 --- a/examples/run/deprecated/dp2.x-lammps-pwmat/machine-slurm-pwmat-single.json +++ b/examples/run/deprecated/dp2.x-lammps-pwmat/machine-slurm-pwmat-single.json @@ -77,4 +77,4 @@ "group_size": 5 } ] -} \ No newline at end of file +} diff --git a/examples/run/deprecated/dp2.x-lammps-pwmat/param_CH4.json b/examples/run/deprecated/dp2.x-lammps-pwmat/param_CH4.json index beacfe0f3..42e791d2c 100644 --- a/examples/run/deprecated/dp2.x-lammps-pwmat/param_CH4.json +++ b/examples/run/deprecated/dp2.x-lammps-pwmat/param_CH4.json @@ -144,4 +144,4 @@ ], "fp_incar": "etot.input", "_comment10": " that's all " -} \ No newline at end of file +} diff --git a/examples/run/deprecated/dp2.x-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.json b/examples/run/deprecated/dp2.x-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.json index b85cd815c..09054a7ad 100644 --- a/examples/run/deprecated/dp2.x-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.json +++ b/examples/run/deprecated/dp2.x-lammps-siesta/dp-lammps-siesta/CH4/param_CH4.json @@ -145,4 +145,4 @@ "_comment3": " that's all " }, "_comment4": " that's all " -} \ No newline at end of file +} diff --git a/examples/run/deprecated/dp2.x-lammps-vasp/Al/param_al_all_gpu.json b/examples/run/deprecated/dp2.x-lammps-vasp/Al/param_al_all_gpu.json index 467a24ea6..a94cc1fba 100644 --- a/examples/run/deprecated/dp2.x-lammps-vasp/Al/param_al_all_gpu.json +++ b/examples/run/deprecated/dp2.x-lammps-vasp/Al/param_al_all_gpu.json @@ -447,4 +447,4 @@ ], "fp_incar": "/gpfs/share/home/1600017784/start/pku_input_set/INCAR_metal_scf_gpu", "_comment10": " that's all " -} \ No newline at end of file +} diff --git a/examples/run/deprecated/dp2.x-lammps-vasp/CH4/param_CH4.json b/examples/run/deprecated/dp2.x-lammps-vasp/CH4/param_CH4.json index 68c5ae374..e339794e2 100644 --- a/examples/run/deprecated/dp2.x-lammps-vasp/CH4/param_CH4.json +++ b/examples/run/deprecated/dp2.x-lammps-vasp/CH4/param_CH4.json @@ -143,4 +143,4 @@ ], "fp_incar": "/gpfs/share/home/1600017784/yuzhi/methane/INCAR_methane", "_comment10": " that's all " -} \ No newline at end of file +} diff --git a/examples/run/deprecated/param-h2oscan-vasp.json b/examples/run/deprecated/param-h2oscan-vasp.json index 0d13136fd..fadeeb98a 100644 --- a/examples/run/deprecated/param-h2oscan-vasp.json +++ b/examples/run/deprecated/param-h2oscan-vasp.json @@ -691,4 +691,4 @@ "_comment19": " that's all " }, "_comment20": " that's all " -} \ No newline at end of file +} diff --git a/examples/run/deprecated/param-mg-vasp-ucloud.json b/examples/run/deprecated/param-mg-vasp-ucloud.json index f6c046ea7..847024691 100644 --- a/examples/run/deprecated/param-mg-vasp-ucloud.json +++ b/examples/run/deprecated/param-mg-vasp-ucloud.json @@ -464,4 +464,4 @@ "_comment14": " that's all " }, "_comment15": " that's all " -} \ No newline at end of file +} diff --git a/examples/run/deprecated/param-mg-vasp.json b/examples/run/deprecated/param-mg-vasp.json index d73b10dc3..716567440 100644 --- a/examples/run/deprecated/param-mg-vasp.json +++ b/examples/run/deprecated/param-mg-vasp.json @@ -471,4 +471,4 @@ "_comment15": " that's all " }, "_comment16": " that's all " -} \ No newline at end of file +} diff --git a/examples/run/deprecated/param-pyridine-pwscf.json b/examples/run/deprecated/param-pyridine-pwscf.json index 663ec5a5f..f619cbcdf 100644 --- a/examples/run/deprecated/param-pyridine-pwscf.json +++ b/examples/run/deprecated/param-pyridine-pwscf.json @@ -325,4 +325,4 @@ "_comment13": " that's all " }, "_comment14": " that's all " -} \ No newline at end of file +} diff --git a/examples/run/dp-calypso-vasp/machine.json b/examples/run/dp-calypso-vasp/machine.json index 7a156efec..a1b0d3ad3 100644 --- a/examples/run/dp-calypso-vasp/machine.json +++ b/examples/run/dp-calypso-vasp/machine.json @@ -79,4 +79,4 @@ } } ] -} \ No newline at end of file +} diff --git a/examples/run/dp-calypso-vasp/param.json b/examples/run/dp-calypso-vasp/param.json index 4dc25b420..e8664f0ca 100644 --- a/examples/run/dp-calypso-vasp/param.json +++ b/examples/run/dp-calypso-vasp/param.json @@ -409,4 +409,4 @@ "POTCAR.Cu" ], "fp_incar": "/home/zhenyu/workplace/dpgen/AA-2400/vasp_input/INCAR" -} \ No newline at end of file +} diff --git a/examples/run/dp-lammps-enhance_sampling/param.json b/examples/run/dp-lammps-enhance_sampling/param.json index 9d7a05942..1045477cd 100644 --- a/examples/run/dp-lammps-enhance_sampling/param.json +++ b/examples/run/dp-lammps-enhance_sampling/param.json @@ -220,4 +220,4 @@ ], "fp_incar": "INCAR", "_comment8": " that's all " -} \ No newline at end of file +} diff --git a/examples/run/dp2.x-gromacs-gaussian/param.json b/examples/run/dp2.x-gromacs-gaussian/param.json index 089ab67a4..10acf1420 100644 --- a/examples/run/dp2.x-gromacs-gaussian/param.json +++ b/examples/run/dp2.x-gromacs-gaussian/param.json @@ -278,4 +278,4 @@ "nproc": 28, "multiplicity": 1 } -} \ No newline at end of file +} diff --git a/examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/machine.json b/examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/machine.json index 705ab5733..e68d992bb 100644 --- a/examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/machine.json +++ b/examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/machine.json @@ -82,4 +82,4 @@ } } ] -} \ No newline at end of file +} diff --git a/examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/param.json b/examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/param.json index 61983b76b..42600e31f 100644 --- a/examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/param.json +++ b/examples/run/dp2.x-lammps-ABACUS-lcao-dpks/methane/param.json @@ -168,4 +168,4 @@ "nspin": 1, "smearing_method": "fixed" } -} \ No newline at end of file +} diff --git a/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/machine.json b/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/machine.json index e9d690ca6..f06bb460c 100644 --- a/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/machine.json +++ b/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/machine.json @@ -102,4 +102,4 @@ ] } } -} \ No newline at end of file +} diff --git a/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/run_param.json b/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/run_param.json index 80349d31d..a83ba5678 100644 --- a/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/run_param.json +++ b/examples/run/dp2.x-lammps-ABACUS-lcao/fcc-al/run_param.json @@ -146,4 +146,4 @@ "mixing_beta": 0.3, "cal_force": 1 } -} \ No newline at end of file +} diff --git a/examples/run/dp2.x-lammps-ABACUS-pw/fcc-al/machine.json b/examples/run/dp2.x-lammps-ABACUS-pw/fcc-al/machine.json index e9d690ca6..f06bb460c 100644 --- a/examples/run/dp2.x-lammps-ABACUS-pw/fcc-al/machine.json +++ b/examples/run/dp2.x-lammps-ABACUS-pw/fcc-al/machine.json @@ -102,4 +102,4 @@ ] } } -} \ No newline at end of file +} diff --git a/examples/run/dp2.x-lammps-ABACUS-pw/fcc-al/run_param.json b/examples/run/dp2.x-lammps-ABACUS-pw/fcc-al/run_param.json index 2e8e7505d..c8cc096ba 100644 --- a/examples/run/dp2.x-lammps-ABACUS-pw/fcc-al/run_param.json +++ b/examples/run/dp2.x-lammps-ABACUS-pw/fcc-al/run_param.json @@ -125,4 +125,4 @@ "Al_ONCV_PBE-1.0.upf" ], "fp_incar": "./INPUT.run" -} \ No newline at end of file +} diff --git a/examples/run/dp2.x-lammps-ABACUS-pw/methane/machine.json b/examples/run/dp2.x-lammps-ABACUS-pw/methane/machine.json index 705ab5733..e68d992bb 100644 --- a/examples/run/dp2.x-lammps-ABACUS-pw/methane/machine.json +++ b/examples/run/dp2.x-lammps-ABACUS-pw/methane/machine.json @@ -82,4 +82,4 @@ } } ] -} \ No newline at end of file +} diff --git a/examples/run/dp2.x-lammps-ABACUS-pw/methane/param.json b/examples/run/dp2.x-lammps-ABACUS-pw/methane/param.json index a8e881eeb..5594cb6cf 100644 --- a/examples/run/dp2.x-lammps-ABACUS-pw/methane/param.json +++ b/examples/run/dp2.x-lammps-ABACUS-pw/methane/param.json @@ -159,4 +159,4 @@ "smearing": "fixed", "sigma": 0.001 } -} \ No newline at end of file +} diff --git a/examples/run/dp2.x-lammps-cp2k/methane/param-ch4.json b/examples/run/dp2.x-lammps-cp2k/methane/param-ch4.json index 20badb2b1..d6cbd3e67 100644 --- a/examples/run/dp2.x-lammps-cp2k/methane/param-ch4.json +++ b/examples/run/dp2.x-lammps-cp2k/methane/param-ch4.json @@ -135,4 +135,4 @@ "fp_task_max": 20, "fp_task_min": 5, "external_input_path": "/data/ybzhuang/methane-dpgen/dpgen-tutorial-2020-08-23/dpgen-tutorial-mathane/cp2k_dpgen/template.inp" -} \ No newline at end of file +} diff --git a/examples/run/dp2.x-lammps-cp2k/param_CH4_deepmd-kit-2.0.1.json b/examples/run/dp2.x-lammps-cp2k/param_CH4_deepmd-kit-2.0.1.json index 1813b7d1d..fd95ebf15 100644 --- a/examples/run/dp2.x-lammps-cp2k/param_CH4_deepmd-kit-2.0.1.json +++ b/examples/run/dp2.x-lammps-cp2k/param_CH4_deepmd-kit-2.0.1.json @@ -148,4 +148,4 @@ } } } -} \ No newline at end of file +} diff --git a/examples/run/dp2.x-lammps-gaussian/machine.json b/examples/run/dp2.x-lammps-gaussian/machine.json index 7cdcb6a20..fd1159f33 100644 --- a/examples/run/dp2.x-lammps-gaussian/machine.json +++ b/examples/run/dp2.x-lammps-gaussian/machine.json @@ -108,4 +108,4 @@ "group_size": 10 } } -} \ No newline at end of file +} diff --git a/examples/run/dp2.x-lammps-gaussian/param_C4H16N4_deepmd-kit-2.0.1.json b/examples/run/dp2.x-lammps-gaussian/param_C4H16N4_deepmd-kit-2.0.1.json index fbe260e9f..82522d36c 100644 --- a/examples/run/dp2.x-lammps-gaussian/param_C4H16N4_deepmd-kit-2.0.1.json +++ b/examples/run/dp2.x-lammps-gaussian/param_C4H16N4_deepmd-kit-2.0.1.json @@ -147,4 +147,4 @@ "nproc": 2, "multiplicity": "auto" } -} \ No newline at end of file +} diff --git a/examples/run/dp2.x-lammps-vasp-et/param_elet.json b/examples/run/dp2.x-lammps-vasp-et/param_elet.json index 351ca68a8..c10faa58d 100644 --- a/examples/run/dp2.x-lammps-vasp-et/param_elet.json +++ b/examples/run/dp2.x-lammps-vasp-et/param_elet.json @@ -128,4 +128,4 @@ ], "fp_incar": "/home/wanghan/study/deep.md/dpgen/almg/vasp/INCAR", "_comment10": " that's all " -} \ No newline at end of file +} diff --git a/examples/run/dp2.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-1.1.0.json b/examples/run/dp2.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-1.1.0.json index 4c4198783..608471119 100644 --- a/examples/run/dp2.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-1.1.0.json +++ b/examples/run/dp2.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-1.1.0.json @@ -427,4 +427,4 @@ ], "fp_incar": "/data1/yfb222333/2_dpgen_gpu_multi/INCAR_metal_scf_gpu", "_comment10": " that's all " -} \ No newline at end of file +} diff --git a/examples/run/dp2.x-lammps-vasp/CH4/param_CH4_deepmd-kit-2.x.json b/examples/run/dp2.x-lammps-vasp/CH4/param_CH4_deepmd-kit-2.x.json index 932d511b9..2501a56fb 100644 --- a/examples/run/dp2.x-lammps-vasp/CH4/param_CH4_deepmd-kit-2.x.json +++ b/examples/run/dp2.x-lammps-vasp/CH4/param_CH4_deepmd-kit-2.x.json @@ -134,4 +134,4 @@ ], "_comments": "We can only provide empty files in public, you should provide valid POTCARS yourself when running DP-GEN", "fp_incar": "/data1/yfb222333/2_dpgen_gpu_multi/INCAR_methane" -} \ No newline at end of file +} diff --git a/examples/run/dp2.x-lammps-vasp/param_CH4_deepmd-kit-2.0.1.json b/examples/run/dp2.x-lammps-vasp/param_CH4_deepmd-kit-2.0.1.json index c1a95190b..e90fc503e 100644 --- a/examples/run/dp2.x-lammps-vasp/param_CH4_deepmd-kit-2.0.1.json +++ b/examples/run/dp2.x-lammps-vasp/param_CH4_deepmd-kit-2.0.1.json @@ -130,4 +130,4 @@ "POTCAR_C" ], "fp_incar": "./INCAR_methane" -} \ No newline at end of file +} diff --git a/examples/run/dp2.x_lammps_gaussian/dodecane/dodecane.json b/examples/run/dp2.x_lammps_gaussian/dodecane/dodecane.json index 4691ff40b..d7b1a2f96 100644 --- a/examples/run/dp2.x_lammps_gaussian/dodecane/dodecane.json +++ b/examples/run/dp2.x_lammps_gaussian/dodecane/dodecane.json @@ -149,4 +149,4 @@ "nproc": 4, "multiplicity": "auto" } -} \ No newline at end of file +} diff --git a/examples/run/dprc/generator.json b/examples/run/dprc/generator.json index 6ae474ff1..2460e4c96 100644 --- a/examples/run/dprc/generator.json +++ b/examples/run/dprc/generator.json @@ -367,4 +367,4 @@ "model_devi_engine": "amber", "fp_style": "amber/diff", "detailed_report_make_fp": true -} \ No newline at end of file +} diff --git a/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/machine.json b/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/machine.json index c48034222..d495823bb 100644 --- a/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/machine.json +++ b/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/machine.json @@ -112,4 +112,4 @@ ] } } -} \ No newline at end of file +} diff --git a/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/simplify.json b/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/simplify.json index fdc7658ae..2538eec74 100644 --- a/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/simplify.json +++ b/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/simplify.json @@ -144,4 +144,4 @@ "model_devi_f_trust_lo": 0.3, "model_devi_f_trust_hi": 100.0, "cvasp": false -} \ No newline at end of file +} diff --git a/examples/simplify/qm7.json b/examples/simplify/qm7.json index d00847568..a9caf52a6 100644 --- a/examples/simplify/qm7.json +++ b/examples/simplify/qm7.json @@ -107,4 +107,4 @@ "model_devi_f_trust_lo": 0.1, "model_devi_f_trust_hi": 0.3, "_comment3": " that's all " -} \ No newline at end of file +} diff --git a/examples/test/deepmd_param.json b/examples/test/deepmd_param.json index 08bf864d3..75e3da5ad 100644 --- a/examples/test/deepmd_param.json +++ b/examples/test/deepmd_param.json @@ -59,4 +59,4 @@ ], "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", "_comment11": "that's all" -} \ No newline at end of file +} diff --git a/examples/test/meam_param.json b/examples/test/meam_param.json index ece70d04c..29ea4e540 100644 --- a/examples/test/meam_param.json +++ b/examples/test/meam_param.json @@ -72,4 +72,4 @@ ], "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", "_comment11": "that's all" -} \ No newline at end of file +} diff --git a/examples/test/vasp_param.json b/examples/test/vasp_param.json index 7284af83c..f06060f76 100644 --- a/examples/test/vasp_param.json +++ b/examples/test/vasp_param.json @@ -51,4 +51,4 @@ ], "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", "_comment11": "that's all" -} \ No newline at end of file +} diff --git a/examples/test/vasp_param_from_incar.json b/examples/test/vasp_param_from_incar.json index 558860831..77221f2fb 100644 --- a/examples/test/vasp_param_from_incar.json +++ b/examples/test/vasp_param_from_incar.json @@ -44,4 +44,4 @@ ], "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", "_comment10": "that's all" -} \ No newline at end of file +} From 2d34f58782dc9e4f86957837a4261951dcf5e54c Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Wed, 23 Aug 2023 15:25:51 -0400 Subject: [PATCH 03/10] fix errors Signed-off-by: Jinzhe Zeng --- .../CH4-refact-dpdispatcher/INCAR_methane | 2 +- examples/init/abacus/fcc-Al-lcao/machine.json | 12 +- examples/init/abacus/fcc-Al-pw/machine.json | 12 +- ...n => param_al_all_gpu-deepmd-kit-2.x.json} | 0 tests/generator/param-mg-vasp-v1.json | 222 ++++++++---------- tests/test_check_examples.py | 28 +-- 6 files changed, 117 insertions(+), 159 deletions(-) rename examples/run/dp2.x-lammps-vasp/Al/{param_al_all_gpu-deepmd-kit-1.1.0.json => param_al_all_gpu-deepmd-kit-2.x.json} (100%) diff --git a/examples/CH4-refact-dpdispatcher/INCAR_methane b/examples/CH4-refact-dpdispatcher/INCAR_methane index b946fb7e5..4d1d7d039 120000 --- a/examples/CH4-refact-dpdispatcher/INCAR_methane +++ b/examples/CH4-refact-dpdispatcher/INCAR_methane @@ -1 +1 @@ -../run/dp1.x-lammps-vasp/CH4/INCAR_methane \ No newline at end of file +../run/dp2.x-lammps-vasp/CH4/INCAR_methane \ No newline at end of file diff --git a/examples/init/abacus/fcc-Al-lcao/machine.json b/examples/init/abacus/fcc-Al-lcao/machine.json index ba74f0297..0d82a2af3 100644 --- a/examples/init/abacus/fcc-Al-lcao/machine.json +++ b/examples/init/abacus/fcc-Al-lcao/machine.json @@ -11,7 +11,7 @@ "remote_profile":{ "email": "", "password": "", - "program_id": , + "program_id": 0, "keep_backup":true, "input_data":{ "job_type": "indicate", @@ -25,8 +25,7 @@ "platform": "", "region":"", "image_name":"", - "on_demand":0, - "job_type":"" + "on_demand":0 } } }, @@ -45,7 +44,7 @@ "remote_profile":{ "email": "", "password": "", - "program_id": , + "program_id": 0, "keep_backup":true, "input_data":{ "job_type": "indicate", @@ -59,8 +58,7 @@ "image_name":"", "checkpoint_files": "sync_files", "checkpoint_time":30, - "on_demand":0, - "job_type":"" + "on_demand":0 } } }, @@ -79,7 +77,7 @@ "remote_profile":{ "email": "", "password": "", - "program_id": , + "program_id": 0, "keep_backup":true, "input_data":{ "job_type": "indicate", diff --git a/examples/init/abacus/fcc-Al-pw/machine.json b/examples/init/abacus/fcc-Al-pw/machine.json index ba74f0297..0d82a2af3 100644 --- a/examples/init/abacus/fcc-Al-pw/machine.json +++ b/examples/init/abacus/fcc-Al-pw/machine.json @@ -11,7 +11,7 @@ "remote_profile":{ "email": "", "password": "", - "program_id": , + "program_id": 0, "keep_backup":true, "input_data":{ "job_type": "indicate", @@ -25,8 +25,7 @@ "platform": "", "region":"", "image_name":"", - "on_demand":0, - "job_type":"" + "on_demand":0 } } }, @@ -45,7 +44,7 @@ "remote_profile":{ "email": "", "password": "", - "program_id": , + "program_id": 0, "keep_backup":true, "input_data":{ "job_type": "indicate", @@ -59,8 +58,7 @@ "image_name":"", "checkpoint_files": "sync_files", "checkpoint_time":30, - "on_demand":0, - "job_type":"" + "on_demand":0 } } }, @@ -79,7 +77,7 @@ "remote_profile":{ "email": "", "password": "", - "program_id": , + "program_id": 0, "keep_backup":true, "input_data":{ "job_type": "indicate", diff --git a/examples/run/dp2.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-1.1.0.json b/examples/run/dp2.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-2.x.json similarity index 100% rename from examples/run/dp2.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-1.1.0.json rename to examples/run/dp2.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-2.x.json diff --git a/tests/generator/param-mg-vasp-v1.json b/tests/generator/param-mg-vasp-v1.json index f2771deac..9355bea0d 100644 --- a/tests/generator/param-mg-vasp-v1.json +++ b/tests/generator/param-mg-vasp-v1.json @@ -1,133 +1,95 @@ { - "type_map": [ - "Al", - "Mg" - ], - "mass_map": [ - 27, - 24 - ], - "use_ele_temp": 0, - "init_data_prefix": "data", - "init_data_sys": [ - "deepmd" - ], - "init_batch_size": [ - 16 - ], - "sys_configs": [ - [ - "data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/000010/POSCAR" + "type_map": ["Al", "Mg"], + "mass_map": [27, 24], + "use_ele_temp": 0, + + "init_data_prefix": "data", + "init_data_sys": ["deepmd" + ], + "init_batch_size": [16], + "sys_configs": [ + ["data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/000010/POSCAR"], + ["data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/00000[8-9]/POSCAR"] ], - [ - "data/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale*/00000[8-9]/POSCAR" - ] - ], - "sys_batch_size": [ - 1, - 1 - ], - "_comment1": " 00.train ", - "numb_models": 4, - "default_training_param": { - "model": { - "descriptor": { - "type": "se_a", - "sel": [ - 90, - 90 - ], - "rcut_smth": 1.8, - "rcut": 6.0, - "neuron": [ - 10, - 20, - 40 - ], - "resnet_dt": false, - "axis_neuron": 4, - "seed": 1 - }, - "fitting_net": { - "neuron": [ - 120, - 120, - 120 - ], - "resnet_dt": true, - "seed": 1 - } + "sys_batch_size": [1,1], + + "_comment": " 00.train ", + "numb_models": 4, + "default_training_param" : { + "model" : { + "descriptor": { + "type": "se_a", + "sel": [90, 90], + "rcut_smth": 1.80, + "rcut": 6.00, + "neuron": [10, 20, 40], + "resnet_dt": false, + "axis_neuron": 4, + "seed": 1 + }, + "fitting_net" : { + "neuron": [120, 120, 120], + "resnet_dt": true, + "seed": 1 + } + }, + + "loss" : { + "start_pref_e": 0.02, + "limit_pref_e": 1, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0, + "limit_pref_v": 0 + }, + + "learning_rate" : { + "start_lr": 0.001, + "decay_steps": 5000, + "decay_rate": 0.95 + }, + + "training" : { + "systems": [], + "set_prefix": "set", + "stop_batch": 1000, + "batch_size": 1, + + "seed": 1, + + "_comment": " display and restart", + "_comment": " frequencies counted in batch", + "disp_file": "lcurve.out", + "disp_freq": 1000, + "numb_test": 1, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "load_ckpt": "model.ckpt", + "disp_training":true, + "time_training":true, + "profiling": false, + "profiling_file": "timeline.json" + } }, - "loss": { - "start_pref_e": 0.02, - "limit_pref_e": 1, - "start_pref_f": 1000, - "limit_pref_f": 1, - "start_pref_v": 0, - "limit_pref_v": 0 - }, - "learning_rate": { - "start_lr": 0.001, - "decay_steps": 5000, - "stop_lr": 0.0009897937816869885 - }, - "training": { - "stop_batch": 1000, - "seed": 1, - "_comment2": " display and restart", - "_comment3": " frequencies counted in batch", - "disp_file": "lcurve.out", - "disp_freq": 1000, - "save_freq": 1000, - "save_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json", - "training_data": { - "systems": [], - "set_prefix": "set", - "batch_size": 1 - } - } - }, - "_comment4": " 01.model_devi ", - "_comment5": "model_devi_skip: the first x of the recorded frames", - "model_devi_dt": 0.002, - "model_devi_skip": 0, - "model_devi_f_trust_lo": 0.05, - "model_devi_f_trust_hi": 0.2, - "model_devi_clean_traj": false, - "model_devi_jobs": [ - { - "_idx": 0, - "ensemble": "npt", - "nsteps": 50, - "press": [ - 1.0, - 2.0 - ], - "sys_idx": [ - 0, - 1 - ], - "temps": [ - 50, - 100 - ], - "trj_freq": 10 - } - ], - "_comment6": " 02.fp ", - "fp_style": "vasp", - "shuffle_poscar": false, - "fp_task_max": 8, - "fp_task_min": 2, - "fp_pp_path": "/home/wanghan/study/deep.md/dpgen/almg/vasp", - "fp_pp_files": [ - "POTCAR.Al", - "POTCAR.Mg" - ], - "fp_incar": "/home/wanghan/study/deep.md/dpgen/almg/vasp/INCAR", - "_comment7": " that's all " -} \ No newline at end of file + + "_comment": " 01.model_devi ", + "_comment": "model_devi_skip: the first x of the recorded frames", + "model_devi_dt": 0.002, + "model_devi_skip": 0, + "model_devi_f_trust_lo": 0.05, + "model_devi_f_trust_hi": 0.20, + "model_devi_clean_traj": false, + "model_devi_jobs": [ + { "_idx": 0, "ensemble": "npt", "nsteps": 50, "press": [1.0,2.0], "sys_idx": [0, 1], "temps": [50,100], "trj_freq": 10 } + ], + "_comment": " 02.fp ", + "fp_style": "vasp", + "shuffle_poscar": false, + "fp_task_max": 8, + "fp_task_min": 2, + "fp_pp_path": "/home/wanghan/study/deep.md/dpgen/almg/vasp", + "fp_pp_files": ["POTCAR.Al", "POTCAR.Mg"], + "fp_incar": "/home/wanghan/study/deep.md/dpgen/almg/vasp/INCAR", + "_comment": " that's all " +} + diff --git a/tests/test_check_examples.py b/tests/test_check_examples.py index 976980b15..8522e8568 100644 --- a/tests/test_check_examples.py +++ b/tests/test_check_examples.py @@ -54,19 +54,19 @@ run_jdata, p_examples / "run" - / "dp1.x-lammps-vasp" + / "dp2.x-lammps-vasp" / "CH4" - / "param_CH4_deepmd-kit-1.1.0.json", + / "param_CH4_deepmd-kit-2.x.json", ), ( run_jdata, p_examples / "run" - / "dp1.x-lammps-vasp" + / "dp2.x-lammps-vasp" / "Al" - / "param_al_all_gpu-deepmd-kit-1.1.0.json", + / "param_al_all_gpu-deepmd-kit-2.x.json", ), - (run_jdata, p_examples / "run" / "dp1.x-lammps-vasp-et" / "param_elet.json"), + (run_jdata, p_examples / "run" / "dp2.x-lammps-vasp-et" / "param_elet.json"), ( run_jdata, p_examples / "run" / "dp2.x-lammps-ABACUS-lcao" / "fcc-al" / "run_param.json", @@ -77,19 +77,19 @@ ), ( run_jdata, - p_examples / "run" / "dp1.x-lammps-cp2k" / "methane" / "param-ch4.json", + p_examples / "run" / "dp2.x-lammps-cp2k" / "methane" / "param-ch4.json", ), ( run_jdata, - p_examples / "run" / "dp1.x-lammps-ABACUS-pw" / "methane" / "param.json", + p_examples / "run" / "dp2.x-lammps-ABACUS-pw" / "methane" / "param.json", ), ( run_jdata, - p_examples / "run" / "dp1.x-lammps-ABACUS-lcao-dpks" / "methane" / "param.json", + p_examples / "run" / "dp2.x-lammps-ABACUS-lcao-dpks" / "methane" / "param.json", ), ( run_jdata, - p_examples / "run" / "dp1.x_lammps_gaussian" / "dodecane" / "dodecane.json", + p_examples / "run" / "dp2.x_lammps_gaussian" / "dodecane" / "dodecane.json", ), (run_jdata, p_examples / "run" / "dp-lammps-enhance_sampling" / "param.json"), # (run_jdata, p_examples / "run" / "deprecated" / "param-mg-vasp.json"), @@ -101,17 +101,17 @@ p_examples / "run" / "deprecated" - / "dp0.12-lammps-cp2k" + / "dp2.x-lammps-cp2k" / "CH4" / "param_CH4.json", ), - # (run_jdata, p_examples / "run" / "deprecated" / "dp0.12-lammps-pwmat" / "param_CH4.json"), + # (run_jdata, p_examples / "run" / "deprecated" / "dp2.x-lammps-pwmat" / "param_CH4.json"), ( run_jdata, p_examples / "run" / "deprecated" - / "dp0.12-lammps-siesta" + / "dp2.x-lammps-siesta" / "dp-lammps-siesta" / "CH4" / "param_CH4.json", @@ -121,7 +121,7 @@ p_examples / "run" / "deprecated" - / "dp0.12-lammps-vasp" + / "dp2.x-lammps-vasp" / "Al" / "param_al_all_gpu.json", ), @@ -130,7 +130,7 @@ p_examples / "run" / "deprecated" - / "dp0.12-lammps-vasp" + / "dp2.x-lammps-vasp" / "CH4" / "param_CH4.json", ), From 6df210717172e090254e90533318d9624b69b55c Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Wed, 23 Aug 2023 15:30:38 -0400 Subject: [PATCH 04/10] exclude symlinks Signed-off-by: Jinzhe Zeng --- .pre-commit-config.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index eab10454f..756209c94 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -13,6 +13,7 @@ repos: - id: check-yaml exclude: "^conda/.*$" - id: check-json + exclude: "^examples/CH4-lebesgue/.*$" - id: check-added-large-files - id: check-merge-conflict - id: check-symlinks From 143bb9945a9271b68e9ede2f5b6e844c81af4fc6 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Wed, 23 Aug 2023 15:32:02 -0400 Subject: [PATCH 05/10] fix json Signed-off-by: Jinzhe Zeng --- tests/generator/param-mg-vasp-v1.json | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/tests/generator/param-mg-vasp-v1.json b/tests/generator/param-mg-vasp-v1.json index 9355bea0d..4275a0fb7 100644 --- a/tests/generator/param-mg-vasp-v1.json +++ b/tests/generator/param-mg-vasp-v1.json @@ -13,7 +13,7 @@ ], "sys_batch_size": [1,1], - "_comment": " 00.train ", + "_comment1": " 00.train ", "numb_models": 4, "default_training_param" : { "model" : { @@ -57,8 +57,8 @@ "seed": 1, - "_comment": " display and restart", - "_comment": " frequencies counted in batch", + "_comment2": " display and restart", + "_comment3": " frequencies counted in batch", "disp_file": "lcurve.out", "disp_freq": 1000, "numb_test": 1, @@ -72,8 +72,8 @@ } }, - "_comment": " 01.model_devi ", - "_comment": "model_devi_skip: the first x of the recorded frames", + "_comment4": " 01.model_devi ", + "_comment5": "model_devi_skip: the first x of the recorded frames", "model_devi_dt": 0.002, "model_devi_skip": 0, "model_devi_f_trust_lo": 0.05, @@ -82,7 +82,7 @@ "model_devi_jobs": [ { "_idx": 0, "ensemble": "npt", "nsteps": 50, "press": [1.0,2.0], "sys_idx": [0, 1], "temps": [50,100], "trj_freq": 10 } ], - "_comment": " 02.fp ", + "_comment6": " 02.fp ", "fp_style": "vasp", "shuffle_poscar": false, "fp_task_max": 8, @@ -90,6 +90,6 @@ "fp_pp_path": "/home/wanghan/study/deep.md/dpgen/almg/vasp", "fp_pp_files": ["POTCAR.Al", "POTCAR.Mg"], "fp_incar": "/home/wanghan/study/deep.md/dpgen/almg/vasp/INCAR", - "_comment": " that's all " + "_comment7": " that's all " } From fb20b459eb2f4fb7e035fc4b52a0d6caee6546ea Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Sat, 26 Aug 2023 23:05:04 -0400 Subject: [PATCH 06/10] add pretty-format-json hook; 4 spaces may be better --- .pre-commit-config.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 756209c94..4ac1241b5 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -19,6 +19,9 @@ repos: - id: check-symlinks exclude: "^tests/tools/run_report_test_output/.*$" - id: check-toml + - id: pretty-format-json + args: ["--no-sort-keys", "--indent 4"] + # Python - repo: https://github.com/psf/black rev: 23.7.0 From 8f413de674dac3f8a5785cfc64d4be9e83d8ca69 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Sun, 27 Aug 2023 03:05:18 +0000 Subject: [PATCH 07/10] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4ac1241b5..77280dc9c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -21,7 +21,7 @@ repos: - id: check-toml - id: pretty-format-json args: ["--no-sort-keys", "--indent 4"] - + # Python - repo: https://github.com/psf/black rev: 23.7.0 From 5ad2ca359fb902e24ffff7d1ca49835243ebf502 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Sat, 26 Aug 2023 23:06:48 -0400 Subject: [PATCH 08/10] fix args --- .pre-commit-config.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 77280dc9c..e377d9dac 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -20,7 +20,8 @@ repos: exclude: "^tests/tools/run_report_test_output/.*$" - id: check-toml - id: pretty-format-json - args: ["--no-sort-keys", "--indent 4"] + args: ["--no-sort-keys", "--indent=4"] + exclude: "^examples/CH4-lebesgue/.*$" # Python - repo: https://github.com/psf/black From dbf710340879d66a344a111137f66527ced7cf72 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Sat, 26 Aug 2023 23:09:52 -0400 Subject: [PATCH 09/10] autofix --- .pre-commit-config.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index e377d9dac..904018833 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -20,7 +20,10 @@ repos: exclude: "^tests/tools/run_report_test_output/.*$" - id: check-toml - id: pretty-format-json - args: ["--no-sort-keys", "--indent=4"] + args: + - "--autofix" + - "--no-sort-keys" + - "--indent=4" exclude: "^examples/CH4-lebesgue/.*$" # Python From 1eb347dc73a232d5ec18b1311801879e411b82ce Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Sun, 27 Aug 2023 03:10:07 +0000 Subject: [PATCH 10/10] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- dpgen/data/jsons/al.diamond.111.json | 68 +- dpgen/data/jsons/al.diamond.222.json | 68 +- dpgen/data/jsons/al.fcc.111.json | 68 +- dpgen/data/jsons/al.fcc.222.json | 68 +- dpgen/data/jsons/al.hcp.111.json | 68 +- dpgen/data/jsons/al.hcp.222.json | 68 +- dpgen/data/jsons/al.hcp.332.json | 68 +- dpgen/data/jsons/al.sc.222.json | 68 +- dpgen/data/jsons/almg.diamond.111.json | 72 +- dpgen/data/jsons/almg.diamond.222.json | 72 +- dpgen/data/jsons/almg.fcc.111.json | 72 +- dpgen/data/jsons/almg.fcc.222.json | 72 +- dpgen/data/jsons/almg.hcp.111.json | 72 +- dpgen/data/jsons/almg.hcp.222.json | 72 +- dpgen/data/jsons/almg.hcp.332.json | 72 +- dpgen/data/jsons/almg.sc.222.json | 72 +- dpgen/data/jsons/almg.sc.333.json | 72 +- dpgen/data/jsons/mg.diamond.111.json | 68 +- dpgen/data/jsons/mg.diamond.222.json | 68 +- dpgen/data/jsons/mg.fcc.111.json | 68 +- dpgen/data/jsons/mg.fcc.222.json | 68 +- dpgen/data/jsons/mg.hcp.111.json | 68 +- dpgen/data/jsons/mg.hcp.222.json | 64 +- dpgen/data/jsons/mg.hcp.332.json | 64 +- dpgen/data/jsons/mg.sc.222.json | 68 +- dpgen/data/jsons/param.json | 76 +- dpgen/data/jsons/si.diamond.111.json | 68 +- dpgen/data/jsons/si.diamond.222.json | 68 +- dpgen/data/jsons/si.fcc.111.json | 68 +- dpgen/data/jsons/si.fcc.222.json | 68 +- dpgen/data/jsons/si.hcp.111.json | 68 +- dpgen/data/jsons/si.hcp.222.json | 68 +- dpgen/data/jsons/si.sc.222.json | 68 +- dpgen/data/jsons/surf.al.fcc.json | 76 +- dpgen/data/jsons/surf.al.hcp.json | 76 +- dpgen/data/jsons/surf.almg.fcc.json | 80 +- dpgen/data/jsons/surf.almg.hcp.json | 80 +- dpgen/data/jsons/surf.mg.fcc.json | 76 +- dpgen/data/jsons/surf.mg.hcp.json | 76 +- dpgen/data/jsons/surf.si.diamond.json | 108 +- dpgen/data/jsons/w.bcc.111.json | 72 +- dpgen/data/jsons/w.bcc.222.json | 72 +- dpgen/data/jsons/w.diamond.111.json | 72 +- dpgen/data/jsons/w.fcc.111.json | 72 +- dpgen/data/jsons/w.hcp.111.json | 72 +- dpgen/data/jsons/water.111.json | 70 +- .../machine-ali-ehpc.json | 176 +- .../machine-dpcloudserver.json | 234 +- examples/database/param_Ti.json | 196 +- examples/init/abacus/CuW/CuW.json | 100 +- examples/init/abacus/fcc-Al-lcao/init.json | 78 +- examples/init/abacus/fcc-Al-lcao/machine.json | 199 +- examples/init/abacus/fcc-Al-pw/init.json | 72 +- examples/init/abacus/fcc-Al-pw/machine.json | 199 +- examples/init/al.json | 60 +- examples/init/ch4.json | 68 +- examples/init/cu.surf.hcp.111.json | 110 +- examples/init/reaction.json | 34 +- examples/init/surf.json | 104 +- .../DeePMD-kit-1.0/machine-local-4GPU.json | 170 +- .../machine/DeePMD-kit-1.x/machine-local.json | 122 +- .../machine-lsf-slurm-cp2k.json | 186 +- .../DeePMD-kit-1.x/machine-pbs-gaussian.json | 168 +- .../DeePMD-kit-1.x/machine-slurm-qe.json | 214 +- .../DeePMD-kit-2.x/lebesgue_v2_machine.json | 196 +- examples/run/ch4/machine.json | 150 +- examples/run/ch4/param.json | 366 +- .../dp2.x-gromacs-gaussian/param.json | 392 +- .../dp2.x-lammps-cp2k/CH4/param_CH4.json | 298 +- .../machine-slurm-pwmat-single.json | 156 +- .../dp2.x-lammps-pwmat/param_CH4.json | 284 +- .../dp-lammps-siesta/CH4/param_CH4.json | 284 +- .../Al/param_al_all_gpu.json | 876 +- .../dp2.x-lammps-vasp/CH4/param_CH4.json | 282 +- .../run/deprecated/param-h2oscan-vasp.json | 1372 +- .../run/deprecated/param-mg-vasp-ucloud.json | 912 +- examples/run/deprecated/param-mg-vasp.json | 926 +- .../run/deprecated/param-pyridine-pwscf.json | 628 +- examples/run/dp-calypso-vasp/machine.json | 160 +- examples/run/dp-calypso-vasp/param.json | 812 +- .../run/dp-lammps-enhance_sampling/param.json | 424 +- .../run/dp2.x-gromacs-gaussian/param.json | 528 +- .../methane/machine.json | 160 +- .../methane/param.json | 328 +- .../fcc-al/machine.json | 194 +- .../fcc-al/run_param.json | 286 +- .../fcc-al/machine.json | 194 +- .../fcc-al/run_param.json | 246 +- .../methane/machine.json | 160 +- .../dp2.x-lammps-ABACUS-pw/methane/param.json | 310 +- .../dp2.x-lammps-cp2k/methane/param-ch4.json | 266 +- .../param_CH4_deepmd-kit-2.0.1.json | 286 +- .../run/dp2.x-lammps-gaussian/machine.json | 206 +- .../param_C4H16N4_deepmd-kit-2.0.1.json | 286 +- .../run/dp2.x-lammps-vasp-et/param_elet.json | 252 +- .../Al/param_al_all_gpu-deepmd-kit-2.x.json | 842 +- .../CH4/param_CH4_deepmd-kit-2.x.json | 262 +- .../param_CH4_deepmd-kit-2.0.1.json | 254 +- .../dodecane/dodecane.json | 292 +- examples/run/dprc/generator.json | 706 +- .../simplify_example/machine.json | 214 +- .../simplify_example/simplify.json | 272 +- examples/simplify/qm7.json | 202 +- examples/test/deepmd_param.json | 118 +- examples/test/meam_param.json | 142 +- examples/test/vasp_param.json | 104 +- examples/test/vasp_param_from_incar.json | 90 +- tests/auto_test/equi/abacus/cell-relax.json | 9554 +++---- tests/auto_test/equi/vasp/Al-fcc.json | 532 +- tests/auto_test/equi/vasp/outcar.json | 9334 +++---- .../output/gamma_00/task.000000/inter.json | 14 +- .../output/gamma_00/task.000000/miller.json | 8 +- .../gamma_00/task.000000/result_task.json | 21358 ++++++++-------- .../output/gamma_00/task.000000/task.json | 66 +- .../output/gamma_00/task.000001/inter.json | 14 +- .../output/gamma_00/task.000001/miller.json | 8 +- .../gamma_00/task.000001/result_task.json | 21358 ++++++++-------- .../output/gamma_00/task.000001/task.json | 66 +- .../output/gamma_00/task.000002/inter.json | 14 +- .../output/gamma_00/task.000002/miller.json | 8 +- .../gamma_00/task.000002/result_task.json | 21358 ++++++++-------- .../output/gamma_00/task.000002/task.json | 66 +- .../output/relaxation/relax_task/result.json | 746 +- tests/data/CuW.json | 90 +- tests/data/al.json | 62 +- tests/data/alloy.json | 60 +- tests/data/ch4.json | 90 +- tests/data/surf.json | 90 +- tests/data/surf_poscar.json | 90 +- tests/database/param_Al.json | 198 +- tests/generator/cluster/cluster1.json | 424 +- .../gromacs/model_devi_case/input.json | 12 +- tests/generator/machine-local-v1.json | 102 +- tests/generator/machine-local.json | 104 +- .../02.fp/task.000.000000/job.json | 4 +- .../02.fp/task.000.000001/job.json | 4 +- .../02.fp/task.001.000000/job.json | 4 +- .../02.fp/task.001.000001/job.json | 4 +- tests/generator/param-amber.json | 126 +- tests/generator/param-custom-fp.json | 616 +- tests/generator/param-methane-abacus-diy.json | 312 +- tests/generator/param-methane-abacus.json | 354 +- tests/generator/param-mg-vasp-diy.json | 258 +- .../generator/param-mg-vasp-multi-trust.json | 310 +- tests/generator/param-mg-vasp-old.json | 284 +- tests/generator/param-mg-vasp-v1-et.json | 260 +- tests/generator/param-mg-vasp-v1.json | 216 +- tests/generator/param-mg-vasp.json | 294 +- tests/generator/param-mg-vasp_merge_traj.json | 294 +- tests/generator/param-mgo-cp2k-exinput.json | 608 +- tests/generator/param-pyridine-cp2k.json | 664 +- tests/generator/param-pyridine-gaussian.json | 612 +- tests/generator/param-pyridine-pwmat.json | 648 +- tests/generator/param-pyridine-pwscf-old.json | 630 +- tests/generator/param-pyridine-pwscf.json | 654 +- tests/generator/param-pyridine-siesta.json | 626 +- tests/sample.json | 4 +- tests/tools/machine_fp_single.json | 32 +- tests/tools/machine_fp_single2.json | 28 +- tests/tools/run_report_test_output/param.json | 256 +- 160 files changed, 57735 insertions(+), 57683 deletions(-) diff --git a/dpgen/data/jsons/al.diamond.111.json b/dpgen/data/jsons/al.diamond.111.json index 83ccf6753..8fe91110c 100644 --- a/dpgen/data/jsons/al.diamond.111.json +++ b/dpgen/data/jsons/al.diamond.111.json @@ -1,36 +1,36 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "Al" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/al.diamond.222.json b/dpgen/data/jsons/al.diamond.222.json index 3d15c40f8..ef9ff78c7 100644 --- a/dpgen/data/jsons/al.diamond.222.json +++ b/dpgen/data/jsons/al.diamond.222.json @@ -1,36 +1,36 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [ - 2, - 2, - 2 - ], - "elements": [ - "Al" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/al.fcc.111.json b/dpgen/data/jsons/al.fcc.111.json index 50866a722..64ec32688 100644 --- a/dpgen/data/jsons/al.fcc.111.json +++ b/dpgen/data/jsons/al.fcc.111.json @@ -1,36 +1,36 @@ { - "cell_type": "fcc", - "latt": 4.04, - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "Al" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": true, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "fcc", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": true, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/al.fcc.222.json b/dpgen/data/jsons/al.fcc.222.json index 14790cdbd..901a43156 100644 --- a/dpgen/data/jsons/al.fcc.222.json +++ b/dpgen/data/jsons/al.fcc.222.json @@ -1,36 +1,36 @@ { - "cell_type": "fcc", - "latt": 4.04, - "super_cell": [ - 2, - 2, - 2 - ], - "elements": [ - "Al" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": true, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "fcc", + "latt": 4.04, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": true, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/al.hcp.111.json b/dpgen/data/jsons/al.hcp.111.json index 2b14badba..b9aa495f8 100644 --- a/dpgen/data/jsons/al.hcp.111.json +++ b/dpgen/data/jsons/al.hcp.111.json @@ -1,36 +1,36 @@ { - "cell_type": "hcp", - "latt": 4.04, - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "Al" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "hcp", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/al.hcp.222.json b/dpgen/data/jsons/al.hcp.222.json index aa1d06abc..85ecc8b9d 100644 --- a/dpgen/data/jsons/al.hcp.222.json +++ b/dpgen/data/jsons/al.hcp.222.json @@ -1,36 +1,36 @@ { - "cell_type": "hcp", - "latt": 4.04, - "super_cell": [ - 2, - 2, - 2 - ], - "elements": [ - "Al" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "hcp", + "latt": 4.04, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/al.hcp.332.json b/dpgen/data/jsons/al.hcp.332.json index 77b2bdedc..990e13e4e 100644 --- a/dpgen/data/jsons/al.hcp.332.json +++ b/dpgen/data/jsons/al.hcp.332.json @@ -1,36 +1,36 @@ { - "cell_type": "hcp", - "latt": 4.04, - "super_cell": [ - 3, - 3, - 2 - ], - "elements": [ - "Al" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "hcp", + "latt": 4.04, + "super_cell": [ + 3, + 3, + 2 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/al.sc.222.json b/dpgen/data/jsons/al.sc.222.json index 1c5a5f43c..9b7d0ee1e 100644 --- a/dpgen/data/jsons/al.sc.222.json +++ b/dpgen/data/jsons/al.sc.222.json @@ -1,36 +1,36 @@ { - "cell_type": "sc", - "latt": 2.5, - "super_cell": [ - 2, - 2, - 2 - ], - "elements": [ - "Al" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "sc", + "latt": 2.5, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/almg.diamond.111.json b/dpgen/data/jsons/almg.diamond.111.json index 251425fd9..d6800a15e 100644 --- a/dpgen/data/jsons/almg.diamond.111.json +++ b/dpgen/data/jsons/almg.diamond.111.json @@ -1,38 +1,38 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "Al", - "Mg" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/almg.diamond.222.json b/dpgen/data/jsons/almg.diamond.222.json index 7b968c24c..968f7a781 100644 --- a/dpgen/data/jsons/almg.diamond.222.json +++ b/dpgen/data/jsons/almg.diamond.222.json @@ -1,38 +1,38 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [ - 2, - 2, - 2 - ], - "elements": [ - "Al", - "Mg" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/almg.fcc.111.json b/dpgen/data/jsons/almg.fcc.111.json index 9246b1b03..7a81d8f7a 100644 --- a/dpgen/data/jsons/almg.fcc.111.json +++ b/dpgen/data/jsons/almg.fcc.111.json @@ -1,38 +1,38 @@ { - "cell_type": "fcc", - "latt": 4.3, - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "Al", - "Mg" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "fcc", + "latt": 4.3, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/almg.fcc.222.json b/dpgen/data/jsons/almg.fcc.222.json index 8370e2025..526296e14 100644 --- a/dpgen/data/jsons/almg.fcc.222.json +++ b/dpgen/data/jsons/almg.fcc.222.json @@ -1,38 +1,38 @@ { - "cell_type": "fcc", - "latt": 4.3, - "super_cell": [ - 2, - 2, - 2 - ], - "elements": [ - "Al", - "Mg" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "fcc", + "latt": 4.3, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/almg.hcp.111.json b/dpgen/data/jsons/almg.hcp.111.json index 31fce16f3..c3e6f959b 100644 --- a/dpgen/data/jsons/almg.hcp.111.json +++ b/dpgen/data/jsons/almg.hcp.111.json @@ -1,38 +1,38 @@ { - "cell_type": "hcp", - "latt": 4.3, - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "Al", - "Mg" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "hcp", + "latt": 4.3, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/almg.hcp.222.json b/dpgen/data/jsons/almg.hcp.222.json index bbff1dec1..bd294960e 100644 --- a/dpgen/data/jsons/almg.hcp.222.json +++ b/dpgen/data/jsons/almg.hcp.222.json @@ -1,38 +1,38 @@ { - "cell_type": "hcp", - "latt": 4.3, - "super_cell": [ - 2, - 2, - 2 - ], - "elements": [ - "Al", - "Mg" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "hcp", + "latt": 4.3, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/almg.hcp.332.json b/dpgen/data/jsons/almg.hcp.332.json index b7477e75b..a42c819d2 100644 --- a/dpgen/data/jsons/almg.hcp.332.json +++ b/dpgen/data/jsons/almg.hcp.332.json @@ -1,38 +1,38 @@ { - "cell_type": "hcp", - "latt": 4.3, - "super_cell": [ - 3, - 3, - 2 - ], - "elements": [ - "Al", - "Mg" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "hcp", + "latt": 4.3, + "super_cell": [ + 3, + 3, + 2 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/almg.sc.222.json b/dpgen/data/jsons/almg.sc.222.json index df9d25f53..f13f31309 100644 --- a/dpgen/data/jsons/almg.sc.222.json +++ b/dpgen/data/jsons/almg.sc.222.json @@ -1,38 +1,38 @@ { - "cell_type": "sc", - "latt": 2.5, - "super_cell": [ - 2, - 2, - 2 - ], - "elements": [ - "Al", - "Mg" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "sc", + "latt": 2.5, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/almg.sc.333.json b/dpgen/data/jsons/almg.sc.333.json index 621b3ca84..48434e6e9 100644 --- a/dpgen/data/jsons/almg.sc.333.json +++ b/dpgen/data/jsons/almg.sc.333.json @@ -1,38 +1,38 @@ { - "cell_type": "sc", - "latt": 2.5, - "super_cell": [ - 3, - 3, - 3 - ], - "elements": [ - "Al", - "Mg" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "sc", + "latt": 2.5, + "super_cell": [ + 3, + 3, + 3 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/mg.diamond.111.json b/dpgen/data/jsons/mg.diamond.111.json index 419154c68..9cf5929cd 100644 --- a/dpgen/data/jsons/mg.diamond.111.json +++ b/dpgen/data/jsons/mg.diamond.111.json @@ -1,36 +1,36 @@ { - "cell_type": "diamond", - "latt": 3.3, - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "Mg" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "diamond", + "latt": 3.3, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/mg.diamond.222.json b/dpgen/data/jsons/mg.diamond.222.json index d3e19bc32..3e57d89fb 100644 --- a/dpgen/data/jsons/mg.diamond.222.json +++ b/dpgen/data/jsons/mg.diamond.222.json @@ -1,36 +1,36 @@ { - "cell_type": "diamond", - "latt": 3.3, - "super_cell": [ - 2, - 2, - 2 - ], - "elements": [ - "Mg" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "diamond", + "latt": 3.3, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/mg.fcc.111.json b/dpgen/data/jsons/mg.fcc.111.json index 42662508b..4b410025d 100644 --- a/dpgen/data/jsons/mg.fcc.111.json +++ b/dpgen/data/jsons/mg.fcc.111.json @@ -1,36 +1,36 @@ { - "cell_type": "fcc", - "latt": 4.48, - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "Mg" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": true, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "fcc", + "latt": 4.48, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": true, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/mg.fcc.222.json b/dpgen/data/jsons/mg.fcc.222.json index 18fd5f789..1c336433a 100644 --- a/dpgen/data/jsons/mg.fcc.222.json +++ b/dpgen/data/jsons/mg.fcc.222.json @@ -1,36 +1,36 @@ { - "cell_type": "fcc", - "latt": 4.48, - "super_cell": [ - 2, - 2, - 2 - ], - "elements": [ - "Mg" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": true, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "fcc", + "latt": 4.48, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": true, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/mg.hcp.111.json b/dpgen/data/jsons/mg.hcp.111.json index 56b8b10ee..de791a650 100644 --- a/dpgen/data/jsons/mg.hcp.111.json +++ b/dpgen/data/jsons/mg.hcp.111.json @@ -1,36 +1,36 @@ { - "cell_type": "hcp", - "latt": 4.48, - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "Mg" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "hcp", + "latt": 4.48, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/mg.hcp.222.json b/dpgen/data/jsons/mg.hcp.222.json index 9d1507ae1..228085b5e 100644 --- a/dpgen/data/jsons/mg.hcp.222.json +++ b/dpgen/data/jsons/mg.hcp.222.json @@ -1,34 +1,34 @@ { - "cell_type": "hcp", - "latt": 4.48, - "super_cell": [ - 2, - 2, - 2 - ], - "elements": [ - "Mg" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "_comment1": "that's all" + "cell_type": "hcp", + "latt": 4.48, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/mg.hcp.332.json b/dpgen/data/jsons/mg.hcp.332.json index e39c3c3bc..c072c16e3 100644 --- a/dpgen/data/jsons/mg.hcp.332.json +++ b/dpgen/data/jsons/mg.hcp.332.json @@ -1,34 +1,34 @@ { - "cell_type": "hcp", - "latt": 4.48, - "super_cell": [ - 3, - 3, - 2 - ], - "elements": [ - "Mg" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "_comment1": "that's all" + "cell_type": "hcp", + "latt": 4.48, + "super_cell": [ + 3, + 3, + 2 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/mg.sc.222.json b/dpgen/data/jsons/mg.sc.222.json index 5c2098ad7..b05669cc3 100644 --- a/dpgen/data/jsons/mg.sc.222.json +++ b/dpgen/data/jsons/mg.sc.222.json @@ -1,36 +1,36 @@ { - "cell_type": "sc", - "latt": 2.7, - "super_cell": [ - 2, - 2, - 2 - ], - "elements": [ - "Mg" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "sc", + "latt": 2.7, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/param.json b/dpgen/data/jsons/param.json index 5581417b7..5527819e0 100644 --- a/dpgen/data/jsons/param.json +++ b/dpgen/data/jsons/param.json @@ -1,40 +1,40 @@ { - "cell_type": "hcp", - "latt": 4.03, - "super_cell": [ - 2, - 1, - 1 - ], - "elements": [ - "Al", - "Mg" - ], - "potcars": [ - "/gpfs/share/home/1600017784/start/data/POTCAR/Al/POTCAR", - "/gpfs/share/home/1600017784/start/data/POTCAR/Mg/POTCAR" - ], - "encut": 600, - "kspacing": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": true, - "relax_incar": "INCAR", - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 20, - "_comment1": "that's all", - "stages": [ - 1, - 2 - ] + "cell_type": "hcp", + "latt": 4.03, + "super_cell": [ + 2, + 1, + 1 + ], + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/gpfs/share/home/1600017784/start/data/POTCAR/Al/POTCAR", + "/gpfs/share/home/1600017784/start/data/POTCAR/Mg/POTCAR" + ], + "encut": 600, + "kspacing": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": true, + "relax_incar": "INCAR", + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 20, + "_comment1": "that's all", + "stages": [ + 1, + 2 + ] } diff --git a/dpgen/data/jsons/si.diamond.111.json b/dpgen/data/jsons/si.diamond.111.json index 808ff33fe..153435fec 100644 --- a/dpgen/data/jsons/si.diamond.111.json +++ b/dpgen/data/jsons/si.diamond.111.json @@ -1,36 +1,36 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "Si" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Si" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/si.diamond.222.json b/dpgen/data/jsons/si.diamond.222.json index 14c147250..8d648cad7 100644 --- a/dpgen/data/jsons/si.diamond.222.json +++ b/dpgen/data/jsons/si.diamond.222.json @@ -1,36 +1,36 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [ - 2, - 2, - 2 - ], - "elements": [ - "Si" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Si" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/si.fcc.111.json b/dpgen/data/jsons/si.fcc.111.json index af33644d2..a63cbcc37 100644 --- a/dpgen/data/jsons/si.fcc.111.json +++ b/dpgen/data/jsons/si.fcc.111.json @@ -1,36 +1,36 @@ { - "cell_type": "fcc", - "latt": 4.04, - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "Si" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "fcc", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Si" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/si.fcc.222.json b/dpgen/data/jsons/si.fcc.222.json index 3c7f41bf6..4c1a48548 100644 --- a/dpgen/data/jsons/si.fcc.222.json +++ b/dpgen/data/jsons/si.fcc.222.json @@ -1,36 +1,36 @@ { - "cell_type": "fcc", - "latt": 4.04, - "super_cell": [ - 2, - 2, - 2 - ], - "elements": [ - "Si" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "fcc", + "latt": 4.04, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Si" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/si.hcp.111.json b/dpgen/data/jsons/si.hcp.111.json index 127c769b0..b3a66a6cd 100644 --- a/dpgen/data/jsons/si.hcp.111.json +++ b/dpgen/data/jsons/si.hcp.111.json @@ -1,36 +1,36 @@ { - "cell_type": "hcp", - "latt": 4.04, - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "Si" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "hcp", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Si" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/si.hcp.222.json b/dpgen/data/jsons/si.hcp.222.json index b92ec401a..a6f7e2157 100644 --- a/dpgen/data/jsons/si.hcp.222.json +++ b/dpgen/data/jsons/si.hcp.222.json @@ -1,36 +1,36 @@ { - "cell_type": "hcp", - "latt": 4.04, - "super_cell": [ - 2, - 2, - 2 - ], - "elements": [ - "Si" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "hcp", + "latt": 4.04, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Si" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/si.sc.222.json b/dpgen/data/jsons/si.sc.222.json index f321c2c79..a136c51f8 100644 --- a/dpgen/data/jsons/si.sc.222.json +++ b/dpgen/data/jsons/si.sc.222.json @@ -1,36 +1,36 @@ { - "cell_type": "sc", - "latt": 2.5, - "super_cell": [ - 2, - 2, - 2 - ], - "elements": [ - "Si" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "sc", + "latt": 2.5, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "Si" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/surf.al.fcc.json b/dpgen/data/jsons/surf.al.fcc.json index bc8a84023..30efd029a 100644 --- a/dpgen/data/jsons/surf.al.fcc.json +++ b/dpgen/data/jsons/surf.al.fcc.json @@ -1,40 +1,40 @@ { - "cell_type": "fcc", - "latt": 4.04, - "super_cell": [ - 1, - 1, - 1 - ], - "z_min": 12, - "vacuum_max": 9, - "vacuum_resol": 0.2, - "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", - "elements": [ - "Al" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "fcc", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "z_min": 12, + "vacuum_max": 9, + "vacuum_resol": 0.2, + "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 5, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/surf.al.hcp.json b/dpgen/data/jsons/surf.al.hcp.json index 9e78a2207..4c28934e7 100644 --- a/dpgen/data/jsons/surf.al.hcp.json +++ b/dpgen/data/jsons/surf.al.hcp.json @@ -1,40 +1,40 @@ { - "cell_type": "hcp", - "latt": 4.04, - "super_cell": [ - 1, - 1, - 1 - ], - "z_min": 12, - "vacuum_max": 9, - "vacuum_resol": 0.2, - "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", - "elements": [ - "Al" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "hcp", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "z_min": 12, + "vacuum_max": 9, + "vacuum_resol": 0.2, + "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", + "elements": [ + "Al" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 5, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/surf.almg.fcc.json b/dpgen/data/jsons/surf.almg.fcc.json index 311d38058..cda94f5ae 100644 --- a/dpgen/data/jsons/surf.almg.fcc.json +++ b/dpgen/data/jsons/surf.almg.fcc.json @@ -1,42 +1,42 @@ { - "cell_type": "fcc", - "latt": 4.04, - "super_cell": [ - 1, - 1, - 1 - ], - "z_min": 12, - "vacuum_max": 9, - "vacuum_resol": 0.2, - "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", - "elements": [ - "Al", - "Mg" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "fcc", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "z_min": 12, + "vacuum_max": 9, + "vacuum_resol": 0.2, + "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 5, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/surf.almg.hcp.json b/dpgen/data/jsons/surf.almg.hcp.json index 2b6b29bac..59fba4af5 100644 --- a/dpgen/data/jsons/surf.almg.hcp.json +++ b/dpgen/data/jsons/surf.almg.hcp.json @@ -1,42 +1,42 @@ { - "cell_type": "hcp", - "latt": 4.04, - "super_cell": [ - 1, - 1, - 1 - ], - "z_min": 12, - "vacuum_max": 9, - "vacuum_resol": 0.2, - "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", - "elements": [ - "Al", - "Mg" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "hcp", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "z_min": 12, + "vacuum_max": 9, + "vacuum_resol": 0.2, + "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", + "elements": [ + "Al", + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Al/POTCAR", + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 5, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/surf.mg.fcc.json b/dpgen/data/jsons/surf.mg.fcc.json index 75504a33a..43a55b0af 100644 --- a/dpgen/data/jsons/surf.mg.fcc.json +++ b/dpgen/data/jsons/surf.mg.fcc.json @@ -1,40 +1,40 @@ { - "cell_type": "fcc", - "latt": 4.48, - "super_cell": [ - 1, - 1, - 1 - ], - "z_min": 12, - "vacuum_max": 9, - "vacuum_resol": 0.2, - "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", - "elements": [ - "Mg" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "fcc", + "latt": 4.48, + "super_cell": [ + 1, + 1, + 1 + ], + "z_min": 12, + "vacuum_max": 9, + "vacuum_resol": 0.2, + "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 5, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/surf.mg.hcp.json b/dpgen/data/jsons/surf.mg.hcp.json index 2ee3c7d4e..c7c91d2df 100644 --- a/dpgen/data/jsons/surf.mg.hcp.json +++ b/dpgen/data/jsons/surf.mg.hcp.json @@ -1,40 +1,40 @@ { - "cell_type": "hcp", - "latt": 4.48, - "super_cell": [ - 1, - 1, - 1 - ], - "z_min": 12, - "vacuum_max": 9, - "vacuum_resol": 0.2, - "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", - "elements": [ - "Mg" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "hcp", + "latt": 4.48, + "super_cell": [ + 1, + 1, + 1 + ], + "z_min": 12, + "vacuum_max": 9, + "vacuum_resol": 0.2, + "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", + "elements": [ + "Mg" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Mg/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 5, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/surf.si.diamond.json b/dpgen/data/jsons/surf.si.diamond.json index c34c05e30..725a9b90f 100644 --- a/dpgen/data/jsons/surf.si.diamond.json +++ b/dpgen/data/jsons/surf.si.diamond.json @@ -1,58 +1,58 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [ - 1, - 1, - 1 - ], - "z_min": 12, - "vacuum_max": 9, - "vacuum_resol": 0.2, - "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", - "pymatgen_surf": true, - "millers": [ - [ - 0, - 0, - 1 + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 1, + 1, + 1 ], - [ - 1, - 1, - 0 + "z_min": 12, + "vacuum_max": 9, + "vacuum_resol": 0.2, + "lmp_cmd": "/home/wanghan/Soft/lammps/lammps-16Mar18/src/lmp_mpi", + "pymatgen_surf": true, + "millers": [ + [ + 0, + 0, + 1 + ], + [ + 1, + 1, + 0 + ], + [ + 1, + 1, + 1 + ] ], - [ - 1, - 1, - 1 - ] - ], - "elements": [ - "Si" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.06, - "kgamma": false, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "elements": [ + "Si" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/Si/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.06, + "kgamma": false, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 5, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/w.bcc.111.json b/dpgen/data/jsons/w.bcc.111.json index 35c696d23..210514e6c 100644 --- a/dpgen/data/jsons/w.bcc.111.json +++ b/dpgen/data/jsons/w.bcc.111.json @@ -1,38 +1,38 @@ { - "cell_type": "bcc", - "latt": 3.2, - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "W" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "ismear": 1, - "sigma": 0.2, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 30, - "pert_box": 0.005, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "bcc", + "latt": 3.2, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "W" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "ismear": 1, + "sigma": 0.2, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 30, + "pert_box": 0.005, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/w.bcc.222.json b/dpgen/data/jsons/w.bcc.222.json index 76731b97b..0fa54012e 100644 --- a/dpgen/data/jsons/w.bcc.222.json +++ b/dpgen/data/jsons/w.bcc.222.json @@ -1,38 +1,38 @@ { - "cell_type": "bcc", - "latt": 3.173, - "super_cell": [ - 2, - 2, - 2 - ], - "elements": [ - "W" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "ismear": 1, - "sigma": 0.2, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": true, - "pert_numb": 100, - "pert_box": 0.005, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "bcc", + "latt": 3.173, + "super_cell": [ + 2, + 2, + 2 + ], + "elements": [ + "W" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "ismear": 1, + "sigma": 0.2, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": true, + "pert_numb": 100, + "pert_box": 0.005, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/w.diamond.111.json b/dpgen/data/jsons/w.diamond.111.json index 3e140a071..89ce0e8af 100644 --- a/dpgen/data/jsons/w.diamond.111.json +++ b/dpgen/data/jsons/w.diamond.111.json @@ -1,38 +1,38 @@ { - "cell_type": "diamond", - "latt": 2.5, - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "W" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "ismear": 1, - "sigma": 0.2, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 30, - "pert_box": 0.005, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "diamond", + "latt": 2.5, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "W" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "ismear": 1, + "sigma": 0.2, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 30, + "pert_box": 0.005, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/w.fcc.111.json b/dpgen/data/jsons/w.fcc.111.json index 1ad0c6cc4..705181620 100644 --- a/dpgen/data/jsons/w.fcc.111.json +++ b/dpgen/data/jsons/w.fcc.111.json @@ -1,38 +1,38 @@ { - "cell_type": "fcc", - "latt": 4.04, - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "W" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "ismear": 1, - "sigma": 0.2, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 30, - "pert_box": 0.005, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "fcc", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "W" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "ismear": 1, + "sigma": 0.2, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 30, + "pert_box": 0.005, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/w.hcp.111.json b/dpgen/data/jsons/w.hcp.111.json index 097daf9d4..dc8093a63 100644 --- a/dpgen/data/jsons/w.hcp.111.json +++ b/dpgen/data/jsons/w.hcp.111.json @@ -1,38 +1,38 @@ { - "cell_type": "hcp", - "latt": 4.04, - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "W" - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" - ], - "encut": 600, - "kspacing_relax": 0.16, - "kspacing_md": 0.08, - "kgamma": false, - "ismear": 1, - "sigma": 0.2, - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 30, - "pert_box": 0.005, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "cell_type": "hcp", + "latt": 4.04, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "W" + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.unknown/potpaw_PBE/W/POTCAR" + ], + "encut": 600, + "kspacing_relax": 0.16, + "kspacing_md": 0.08, + "kgamma": false, + "ismear": 1, + "sigma": 0.2, + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 30, + "pert_box": 0.005, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/dpgen/data/jsons/water.111.json b/dpgen/data/jsons/water.111.json index 261575b03..6cd01b135 100644 --- a/dpgen/data/jsons/water.111.json +++ b/dpgen/data/jsons/water.111.json @@ -1,37 +1,37 @@ { - "_comment1": "init poscars form a crystal structure", - "cell_type": "diamond", - "latt": 2.5, - "elements": [ - "Si" - ], - "_comment2": "if set from poscar, the options above will be ignored", - "from_poscar": true, - "from_poscar_path": "ice6.POSCAR", - "_comment3": "", - "super_cell": [ - 1, - 1, - 1 - ], - "potcars": [ - "/home/wanghan/Soft/vasp/potcar.52/potpaw_PBE.52/O/POTCAR", - "/home/wanghan/Soft/vasp/potcar.52/potpaw_PBE.52/H/POTCAR" - ], - "encut": 900, - "kspacing_relax": 0.75, - "kspacing_md": 0.75, - "kgamma": false, - "scale": [ - 1.0 - ], - "skip_relax": true, - "pert_numb": 100, - "pert_box": 0.03, - "pert_atom": 0.01, - "md_temp": 100, - "md_nstep": 10, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment4": "that's all" + "_comment1": "init poscars form a crystal structure", + "cell_type": "diamond", + "latt": 2.5, + "elements": [ + "Si" + ], + "_comment2": "if set from poscar, the options above will be ignored", + "from_poscar": true, + "from_poscar_path": "ice6.POSCAR", + "_comment3": "", + "super_cell": [ + 1, + 1, + 1 + ], + "potcars": [ + "/home/wanghan/Soft/vasp/potcar.52/potpaw_PBE.52/O/POTCAR", + "/home/wanghan/Soft/vasp/potcar.52/potpaw_PBE.52/H/POTCAR" + ], + "encut": 900, + "kspacing_relax": 0.75, + "kspacing_md": 0.75, + "kgamma": false, + "scale": [ + 1.0 + ], + "skip_relax": true, + "pert_numb": 100, + "pert_box": 0.03, + "pert_atom": 0.01, + "md_temp": 100, + "md_nstep": 10, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment4": "that's all" } diff --git a/examples/CH4-refact-dpdispatcher/machine-ali-ehpc.json b/examples/CH4-refact-dpdispatcher/machine-ali-ehpc.json index 9222aed6f..372545587 100644 --- a/examples/CH4-refact-dpdispatcher/machine-ali-ehpc.json +++ b/examples/CH4-refact-dpdispatcher/machine-ali-ehpc.json @@ -1,92 +1,92 @@ { - "api_version": "1.0", - "train": { - "command": "dp", - "machine": { - "batch_type": "PBS", - "context_type": "SSHContext", - "local_root": "./", - "remote_root": "/home/fengbo/work_path_dpdispatcher_test", - "remote_profile": { - "hostname": "39.xxx.xx.xx", - "username": "fengbo" - } + "api_version": "1.0", + "train": { + "command": "dp", + "machine": { + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/fengbo/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "fengbo" + } + }, + "resources": { + "batch_type": "PBS", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "T4_4_15", + "group_size": 1, + "custom_flags": [ + "#SBATCH --mem=32G" + ], + "strategy": { + "if_cuda_multi_devices": true + }, + "para_deg": 3, + "source_list": [ + "/home/fengbo/deepmd.1.2.4.env" + ] + } }, - "resources": { - "batch_type": "PBS", - "number_node": 1, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "T4_4_15", - "group_size": 1, - "custom_flags": [ - "#SBATCH --mem=32G" - ], - "strategy": { - "if_cuda_multi_devices": true - }, - "para_deg": 3, - "source_list": [ - "/home/fengbo/deepmd.1.2.4.env" - ] - } - }, - "model_devi": { - "command": "lmp", - "machine": { - "batch_type": "PBS", - "context_type": "SSHContext", - "local_root": "./", - "remote_root": "/home/fengbo/work_path_dpdispatcher_test", - "remote_profile": { - "hostname": "39.xxx.xx.xx", - "username": "fengbo" - } - }, - "resources": { - "batch_type": "PBS", - "number_node": 1, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "T4_4_15", - "group_size": 5, - "source_list": [ - "/home/fengbo/deepmd.1.2.4.env" - ] - }, - "_comments": "In user_backward_files, define output files to be collected.", - "user_forward_files": [], - "user_backward_files": [ - "HILLS" - ] - }, - "fp": { - "command": "vasp_std", - "machine": { - "batch_type": "PBS", - "context_type": "SSHContext", - "local_root": "./", - "remote_root": "/home/fengbo/work_path_dpdispatcher_test", - "remote_profile": { - "hostname": "39.xxx.xx.xx", - "username": "fengbo" - } + "model_devi": { + "command": "lmp", + "machine": { + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/fengbo/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "fengbo" + } + }, + "resources": { + "batch_type": "PBS", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "T4_4_15", + "group_size": 5, + "source_list": [ + "/home/fengbo/deepmd.1.2.4.env" + ] + }, + "_comments": "In user_backward_files, define output files to be collected.", + "user_forward_files": [], + "user_backward_files": [ + "HILLS" + ] }, - "resources": { - "batch_type": "PBS", - "number_node": 1, - "cpu_per_node": 32, - "gpu_per_node": 0, - "queue_name": "G_32_128", - "group_size": 1, - "source_list": [ - "~/vasp.env" - ] - }, - "_comments": "In user_backward_files, define output files to be collected.", - "user_forward_files": [ - "vdw_kernel.bindat" - ], - "user_backward_files": [] - } + "fp": { + "command": "vasp_std", + "machine": { + "batch_type": "PBS", + "context_type": "SSHContext", + "local_root": "./", + "remote_root": "/home/fengbo/work_path_dpdispatcher_test", + "remote_profile": { + "hostname": "39.xxx.xx.xx", + "username": "fengbo" + } + }, + "resources": { + "batch_type": "PBS", + "number_node": 1, + "cpu_per_node": 32, + "gpu_per_node": 0, + "queue_name": "G_32_128", + "group_size": 1, + "source_list": [ + "~/vasp.env" + ] + }, + "_comments": "In user_backward_files, define output files to be collected.", + "user_forward_files": [ + "vdw_kernel.bindat" + ], + "user_backward_files": [] + } } diff --git a/examples/CH4-refact-dpdispatcher/machine-dpcloudserver.json b/examples/CH4-refact-dpdispatcher/machine-dpcloudserver.json index c27db8859..d3a1c9db1 100644 --- a/examples/CH4-refact-dpdispatcher/machine-dpcloudserver.json +++ b/examples/CH4-refact-dpdispatcher/machine-dpcloudserver.json @@ -1,128 +1,128 @@ { - "api_version": "1.0", - "train": { - "command": "dp", - "machine": { - "batch_type": "DpCloudServer", - "context_type": "DpCloudServerContext", - "local_root": "./", - "remote_profile": { - "email": "yfb222333", - "password": "", - "program_id": 0, - "input_data": { - "job_type": "indicate", - "log_file": "dp_cloud_server.log", - "command": null, - "backward_files": [], - "job_name": "dpgen_20210630_job", - "machine": { - "platform": "ali", - "resources": { - "gpu_type": "1 * NVIDIA P100", - "cpu_num": 4, - "mem_limit": 30, - "disk_size": 100, - "region": "cn-beijing", - "time_limit": "2:00:00", - "image_name": "yfb-deepmd-kit-1.2.4-cuda10" + "api_version": "1.0", + "train": { + "command": "dp", + "machine": { + "batch_type": "DpCloudServer", + "context_type": "DpCloudServerContext", + "local_root": "./", + "remote_profile": { + "email": "yfb222333", + "password": "", + "program_id": 0, + "input_data": { + "job_type": "indicate", + "log_file": "dp_cloud_server.log", + "command": null, + "backward_files": [], + "job_name": "dpgen_20210630_job", + "machine": { + "platform": "ali", + "resources": { + "gpu_type": "1 * NVIDIA P100", + "cpu_num": 4, + "mem_limit": 30, + "disk_size": 100, + "region": "cn-beijing", + "time_limit": "2:00:00", + "image_name": "yfb-deepmd-kit-1.2.4-cuda10" + } + }, + "job_resources": null + } } - }, - "job_resources": null + }, + "resources": { + "batch_type": "DpCloudServer", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "GPU", + "group_size": 1 } - } }, - "resources": { - "batch_type": "DpCloudServer", - "number_node": 1, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "GPU", - "group_size": 1 - } - }, - "model_devi": { - "command": "lmp -i input.lammps -v restart 0", - "machine": { - "batch_type": "DpCloudServer", - "context_type": "DpCloudServerContext", - "local_root": "./", - "remote_profile": { - "email": "yfb222333", - "password": "", - "program_id": 0, - "input_data": { - "job_type": "indicate", - "log_file": "dp_cloud_server.log", - "command": null, - "backward_files": [], - "job_name": "dpgen_20210630_job", - "machine": { - "platform": "ali", - "resources": { - "gpu_type": "1 * NVIDIA P100", - "cpu_num": 4, - "mem_limit": 30, - "disk_size": 100, - "region": "cn-beijing", - "time_limit": "2:00:00", - "image_name": "yfb-deepmd-kit-1.2.4-cuda10" + "model_devi": { + "command": "lmp -i input.lammps -v restart 0", + "machine": { + "batch_type": "DpCloudServer", + "context_type": "DpCloudServerContext", + "local_root": "./", + "remote_profile": { + "email": "yfb222333", + "password": "", + "program_id": 0, + "input_data": { + "job_type": "indicate", + "log_file": "dp_cloud_server.log", + "command": null, + "backward_files": [], + "job_name": "dpgen_20210630_job", + "machine": { + "platform": "ali", + "resources": { + "gpu_type": "1 * NVIDIA P100", + "cpu_num": 4, + "mem_limit": 30, + "disk_size": 100, + "region": "cn-beijing", + "time_limit": "2:00:00", + "image_name": "yfb-deepmd-kit-1.2.4-cuda10" + } + }, + "job_resources": null + } } - }, - "job_resources": null + }, + "resources": { + "batch_type": "DpCloudServer", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "GPU", + "group_size": 5 } - } }, - "resources": { - "batch_type": "DpCloudServer", - "number_node": 1, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "GPU", - "group_size": 5 - } - }, - "fp": { - "command": "mpirun -n 16 vasp_std", - "machine": { - "batch_type": "DpCloudServer", - "context_type": "DpCloudServerContext", - "local_root": "./", - "remote_profile": { - "email": "yfb222333", - "password": "", - "program_id": 0, - "input_data": { - "job_type": "indicate", - "log_file": "dp_cloud_server.log", - "command": null, - "backward_files": [], - "job_name": "dpgen_20210630_job", - "machine": { - "platform": "ali", - "resources": { - "cpu_num": 32, - "mem_limit": 64, - "disk_size": 200, - "region": "cn-beijing", - "time_limit": "2:00:00", - "image_name": "deepmd-vasp-cloudserver-v8" + "fp": { + "command": "mpirun -n 16 vasp_std", + "machine": { + "batch_type": "DpCloudServer", + "context_type": "DpCloudServerContext", + "local_root": "./", + "remote_profile": { + "email": "yfb222333", + "password": "", + "program_id": 0, + "input_data": { + "job_type": "indicate", + "log_file": "dp_cloud_server.log", + "command": null, + "backward_files": [], + "job_name": "dpgen_20210630_job", + "machine": { + "platform": "ali", + "resources": { + "cpu_num": 32, + "mem_limit": 64, + "disk_size": 200, + "region": "cn-beijing", + "time_limit": "2:00:00", + "image_name": "deepmd-vasp-cloudserver-v8" + } + }, + "job_resources": null + } } - }, - "job_resources": null + }, + "resources": { + "batch_type": "DpCloudServer", + "number_node": 1, + "cpu_per_node": 32, + "gpu_per_node": 0, + "queue_name": "CPU", + "group_size": 5, + "source_list": [ + "/opt/intel/oneapi/setvars.sh" + ] } - } - }, - "resources": { - "batch_type": "DpCloudServer", - "number_node": 1, - "cpu_per_node": 32, - "gpu_per_node": 0, - "queue_name": "CPU", - "group_size": 5, - "source_list": [ - "/opt/intel/oneapi/setvars.sh" - ] } - } } diff --git a/examples/database/param_Ti.json b/examples/database/param_Ti.json index 5560b31f9..ed2e6b556 100644 --- a/examples/database/param_Ti.json +++ b/examples/database/param_Ti.json @@ -1,100 +1,100 @@ { - "path": "/path/to/Ti", - "calculator": "vasp", - "_comment1": "Current only support VASP", - "output": "./db_Ti.json", - "id_prefix": "", - "config_info_dict": { - "fcc-bulk": [ - 0, - 1, - 2, - 3, - 4, - 5, - 6, - 7 - ], - "hcp-bulk": [ - 8, - 9, - 10, - 11, - 12, - 13, - 14, - 15 - ], - "bcc-bulk": [ - 16, - 17, - 18, - 19, - 20, - 21, - 22, - 23 - ], - "fcc-surf-100": [ - 24, - 25, - 26, - 27, - 28, - 29, - 30, - 31 - ], - "fcc-surf-111": [ - 32, - 33, - 34, - 35, - 36, - 37, - 38, - 39 - ], - "fcc-surf-110": [ - 40, - 41, - 42, - 43, - 44, - 45, - 46, - 47 - ], - "hcp-surf-001": [ - 48, - 49, - 50, - 51, - 52, - 53, - 54, - 55 - ], - "hcp-surf-100": [ - 56, - 57, - 58, - 59, - 60, - 61, - 62, - 63 - ], - "hcp-surf-110": [ - 64, - 65, - 66, - 67, - 68, - 69, - 70, - 71 - ] - }, - "skip_init": true + "path": "/path/to/Ti", + "calculator": "vasp", + "_comment1": "Current only support VASP", + "output": "./db_Ti.json", + "id_prefix": "", + "config_info_dict": { + "fcc-bulk": [ + 0, + 1, + 2, + 3, + 4, + 5, + 6, + 7 + ], + "hcp-bulk": [ + 8, + 9, + 10, + 11, + 12, + 13, + 14, + 15 + ], + "bcc-bulk": [ + 16, + 17, + 18, + 19, + 20, + 21, + 22, + 23 + ], + "fcc-surf-100": [ + 24, + 25, + 26, + 27, + 28, + 29, + 30, + 31 + ], + "fcc-surf-111": [ + 32, + 33, + 34, + 35, + 36, + 37, + 38, + 39 + ], + "fcc-surf-110": [ + 40, + 41, + 42, + 43, + 44, + 45, + 46, + 47 + ], + "hcp-surf-001": [ + 48, + 49, + 50, + 51, + 52, + 53, + 54, + 55 + ], + "hcp-surf-100": [ + 56, + 57, + 58, + 59, + 60, + 61, + 62, + 63 + ], + "hcp-surf-110": [ + 64, + 65, + 66, + 67, + 68, + 69, + 70, + 71 + ] + }, + "skip_init": true } diff --git a/examples/init/abacus/CuW/CuW.json b/examples/init/abacus/CuW/CuW.json index b351af657..0703bfb21 100644 --- a/examples/init/abacus/CuW/CuW.json +++ b/examples/init/abacus/CuW/CuW.json @@ -1,52 +1,52 @@ { - "init_fp_style": "ABACUS", - "stages": [ - 1, - 2, - 3, - 4 - ], - "cell_type": "fcc", - "latt": 3.76, - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "Cu", - "W" - ], - "atom_masses": [ - 63.55, - 183.8 - ], - "potcars": [ - "Cu_ONCV_PBE-1.0.upf", - "W_ONCV_PBE-1.0.upf" - ], - "orb_files": [ - "Cu_gga_9au_60Ry_4s2p2d1f.orb", - "W_gga_10au_60Ry_4s2p2d2f.orb" - ], - "relax_incar": "INPUT", - "relax_kpt": "KPT", - "md_kpt": "KPT", - "md_incar": "INPUT.md", - "dpks_descriptor": "jle.orb", - "dpks_model": "model.ptg", - "scale": [ - 0.99 - ], - "skip_relax": true, - "pert_numb": 2, - "md_nstep": 2, - "pert_box": 0.01, - "pert_atom": 0.01, - "coll_ndata": 12, - "type_map": [ - "Cu", - "W" - ], - "_comment1": "that's all" + "init_fp_style": "ABACUS", + "stages": [ + 1, + 2, + 3, + 4 + ], + "cell_type": "fcc", + "latt": 3.76, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Cu", + "W" + ], + "atom_masses": [ + 63.55, + 183.8 + ], + "potcars": [ + "Cu_ONCV_PBE-1.0.upf", + "W_ONCV_PBE-1.0.upf" + ], + "orb_files": [ + "Cu_gga_9au_60Ry_4s2p2d1f.orb", + "W_gga_10au_60Ry_4s2p2d2f.orb" + ], + "relax_incar": "INPUT", + "relax_kpt": "KPT", + "md_kpt": "KPT", + "md_incar": "INPUT.md", + "dpks_descriptor": "jle.orb", + "dpks_model": "model.ptg", + "scale": [ + 0.99 + ], + "skip_relax": true, + "pert_numb": 2, + "md_nstep": 2, + "pert_box": 0.01, + "pert_atom": 0.01, + "coll_ndata": 12, + "type_map": [ + "Cu", + "W" + ], + "_comment1": "that's all" } diff --git a/examples/init/abacus/fcc-Al-lcao/init.json b/examples/init/abacus/fcc-Al-lcao/init.json index 76507f0df..1095fa54b 100644 --- a/examples/init/abacus/fcc-Al-lcao/init.json +++ b/examples/init/abacus/fcc-Al-lcao/init.json @@ -1,41 +1,41 @@ { - "init_fp_style": "ABACUS", - "stages": [ - 1, - 2, - 3, - 4 - ], - "cell_type": "diamond", - "super_cell": [ - 2, - 1, - 1 - ], - "elements": [ - "Al" - ], - "from_poscar": true, - "from_poscar_path": "./Al.STRU", - "potcars": [ - "Al_ONCV_PBE-1.0.upf" - ], - "orb_files": [ - "Al_gga_9au_100Ry_4s4p1d.orb" - ], - "relax_incar": "./INPUT.rlx", - "md_incar": "./INPUT.md", - "relax_kpt": "./KPT.rlx", - "md_kpt": "./KPT.md", - "md_nstep": 3, - "scale": [ - 1.0 - ], - "skip_relax": false, - "pert_numb": 2, - "pert_box": 0.03, - "pert_atom": 0.01, - "deepgen_templ": "../generator/template/", - "coll_ndata": 5000, - "_comment1": "that's all" + "init_fp_style": "ABACUS", + "stages": [ + 1, + 2, + 3, + 4 + ], + "cell_type": "diamond", + "super_cell": [ + 2, + 1, + 1 + ], + "elements": [ + "Al" + ], + "from_poscar": true, + "from_poscar_path": "./Al.STRU", + "potcars": [ + "Al_ONCV_PBE-1.0.upf" + ], + "orb_files": [ + "Al_gga_9au_100Ry_4s4p1d.orb" + ], + "relax_incar": "./INPUT.rlx", + "md_incar": "./INPUT.md", + "relax_kpt": "./KPT.rlx", + "md_kpt": "./KPT.md", + "md_nstep": 3, + "scale": [ + 1.0 + ], + "skip_relax": false, + "pert_numb": 2, + "pert_box": 0.03, + "pert_atom": 0.01, + "deepgen_templ": "../generator/template/", + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/examples/init/abacus/fcc-Al-lcao/machine.json b/examples/init/abacus/fcc-Al-lcao/machine.json index 0d82a2af3..1a35c7107 100644 --- a/examples/init/abacus/fcc-Al-lcao/machine.json +++ b/examples/init/abacus/fcc-Al-lcao/machine.json @@ -1,104 +1,111 @@ { - "api_version": "1.0", - "deepmd_version": "2.0.1", - "train" :[ - { - "command": "dp", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": 0, - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "00*/train.log", - "grouped":true, - "job_name": "dpgen_train_job", - "disk_size": 200, - "scass_type":"", - "checkpoint_files":["00*/checkpoint","00*/model.ckpt*"], - "checkpoint_time":30, - "platform": "", - "region":"", - "image_name":"", - "on_demand":0 + "api_version": "1.0", + "deepmd_version": "2.0.1", + "train": [ + { + "command": "dp", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "00*/train.log", + "grouped": true, + "job_name": "dpgen_train_job", + "disk_size": 200, + "scass_type": "", + "checkpoint_files": [ + "00*/checkpoint", + "00*/model.ckpt*" + ], + "checkpoint_time": 30, + "platform": "", + "region": "", + "image_name": "", + "on_demand": 0 + } + } + }, + "resources": { + "local_root": "./", + "group_size": 1 } } - }, - "resources": { - "local_root":"./", - "group_size": 1 - } - }], - "model_devi": - [{ - "command": "lmp -i input.lammps -v restart 0", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": 0, - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "*/model_devi.log", - "grouped":true, - "job_name": "dpgen_model_devi_job", - "disk_size": 200, - "scass_type":"", - "platform": "", - "region":"", - "image_name":"", - "checkpoint_files": "sync_files", - "checkpoint_time":30, - "on_demand":0 + ], + "model_devi": [ + { + "command": "lmp -i input.lammps -v restart 0", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "*/model_devi.log", + "grouped": true, + "job_name": "dpgen_model_devi_job", + "disk_size": 200, + "scass_type": "", + "platform": "", + "region": "", + "image_name": "", + "checkpoint_files": "sync_files", + "checkpoint_time": 30, + "on_demand": 0 + } + } + }, + "resources": { + "local_root": "./", + "group_size": 50 } } - }, - "resources": { - "local_root":"./", - "group_size": 50 - } - }], - "fp": - [{ - "command": "OMP_NUM_THREADS=1 mpirun -n 8 abacus", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": 0, - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "task*/fp.log", - "grouped":true, - "job_name": "dpgen_fp_job", - "disk_size": 100, - "checkpoint_files": "sync_files", - "checkpoint_time":30, - "scass_type":"", - "platform": "", - "image_name":"", - "on_demand":0 + ], + "fp": [ + { + "command": "OMP_NUM_THREADS=1 mpirun -n 8 abacus", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "task*/fp.log", + "grouped": true, + "job_name": "dpgen_fp_job", + "disk_size": 100, + "checkpoint_files": "sync_files", + "checkpoint_time": 30, + "scass_type": "", + "platform": "", + "image_name": "", + "on_demand": 0 + } + } + }, + "resources": { + "group_size": 50, + "local_root": "./", + "source_list": [ + "" + ] } } - }, - "resources": { - "group_size": 50, - "local_root":"./", - "source_list": [""] - } - } - ] + ] } diff --git a/examples/init/abacus/fcc-Al-pw/init.json b/examples/init/abacus/fcc-Al-pw/init.json index a20ca4c87..d90cef3bd 100644 --- a/examples/init/abacus/fcc-Al-pw/init.json +++ b/examples/init/abacus/fcc-Al-pw/init.json @@ -1,38 +1,38 @@ { - "init_fp_style": "ABACUS", - "stages": [ - 1, - 2, - 3, - 4 - ], - "cell_type": "fcc", - "super_cell": [ - 2, - 1, - 1 - ], - "elements": [ - "Al" - ], - "from_poscar": true, - "from_poscar_path": "./Al.STRU", - "potcars": [ - "Al_ONCV_PBE-1.0.upf" - ], - "relax_incar": "INPUT.rlx", - "relax_kpt": "KPT", - "md_incar": "INPUT.md", - "md_kpt": "KPT", - "skip_relax": false, - "scale": [ - 1.0 - ], - "pert_numb": 10, - "md_nstep": 10, - "pert_box": 0.01, - "pert_atom": 0.01, - "deepgen_templ": "../generator/template/", - "coll_ndata": 10, - "_comment1": "that's all" + "init_fp_style": "ABACUS", + "stages": [ + 1, + 2, + 3, + 4 + ], + "cell_type": "fcc", + "super_cell": [ + 2, + 1, + 1 + ], + "elements": [ + "Al" + ], + "from_poscar": true, + "from_poscar_path": "./Al.STRU", + "potcars": [ + "Al_ONCV_PBE-1.0.upf" + ], + "relax_incar": "INPUT.rlx", + "relax_kpt": "KPT", + "md_incar": "INPUT.md", + "md_kpt": "KPT", + "skip_relax": false, + "scale": [ + 1.0 + ], + "pert_numb": 10, + "md_nstep": 10, + "pert_box": 0.01, + "pert_atom": 0.01, + "deepgen_templ": "../generator/template/", + "coll_ndata": 10, + "_comment1": "that's all" } diff --git a/examples/init/abacus/fcc-Al-pw/machine.json b/examples/init/abacus/fcc-Al-pw/machine.json index 0d82a2af3..1a35c7107 100644 --- a/examples/init/abacus/fcc-Al-pw/machine.json +++ b/examples/init/abacus/fcc-Al-pw/machine.json @@ -1,104 +1,111 @@ { - "api_version": "1.0", - "deepmd_version": "2.0.1", - "train" :[ - { - "command": "dp", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": 0, - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "00*/train.log", - "grouped":true, - "job_name": "dpgen_train_job", - "disk_size": 200, - "scass_type":"", - "checkpoint_files":["00*/checkpoint","00*/model.ckpt*"], - "checkpoint_time":30, - "platform": "", - "region":"", - "image_name":"", - "on_demand":0 + "api_version": "1.0", + "deepmd_version": "2.0.1", + "train": [ + { + "command": "dp", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "00*/train.log", + "grouped": true, + "job_name": "dpgen_train_job", + "disk_size": 200, + "scass_type": "", + "checkpoint_files": [ + "00*/checkpoint", + "00*/model.ckpt*" + ], + "checkpoint_time": 30, + "platform": "", + "region": "", + "image_name": "", + "on_demand": 0 + } + } + }, + "resources": { + "local_root": "./", + "group_size": 1 } } - }, - "resources": { - "local_root":"./", - "group_size": 1 - } - }], - "model_devi": - [{ - "command": "lmp -i input.lammps -v restart 0", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": 0, - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "*/model_devi.log", - "grouped":true, - "job_name": "dpgen_model_devi_job", - "disk_size": 200, - "scass_type":"", - "platform": "", - "region":"", - "image_name":"", - "checkpoint_files": "sync_files", - "checkpoint_time":30, - "on_demand":0 + ], + "model_devi": [ + { + "command": "lmp -i input.lammps -v restart 0", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "*/model_devi.log", + "grouped": true, + "job_name": "dpgen_model_devi_job", + "disk_size": 200, + "scass_type": "", + "platform": "", + "region": "", + "image_name": "", + "checkpoint_files": "sync_files", + "checkpoint_time": 30, + "on_demand": 0 + } + } + }, + "resources": { + "local_root": "./", + "group_size": 50 } } - }, - "resources": { - "local_root":"./", - "group_size": 50 - } - }], - "fp": - [{ - "command": "OMP_NUM_THREADS=1 mpirun -n 8 abacus", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root" : "./", - "remote_profile":{ - "email": "", - "password": "", - "program_id": 0, - "keep_backup":true, - "input_data":{ - "job_type": "indicate", - "log_file": "task*/fp.log", - "grouped":true, - "job_name": "dpgen_fp_job", - "disk_size": 100, - "checkpoint_files": "sync_files", - "checkpoint_time":30, - "scass_type":"", - "platform": "", - "image_name":"", - "on_demand":0 + ], + "fp": [ + { + "command": "OMP_NUM_THREADS=1 mpirun -n 8 abacus", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "task*/fp.log", + "grouped": true, + "job_name": "dpgen_fp_job", + "disk_size": 100, + "checkpoint_files": "sync_files", + "checkpoint_time": 30, + "scass_type": "", + "platform": "", + "image_name": "", + "on_demand": 0 + } + } + }, + "resources": { + "group_size": 50, + "local_root": "./", + "source_list": [ + "" + ] } } - }, - "resources": { - "group_size": 50, - "local_root":"./", - "source_list": [""] - } - } - ] + ] } diff --git a/examples/init/al.json b/examples/init/al.json index 76506d76d..6f1fbb2ab 100644 --- a/examples/init/al.json +++ b/examples/init/al.json @@ -1,32 +1,32 @@ { - "cell_type": "fcc", - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "Al" - ], - "from_poscar": true, - "from_poscar_path": "al.POSCAR", - "potcars": [ - "POTCAR" - ], - "relax_incar": "INCAR.rlx", - "md_incar": "INCAR.md", - "scale": [ - 1.0 - ], - "skip_relax": true, - "pert_numb": 30, - "md_nstep": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "coll_ndata": 10, - "type_map": [ - "Mg", - "Al" - ], - "_comment1": "that's all" + "cell_type": "fcc", + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al" + ], + "from_poscar": true, + "from_poscar_path": "al.POSCAR", + "potcars": [ + "POTCAR" + ], + "relax_incar": "INCAR.rlx", + "md_incar": "INCAR.md", + "scale": [ + 1.0 + ], + "skip_relax": true, + "pert_numb": 30, + "md_nstep": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "coll_ndata": 10, + "type_map": [ + "Mg", + "Al" + ], + "_comment1": "that's all" } diff --git a/examples/init/ch4.json b/examples/init/ch4.json index d28e7ac26..622b74b5f 100644 --- a/examples/init/ch4.json +++ b/examples/init/ch4.json @@ -1,36 +1,36 @@ { - "stages": [ - 1, - 2, - 3, - 4 - ], - "cell_type": "diamond", - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "H", - "C" - ], - "from_poscar": true, - "from_poscar_path": "./CH4.POSCAR", - "potcars": [ - "./POTCAR_H", - "./POTCAR_C" - ], - "relax_incar": "./INCAR_methane.rlx", - "md_incar": "./INCAR_methane.md", - "scale": [ - 1.0 - ], - "skip_relax": false, - "pert_numb": 30, - "md_nstep": 10, - "pert_box": 0.03, - "pert_atom": 0.01, - "coll_ndata": 5000, - "_comment1": "that's all" + "stages": [ + 1, + 2, + 3, + 4 + ], + "cell_type": "diamond", + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "H", + "C" + ], + "from_poscar": true, + "from_poscar_path": "./CH4.POSCAR", + "potcars": [ + "./POTCAR_H", + "./POTCAR_C" + ], + "relax_incar": "./INCAR_methane.rlx", + "md_incar": "./INCAR_methane.md", + "scale": [ + 1.0 + ], + "skip_relax": false, + "pert_numb": 30, + "md_nstep": 10, + "pert_box": 0.03, + "pert_atom": 0.01, + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/examples/init/cu.surf.hcp.111.json b/examples/init/cu.surf.hcp.111.json index 7d29774fc..7ed24507f 100644 --- a/examples/init/cu.surf.hcp.111.json +++ b/examples/init/cu.surf.hcp.111.json @@ -1,59 +1,59 @@ { - "_comments": "Last modified on 2019.8.27 by Yuzhi Zhang.", - "stages": [ - 1, - 2 - ], - "cell_type": "hcp", - "latt": 3.63, - "super_cell": [ - 1, - 1, - 1 - ], - "z_min": 10, - "vacuum_max": 10, - "vacuum_resol": [ - 0.5, - 1 - ], - "mid_point": 4.0, - "millers": [ - [ - 1, - 0, - 0 + "_comments": "Last modified on 2019.8.27 by Yuzhi Zhang.", + "stages": [ + 1, + 2 ], - [ - 1, - 1, - 0 + "cell_type": "hcp", + "latt": 3.63, + "super_cell": [ + 1, + 1, + 1 ], - [ - 0, - 0, - 1 - ] - ], - "elements": [ - "Cu" - ], - "potcars": [ - "PATH/POTCAR" - ], - "relax_incar": "PATH/INCAR_surf_rlx", - "scale": [ - 0.96, - 0.98, - 1.0, - 1.02, - 1.04, - 1.06 - ], - "skip_relax": false, - "pert_numb": 20, - "pert_box": 0.03, - "pert_atom": 0.01, - "lmp_cmd": "PATH/lmp_serial", - "_comment1": "that's all" + "z_min": 10, + "vacuum_max": 10, + "vacuum_resol": [ + 0.5, + 1 + ], + "mid_point": 4.0, + "millers": [ + [ + 1, + 0, + 0 + ], + [ + 1, + 1, + 0 + ], + [ + 0, + 0, + 1 + ] + ], + "elements": [ + "Cu" + ], + "potcars": [ + "PATH/POTCAR" + ], + "relax_incar": "PATH/INCAR_surf_rlx", + "scale": [ + 0.96, + 0.98, + 1.0, + 1.02, + 1.04, + 1.06 + ], + "skip_relax": false, + "pert_numb": 20, + "pert_box": 0.03, + "pert_atom": 0.01, + "lmp_cmd": "PATH/lmp_serial", + "_comment1": "that's all" } diff --git a/examples/init/reaction.json b/examples/init/reaction.json index 0d163343e..8bf070726 100644 --- a/examples/init/reaction.json +++ b/examples/init/reaction.json @@ -1,19 +1,19 @@ { - "type_map": [ - "H", - "O" - ], - "reaxff": { - "data": "data.hydrogen", - "ff": "ffield.reax.cho", - "control": "lmp_control", - "temp": 3000, - "tau_t": 100, - "dt": 0.1, - "nstep": 10000, - "dump_freq": 100 - }, - "cutoff": 3.5, - "dataset_size": 100, - "qmkeywords": "b3lyp/6-31g** force Geom=PrintInputOrient" + "type_map": [ + "H", + "O" + ], + "reaxff": { + "data": "data.hydrogen", + "ff": "ffield.reax.cho", + "control": "lmp_control", + "temp": 3000, + "tau_t": 100, + "dt": 0.1, + "nstep": 10000, + "dump_freq": 100 + }, + "cutoff": 3.5, + "dataset_size": 100, + "qmkeywords": "b3lyp/6-31g** force Geom=PrintInputOrient" } diff --git a/examples/init/surf.json b/examples/init/surf.json index 4bb00df97..08ec0f05a 100644 --- a/examples/init/surf.json +++ b/examples/init/surf.json @@ -1,56 +1,56 @@ { - "stages": [ - 1, - 2 - ], - "cell_type": "fcc", - "latt": 4.1, - "super_cell": [ - 1, - 1, - 1 - ], - "z_min": 9, - "vacuum_max": 9.0, - "vacuum_resol": [ - 0.5, - 1 - ], - "mid_point": 4.0, - "head_ratio": 0.6, - "vacuum_numb": 20, - "millers": [ - [ - 1, - 0, - 0 + "stages": [ + 1, + 2 ], - [ - 1, - 1, - 0 + "cell_type": "fcc", + "latt": 4.1, + "super_cell": [ + 1, + 1, + 1 ], - [ - 1, - 1, - 1 - ] - ], - "elements": [ - "Al" - ], - "potcars": [ - "./POTCAR" - ], - "relax_incar": "INCAR_metal_rlx_low", - "scale": [ - 0.98, - 1.0 - ], - "skip_relax": true, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "coll_ndata": 5000, - "_comment1": "that's all" + "z_min": 9, + "vacuum_max": 9.0, + "vacuum_resol": [ + 0.5, + 1 + ], + "mid_point": 4.0, + "head_ratio": 0.6, + "vacuum_numb": 20, + "millers": [ + [ + 1, + 0, + 0 + ], + [ + 1, + 1, + 0 + ], + [ + 1, + 1, + 1 + ] + ], + "elements": [ + "Al" + ], + "potcars": [ + "./POTCAR" + ], + "relax_incar": "INCAR_metal_rlx_low", + "scale": [ + 0.98, + 1.0 + ], + "skip_relax": true, + "pert_numb": 5, + "pert_box": 0.03, + "pert_atom": 0.01, + "coll_ndata": 5000, + "_comment1": "that's all" } diff --git a/examples/machine/DeePMD-kit-1.0/machine-local-4GPU.json b/examples/machine/DeePMD-kit-1.0/machine-local-4GPU.json index 37526ab2f..854ee01ba 100644 --- a/examples/machine/DeePMD-kit-1.0/machine-local-4GPU.json +++ b/examples/machine/DeePMD-kit-1.0/machine-local-4GPU.json @@ -1,90 +1,90 @@ { - "_comment1": "This is an example of DP-GEN on Local device running with 4 GPUs", - "_comment2": "Last updated on 2021.5.9 for DP-GEN 0.9.2 by Ke XU", - "train": { - "_comment3": "Specify the installed path of DeePMD-kit", - "command": "/home/user/anaconda3/bin/dp", - "_comment4": "Specify machine settings", - "machine": { - "_comment5": "Supported batches include slurm, pbs, shell, lsf.", - "batch_type": "shell", - "context_type": "local", - "remote_root": "/tmp/dpwork", - "local_root": "./" + "_comment1": "This is an example of DP-GEN on Local device running with 4 GPUs", + "_comment2": "Last updated on 2021.5.9 for DP-GEN 0.9.2 by Ke XU", + "train": { + "_comment3": "Specify the installed path of DeePMD-kit", + "command": "/home/user/anaconda3/bin/dp", + "_comment4": "Specify machine settings", + "machine": { + "_comment5": "Supported batches include slurm, pbs, shell, lsf.", + "batch_type": "shell", + "context_type": "local", + "remote_root": "/tmp/dpwork", + "local_root": "./" + }, + "resources": { + "module_list": [], + "_comment6": "Environment to be activated. This will generate source xxx/psxevars.sh in scripts. ", + "source_list": [ + "/opt/intel/parallel_studio_xe_2020/psxevars.sh" + ], + "batch_type": "shell", + "_comment7": "DP-GEN will put 4 tasks together in one submitting script.", + "group_size": 4, + "_comment8": "The number of nodes.", + "number_node": 1, + "_comment9": "The number of CPUs.", + "cpu_per_node": 4, + "_comment10": "If you choose to run with multiple GPUs simultaneously, just ignore numb_gpu.", + "gpu_per_node": 0, + "kwargs": {}, + "strategy": { + "_comment11": "Allow the multi-GPU task running.", + "if_cuda_multi_devices": true + }, + "para_deg": 4, + "queue_name": "" + } }, - "resources": { - "module_list": [], - "_comment6": "Environment to be activated. This will generate source xxx/psxevars.sh in scripts. ", - "source_list": [ - "/opt/intel/parallel_studio_xe_2020/psxevars.sh" - ], - "batch_type": "shell", - "_comment7": "DP-GEN will put 4 tasks together in one submitting script.", - "group_size": 4, - "_comment8": "The number of nodes.", - "number_node": 1, - "_comment9": "The number of CPUs.", - "cpu_per_node": 4, - "_comment10": "If you choose to run with multiple GPUs simultaneously, just ignore numb_gpu.", - "gpu_per_node": 0, - "kwargs": {}, - "strategy": { - "_comment11": "Allow the multi-GPU task running.", - "if_cuda_multi_devices": true - }, - "para_deg": 4, - "queue_name": "" - } - }, - "model_devi": { - "machine": { - "batch_type": "shell", - "context_type": "local", - "remote_root": "/tmp/dpwork", - "local_root": "./" + "model_devi": { + "machine": { + "batch_type": "shell", + "context_type": "local", + "remote_root": "/tmp/dpwork", + "local_root": "./" + }, + "resources": { + "source_list": [], + "module_list": [], + "batch_type": "shell", + "group_size": 4, + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 0, + "kwargs": {}, + "strategy": { + "if_cuda_multi_devices": true + }, + "para_deg": 4, + "queue_name": "" + }, + "command": "/home/user/Soft/Deepmd/lammps-stable_29Oct2020/src/lmp_mpi" }, - "resources": { - "source_list": [], - "module_list": [], - "batch_type": "shell", - "group_size": 4, - "number_node": 1, - "cpu_per_node": 4, - "gpu_per_node": 0, - "kwargs": {}, - "strategy": { - "if_cuda_multi_devices": true - }, - "para_deg": 4, - "queue_name": "" + "fp": { + "machine": { + "batch_type": "shell", + "context_type": "local", + "remote_root": "/tmp/dpwork", + "local_root": "./" + }, + "resources": { + "_comment12": "Load the intel compiler.", + "source_list": [ + "/opt/intel/parallel_studio_xe_2020/psxevars.sh" + ], + "_comment13": "This will generate export PATH=/home/user/Soft/VASP/vasp.5.4.4-allbak/bin:$PATH in scripts;", + "envs": { + "PATH": "/home/user/Soft/VASP/vasp.5.4.4-allbak/bin:$PATH" + }, + "batch_type": "shell", + "group_size": 1, + "cpu_per_node": 16, + "kwargs": {}, + "queue_name": "", + "number_node": 1, + "gpu_per_node": 1 + }, + "command": "mpirun -n 16 vasp_std || :" }, - "command": "/home/user/Soft/Deepmd/lammps-stable_29Oct2020/src/lmp_mpi" - }, - "fp": { - "machine": { - "batch_type": "shell", - "context_type": "local", - "remote_root": "/tmp/dpwork", - "local_root": "./" - }, - "resources": { - "_comment12": "Load the intel compiler.", - "source_list": [ - "/opt/intel/parallel_studio_xe_2020/psxevars.sh" - ], - "_comment13": "This will generate export PATH=/home/user/Soft/VASP/vasp.5.4.4-allbak/bin:$PATH in scripts;", - "envs": { - "PATH": "/home/user/Soft/VASP/vasp.5.4.4-allbak/bin:$PATH" - }, - "batch_type": "shell", - "group_size": 1, - "cpu_per_node": 16, - "kwargs": {}, - "queue_name": "", - "number_node": 1, - "gpu_per_node": 1 - }, - "command": "mpirun -n 16 vasp_std || :" - }, - "api_version": "1.0" + "api_version": "1.0" } diff --git a/examples/machine/DeePMD-kit-1.x/machine-local.json b/examples/machine/DeePMD-kit-1.x/machine-local.json index 6da8a09cb..eaac4cb5d 100644 --- a/examples/machine/DeePMD-kit-1.x/machine-local.json +++ b/examples/machine/DeePMD-kit-1.x/machine-local.json @@ -1,65 +1,65 @@ { - "api_version": "1.0", - "train": { - "_comment1": "training on localhost", - "machine": { - "batch_type": "shell", - "context_type": "local", - "remote_root": "/home/wanghan/tmp/subs/", - "local_root": "./" + "api_version": "1.0", + "train": { + "_comment1": "training on localhost", + "machine": { + "batch_type": "shell", + "context_type": "local", + "remote_root": "/home/wanghan/tmp/subs/", + "local_root": "./" + }, + "resources": { + "envs": {}, + "batch_type": "shell", + "group_size": 1, + "kwargs": {}, + "queue_name": "", + "number_node": 1, + "cpu_per_node": 1, + "gpu_per_node": 1 + }, + "command": "/home/wanghan/local/deepmd/1.*/dp" }, - "resources": { - "envs": {}, - "batch_type": "shell", - "group_size": 1, - "kwargs": {}, - "queue_name": "", - "number_node": 1, - "cpu_per_node": 1, - "gpu_per_node": 1 + "model_devi": { + "_comment2": "model devi on localhost", + "machine": { + "_comment3": "If lazy_local, calculations are done directly in current folders.", + "batch_type": "shell", + "context_type": "lazylocal", + "local_root": "./" + }, + "resources": { + "batch_type": "shell", + "group_size": 5, + "kwargs": {}, + "queue_name": "", + "number_node": 1, + "cpu_per_node": 1, + "gpu_per_node": 1 + }, + "command": "/home/wanghan/local/bin/lmp_mpi_010" }, - "command": "/home/wanghan/local/deepmd/1.*/dp" - }, - "model_devi": { - "_comment2": "model devi on localhost", - "machine": { - "_comment3": "If lazy_local, calculations are done directly in current folders.", - "batch_type": "shell", - "context_type": "lazylocal", - "local_root": "./" - }, - "resources": { - "batch_type": "shell", - "group_size": 5, - "kwargs": {}, - "queue_name": "", - "number_node": 1, - "cpu_per_node": 1, - "gpu_per_node": 1 - }, - "command": "/home/wanghan/local/bin/lmp_mpi_010" - }, - "fp": { - "_comment4": "fp on localhost", - "machine": { - "batch_type": "shell", - "context_type": "local", - "remote_root": "/home/wanghan/tmp/subs/", - "local_root": "./" - }, - "resources": { - "module_list": [ - "mpi" - ], - "_comment5": "that's all", - "batch_type": "shell", - "group_size": 2, - "cpu_per_node": 4, - "kwargs": {}, - "queue_name": "", - "number_node": 1, - "gpu_per_node": 1 - }, - "command": "mpirun -n 4 /home/wanghan/local/bin/vasp_std" - } + "fp": { + "_comment4": "fp on localhost", + "machine": { + "batch_type": "shell", + "context_type": "local", + "remote_root": "/home/wanghan/tmp/subs/", + "local_root": "./" + }, + "resources": { + "module_list": [ + "mpi" + ], + "_comment5": "that's all", + "batch_type": "shell", + "group_size": 2, + "cpu_per_node": 4, + "kwargs": {}, + "queue_name": "", + "number_node": 1, + "gpu_per_node": 1 + }, + "command": "mpirun -n 4 /home/wanghan/local/bin/vasp_std" + } } diff --git a/examples/machine/DeePMD-kit-1.x/machine-lsf-slurm-cp2k.json b/examples/machine/DeePMD-kit-1.x/machine-lsf-slurm-cp2k.json index 634df15f5..0fab6e8b9 100644 --- a/examples/machine/DeePMD-kit-1.x/machine-lsf-slurm-cp2k.json +++ b/examples/machine/DeePMD-kit-1.x/machine-lsf-slurm-cp2k.json @@ -1,98 +1,98 @@ { - "train": { - "machine": { - "batch_type": "slurm", - "context_type": "ssh", - "remote_profile": { - "hostname": "210.34.15.205", - "port": 22, - "username": "ybzhuang" - }, - "remote_root": "/home/ybzhuang/workdir", - "local_root": "./" + "train": { + "machine": { + "batch_type": "slurm", + "context_type": "ssh", + "remote_profile": { + "hostname": "210.34.15.205", + "port": 22, + "username": "ybzhuang" + }, + "remote_root": "/home/ybzhuang/workdir", + "local_root": "./" + }, + "resources": { + "source_list": [], + "module_list": [ + "deepmd/1.2" + ], + "batch_type": "slurm", + "number_node": 1, + "cpu_per_node": 1, + "gpu_per_node": 1, + "queue_name": "emergency", + "custom_flags": [ + "#SBATCH -t 96:0:0" + ], + "kwargs": {}, + "wait_time": 60, + "group_size": 1 + }, + "command": "/share/apps/deepmd/compress/bin/python3.8-m deepmd" }, - "resources": { - "source_list": [], - "module_list": [ - "deepmd/1.2" - ], - "batch_type": "slurm", - "number_node": 1, - "cpu_per_node": 1, - "gpu_per_node": 1, - "queue_name": "emergency", - "custom_flags": [ - "#SBATCH -t 96:0:0" - ], - "kwargs": {}, - "wait_time": 60, - "group_size": 1 + "model_devi": { + "machine": { + "batch_type": "slurm", + "context_type": "ssh", + "remote_profile": { + "hostname": "210.34.15.205", + "port": 22, + "username": "ybzhuang" + }, + "remote_root": "/home/ybzhuang/workdir", + "local_root": "./" + }, + "resources": { + "source_list": [], + "module_list": [ + "deepmd/1.2" + ], + "batch_type": "slurm", + "group_size": 5, + "number_node": 1, + "cpu_per_node": 1, + "gpu_per_node": 1, + "queue_name": "emergency", + "custom_flags": [ + "#SBATCH -t 96:0:0" + ], + "kwargs": {}, + "wait_time": 60 + }, + "command": "lmp_mpi" }, - "command": "/share/apps/deepmd/compress/bin/python3.8-m deepmd" - }, - "model_devi": { - "machine": { - "batch_type": "slurm", - "context_type": "ssh", - "remote_profile": { - "hostname": "210.34.15.205", - "port": 22, - "username": "ybzhuang" - }, - "remote_root": "/home/ybzhuang/workdir", - "local_root": "./" + "fp": { + "machine": { + "batch_type": "lsf", + "context_type": "ssh", + "remote_profile": { + "hostname": "localhost", + "port": 6666, + "username": "ybzhuang" + }, + "remote_root": "/data/ybzhuang/methane-dpgen/dpgen-tutorial-2020-08-23/dpgen-tutorial-mathane/workpath", + "local_root": "./" + }, + "resources": { + "source_list": [], + "module_list": [ + "intel/17.5.239", + "mpi/intel/2017.5.239", + "gcc/5.5.0", + "cp2k/7.1" + ], + "batch_type": "lsf", + "group_size": 50, + "number_node": 1, + "cpu_per_node": 32, + "queue_name": "53-medium", + "custom_flags": [ + "#BSUB -W 12:00:00" + ], + "kwargs": {}, + "gpu_per_node": 1 + }, + "command": "mpirun -n 32 cp2k.popt -i input.inp" }, - "resources": { - "source_list": [], - "module_list": [ - "deepmd/1.2" - ], - "batch_type": "slurm", - "group_size": 5, - "number_node": 1, - "cpu_per_node": 1, - "gpu_per_node": 1, - "queue_name": "emergency", - "custom_flags": [ - "#SBATCH -t 96:0:0" - ], - "kwargs": {}, - "wait_time": 60 - }, - "command": "lmp_mpi" - }, - "fp": { - "machine": { - "batch_type": "lsf", - "context_type": "ssh", - "remote_profile": { - "hostname": "localhost", - "port": 6666, - "username": "ybzhuang" - }, - "remote_root": "/data/ybzhuang/methane-dpgen/dpgen-tutorial-2020-08-23/dpgen-tutorial-mathane/workpath", - "local_root": "./" - }, - "resources": { - "source_list": [], - "module_list": [ - "intel/17.5.239", - "mpi/intel/2017.5.239", - "gcc/5.5.0", - "cp2k/7.1" - ], - "batch_type": "lsf", - "group_size": 50, - "number_node": 1, - "cpu_per_node": 32, - "queue_name": "53-medium", - "custom_flags": [ - "#BSUB -W 12:00:00" - ], - "kwargs": {}, - "gpu_per_node": 1 - }, - "command": "mpirun -n 32 cp2k.popt -i input.inp" - }, - "api_version": "1.0" + "api_version": "1.0" } diff --git a/examples/machine/DeePMD-kit-1.x/machine-pbs-gaussian.json b/examples/machine/DeePMD-kit-1.x/machine-pbs-gaussian.json index d7c0836cb..cc8eca816 100644 --- a/examples/machine/DeePMD-kit-1.x/machine-pbs-gaussian.json +++ b/examples/machine/DeePMD-kit-1.x/machine-pbs-gaussian.json @@ -1,88 +1,88 @@ { - "api_version": "1.0", - "train": { - "machine": { - "batch_type": "lsf", - "context_type": "ssh", - "remote_profile": { - "hostname": "xxx.xxx.xxx.xxx", - "port": 22, - "username": "tzhu" - }, - "remote_root": "/gpfs/home/tzhu/jzzeng/dpgen_workdir", - "local_root": "./" + "api_version": "1.0", + "train": { + "machine": { + "batch_type": "lsf", + "context_type": "ssh", + "remote_profile": { + "hostname": "xxx.xxx.xxx.xxx", + "port": 22, + "username": "tzhu" + }, + "remote_root": "/gpfs/home/tzhu/jzzeng/dpgen_workdir", + "local_root": "./" + }, + "resources": { + "source_list": [ + "activate deepmd" + ], + "envs": { + "KMP_BLOCKTIME": 0, + "KMP_AFFINITY": "granularity=fine,verbose,compact,1,0" + }, + "batch_type": "lsf", + "group_size": 1, + "number_node": 1, + "cpu_per_node": 0, + "gpu_per_node": 1, + "queue_name": "newgpu", + "kwargs": {} + }, + "command": "/gpfs/home/tzhu/anaconda3/envs/python3.6/bin/dp" }, - "resources": { - "source_list": [ - "activate deepmd" - ], - "envs": { - "KMP_BLOCKTIME": 0, - "KMP_AFFINITY": "granularity=fine,verbose,compact,1,0" - }, - "batch_type": "lsf", - "group_size": 1, - "number_node": 1, - "cpu_per_node": 0, - "gpu_per_node": 1, - "queue_name": "newgpu", - "kwargs": {} + "model_devi": { + "machine": { + "batch_type": "lsf", + "context_type": "ssh", + "remote_profile": { + "hostname": "xxx.xxx.xxx.xxx", + "port": 22, + "username": "tzhu" + }, + "remote_root": "/gpfs/home/tzhu/jzzeng/dpgen_workdir", + "local_root": "./" + }, + "resources": { + "envs": { + "KMP_BLOCKTIME": 0 + }, + "source_list": [ + "activate deepmd" + ], + "batch_type": "lsf", + "group_size": 1, + "number_node": 1, + "cpu_per_node": 0, + "gpu_per_node": 1, + "queue_name": "newgpu", + "kwargs": {} + }, + "command": "mpirun -n 0 /gpfs/home/tzhu/lammps-stable_5Jun2019/src/lmp_intel_cpu_intelmpi -pk intel 0 omp 2" }, - "command": "/gpfs/home/tzhu/anaconda3/envs/python3.6/bin/dp" - }, - "model_devi": { - "machine": { - "batch_type": "lsf", - "context_type": "ssh", - "remote_profile": { - "hostname": "xxx.xxx.xxx.xxx", - "port": 22, - "username": "tzhu" - }, - "remote_root": "/gpfs/home/tzhu/jzzeng/dpgen_workdir", - "local_root": "./" - }, - "resources": { - "envs": { - "KMP_BLOCKTIME": 0 - }, - "source_list": [ - "activate deepmd" - ], - "batch_type": "lsf", - "group_size": 1, - "number_node": 1, - "cpu_per_node": 0, - "gpu_per_node": 1, - "queue_name": "newgpu", - "kwargs": {} - }, - "command": "mpirun -n 0 /gpfs/home/tzhu/lammps-stable_5Jun2019/src/lmp_intel_cpu_intelmpi -pk intel 0 omp 2" - }, - "fp": { - "machine": { - "batch_type": "pbs", - "context_type": "ssh", - "remote_profile": { - "hostname": "xxx.xxx.xxx.xxx", - "port": 2323, - "username": "tzhu" - }, - "remote_root": "/public/home/tzhu/jzzeng/dpgen_workdir", - "local_root": "./" - }, - "resources": { - "batch_type": "pbs", - "group_size": 1, - "number_node": 1, - "cpu_per_node": 28, - "queue_name": "small", - "custom_flags": [ - "#PBS -l walltime=10:00:00" - ], - "kwargs": {}, - "gpu_per_node": 1 - }, - "command": "/public/home/tzhu/g16/g16 < input || :" - } + "fp": { + "machine": { + "batch_type": "pbs", + "context_type": "ssh", + "remote_profile": { + "hostname": "xxx.xxx.xxx.xxx", + "port": 2323, + "username": "tzhu" + }, + "remote_root": "/public/home/tzhu/jzzeng/dpgen_workdir", + "local_root": "./" + }, + "resources": { + "batch_type": "pbs", + "group_size": 1, + "number_node": 1, + "cpu_per_node": 28, + "queue_name": "small", + "custom_flags": [ + "#PBS -l walltime=10:00:00" + ], + "kwargs": {}, + "gpu_per_node": 1 + }, + "command": "/public/home/tzhu/g16/g16 < input || :" + } } diff --git a/examples/machine/DeePMD-kit-1.x/machine-slurm-qe.json b/examples/machine/DeePMD-kit-1.x/machine-slurm-qe.json index 0c40266e1..40ed09746 100644 --- a/examples/machine/DeePMD-kit-1.x/machine-slurm-qe.json +++ b/examples/machine/DeePMD-kit-1.x/machine-slurm-qe.json @@ -1,112 +1,112 @@ { - "_comment1": "Last updated on 2021.4.30 for DP-GEN 0.9.2 by Yuzhi Zhang", - "train": { - "_comment2": "Specify the installed path of DeePMD-kit", - "command": "PATH_TO_DEEPMD/dp", - "_comment3": "Specify machine settings", - "machine": { - "batch_type": "slurm", - "context_type": "ssh", - "remote_profile": { - "hostname": "localhost", - "_comment4": "The port for connection, most common settings is 22", - "port": 22, - "_comment5": "Specify your username.", - "username": "USERNAME" - }, - "_comment6": "You should alwasy make sure that directory of work_path exits. ", - "remote_root": "PATH_TO_WORK", - "local_root": "./" + "_comment1": "Last updated on 2021.4.30 for DP-GEN 0.9.2 by Yuzhi Zhang", + "train": { + "_comment2": "Specify the installed path of DeePMD-kit", + "command": "PATH_TO_DEEPMD/dp", + "_comment3": "Specify machine settings", + "machine": { + "batch_type": "slurm", + "context_type": "ssh", + "remote_profile": { + "hostname": "localhost", + "_comment4": "The port for connection, most common settings is 22", + "port": 22, + "_comment5": "Specify your username.", + "username": "USERNAME" + }, + "_comment6": "You should alwasy make sure that directory of work_path exits. ", + "remote_root": "PATH_TO_WORK", + "local_root": "./" + }, + "resources": { + "_comment7": "Environment to be activated. This will generate source PATH/train_new.env . ", + "source_list": [ + "PATH/train_new.env" + ], + "_comment8": " Module is a common tools on HPC clustes to manage softwares for multiple users.", + "_comment9": "Modules to be loaded. This will generate module load intel", + "module_list": [ + "intel" + ], + "batch_type": "slurm", + "_comment10": "The number of nodes. This will generate #SBATCH -N 1 in your script. ", + "number_node": 1, + "_comment11": "The number of CPUs. #SBATCH -n 4", + "cpu_per_node": 4, + "_comment12": "The number of GPU cards. #SBATCH --gres=gpu:1", + "gpu_per_node": 1, + "queue_name": "all", + "custom_flags": [ + "#SBATCH -t 23:0:0", + "#SBATCH --mem=16G", + "#SBATCH --exclude=gpu06,gpu07" + ], + "kwargs": {}, + "group_size": 1 + } }, - "resources": { - "_comment7": "Environment to be activated. This will generate source PATH/train_new.env . ", - "source_list": [ - "PATH/train_new.env" - ], - "_comment8": " Module is a common tools on HPC clustes to manage softwares for multiple users.", - "_comment9": "Modules to be loaded. This will generate module load intel", - "module_list": [ - "intel" - ], - "batch_type": "slurm", - "_comment10": "The number of nodes. This will generate #SBATCH -N 1 in your script. ", - "number_node": 1, - "_comment11": "The number of CPUs. #SBATCH -n 4", - "cpu_per_node": 4, - "_comment12": "The number of GPU cards. #SBATCH --gres=gpu:1", - "gpu_per_node": 1, - "queue_name": "all", - "custom_flags": [ - "#SBATCH -t 23:0:0", - "#SBATCH --mem=16G", - "#SBATCH --exclude=gpu06,gpu07" - ], - "kwargs": {}, - "group_size": 1 - } - }, - "model_devi": { - "machine": { - "batch_type": "slurm", - "context_type": "ssh", - "remote_profile": { - "hostname": "localhost", - "port": 22, - "username": "USERNAME" - }, - "remote_root": "PATH_TO_WORK", - "local_root": "./" + "model_devi": { + "machine": { + "batch_type": "slurm", + "context_type": "ssh", + "remote_profile": { + "hostname": "localhost", + "port": 22, + "username": "USERNAME" + }, + "remote_root": "PATH_TO_WORK", + "local_root": "./" + }, + "resources": { + "source_list": [ + "PATH/lmp_new.env" + ], + "module_list": [], + "batch_type": "slurm", + "_comment13": "DP-GEN will put 5 tasks together in one submitting script.", + "group_size": 5, + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "all", + "custom_flags": [ + "#SBATCH -t 23:0:0", + "#SBATCH --mem=16G", + "#SBATCH --exclude=" + ], + "kwargs": {} + }, + "command": "lmp_serial" }, - "resources": { - "source_list": [ - "PATH/lmp_new.env" - ], - "module_list": [], - "batch_type": "slurm", - "_comment13": "DP-GEN will put 5 tasks together in one submitting script.", - "group_size": 5, - "number_node": 1, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "all", - "custom_flags": [ - "#SBATCH -t 23:0:0", - "#SBATCH --mem=16G", - "#SBATCH --exclude=" - ], - "kwargs": {} + "fp": { + "machine": { + "batch_type": "slurm", + "context_type": "ssh", + "remote_profile": { + "hostname": "xxx.xxx.xxx.xxx", + "port": 22, + "username": "USERNAME" + }, + "remote_root": "PATH_TO_WORK", + "local_root": "./" + }, + "resources": { + "source_list": [], + "module_list": [ + "mpich/3.2.1-intel-2017.1" + ], + "batch_type": "slurm", + "group_size": 1, + "cpu_per_node": 8, + "gpu_per_node": 0, + "queue_name": "C032M0128G", + "custom_flags": [ + "#SBATCH -t 120:0:0" + ], + "kwargs": {}, + "number_node": 1 + }, + "command": "mpirun -n 8 /gpfs/share/home/1600017784/yuzhi/soft/QE-mpi/PW/src/pw.x < input" }, - "command": "lmp_serial" - }, - "fp": { - "machine": { - "batch_type": "slurm", - "context_type": "ssh", - "remote_profile": { - "hostname": "xxx.xxx.xxx.xxx", - "port": 22, - "username": "USERNAME" - }, - "remote_root": "PATH_TO_WORK", - "local_root": "./" - }, - "resources": { - "source_list": [], - "module_list": [ - "mpich/3.2.1-intel-2017.1" - ], - "batch_type": "slurm", - "group_size": 1, - "cpu_per_node": 8, - "gpu_per_node": 0, - "queue_name": "C032M0128G", - "custom_flags": [ - "#SBATCH -t 120:0:0" - ], - "kwargs": {}, - "number_node": 1 - }, - "command": "mpirun -n 8 /gpfs/share/home/1600017784/yuzhi/soft/QE-mpi/PW/src/pw.x < input" - }, - "api_version": "1.0" + "api_version": "1.0" } diff --git a/examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine.json b/examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine.json index 49d0d4338..8fdd1db35 100644 --- a/examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine.json +++ b/examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine.json @@ -1,106 +1,106 @@ { - "api_version": "1.0", - "deepmd_version": "2.0.1", - "train": { - "command": "dp", - "machine": { - "batch_type": "DpCloudServer", - "context_type": "DpCloudServerContext", - "local_root": "./", - "remote_profile": { - "email": "your lebesgue register email", - "password": "your lebesgue password", - "program_id": 0, - "input_data": { - "api_version": 2, - "job_type": "indicate", - "log_file": "00*/train.log", - "grouped": true, - "job_name": "dpgen_train_job", - "disk_size": 100, - "scass_type": "c8_m60_1 * NVIDIA P100", - "platform": "ali", - "image_name": "deepmd-kit:2.0.1", - "on_demand": 0 + "api_version": "1.0", + "deepmd_version": "2.0.1", + "train": { + "command": "dp", + "machine": { + "batch_type": "DpCloudServer", + "context_type": "DpCloudServerContext", + "local_root": "./", + "remote_profile": { + "email": "your lebesgue register email", + "password": "your lebesgue password", + "program_id": 0, + "input_data": { + "api_version": 2, + "job_type": "indicate", + "log_file": "00*/train.log", + "grouped": true, + "job_name": "dpgen_train_job", + "disk_size": 100, + "scass_type": "c8_m60_1 * NVIDIA P100", + "platform": "ali", + "image_name": "deepmd-kit:2.0.1", + "on_demand": 0 + } + } + }, + "resources": { + "batch_type": "DpCloudServer", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "GPU", + "group_size": 1 } - } }, - "resources": { - "batch_type": "DpCloudServer", - "number_node": 1, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "GPU", - "group_size": 1 - } - }, - "model_devi": { - "command": "lmp -i input.lammps -v restart 0", - "machine": { - "batch_type": "DpCloudServer", - "context_type": "DpCloudServerContext", - "local_root": "./", - "remote_profile": { - "email": "your lebesgue register email", - "password": "your lebesgue password", - "program_id": 0, - "input_data": { - "api_version": 2, - "job_type": "indicate", - "log_file": "*/model_devi.log", - "grouped": true, - "job_name": "dpgen_model_devi_job", - "disk_size": 200, - "scass_type": "c8_m60_1 * NVIDIA P100", - "platform": "ali", - "image_name": "deepmd-kit:2.0.1", - "on_demand": 0 + "model_devi": { + "command": "lmp -i input.lammps -v restart 0", + "machine": { + "batch_type": "DpCloudServer", + "context_type": "DpCloudServerContext", + "local_root": "./", + "remote_profile": { + "email": "your lebesgue register email", + "password": "your lebesgue password", + "program_id": 0, + "input_data": { + "api_version": 2, + "job_type": "indicate", + "log_file": "*/model_devi.log", + "grouped": true, + "job_name": "dpgen_model_devi_job", + "disk_size": 200, + "scass_type": "c8_m60_1 * NVIDIA P100", + "platform": "ali", + "image_name": "deepmd-kit:2.0.1", + "on_demand": 0 + } + } + }, + "resources": { + "batch_type": "DpCloudServer", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "GPU", + "group_size": 5 } - } }, - "resources": { - "batch_type": "DpCloudServer", - "number_node": 1, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "GPU", - "group_size": 5 - } - }, - "fp": { - "command": "mpirun -n 16 vasp_std", - "machine": { - "batch_type": "DpCloudServer", - "context_type": "DpCloudServerContext", - "local_root": "./", - "remote_profile": { - "email": "your lebesgue register email", - "password": "your lebesgue password", - "program_id": 0, - "input_data": { - "api_version": 2, - "job_type": "indicate", - "log_file": "task*/fp.log", - "grouped": true, - "job_name": "dpgen_fp_job", - "disk_size": 100, - "scass_type": "c8_m8_cpu", - "platform": "ali", - "image_name": "vasp:5.4.4", - "on_demand": 0 + "fp": { + "command": "mpirun -n 16 vasp_std", + "machine": { + "batch_type": "DpCloudServer", + "context_type": "DpCloudServerContext", + "local_root": "./", + "remote_profile": { + "email": "your lebesgue register email", + "password": "your lebesgue password", + "program_id": 0, + "input_data": { + "api_version": 2, + "job_type": "indicate", + "log_file": "task*/fp.log", + "grouped": true, + "job_name": "dpgen_fp_job", + "disk_size": 100, + "scass_type": "c8_m8_cpu", + "platform": "ali", + "image_name": "vasp:5.4.4", + "on_demand": 0 + } + } + }, + "resources": { + "batch_type": "DpCloudServer", + "number_node": 1, + "cpu_per_node": 32, + "gpu_per_node": 0, + "queue_name": "CPU", + "group_size": 5, + "source_list": [ + "/opt/intel/oneapi/setvars.sh" + ] } - } - }, - "resources": { - "batch_type": "DpCloudServer", - "number_node": 1, - "cpu_per_node": 32, - "gpu_per_node": 0, - "queue_name": "CPU", - "group_size": 5, - "source_list": [ - "/opt/intel/oneapi/setvars.sh" - ] } - } } diff --git a/examples/run/ch4/machine.json b/examples/run/ch4/machine.json index 9c2431024..70b8ee67a 100644 --- a/examples/run/ch4/machine.json +++ b/examples/run/ch4/machine.json @@ -1,77 +1,77 @@ { - "deepmd_path": "/sharedext4/local/deepmd-kit-0.12.4/", - "train_machine": { - "machine_type": "slurm", - "hostname": "localhost", - "port": 22, - "username": "root", - "work_path": "/sharedext4/generator/example/deep.gen/generator/ch4/", - "_comment1": "that's all" - }, - "train_resources": { - "numb_node": 1, - "numb_gpu": 1, - "task_per_node": 8, - "partition": "GPU-H", - "exclude_list": [], - "source_list": [ - "/sharedext4/local/deepmd-kit-0.12.4/bin/activate" - ], - "module_list": [], - "time_limit": "23:0:0", - "mem_limit": 32, - "_comment2": "that's all" - }, - "model_devi_command": "/sharedext4/softwares/lammps/bin/lmp_serial", - "model_devi_group_size": 1, - "_comment3": "model_devi on localhost", - "model_devi_machine": { - "machine_type": "slurm", - "hostname": "localhost", - "port": 22, - "username": "root", - "work_path": "/sharedext4/generator/example/deep.gen/generator/ch4/", - "_comment4": "that's all" - }, - "_comment5": " if use GPU, numb_nodes(nn) should always be 1 ", - "_comment6": " if numb_nodes(nn) = 1 multi-threading rather than mpi is assumed", - "model_devi_resources": { - "numb_node": 1, - "numb_gpu": 0, - "task_per_node": 1, - "source_list": [ - "/sharedext4/local/deepmd-kit-0.12.4/bin/lammps.activate" - ], - "module_list": [], - "time_limit": "19:0:0", - "mem_limit": 32, - "partition": "GPU-All", - "_comment7": "that's all" - }, - "_comment8": "fp on localhost ", - "fp_command": "/sharedext4/vasp/vasp.5.4.4/bin/vasp_std", - "fp_group_size": 1, - "fp_machine": { - "machine_type": "slurm", - "hostname": "localhost", - "port": 22, - "username": "root", - "work_path": "/sharedext4/generator/example/deep.gen/generator/ch4/", - "_comment9": "that's all" - }, - "fp_resources": { - "numb_node": 1, - "task_per_node": 1, - "numb_gpu": 0, - "exclude_list": [], - "source_list": [ - "/sharedext4/softwares/source/vasp_cpu.activate" - ], - "module_list": [], - "with_mpi": 1, - "time_limit": "1:0:0", - "partition": "GPU-All", - "_comment10": "that's all" - }, - "_comment11": " that's all " + "deepmd_path": "/sharedext4/local/deepmd-kit-0.12.4/", + "train_machine": { + "machine_type": "slurm", + "hostname": "localhost", + "port": 22, + "username": "root", + "work_path": "/sharedext4/generator/example/deep.gen/generator/ch4/", + "_comment1": "that's all" + }, + "train_resources": { + "numb_node": 1, + "numb_gpu": 1, + "task_per_node": 8, + "partition": "GPU-H", + "exclude_list": [], + "source_list": [ + "/sharedext4/local/deepmd-kit-0.12.4/bin/activate" + ], + "module_list": [], + "time_limit": "23:0:0", + "mem_limit": 32, + "_comment2": "that's all" + }, + "model_devi_command": "/sharedext4/softwares/lammps/bin/lmp_serial", + "model_devi_group_size": 1, + "_comment3": "model_devi on localhost", + "model_devi_machine": { + "machine_type": "slurm", + "hostname": "localhost", + "port": 22, + "username": "root", + "work_path": "/sharedext4/generator/example/deep.gen/generator/ch4/", + "_comment4": "that's all" + }, + "_comment5": " if use GPU, numb_nodes(nn) should always be 1 ", + "_comment6": " if numb_nodes(nn) = 1 multi-threading rather than mpi is assumed", + "model_devi_resources": { + "numb_node": 1, + "numb_gpu": 0, + "task_per_node": 1, + "source_list": [ + "/sharedext4/local/deepmd-kit-0.12.4/bin/lammps.activate" + ], + "module_list": [], + "time_limit": "19:0:0", + "mem_limit": 32, + "partition": "GPU-All", + "_comment7": "that's all" + }, + "_comment8": "fp on localhost ", + "fp_command": "/sharedext4/vasp/vasp.5.4.4/bin/vasp_std", + "fp_group_size": 1, + "fp_machine": { + "machine_type": "slurm", + "hostname": "localhost", + "port": 22, + "username": "root", + "work_path": "/sharedext4/generator/example/deep.gen/generator/ch4/", + "_comment9": "that's all" + }, + "fp_resources": { + "numb_node": 1, + "task_per_node": 1, + "numb_gpu": 0, + "exclude_list": [], + "source_list": [ + "/sharedext4/softwares/source/vasp_cpu.activate" + ], + "module_list": [], + "with_mpi": 1, + "time_limit": "1:0:0", + "partition": "GPU-All", + "_comment10": "that's all" + }, + "_comment11": " that's all " } diff --git a/examples/run/ch4/param.json b/examples/run/ch4/param.json index d015c8bd8..9983473b8 100644 --- a/examples/run/ch4/param.json +++ b/examples/run/ch4/param.json @@ -1,193 +1,193 @@ { - "type_map": [ - "H", - "C" - ], - "mass_map": [ - 1, - 12 - ], - "init_data_prefix": "/sharedext4/generator/example/deep.gen/data/", - "init_data_sys": [ - "/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd" - ], - "init_batch_size": [ - 8 - ], - "sys_configs": [ - [ - "/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000[0-4]/POSCAR" + "type_map": [ + "H", + "C" ], - [ - "/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000[5-9]/POSCAR" + "mass_map": [ + 1, + 12 ], - [ - "/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00001*/POSCAR" + "init_data_prefix": "/sharedext4/generator/example/deep.gen/data/", + "init_data_sys": [ + "/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd" ], - [ - "/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00002*/POSCAR" - ] - ], - "_comment1": "0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25", - "sys_batch_size": [ - 8, - 8, - 8, - 8 - ], - "_comment2": " 00.train ", - "numb_models": 4, - "default_training_param": { - "model": { - "descriptor": { - "seed": 0, - "type": "se_a", - "sel": [ - 16, - 4 + "init_batch_size": [ + 8 + ], + "sys_configs": [ + [ + "/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000[0-4]/POSCAR" ], - "rcut": 5, - "rcut_smth": 0.5, - "neuron": [ - 10, - 20, - 40 + [ + "/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000[5-9]/POSCAR" ], - "axis_neuron": 12, - "resnet_dt": false - }, - "fitting_net": { - "seed": 0, - "neuron": [ - 120, - 120, - 120 + [ + "/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00001*/POSCAR" ], - "resnet_dt": true - } - }, - "learning_rate": { - "type": "exp", - "decay_steps": 150, - "start_lr": 0.001, - "stop_lr": 3.505266624882874e-08 - }, - "loss": { - "start_pref_e": 0.02, - "limit_pref_e": 2, - "start_pref_f": 1000, - "limit_pref_f": 1, - "start_pref_v": 0.0, - "limit_pref_v": 0.0 - }, - "training": { - "seed": 0, - "stop_batch": 30000, - "disp_file": "lcurve.out", - "disp_freq": 1000, - "save_freq": 1000, - "save_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "training_data": { - "systems": [], - "set_prefix": "set", - "batch_size": 1 - } - } - }, - "_comment8": " 01.model_devi ", - "_comment9": "model_devi_skip: the first x of the recorded frames", - "model_devi_dt": 0.002, - "model_devi_skip": 0, - "model_devi_f_trust_lo": 0.05, - "model_devi_f_trust_hi": 0.15, - "model_devi_clean_traj": true, - "model_devi_jobs": [ - { - "sys_idx": [ - 0 - ], - "temps": [ - 100 - ], - "press": [ - 1.0 - ], - "trj_freq": 10, - "nsteps": 300, - "ensemble": "npt", - "_idx": "00" - }, - { - "sys_idx": [ - 1 - ], - "temps": [ - 100 - ], - "press": [ - 1.0 - ], - "trj_freq": 10, - "nsteps": 1000, - "ensemble": "npt", - "_idx": "01" + [ + "/sharedext4/generator/example/deep.gen/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00002*/POSCAR" + ] + ], + "_comment1": "0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25", + "sys_batch_size": [ + 8, + 8, + 8, + 8 + ], + "_comment2": " 00.train ", + "numb_models": 4, + "default_training_param": { + "model": { + "descriptor": { + "seed": 0, + "type": "se_a", + "sel": [ + 16, + 4 + ], + "rcut": 5, + "rcut_smth": 0.5, + "neuron": [ + 10, + 20, + 40 + ], + "axis_neuron": 12, + "resnet_dt": false + }, + "fitting_net": { + "seed": 0, + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true + } + }, + "learning_rate": { + "type": "exp", + "decay_steps": 150, + "start_lr": 0.001, + "stop_lr": 3.505266624882874e-08 + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0.0, + "limit_pref_v": 0.0 + }, + "training": { + "seed": 0, + "stop_batch": 30000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "training_data": { + "systems": [], + "set_prefix": "set", + "batch_size": 1 + } + } }, - { - "sys_idx": [ - 2 - ], - "temps": [ - 100 - ], - "press": [ - 1.0 - ], - "trj_freq": 10, - "nsteps": 3000, - "ensemble": "npt", - "_idx": "02" + "_comment8": " 01.model_devi ", + "_comment9": "model_devi_skip: the first x of the recorded frames", + "model_devi_dt": 0.002, + "model_devi_skip": 0, + "model_devi_f_trust_lo": 0.05, + "model_devi_f_trust_hi": 0.15, + "model_devi_clean_traj": true, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 100 + ], + "press": [ + 1.0 + ], + "trj_freq": 10, + "nsteps": 300, + "ensemble": "npt", + "_idx": "00" + }, + { + "sys_idx": [ + 1 + ], + "temps": [ + 100 + ], + "press": [ + 1.0 + ], + "trj_freq": 10, + "nsteps": 1000, + "ensemble": "npt", + "_idx": "01" + }, + { + "sys_idx": [ + 2 + ], + "temps": [ + 100 + ], + "press": [ + 1.0 + ], + "trj_freq": 10, + "nsteps": 3000, + "ensemble": "npt", + "_idx": "02" + }, + { + "sys_idx": [ + 3 + ], + "temps": [ + 100 + ], + "press": [ + 1.0 + ], + "trj_freq": 10, + "nsteps": 3000, + "ensemble": "npt", + "_idx": "03" + } + ], + "_comment10": " 02.fp ", + "fp_style": "vasp", + "shuffle_poscar": false, + "fp_task_max": 30, + "fp_task_min": 5, + "fp_pp_path": "/sharedext4/generator/example/deep.gen/data/ch4/", + "fp_pp_files": [ + "POTCAR" + ], + "fp_params": { + "_comment11": "given in unit depending on the fp method", + "ecut": 400, + "ediff": 1e-06, + "kspacing": 2, + "_comment12": "gauss, mp:N(methfessel-paxton:order by default order=1), fd(Fermi-Dirac)", + "smearing": "gauss", + "sigma": 0.05, + "_comment13": "only for vasp, can be NONE, SCAN, TPSS, RTPSS, M06L or MBJ", + "metagga": "NONE", + "npar": 4, + "kpar": 1, + "_comment14": " that's all " }, - { - "sys_idx": [ - 3 - ], - "temps": [ - 100 - ], - "press": [ - 1.0 - ], - "trj_freq": 10, - "nsteps": 3000, - "ensemble": "npt", - "_idx": "03" - } - ], - "_comment10": " 02.fp ", - "fp_style": "vasp", - "shuffle_poscar": false, - "fp_task_max": 30, - "fp_task_min": 5, - "fp_pp_path": "/sharedext4/generator/example/deep.gen/data/ch4/", - "fp_pp_files": [ - "POTCAR" - ], - "fp_params": { - "_comment11": "given in unit depending on the fp method", - "ecut": 400, - "ediff": 1e-06, - "kspacing": 2, - "_comment12": "gauss, mp:N(methfessel-paxton:order by default order=1), fd(Fermi-Dirac)", - "smearing": "gauss", - "sigma": 0.05, - "_comment13": "only for vasp, can be NONE, SCAN, TPSS, RTPSS, M06L or MBJ", - "metagga": "NONE", - "npar": 4, - "kpar": 1, - "_comment14": " that's all " - }, - "_comment15": " that's all " + "_comment15": " that's all " } diff --git a/examples/run/deprecated/dp2.x-gromacs-gaussian/param.json b/examples/run/deprecated/dp2.x-gromacs-gaussian/param.json index 639039a5a..99842df95 100644 --- a/examples/run/deprecated/dp2.x-gromacs-gaussian/param.json +++ b/examples/run/deprecated/dp2.x-gromacs-gaussian/param.json @@ -1,209 +1,209 @@ { - "type_map": [ - "H", - "C", - "N", - "O", - "Cl" - ], - "mass_map": [ - 2, - 12, - 14, - 16, - 35 - ], - "init_data_prefix": "somplace/tyk2-dpgen", - "init_data_sys": [ - "init_data", - "mdtraj_data" - ], - "sys_configs_prefix": "somplace/tyk2-dpgen", - "sys_configs": [ - [ - "model_devi/lig_ejm_31" - ], - [ - "model_devi/lig_ejm_42" - ], - [ - "model_devi/lig_ejm_43" - ], - [ - "model_devi/lig_ejm_44" - ], - [ - "model_devi/lig_ejm_45" - ], - [ - "model_devi/lig_ejm_46" - ], - [ - "model_devi/lig_ejm_47" - ], - [ - "model_devi/lig_ejm_48" - ], - [ - "model_devi/lig_ejm_49" - ], - [ - "model_devi/lig_ejm_50" - ], - [ - "model_devi/lig_ejm_54" - ], - [ - "model_devi/lig_ejm_55" - ], - [ - "model_devi/lig_jmc_27" - ], - [ - "model_devi/lig_jmc_28" - ], - [ - "model_devi/lig_jmc_30" - ] - ], - "sys_format": "gromacs/gro", - "numb_models": 4, - "training_reuse_iter": 1, - "training_reuse_old_ratio": 0.3, - "training_reuse_start_lr": 0.0001, - "training_reuse_decay_steps": 500, - "training_reuse_stop_batch": 200000, - "training_reuse_start_pref_e": 1, - "training_reuse_start_pref_f": 100, - "train_param": "input.json", - "default_training_param": { - "model": { - "type_map": [ + "type_map": [ "H", "C", "N", "O", "Cl" - ], - "descriptor": { - "type": "se_a", - "sel": [ - 40, - 48, - 48, - 48, - 48 + ], + "mass_map": [ + 2, + 12, + 14, + 16, + 35 + ], + "init_data_prefix": "somplace/tyk2-dpgen", + "init_data_sys": [ + "init_data", + "mdtraj_data" + ], + "sys_configs_prefix": "somplace/tyk2-dpgen", + "sys_configs": [ + [ + "model_devi/lig_ejm_31" ], - "rcut_smth": 0.5, - "rcut": 6.0, - "neuron": [ - 25, - 50, - 100 + [ + "model_devi/lig_ejm_42" ], - "resnet_dt": false, - "axis_neuron": 16, - "type_one_side": true - }, - "fitting_net": { - "neuron": [ - 60, - 60, - 60 + [ + "model_devi/lig_ejm_43" ], - "resnet_dt": true - } - }, - "learning_rate": { - "type": "exp", - "start_lr": 0.001, - "decay_steps": 2000, - "stop_lr": 7.274491561439049e-15 + [ + "model_devi/lig_ejm_44" + ], + [ + "model_devi/lig_ejm_45" + ], + [ + "model_devi/lig_ejm_46" + ], + [ + "model_devi/lig_ejm_47" + ], + [ + "model_devi/lig_ejm_48" + ], + [ + "model_devi/lig_ejm_49" + ], + [ + "model_devi/lig_ejm_50" + ], + [ + "model_devi/lig_ejm_54" + ], + [ + "model_devi/lig_ejm_55" + ], + [ + "model_devi/lig_jmc_27" + ], + [ + "model_devi/lig_jmc_28" + ], + [ + "model_devi/lig_jmc_30" + ] + ], + "sys_format": "gromacs/gro", + "numb_models": 4, + "training_reuse_iter": 1, + "training_reuse_old_ratio": 0.3, + "training_reuse_start_lr": 0.0001, + "training_reuse_decay_steps": 500, + "training_reuse_stop_batch": 200000, + "training_reuse_start_pref_e": 1, + "training_reuse_start_pref_f": 100, + "train_param": "input.json", + "default_training_param": { + "model": { + "type_map": [ + "H", + "C", + "N", + "O", + "Cl" + ], + "descriptor": { + "type": "se_a", + "sel": [ + 40, + 48, + 48, + 48, + 48 + ], + "rcut_smth": 0.5, + "rcut": 6.0, + "neuron": [ + 25, + 50, + 100 + ], + "resnet_dt": false, + "axis_neuron": 16, + "type_one_side": true + }, + "fitting_net": { + "neuron": [ + 60, + 60, + 60 + ], + "resnet_dt": true + } + }, + "learning_rate": { + "type": "exp", + "start_lr": 0.001, + "decay_steps": 2000, + "stop_lr": 7.274491561439049e-15 + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 8, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0, + "limit_pref_v": 0, + "start_pref_pf": 0, + "limit_pref_pf": 0 + }, + "training": { + "stop_batch": 1000000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "training_data": { + "set_prefix": "set" + } + } }, - "loss": { - "start_pref_e": 0.02, - "limit_pref_e": 8, - "start_pref_f": 1000, - "limit_pref_f": 1, - "start_pref_v": 0, - "limit_pref_v": 0, - "start_pref_pf": 0, - "limit_pref_pf": 0 + "model_devi_engine": "gromacs", + "gromacs_settings": { + "mdp_filename": "md.mdp", + "topol_filename": "processed.top", + "conf_filename": "npt.gro", + "index_filename": "index.raw", + "ref_filename": "em.tpr", + "model_devi_script": "model_devi.py", + "traj_filename": "deepmd_traj.gro" }, - "training": { - "stop_batch": 1000000, - "disp_file": "lcurve.out", - "disp_freq": 1000, - "save_freq": 1000, - "save_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json", - "training_data": { - "set_prefix": "set" - } - } - }, - "model_devi_engine": "gromacs", - "gromacs_settings": { - "mdp_filename": "md.mdp", - "topol_filename": "processed.top", - "conf_filename": "npt.gro", - "index_filename": "index.raw", - "ref_filename": "em.tpr", - "model_devi_script": "model_devi.py", - "traj_filename": "deepmd_traj.gro" - }, - "model_devi_dt": 0.001, - "model_devi_f_trust_lo": 0.2, - "model_devi_f_trust_hi": 0.4, - "model_devi_clean_traj": false, - "model_devi_skip": 0, - "model_devi_nopbc": true, - "model_devi_activation_func": [ - "tanh", - "tanh", - "gelu", - "gelu" - ], - "model_devi_jobs": [ - { - "_idx": 0, - "ensemble": "nvt", - "nsteps": 5000, - "press": [], - "sys_idx": [ - 0, - 1, - 2, - 3, - 4, - 5, - 6, - 7, - 8, - 9, - 10, - 11, - 12, - 13, - 14 - ], - "temps": [], - "trj_freq": 10, - "_comment1": "trj_freq should be consistent with nstxout in mdp" + "model_devi_dt": 0.001, + "model_devi_f_trust_lo": 0.2, + "model_devi_f_trust_hi": 0.4, + "model_devi_clean_traj": false, + "model_devi_skip": 0, + "model_devi_nopbc": true, + "model_devi_activation_func": [ + "tanh", + "tanh", + "gelu", + "gelu" + ], + "model_devi_jobs": [ + { + "_idx": 0, + "ensemble": "nvt", + "nsteps": 5000, + "press": [], + "sys_idx": [ + 0, + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11, + 12, + 13, + 14 + ], + "temps": [], + "trj_freq": 10, + "_comment1": "trj_freq should be consistent with nstxout in mdp" + } + ], + "fp_style": "gaussian", + "shuffle_poscar": false, + "fp_task_max": 20, + "fp_task_min": 1, + "fp_pp_path": "./", + "fp_pp_files": [], + "fp_params": { + "keywords": "force m062x/6-31g(d) nosymm", + "nproc": 16, + "multiplicity": "auto" } - ], - "fp_style": "gaussian", - "shuffle_poscar": false, - "fp_task_max": 20, - "fp_task_min": 1, - "fp_pp_path": "./", - "fp_pp_files": [], - "fp_params": { - "keywords": "force m062x/6-31g(d) nosymm", - "nproc": 16, - "multiplicity": "auto" - } } diff --git a/examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.json b/examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.json index 061914c8c..bc07d204a 100644 --- a/examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.json +++ b/examples/run/deprecated/dp2.x-lammps-cp2k/CH4/param_CH4.json @@ -1,156 +1,156 @@ { - "type_map": [ - "H", - "C" - ], - "mass_map": [ - 1, - 12 - ], - "init_data_prefix": "/public/data/deepmd-tutorial/data/", - "init_data_sys": [ - "deepmd" - ], - "init_batch_size": [ - 8 - ], - "sys_configs": [ - [ - "/public/data/deepmd-tutorial/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00000*/POSCAR" + "type_map": [ + "H", + "C" ], - [ - "/public/data/deepmd-tutorial/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00001*/POSCAR" - ] - ], - "sys_batch_size": [ - 8, - 8, - 8, - 8 - ], - "_comment1": " that's all ", - "numb_models": 4, - "default_training_param": { - "model": { - "descriptor": { - "seed": 0, - "type": "se_a", - "sel": [ - 16, - 4 + "mass_map": [ + 1, + 12 + ], + "init_data_prefix": "/public/data/deepmd-tutorial/data/", + "init_data_sys": [ + "deepmd" + ], + "init_batch_size": [ + 8 + ], + "sys_configs": [ + [ + "/public/data/deepmd-tutorial/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00000*/POSCAR" ], - "rcut": 5, - "rcut_smth": 0.5, - "neuron": [ - 10, - 20, - 40 + [ + "/public/data/deepmd-tutorial/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00001*/POSCAR" + ] + ], + "sys_batch_size": [ + 8, + 8, + 8, + 8 + ], + "_comment1": " that's all ", + "numb_models": 4, + "default_training_param": { + "model": { + "descriptor": { + "seed": 0, + "type": "se_a", + "sel": [ + 16, + 4 + ], + "rcut": 5, + "rcut_smth": 0.5, + "neuron": [ + 10, + 20, + 40 + ], + "axis_neuron": 12, + "resnet_dt": false + }, + "fitting_net": { + "seed": 0, + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true + } + }, + "learning_rate": { + "type": "exp", + "decay_steps": 200, + "start_lr": 0.001, + "stop_lr": 3.505266624882874e-08 + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0, + "limit_pref_v": 0 + }, + "training": { + "seed": 0, + "stop_batch": 40000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "training_data": { + "systems": [], + "set_prefix": "set", + "batch_size": 1 + } + } + }, + "model_devi_dt": 0.002, + "model_devi_skip": 0, + "model_devi_f_trust_lo": 0.05, + "model_devi_f_trust_hi": 0.15, + "model_devi_clean_traj": true, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 100 + ], + "press": [ + 1 + ], + "trj_freq": 10, + "nsteps": 1000, + "ensemble": "nvt", + "_idx": "00" + }, + { + "sys_idx": [ + 1 + ], + "temps": [ + 100 + ], + "press": [ + 1 + ], + "trj_freq": 10, + "nsteps": 5000, + "ensemble": "nvt", + "_idx": "01" + } + ], + "fp_style": "cp2k", + "shuffle_poscar": false, + "fp_task_max": 20, + "fp_task_min": 5, + "fp_params": { + "cutoff": "400", + "rel_cutoff": "50", + "functional": "PBE", + "pair_potential_path": "dftd3.dat", + "pair_ref_functional": "PBE", + "basis_path": "BASIS_MOLOPT", + "pp_path": "GTH_POTENTIALS", + "element_list": [ + "H", + "C" ], - "axis_neuron": 12, - "resnet_dt": false - }, - "fitting_net": { - "seed": 0, - "neuron": [ - 120, - 120, - 120 + "basis_list": [ + "DZVP-MOLOPT-GTH", + "DZVP-MOLOPT-GTH" ], - "resnet_dt": true - } - }, - "learning_rate": { - "type": "exp", - "decay_steps": 200, - "start_lr": 0.001, - "stop_lr": 3.505266624882874e-08 - }, - "loss": { - "start_pref_e": 0.02, - "limit_pref_e": 2, - "start_pref_f": 1000, - "limit_pref_f": 1, - "start_pref_v": 0, - "limit_pref_v": 0 - }, - "training": { - "seed": 0, - "stop_batch": 40000, - "disp_file": "lcurve.out", - "disp_freq": 1000, - "save_freq": 1000, - "save_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "training_data": { - "systems": [], - "set_prefix": "set", - "batch_size": 1 - } + "_comment3": "elment_list, basis_list, pp_list should be one to one correspondance", + "pp_list": [ + "GTH-PBE-q1", + "GTH-PBE-q4" + ] } - }, - "model_devi_dt": 0.002, - "model_devi_skip": 0, - "model_devi_f_trust_lo": 0.05, - "model_devi_f_trust_hi": 0.15, - "model_devi_clean_traj": true, - "model_devi_jobs": [ - { - "sys_idx": [ - 0 - ], - "temps": [ - 100 - ], - "press": [ - 1 - ], - "trj_freq": 10, - "nsteps": 1000, - "ensemble": "nvt", - "_idx": "00" - }, - { - "sys_idx": [ - 1 - ], - "temps": [ - 100 - ], - "press": [ - 1 - ], - "trj_freq": 10, - "nsteps": 5000, - "ensemble": "nvt", - "_idx": "01" - } - ], - "fp_style": "cp2k", - "shuffle_poscar": false, - "fp_task_max": 20, - "fp_task_min": 5, - "fp_params": { - "cutoff": "400", - "rel_cutoff": "50", - "functional": "PBE", - "pair_potential_path": "dftd3.dat", - "pair_ref_functional": "PBE", - "basis_path": "BASIS_MOLOPT", - "pp_path": "GTH_POTENTIALS", - "element_list": [ - "H", - "C" - ], - "basis_list": [ - "DZVP-MOLOPT-GTH", - "DZVP-MOLOPT-GTH" - ], - "_comment3": "elment_list, basis_list, pp_list should be one to one correspondance", - "pp_list": [ - "GTH-PBE-q1", - "GTH-PBE-q4" - ] - } } diff --git a/examples/run/deprecated/dp2.x-lammps-pwmat/machine-slurm-pwmat-single.json b/examples/run/deprecated/dp2.x-lammps-pwmat/machine-slurm-pwmat-single.json index c63ac9613..be8a6b027 100644 --- a/examples/run/deprecated/dp2.x-lammps-pwmat/machine-slurm-pwmat-single.json +++ b/examples/run/deprecated/dp2.x-lammps-pwmat/machine-slurm-pwmat-single.json @@ -1,80 +1,80 @@ { - "train": [ - { - "machine": { - "machine_type": "slurm", - "hostname": "mstation", - "port": 22, - "username": "test", - "password": "PWmat2019", - "work_path": "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/work_train" - }, - "resources": { - "numb_node": 1, - "numb_gpu": 4, - "task_per_node": 4, - "partition": "control", - "exclude_list": [], - "source_list": [ - "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/train.env" - ], - "module_list": [], - "time_limit": "23:0:0" - }, - "deepmd_path": "/home/test/anaconda2/envs/python3/" - } - ], - "model_devi": [ - { - "machine": { - "machine_type": "slurm", - "hostname": "mstation", - "port": 22, - "username": "test", - "password": "PWmat2019", - "work_path": "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/work_model" - }, - "resources": { - "numb_node": 1, - "numb_gpu": 4, - "task_per_node": 4, - "partition": "control", - "exclude_list": [], - "source_list": [ - "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/train.env" - ], - "module_list": [], - "time_limit": "23:0:0" - }, - "command": "srun --mpi=pmi2 lmp_mpi", - "group_size": 10 - } - ], - "fp": [ - { - "machine": { - "machine_type": "slurm", - "hostname": "mstation", - "port": 22, - "username": "test", - "password": "PWmat2019", - "work_path": "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/work_fp" - }, - "resources": { - "task_per_node": 4, - "numb_gpu": 4, - "exclude_list": [], - "with_mpi": false, - "source_list": [], - "module_list": [ - "cuda/8.0" - ], - "time_limit": "120:0:0", - "partition": "control", - "_comment1": "that's All" - }, - "command": "mpirun -np 4 PWmat", - "group_size": 5 - } - ] + "train": [ + { + "machine": { + "machine_type": "slurm", + "hostname": "mstation", + "port": 22, + "username": "test", + "password": "PWmat2019", + "work_path": "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/work_train" + }, + "resources": { + "numb_node": 1, + "numb_gpu": 4, + "task_per_node": 4, + "partition": "control", + "exclude_list": [], + "source_list": [ + "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/train.env" + ], + "module_list": [], + "time_limit": "23:0:0" + }, + "deepmd_path": "/home/test/anaconda2/envs/python3/" + } + ], + "model_devi": [ + { + "machine": { + "machine_type": "slurm", + "hostname": "mstation", + "port": 22, + "username": "test", + "password": "PWmat2019", + "work_path": "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/work_model" + }, + "resources": { + "numb_node": 1, + "numb_gpu": 4, + "task_per_node": 4, + "partition": "control", + "exclude_list": [], + "source_list": [ + "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/train.env" + ], + "module_list": [], + "time_limit": "23:0:0" + }, + "command": "srun --mpi=pmi2 lmp_mpi", + "group_size": 10 + } + ], + "fp": [ + { + "machine": { + "machine_type": "slurm", + "hostname": "mstation", + "port": 22, + "username": "test", + "password": "PWmat2019", + "work_path": "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/work_fp" + }, + "resources": { + "task_per_node": 4, + "numb_gpu": 4, + "exclude_list": [], + "with_mpi": false, + "source_list": [], + "module_list": [ + "cuda/8.0" + ], + "time_limit": "120:0:0", + "partition": "control", + "_comment1": "that's All" + }, + "command": "mpirun -np 4 PWmat", + "group_size": 5 + } + ] } diff --git a/examples/run/deprecated/dp2.x-lammps-pwmat/param_CH4.json b/examples/run/deprecated/dp2.x-lammps-pwmat/param_CH4.json index 42e791d2c..3c2ebfdef 100644 --- a/examples/run/deprecated/dp2.x-lammps-pwmat/param_CH4.json +++ b/examples/run/deprecated/dp2.x-lammps-pwmat/param_CH4.json @@ -1,147 +1,147 @@ { - "type_map": [ - "H", - "C" - ], - "mass_map": [ - 1, - 12 - ], - "init_data_prefix": "/home/test/software/dpgen/examples/run/dp-lammps-pwmat/", - "init_data_sys": 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1, + "source_list": [ + "~/abacus.env" + ] + } } - }, - "resources": { - "number_node": 1, - "cpu_per_node": 32, - "gpu_per_node": 0, - "queue_name": "G_32_128", - "group_size": 1, - "source_list": [ - "~/abacus.env" - ] - } - } - ] + ] } diff --git a/examples/run/dp2.x-lammps-ABACUS-pw/methane/param.json b/examples/run/dp2.x-lammps-ABACUS-pw/methane/param.json index 5594cb6cf..d0ebc40a0 100644 --- a/examples/run/dp2.x-lammps-ABACUS-pw/methane/param.json +++ b/examples/run/dp2.x-lammps-ABACUS-pw/methane/param.json @@ -1,162 +1,162 @@ { - "type_map": [ - "H", - "C" - ], - "mass_map": [ - 1.0, - 12.0 - ], - "_comment1": "initial data set for Training and the number of frames in each training batch", - "init_data_prefix": "/home/mhchen_pkuhpc/mhchen_cls/lustre2/5_liurenxi/5_ABACUS_dpgen_interface/5_dpgen_examples/dpgen-example/run_abacus/", - "init_data_sys": [ - "abacus_init_data" - ], - "init_batch_size": [ - 8 - ], - "_comment2": "configurations for starting MD in Exploration and batch 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b/examples/run/dp2.x-lammps-cp2k/methane/param-ch4.json index d6cbd3e67..9f998fb46 100644 --- a/examples/run/dp2.x-lammps-cp2k/methane/param-ch4.json +++ b/examples/run/dp2.x-lammps-cp2k/methane/param-ch4.json @@ -1,138 +1,138 @@ { - "type_map": [ - "H", - "C" - ], - "mass_map": [ - 1, - 12 - ], - "init_data_prefix": "/data/ybzhuang/methane-dpgen/dpgen-tutorial-2020-08-23/dpgen-tutorial-mathane/data", - "init_data_sys": [ - "deepmd" - ], - "init_batch_size": [ - 8 - ], - "sys_configs": [ - [ - "/data/ybzhuang/methane-dpgen/dpgen-tutorial-2020-08-23/dpgen-tutorial-mathane/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00000*/POSCAR" + "type_map": [ + "H", + "C" ], - [ - "/data/ybzhuang/methane-dpgen/dpgen-tutorial-2020-08-23/dpgen-tutorial-mathane/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00000*/POSCAR" - ] - ], - "sys_batch_size": [ - 8, - 8, - 8, - 8 - ], - "_comment1": " that's all ", - "numb_models": 4, - "default_training_param": { - "model": { - "descriptor": { - "type": "se_a", - "sel": [ - 16, - 4 - ], - "rcut_smth": 0.5, - "rcut": 5.0, - "_comment2": "modify according your system", - "neuron": [ - 10, - 20, - 40 - ], - "resnet_dt": false, - "axis_neuron": 12, - "seed": 1 - }, - "fitting_net": { - "neuron": [ - 120, - 120, - 120 + "mass_map": [ + 1, + 12 + ], + "init_data_prefix": "/data/ybzhuang/methane-dpgen/dpgen-tutorial-2020-08-23/dpgen-tutorial-mathane/data", + "init_data_sys": [ + "deepmd" + ], + "init_batch_size": [ + 8 + ], + "sys_configs": [ + [ + "/data/ybzhuang/methane-dpgen/dpgen-tutorial-2020-08-23/dpgen-tutorial-mathane/data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00000*/POSCAR" ], - "resnet_dt": true, - "seed": 1 - } - }, - "learning_rate": { - "type": "exp", - "start_lr": 0.001, - "decay_steps": 100, - "_comment3": "nope", - "stop_lr": 0.0003584859224085419 - }, - "loss": { - "start_pref_e": 0.02, - "limit_pref_e": 2, - "start_pref_f": 1000, - "limit_pref_f": 1, - 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"/data/ybzhuang/methane-dpgen/dpgen-tutorial-2020-08-23/dpgen-tutorial-mathane/cp2k_dpgen/template.inp" } diff --git a/examples/run/dp2.x-lammps-cp2k/param_CH4_deepmd-kit-2.0.1.json b/examples/run/dp2.x-lammps-cp2k/param_CH4_deepmd-kit-2.0.1.json index fd95ebf15..7c7f5acbb 100644 --- a/examples/run/dp2.x-lammps-cp2k/param_CH4_deepmd-kit-2.0.1.json +++ b/examples/run/dp2.x-lammps-cp2k/param_CH4_deepmd-kit-2.0.1.json @@ -1,151 +1,151 @@ { - "type_map": [ - "H", - "C" - ], - "mass_map": [ - 1, - 12 - ], - "init_data_prefix": "./data", - "init_data_sys": [ - "deepmd" - ], - "sys_configs": [ - [ - "./data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00000*/POSCAR" - ], - [ - "./data/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale-1.000/00001*/POSCAR" - ] - ], - "_comment1": " that's all ", - "numb_models": 4, - "default_training_param": { - "model": { - "type_map": [ + "type_map": [ "H", "C" - ], - "descriptor": { - "type": "se_a", - "sel": [ - 16, - 4 - ], - 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b/examples/run/dp2.x-lammps-gaussian/machine.json index fd1159f33..450baa944 100644 --- a/examples/run/dp2.x-lammps-gaussian/machine.json +++ b/examples/run/dp2.x-lammps-gaussian/machine.json @@ -1,111 +1,111 @@ { - "api_version": "1.0", - "deepmd_version": "2.1.0", - "train": { - "command": "dp", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root": "./", - "remote_profile": { - "email": "xxx", - "password": "xxx", - "program_id": 123, - "keep_backup": true, - "input_data": { - "job_type": "indicate", - "log_file": "00*/train.log", - "grouped": true, - "job_name": "dpgen_train_job", - "disk_size": 100, - "scass_type": "c4_m15_1 * NVIDIA T4", - "checkpoint_files": [ - "00*/checkpoint", - "00*/model.ckpt*" - ], - "checkpoint_time": 30, - "platform": "ali", - "image_name": "LBG_DeePMD-kit_2.1.0_v1", - "on_demand": 0 + "api_version": "1.0", + "deepmd_version": "2.1.0", + "train": { + "command": "dp", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "xxx", + "password": "xxx", + "program_id": 123, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "00*/train.log", + "grouped": true, + "job_name": "dpgen_train_job", + "disk_size": 100, + "scass_type": "c4_m15_1 * NVIDIA T4", + "checkpoint_files": [ + "00*/checkpoint", + "00*/model.ckpt*" + ], + "checkpoint_time": 30, + "platform": "ali", + "image_name": "LBG_DeePMD-kit_2.1.0_v1", + "on_demand": 0 + } + } + }, + "resources": { + "batch_type": "Lebesgue", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "T4_4_15", + "group_size": 1 } - } }, - "resources": { - "batch_type": "Lebesgue", - "number_node": 1, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "T4_4_15", - "group_size": 1 - } - }, - "model_devi": { - "command": "lmp", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root": "./", - "remote_profile": { - "email": "xxx", - "password": "xxx", - "program_id": 123, - "keep_backup": true, - "input_data": { - "job_type": "indicate", - "log_file": "*/model_devi.log", - "grouped": true, - "job_name": "dpgen_model_devi_job", - "disk_size": 200, - "scass_type": "c4_m15_1 * NVIDIA T4", - "platform": "ali", - "image_name": "LBG_DeePMD-kit_2.1.0_v1", - "on_demand": 0 + "model_devi": { + "command": "lmp", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "xxx", + "password": "xxx", + "program_id": 123, + "keep_backup": true, + "input_data": { + "job_type": "indicate", + "log_file": "*/model_devi.log", + "grouped": true, + "job_name": "dpgen_model_devi_job", + "disk_size": 200, + "scass_type": "c4_m15_1 * NVIDIA T4", + "platform": "ali", + "image_name": "LBG_DeePMD-kit_2.1.0_v1", + "on_demand": 0 + } + } + }, + "resources": { + "batch_type": "Lebesgue", + "number_node": 1, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "T4_4_15", + "group_size": 50 } - } }, - "resources": { - "batch_type": "Lebesgue", - "number_node": 1, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "T4_4_15", - "group_size": 50 - } - }, - "fp": { - "command": "g09 < input > output ||:", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root": "./", - "remote_profile": { - "email": "xxx", - "password": "xxx", - "program_id": 123, - "input_data": { - "api_version": 2, - "job_type": "indicate", - "log_file": "task*/fp.log", - "grouped": true, - "job_name": "dpgen_fp_job", - "disk_size": 100, - "scass_type": "c16_m32_cpu", - "platform": "ali", - "image_name": "LBG_Gaussian_09_v2", - "on_demand": 0 + "fp": { + "command": "g09 < input > output ||:", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "xxx", + "password": "xxx", + "program_id": 123, + "input_data": { + "api_version": 2, + "job_type": "indicate", + "log_file": "task*/fp.log", + "grouped": true, + "job_name": "dpgen_fp_job", + "disk_size": 100, + "scass_type": "c16_m32_cpu", + "platform": "ali", + "image_name": "LBG_Gaussian_09_v2", + "on_demand": 0 + } + } + }, + "resources": { + "batch_type": "Lebesgue", + "source_list": [ + "/root/g09.sh" + ], + "number_node": 1, + "cpu_per_node": 16, + "gpu_per_node": 0, + "queue_name": "CPU", + "group_size": 10 } - } - }, - "resources": { - "batch_type": "Lebesgue", - "source_list": [ - "/root/g09.sh" - ], - "number_node": 1, - "cpu_per_node": 16, - "gpu_per_node": 0, - "queue_name": "CPU", - "group_size": 10 } - } } diff --git a/examples/run/dp2.x-lammps-gaussian/param_C4H16N4_deepmd-kit-2.0.1.json b/examples/run/dp2.x-lammps-gaussian/param_C4H16N4_deepmd-kit-2.0.1.json index 82522d36c..5dac25455 100644 --- a/examples/run/dp2.x-lammps-gaussian/param_C4H16N4_deepmd-kit-2.0.1.json +++ b/examples/run/dp2.x-lammps-gaussian/param_C4H16N4_deepmd-kit-2.0.1.json @@ -1,150 +1,150 @@ { - "type_map": [ - "H", - "C", - "N" - ], - "mass_map": [ - 1, - 12, - 14 - ], - "init_data_prefix": "./data/deepmd/", - "init_data_sys": [ - "data.000", - "data.001", - "data.002", - "data.003", - "data.004", - "data.005" - ], - "init_batch_size": [ - "auto", - "auto", - "auto", - "auto", - "auto", - "auto" - ], - "sys_configs": [ - [ - "./data/md_sys/data.ch4n2" - ] - ], - "_comment1": " that's all ", - "numb_models": 4, - "sys_format": "lammps/lmp", - "default_training_param": { - "model": { - "type_map": [ + "type_map": [ "H", "C", "N" - ], - "descriptor": { - "type": "se_e2_a", - "sel": [ - 16, - 4, - 4 - ], - "rcut_smth": 0.5, - "rcut": 5.0, - "neuron": [ - 25, - 50, - 100 - ], - "resnet_dt": true, - "axis_neuron": 12, - "seed": 1 - }, - "fitting_net": { - "neuron": [ - 120, - 120, - 120 - ], - "resnet_dt": false, - "seed": 1 - } + ], + "mass_map": [ + 1, + 12, + 14 + ], + 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- ], - "temps": [ - 100 - ], - "press": [ - 1 - ], - "trj_freq": 10, - "nsteps": 2000, - "ensemble": "nvt", - "_idx": "00" - }, - { - "sys_idx": [ - 0 - ], - "temps": [ - 100 - ], - "press": [ - 1 - ], - "trj_freq": 10, - "nsteps": 5000, - "ensemble": "nvt", - "_idx": "01" + "model_devi_dt": 0.002, + "model_devi_skip": 0, + "model_devi_f_trust_lo": 0.02, + "model_devi_f_trust_hi": 1.95, + "model_devi_clean_traj": true, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 100 + ], + "press": [ + 1 + ], + "trj_freq": 10, + "nsteps": 2000, + "ensemble": "nvt", + "_idx": "00" + }, + { + "sys_idx": [ + 0 + ], + "temps": [ + 100 + ], + "press": [ + 1 + ], + "trj_freq": 10, + "nsteps": 5000, + "ensemble": "nvt", + "_idx": "01" + } + ], + "use_clusters": true, + "cluster_cutoff": 5.0, + "cluster_minify": true, + "use_relative": true, + "epsilon": 1.0, + "ratio_failed": 0.2, + "fp_style": "gaussian", + "shuffle_poscar": false, + "fp_task_max": 20, + "fp_task_min": 5, + "fp_params": { + "keywords": "force B3LYP 6-31g(d,p) nosymm", + "nproc": 2, + "multiplicity": "auto" } - ], - "use_clusters": true, - "cluster_cutoff": 5.0, - "cluster_minify": true, - "use_relative": true, - "epsilon": 1.0, - "ratio_failed": 0.2, - "fp_style": "gaussian", - "shuffle_poscar": false, - "fp_task_max": 20, - "fp_task_min": 5, - "fp_params": { - "keywords": "force B3LYP 6-31g(d,p) nosymm", - "nproc": 2, - "multiplicity": "auto" - } } diff --git a/examples/run/dp2.x-lammps-vasp-et/param_elet.json b/examples/run/dp2.x-lammps-vasp-et/param_elet.json index c10faa58d..92c34262a 100644 --- a/examples/run/dp2.x-lammps-vasp-et/param_elet.json +++ b/examples/run/dp2.x-lammps-vasp-et/param_elet.json @@ -1,131 +1,131 @@ { - "type_map": [ - "Al", - "Mg" - ], - "mass_map": [ - 27, - 24 - ], - "use_ele_temp": 2, - "init_data_prefix": "/home/wanghan/study/deep.md/data/almgop.20/init//", - "init_data_sys": [ - "al.fcc.01x01x01/02.md/sys-0004/deepmd", - "mg.fcc.01x01x01/02.md/sys-0004/deepmd" - ], - "sys_configs": [ - [ - "/home/wanghan/study/deep.md/data/almgop.20/init/al.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00000[0-4]/POSCAR" + "type_map": [ + "Al", + "Mg" ], - [ - "/home/wanghan/study/deep.md/data/almgop.20/init/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00000[0-4]/POSCAR" - ] - ], - "_comment1": " 00.train ", - "numb_models": 4, - "default_training_param": { - "_comment2": " model parameters", - "model": { - "descriptor": { - "type": "se_a", - "sel": [ - 90, - 90 - ], - "rcut_smth": 1.8, - "rcut": 6.0, - "neuron": [ - 10, - 20, - 40 - ], - "resnet_dt": false, - "axis_neuron": 4, - "seed": 1 - }, - "fitting_net": { - "neuron": [ - 120, - 120, - 120 + "mass_map": [ + 27, + 24 + ], + "use_ele_temp": 2, + "init_data_prefix": "/home/wanghan/study/deep.md/data/almgop.20/init//", + "init_data_sys": [ + "al.fcc.01x01x01/02.md/sys-0004/deepmd", + "mg.fcc.01x01x01/02.md/sys-0004/deepmd" + ], + "sys_configs": [ + [ + "/home/wanghan/study/deep.md/data/almgop.20/init/al.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00000[0-4]/POSCAR" ], - "resnet_dt": true, - "numb_fparam": 10, - "seed": 1 - } - }, - "loss": { - "start_pref_e": 0.02, - "limit_pref_e": 1, - "start_pref_f": 1000, - "limit_pref_f": 1, - "start_pref_v": 0, - "limit_pref_v": 0 - }, - "learning_rate": { - "start_lr": 0.001, - "decay_steps": 5000, - "stop_lr": 0.0009897937816869885 - }, - "_comment3": " traing controls", - "training": { - "stop_batch": 1000, - "seed": 1, - "_comment4": " display and restart", - "_comment5": " frequencies counted in batch", - "disp_file": "lcurve.out", - "disp_freq": 1000, - "save_freq": 1000, - "save_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json", - "training_data": { - "systems": [], - "set_prefix": "set", - "batch_size": 1 - } + [ + "/home/wanghan/study/deep.md/data/almgop.20/init/mg.fcc.02x02x02/01.scale_pert/sys-0032/scale-1.000/00000[0-4]/POSCAR" + ] + ], + "_comment1": " 00.train ", + "numb_models": 4, + "default_training_param": { + "_comment2": " model parameters", + "model": { + "descriptor": { + "type": "se_a", + "sel": [ + 90, + 90 + ], + "rcut_smth": 1.8, + "rcut": 6.0, + "neuron": [ + 10, + 20, + 40 + ], + "resnet_dt": false, + "axis_neuron": 4, + "seed": 1 + }, + "fitting_net": { + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true, + "numb_fparam": 10, + "seed": 1 + } + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 1, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0, + "limit_pref_v": 0 + }, + "learning_rate": { + "start_lr": 0.001, + "decay_steps": 5000, + "stop_lr": 0.0009897937816869885 + }, + "_comment3": " traing controls", + "training": { + "stop_batch": 1000, + "seed": 1, + "_comment4": " display and restart", + "_comment5": " frequencies counted in batch", + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "training_data": { + "systems": [], + "set_prefix": "set", + "batch_size": 1 + } + }, + "_comment6": "that's all" }, - "_comment6": "that's all" - }, - "_comment7": " 01.model_devi ", - "_comment8": "model_devi_skip: the first x of the recorded frames", - "model_devi_dt": 0.002, - "model_devi_skip": 0, - "model_devi_f_trust_lo": 0.05, - "model_devi_f_trust_hi": 0.2, - "model_devi_clean_traj": false, - "model_devi_jobs": [ - { - "_idx": 0, - "ensemble": "npt", - "nsteps": 50, - "press": [ - 1.0, - 2.0 - ], - "sys_idx": [ - 0, - 1 - ], - "temps": [ - 50, - 100 - ], - "trj_freq": 10 - } - ], - "_comment9": " 02.fp ", - "fp_style": "vasp", - "shuffle_poscar": false, - "fp_task_max": 8, - "fp_task_min": 2, - "fp_pp_path": "/home/wanghan/study/deep.md/dpgen/almg/vasp", - "fp_pp_files": [ - "POTCAR.Al", - "POTCAR.Mg" - ], - "fp_incar": "/home/wanghan/study/deep.md/dpgen/almg/vasp/INCAR", - "_comment10": " that's all " + "_comment7": " 01.model_devi ", + "_comment8": "model_devi_skip: the first x of the recorded frames", + "model_devi_dt": 0.002, + "model_devi_skip": 0, + "model_devi_f_trust_lo": 0.05, + "model_devi_f_trust_hi": 0.2, + "model_devi_clean_traj": false, + "model_devi_jobs": [ + { + "_idx": 0, + "ensemble": "npt", + "nsteps": 50, + "press": [ + 1.0, + 2.0 + ], + "sys_idx": [ + 0, + 1 + ], + "temps": [ + 50, + 100 + ], + "trj_freq": 10 + } + ], + "_comment9": " 02.fp ", + "fp_style": "vasp", + "shuffle_poscar": false, + "fp_task_max": 8, + "fp_task_min": 2, + "fp_pp_path": "/home/wanghan/study/deep.md/dpgen/almg/vasp", + "fp_pp_files": [ + "POTCAR.Al", + "POTCAR.Mg" + ], + "fp_incar": "/home/wanghan/study/deep.md/dpgen/almg/vasp/INCAR", + "_comment10": " that's all " } diff --git a/examples/run/dp2.x-lammps-vasp/Al/param_al_all_gpu-deepmd-kit-2.x.json 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a/examples/run/dp2.x-lammps-vasp/CH4/param_CH4_deepmd-kit-2.x.json +++ b/examples/run/dp2.x-lammps-vasp/CH4/param_CH4_deepmd-kit-2.x.json @@ -1,137 +1,137 @@ { - "type_map": [ - "H", - "C" - ], - "mass_map": [ - 1, - 12 - ], - "init_data_prefix": "/data1/yfb222333/2_dpgen_gpu_multi", - "init_data_sys": [ - "CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd" - ], - "sys_configs_prefix": "/data1/yfb222333/2_dpgen_gpu_multi", - "sys_configs": [ - [ - "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000*/POSCAR" - ], - [ - "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00001*/POSCAR" - ] - ], - "_comment1": " that's all ", - "numb_models": 4, - "default_training_param": { - "model": { - "type_map": [ + "type_map": [ "H", "C" - ], - "descriptor": { - "type": "se_a", - "sel": [ - 16, - 4 - ], - "rcut_smth": 0.5, - "rcut": 5, - "neuron": [ - 120, - 120, - 120 - ], - "resnet_dt": true, - "axis_neuron": 12, - "seed": 1 - }, - "fitting_net": { - "neuron": [ - 25, - 50, - 100 + ], + "mass_map": [ + 1, + 12 + ], + "init_data_prefix": "/data1/yfb222333/2_dpgen_gpu_multi", + "init_data_sys": [ + "CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd" + ], + "sys_configs_prefix": "/data1/yfb222333/2_dpgen_gpu_multi", + "sys_configs": [ + [ + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000*/POSCAR" ], - "resnet_dt": false, - "seed": 1 - } - }, - "learning_rate": { - "type": "exp", - "start_lr": 0.001, - "decay_steps": 100, - "stop_lr": 0.0003584859224085419 - }, - "loss": { - "start_pref_e": 0.02, - "limit_pref_e": 2, - "start_pref_f": 1000, - "limit_pref_f": 1, - "start_pref_v": 0.0, - "limit_pref_v": 0.0 - }, - "training": { - "stop_batch": 2000, - "disp_file": "lcurve.out", - "disp_freq": 1000, - "save_freq": 1000, - "save_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json", - "_comment2": "that's all", - "training_data": { - "set_prefix": "set", - "batch_size": 1 - } - } - }, - "model_devi_dt": 0.002, - "model_devi_skip": 0, - "model_devi_f_trust_lo": 0.05, - "model_devi_f_trust_hi": 0.15, - "model_devi_clean_traj": true, - "model_devi_jobs": [ - { - "sys_idx": [ - 0 - ], - "temps": [ - 100 - ], - "press": [ - 1.0 - ], - "trj_freq": 10, - "nsteps": 300, - "ensemble": "nvt", - "_idx": "00" + [ + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00001*/POSCAR" + ] + ], + "_comment1": " that's all ", + "numb_models": 4, + "default_training_param": { + "model": { + "type_map": [ + "H", + "C" + ], + "descriptor": { + "type": "se_a", + "sel": [ + 16, + 4 + ], + "rcut_smth": 0.5, + "rcut": 5, + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true, + "axis_neuron": 12, + "seed": 1 + }, + "fitting_net": { + "neuron": [ + 25, + 50, + 100 + ], + "resnet_dt": false, + "seed": 1 + } + }, + "learning_rate": { + "type": "exp", + "start_lr": 0.001, + "decay_steps": 100, + "stop_lr": 0.0003584859224085419 + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0.0, + "limit_pref_v": 0.0 + }, + "training": { + "stop_batch": 2000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "_comment2": "that's all", + "training_data": { + "set_prefix": "set", + "batch_size": 1 + } + } }, - { - "sys_idx": [ - 1 - ], - "temps": [ - 100 - ], - "press": [ - 1.0 - ], - "trj_freq": 10, - "nsteps": 3000, - "ensemble": "nvt", - "_idx": "01" - } - ], - "fp_style": "vasp", - "shuffle_poscar": false, - "fp_task_max": 20, - "fp_task_min": 5, - "fp_pp_path": "/data1/yfb222333/2_dpgen_gpu_multi", - "fp_pp_files": [ - "POTCAR_H", - "POTCAR_C" - ], - "_comments": "We can only provide empty files in public, you should provide valid POTCARS yourself when running DP-GEN", - "fp_incar": "/data1/yfb222333/2_dpgen_gpu_multi/INCAR_methane" + "model_devi_dt": 0.002, + "model_devi_skip": 0, + "model_devi_f_trust_lo": 0.05, + "model_devi_f_trust_hi": 0.15, + "model_devi_clean_traj": true, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 100 + ], + "press": [ + 1.0 + ], + "trj_freq": 10, + "nsteps": 300, + "ensemble": "nvt", + "_idx": "00" + }, + { + "sys_idx": [ + 1 + ], + "temps": [ + 100 + ], + "press": [ + 1.0 + ], + "trj_freq": 10, + "nsteps": 3000, + "ensemble": "nvt", + "_idx": "01" + } + ], + "fp_style": "vasp", + "shuffle_poscar": false, + "fp_task_max": 20, + "fp_task_min": 5, + "fp_pp_path": "/data1/yfb222333/2_dpgen_gpu_multi", + "fp_pp_files": [ + "POTCAR_H", + "POTCAR_C" + ], + "_comments": "We can only provide empty files in public, you should provide valid POTCARS yourself when running DP-GEN", + "fp_incar": "/data1/yfb222333/2_dpgen_gpu_multi/INCAR_methane" } diff --git a/examples/run/dp2.x-lammps-vasp/param_CH4_deepmd-kit-2.0.1.json b/examples/run/dp2.x-lammps-vasp/param_CH4_deepmd-kit-2.0.1.json index e90fc503e..a59f44f9f 100644 --- a/examples/run/dp2.x-lammps-vasp/param_CH4_deepmd-kit-2.0.1.json +++ b/examples/run/dp2.x-lammps-vasp/param_CH4_deepmd-kit-2.0.1.json @@ -1,133 +1,133 @@ { - "type_map": [ - "H", - "C" - ], - "mass_map": [ - 1, - 12 - ], - "init_data_prefix": "./", - "init_data_sys": [ - "CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd" - ], - "sys_configs_prefix": "./", - "sys_configs": [ - [ - "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000*/POSCAR" - ], - [ - "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00001*/POSCAR" - ] - ], - "_comment1": " that's all ", - "numb_models": 4, - "default_training_param": { - "model": { - "type_map": [ + "type_map": [ "H", "C" - ], - "descriptor": { - "type": "se_a", - "sel": [ - 16, - 4 - ], - "rcut_smth": 0.5, - "rcut": 5.0, - "neuron": [ - 120, - 120, - 120 - ], - "resnet_dt": true, - "axis_neuron": 12, - "seed": 1 - }, - "fitting_net": { - "neuron": [ - 25, - 50, - 100 + ], + "mass_map": [ + 1, + 12 + ], + "init_data_prefix": "./", + "init_data_sys": [ + "CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd" + ], + "sys_configs_prefix": "./", + "sys_configs": [ + [ + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00000*/POSCAR" ], - "resnet_dt": false, - "seed": 1 - } - }, - "learning_rate": { - "type": "exp", - "start_lr": 0.001, - "decay_steps": 100 - }, - "loss": { - "start_pref_e": 0.02, - "limit_pref_e": 2, - "start_pref_f": 1000, - "limit_pref_f": 1, - "start_pref_v": 0.0, - "limit_pref_v": 0.0 - }, - "training": { - "set_prefix": "set", - "numb_steps": 2000, - "batch_size": 1, - "disp_file": "lcurve.out", - "disp_freq": 1000, - "save_freq": 1000, - "save_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json", - "_comment2": "that's all" - } - }, - "model_devi_dt": 0.002, - "model_devi_skip": 0, - "model_devi_f_trust_lo": 0.05, - "model_devi_f_trust_hi": 0.15, - "model_devi_clean_traj": true, - "model_devi_jobs": [ - { - "sys_idx": [ - 0 - ], - "temps": [ - 100 - ], - "press": [ - 1.0 - ], - "trj_freq": 10, - "nsteps": 300, - "ensemble": "nvt", - "_idx": "00" + [ + "CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale*/00001*/POSCAR" + ] + ], + "_comment1": " that's all ", + "numb_models": 4, + "default_training_param": { + "model": { + "type_map": [ + "H", + "C" + ], + "descriptor": { + "type": "se_a", + "sel": [ + 16, + 4 + ], + "rcut_smth": 0.5, + "rcut": 5.0, + "neuron": [ + 120, + 120, + 120 + ], + "resnet_dt": true, + "axis_neuron": 12, + "seed": 1 + }, + "fitting_net": { + "neuron": [ + 25, + 50, + 100 + ], + "resnet_dt": false, + "seed": 1 + } + }, + "learning_rate": { + "type": "exp", + "start_lr": 0.001, + "decay_steps": 100 + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0.0, + "limit_pref_v": 0.0 + }, + "training": { + "set_prefix": "set", + "numb_steps": 2000, + "batch_size": 1, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "_comment2": "that's all" + } }, - { - "sys_idx": [ - 1 - ], - "temps": [ - 100 - ], - "press": [ - 1.0 - ], - "trj_freq": 10, - "nsteps": 3000, - "ensemble": "nvt", - "_idx": "01" - } - ], - "fp_style": "vasp", - "shuffle_poscar": false, - "fp_task_max": 20, - "fp_task_min": 5, - "fp_pp_path": "./", - "fp_pp_files": [ - "POTCAR_H", - "POTCAR_C" - ], - "fp_incar": "./INCAR_methane" + "model_devi_dt": 0.002, + "model_devi_skip": 0, + "model_devi_f_trust_lo": 0.05, + "model_devi_f_trust_hi": 0.15, + "model_devi_clean_traj": true, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 100 + ], + "press": [ + 1.0 + ], + "trj_freq": 10, + "nsteps": 300, + "ensemble": "nvt", + "_idx": "00" + }, + { + "sys_idx": [ + 1 + ], + "temps": [ + 100 + ], + "press": [ + 1.0 + ], + "trj_freq": 10, + "nsteps": 3000, + "ensemble": "nvt", + "_idx": "01" + } + ], + "fp_style": "vasp", + "shuffle_poscar": false, + "fp_task_max": 20, + "fp_task_min": 5, + "fp_pp_path": "./", + "fp_pp_files": [ + "POTCAR_H", + "POTCAR_C" + ], + "fp_incar": "./INCAR_methane" } diff --git a/examples/run/dp2.x_lammps_gaussian/dodecane/dodecane.json b/examples/run/dp2.x_lammps_gaussian/dodecane/dodecane.json index d7b1a2f96..e28574bb9 100644 --- a/examples/run/dp2.x_lammps_gaussian/dodecane/dodecane.json +++ b/examples/run/dp2.x_lammps_gaussian/dodecane/dodecane.json @@ -1,152 +1,152 @@ { - "type_map": [ - "C", - "H" - ], - "mass_map": [ - 12.011, - 1.008 - ], - "init_data_prefix": "/home/jzzeng/0719dodecane/gen/", - "init_data_sys": [ - "init_data" - ], - "sys_configs": [ - [ - "/home/jzzeng/0719dodecane/gen/data.dodecane.atomic" - ] - ], - "sys_format": "lammps/lmp", - "numb_models": 4, - "default_training_param": { - "model": { - "type_map": [ + "type_map": [ "C", "H" - ], - "descriptor": { - "type": "se_a", - "sel": [ - 40, - 80 - ], - "rcut_smth": 1.0, - "rcut": 6.0, - "neuron": [ - 25, - 50, - 100 - ], - "resnet_dt": false, - "axis_neuron": 12 - }, - "fitting_net": { - "neuron": [ - 240, - 240, - 240 - ], - "resnet_dt": true - } + ], + "mass_map": [ + 12.011, + 1.008 + ], + "init_data_prefix": "/home/jzzeng/0719dodecane/gen/", + "init_data_sys": [ + "init_data" + ], + "sys_configs": [ + [ + "/home/jzzeng/0719dodecane/gen/data.dodecane.atomic" + ] + ], + "sys_format": "lammps/lmp", + "numb_models": 4, + "default_training_param": { + "model": { + "type_map": [ + "C", + "H" + ], + "descriptor": { + "type": "se_a", + "sel": [ + 40, + 80 + ], + "rcut_smth": 1.0, + "rcut": 6.0, + "neuron": [ + 25, + 50, + 100 + ], + "resnet_dt": false, + "axis_neuron": 12 + }, + "fitting_net": { + "neuron": [ + 240, + 240, + 240 + ], + "resnet_dt": true + } + }, + "learning_rate": { + "type": "exp", + "start_lr": 0.001, + "decay_steps": 400, + "stop_lr": 4.317124741065782e-08 + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 1, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0, + "limit_pref_v": 0, + "start_pref_pf": 0, + "limit_pref_pf": 0 + }, + "training": { + "stop_batch": 400000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "training_data": { + "set_prefix": "set" + } + } }, - "learning_rate": { - "type": "exp", - "start_lr": 0.001, - "decay_steps": 400, - "stop_lr": 4.317124741065782e-08 - }, - "loss": { - "start_pref_e": 0.02, - "limit_pref_e": 1, - "start_pref_f": 1000, - "limit_pref_f": 1, - "start_pref_v": 0, - "limit_pref_v": 0, - "start_pref_pf": 0, - "limit_pref_pf": 0 - }, - "training": { - "stop_batch": 400000, - "disp_file": "lcurve.out", - "disp_freq": 1000, - "save_freq": 1000, - "save_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json", - "training_data": { - "set_prefix": "set" - } - } - }, - "use_clusters": true, - "cluster_cutoff": 3.5, - "cluster_minify": true, - "use_relative": true, - "epsilon": 1.0, - "model_devi_dt": 0.0001, - "model_devi_skip": 100, - "model_devi_f_trust_lo": 0.2, - "model_devi_f_trust_hi": 0.45, - "model_devi_clean_traj": false, - "model_devi_jobs": [ - { - "sys_idx": [ - 0 - ], - "temps": [ - 3000 - ], - "trj_freq": 10, - "nsteps": 2000, - "ensemble": "nvt", - "_idx": "00" - }, - { - "sys_idx": [ - 0 - ], - "temps": [ - 3000 - ], - "trj_freq": 10, - "nsteps": 4000, - "ensemble": "nvt", - "_idx": "01" - }, - { - "sys_idx": [ - 0 - ], - "temps": [ - 3000 - ], - "trj_freq": 10, - "nsteps": 8000, - "ensemble": "nvt", - "_idx": "02" - }, - { - "sys_idx": [ - 0 - ], - "temps": [ - 3000 - ], - "trj_freq": 10, - "nsteps": 16000, - "ensemble": "nvt", - "_idx": "03" + "use_clusters": true, + "cluster_cutoff": 3.5, + "cluster_minify": true, + "use_relative": true, + "epsilon": 1.0, + "model_devi_dt": 0.0001, + "model_devi_skip": 100, + "model_devi_f_trust_lo": 0.2, + "model_devi_f_trust_hi": 0.45, + "model_devi_clean_traj": false, + "model_devi_jobs": [ + { + "sys_idx": [ + 0 + ], + "temps": [ + 3000 + ], + "trj_freq": 10, + "nsteps": 2000, + "ensemble": "nvt", + "_idx": "00" + }, + { + "sys_idx": [ + 0 + ], + "temps": [ + 3000 + ], + "trj_freq": 10, + "nsteps": 4000, + "ensemble": "nvt", + "_idx": "01" + }, + { + "sys_idx": [ + 0 + ], + "temps": [ + 3000 + ], + "trj_freq": 10, + "nsteps": 8000, + "ensemble": "nvt", + "_idx": "02" + }, + { + "sys_idx": [ + 0 + ], + "temps": [ + 3000 + ], + "trj_freq": 10, + "nsteps": 16000, + "ensemble": "nvt", + "_idx": "03" + } + ], + "fp_style": "gaussian", + "shuffle_poscar": false, + "fp_task_max": 1000, + "fp_task_min": 10, + "fp_params": { + "keywords": "force mn15/6-31g**", + "nproc": 4, + "multiplicity": "auto" } - ], - "fp_style": "gaussian", - "shuffle_poscar": false, - "fp_task_max": 1000, - "fp_task_min": 10, - "fp_params": { - "keywords": "force mn15/6-31g**", - "nproc": 4, - "multiplicity": "auto" - } } diff --git a/examples/run/dprc/generator.json b/examples/run/dprc/generator.json index 2460e4c96..44fe4e851 100644 --- a/examples/run/dprc/generator.json +++ b/examples/run/dprc/generator.json @@ -1,51 +1,5 @@ { - "type_map": [ - "C", - "H", - "O", - "N", - "P", - "HW", - "OW" - ], - "init_data_sys": [ - "/path/to/initial_data" - ], - "qm_region": [ - ":1" - ], - "qm_charge": [ - 0 - ], - "parm7": [ - "/path/to/MON.parm7" - ], - "mdin": [ - "/path/to/ml.mdin" - ], - "disang": [ - "/path/to/mon.disang" - ], - "sys_configs": [ - [ - "/path/to/init_-1.20.rst7", - "/path/to/init_-0.80.rst7", - "/path/to/init_-0.40.rst7", - "/path/to/init_0.00.rst7" - ] - ], - "r": [ - [ - -1.2, - -0.8, - -0.4, - 0.0 - ] - ], - "numb_models": 4, - "default_training_param": { - "model": { - "type_map": [ + "type_map": [ "C", "H", "O", @@ -53,318 +7,364 @@ "P", "HW", "OW" - ], - "descriptor": { - "type": "hybrid", - "list": [ - { - "type": "se_a", - "sel": [ - 6, - 7, - 6, - 1, - 1, - 0, - 0 + ], + "init_data_sys": [ + "/path/to/initial_data" + ], + "qm_region": [ + ":1" + ], + "qm_charge": [ + 0 + ], + "parm7": [ + "/path/to/MON.parm7" + ], + "mdin": [ + "/path/to/ml.mdin" + ], + "disang": [ + "/path/to/mon.disang" + ], + "sys_configs": [ + [ + "/path/to/init_-1.20.rst7", + "/path/to/init_-0.80.rst7", + "/path/to/init_-0.40.rst7", + "/path/to/init_0.00.rst7" + ] + ], + "r": [ + [ + -1.2, + -0.8, + -0.4, + 0.0 + ] + ], + "numb_models": 4, + "default_training_param": { + "model": { + "type_map": [ + "C", + "H", + "O", + "N", + "P", + "HW", + "OW" ], - "rcut_smth": 1.0, - "rcut": 9.0, - "neuron": [ - 25, - 50, - 100 + "descriptor": { + "type": "hybrid", + "list": [ + { + "type": "se_a", + "sel": [ + 6, + 7, + 6, + 1, + 1, + 0, + 0 + ], + "rcut_smth": 1.0, + "rcut": 9.0, + "neuron": [ + 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"low_level_mdin": "/path/to/low_level.mdin", - "high_level_mdin": "/path/to/high_level.mdin" - }, - "low_level": "MNDOD", - "high_level": "PBE0", - "cutoff": 6.0, - "sys_format": "amber/rst7", - "model_devi_engine": "amber", - "fp_style": "amber/diff", - "detailed_report_make_fp": true + "low_level": "MNDOD", + "high_level": "PBE0", + "cutoff": 6.0, + "sys_format": "amber/rst7", + "model_devi_engine": "amber", + "fp_style": "amber/diff", + "detailed_report_make_fp": true } diff --git a/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/machine.json b/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/machine.json index d495823bb..967735fb5 100644 --- a/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/machine.json +++ b/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/machine.json @@ -1,115 +1,115 @@ { - "api_version": "1.0", - "_comment1": "dependent on dpdispatcher 0.4.15", - "train": { - "command": "dp", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root": "./", - "remote_profile": { - "email": "", - "password": "", - "program_id": 0, - "input_data": { - "api_version": 2, - "job_type": "indicate", - "log_file": "00*/lcurve.out", - "grouped": true, - "job_name": "simplify_MAPbI3-scan_train_job", - "disk_size": 100, - "scass_type": "c8_m32_1 * NVIDIA V100", - "platform": "ali", - "checkpoint_files": [ - "00*/model.ckpt*", - "00*/checkpoint" - ], - "checkpoint_time": 15, - "image_name": "LBG_DeePMD-kit_2.1.1_v1.1", - "on_demand": 0 + "api_version": "1.0", + "_comment1": "dependent on dpdispatcher 0.4.15", + "train": { + "command": "dp", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "input_data": { + "api_version": 2, + "job_type": "indicate", + "log_file": "00*/lcurve.out", + "grouped": true, + "job_name": "simplify_MAPbI3-scan_train_job", + "disk_size": 100, + "scass_type": "c8_m32_1 * NVIDIA V100", + "platform": "ali", + "checkpoint_files": [ + "00*/model.ckpt*", + "00*/checkpoint" + ], + "checkpoint_time": 15, + "image_name": "LBG_DeePMD-kit_2.1.1_v1.1", + "on_demand": 0 + } + } + }, + "resources": { + "batch_type": "Lebesgue", + "number_node": 15, + "cpu_per_node": 4, + "gpu_per_node": 1, + "queue_name": "V100_8_32", + "group_size": 1 } - } }, - "resources": { - "batch_type": "Lebesgue", - "number_node": 15, - "cpu_per_node": 4, - "gpu_per_node": 1, - "queue_name": "V100_8_32", - "group_size": 1 - } - }, - "model_devi": { - "command": "dp", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root": "./", - "remote_profile": { - "email": "", - "password": "", - "program_id": 0, - "input_data": { - "api_version": 2, - "job_type": "indicate", - "log_file": "cubic-*/*/md.log", - "grouped": true, - "job_name": "MAPbI3-scan_md_job", - "disk_size": 100, - "scass_type": "c8_m32_1 * NVIDIA V100", - "platform": 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"queue_name": "V100_8_32", - "group_size": 10 - } - }, - "fp": { - "command": "ulimit -m unlimited; ulimit -s unlimited; mpirun -n 32 vasp_std", - "machine": { - "batch_type": "Lebesgue", - "context_type": "LebesgueContext", - "local_root": "./", - "remote_profile": { - "email": "", - "password": "", - "program_id": 0, - "input_data": { - "api_version": 2, - "job_type": "indicate", - "log_file": "**/fp.log", - "grouped": true, - "job_name": "simplify_MAPbI3-scan_fp_job", - "disk_size": 100, - "scass_type": "c32_m64_cpu", - "platform": "ali", - "checkpoint_files": "sync_files", - "checkpoint_time": 15, - "image_name": "LBG_vasp-5-4-4_v1", - "on_demand": 0 + "fp": { + "command": "ulimit -m unlimited; ulimit -s unlimited; mpirun -n 32 vasp_std", + "machine": { + "batch_type": "Lebesgue", + "context_type": "LebesgueContext", + "local_root": "./", + "remote_profile": { + "email": "", + "password": "", + "program_id": 0, + "input_data": { + "api_version": 2, + "job_type": "indicate", + "log_file": "**/fp.log", + "grouped": true, + "job_name": "simplify_MAPbI3-scan_fp_job", + "disk_size": 100, + "scass_type": "c32_m64_cpu", + "platform": "ali", + "checkpoint_files": "sync_files", + "checkpoint_time": 15, + "image_name": "LBG_vasp-5-4-4_v1", + "on_demand": 0 + } + } + }, + "resources": { + "batch_type": "Lebesgue", + "number_node": 15, + "cpu_per_node": 32, + "gpu_per_node": 0, + "queue_name": "CPU", + "group_size": 10, + "source_list": [ + "/opt/intel/oneapi/setvars.sh" + ] } - } - }, - "resources": { - "batch_type": "Lebesgue", - "number_node": 15, - "cpu_per_node": 32, - "gpu_per_node": 0, - "queue_name": "CPU", - "group_size": 10, - "source_list": [ - "/opt/intel/oneapi/setvars.sh" - ] } - } } diff --git a/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/simplify.json b/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/simplify.json index 2538eec74..23d0f8083 100644 --- a/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/simplify.json +++ b/examples/simplify-MAPbI3-scan-lebesgue/simplify_example/simplify.json @@ -1,147 +1,147 @@ { - "type_map": [ - "I", - "Pb", - "C", - "N", - "H" - ], - "mass_map": [ - 126.90447, - 207.2, - 12.0108, - 14.0067, - 1.00795 - ], - "pick_data": "../data", - "init_data_prefix": "", - "init_data_sys": [], - "sys_configs": [ - null - ], - "sys_batch_size": [ - 1 - ], - "_comment1": " 00.train ", - "numb_models": 4, - "model_devi_activation_func": [ - [ - "tanh", - "tanh" - ], - [ - "tanh", - "gelu" - ], - [ - "gelu", - "gelu" - ], - [ - "gelu", - "tanh" - ] - ], - "default_training_param": { - "model": { - "type_map": [ + "type_map": [ "I", "Pb", "C", "N", "H" - ], - "descriptor": { - "type": "se_e2_a", - "sel": [ - 20, - 8, - 8, - 8, - 48 - ], - "rcut_smth": 2.0, - "rcut": 6.0, - "neuron": [ - 25, - 50, - 100 + ], + "mass_map": [ + 126.90447, + 207.2, + 12.0108, + 14.0067, + 1.00795 + ], + "pick_data": "../data", + "init_data_prefix": "", + "init_data_sys": [], + "sys_configs": [ + null + ], + "sys_batch_size": [ + 1 + ], + "_comment1": " 00.train ", + "numb_models": 4, + "model_devi_activation_func": [ + [ + "tanh", + "tanh" ], - "resnet_dt": false, - "type_one_side": true, - "trainable": true, - "axis_neuron": 12, - "seed": 0 - }, - "fitting_net": { - "neuron": [ - 240, - 240, - 240 + [ + "tanh", + "gelu" ], - "resnet_dt": true, - "trainable": [ - true, - true, - true, - true + [ + "gelu", + "gelu" ], - "seed": 0 - } - }, - "loss": { - "start_pref_e": 0.02, - "limit_pref_e": 2, - "start_pref_f": 1000, - "limit_pref_f": 2, - "start_pref_v": 0.01, - "limit_pref_v": 1 - }, - "learning_rate": { - "type": "exp", - "start_lr": 0.001, - "decay_steps": 25, - "stop_lr": 3.505266624882874e-08 + [ + "gelu", + "tanh" + ] + ], + "default_training_param": { + "model": { + "type_map": [ + "I", + "Pb", + "C", + "N", + "H" + ], + "descriptor": { + "type": "se_e2_a", + "sel": [ + 20, + 8, + 8, + 8, + 48 + ], + "rcut_smth": 2.0, + "rcut": 6.0, + "neuron": [ + 25, + 50, + 100 + ], + "resnet_dt": false, + "type_one_side": true, + "trainable": true, + "axis_neuron": 12, + "seed": 0 + }, + "fitting_net": { + "neuron": [ + 240, + 240, + 240 + ], + "resnet_dt": true, + "trainable": [ + true, + true, + true, + true + ], + "seed": 0 + } + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 2, + "start_pref_f": 1000, + "limit_pref_f": 2, + "start_pref_v": 0.01, + "limit_pref_v": 1 + }, + "learning_rate": { + "type": "exp", + "start_lr": 0.001, + "decay_steps": 25, + "stop_lr": 3.505266624882874e-08 + }, + "training": { + "stop_batch": 5000, + "seed": 1, + "_comment2": "frequencies counted in batch", + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 10000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "training_data": { + "set_prefix": "set", + "batch_size": "auto" + } + } }, - "training": { - "stop_batch": 5000, - "seed": 1, - "_comment2": "frequencies counted in batch", - "disp_file": "lcurve.out", - "disp_freq": 1000, - "save_freq": 10000, - "save_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json", - "training_data": { - "set_prefix": "set", - "batch_size": "auto" - } - } - }, - "_comment3": "02.fp", - "fp_style": "vasp", - "fp_skip_bad_box": "length_ratio:5;height_ratio:5", - "fp_accurate_threshold": 0.1, - "fp_accurate_soft_threshold": 0.0, - "fp_task_max": 20, - "fp_task_min": 5, - "ratio_failed": 0.3, - "fp_pp_path": "../vasp_inputs/", - "fp_pp_files": [ - "POTCAR_I", - "POTCAR_Pb_d", - "POTCAR_C", - "POTCAR_N", - "POTCAR_H" - ], - "fp_incar": "INCAR", - "labeled": false, - "init_pick_number": 5, - "iter_pick_number": 5, - "model_devi_f_trust_lo": 0.3, - "model_devi_f_trust_hi": 100.0, - "cvasp": false + "_comment3": "02.fp", + "fp_style": "vasp", + "fp_skip_bad_box": "length_ratio:5;height_ratio:5", + "fp_accurate_threshold": 0.1, + "fp_accurate_soft_threshold": 0.0, + "fp_task_max": 20, + "fp_task_min": 5, + "ratio_failed": 0.3, + "fp_pp_path": "../vasp_inputs/", + "fp_pp_files": [ + "POTCAR_I", + "POTCAR_Pb_d", + "POTCAR_C", + "POTCAR_N", + "POTCAR_H" + ], + "fp_incar": "INCAR", + "labeled": false, + "init_pick_number": 5, + "iter_pick_number": 5, + "model_devi_f_trust_lo": 0.3, + "model_devi_f_trust_hi": 100.0, + "cvasp": false } diff --git a/examples/simplify/qm7.json b/examples/simplify/qm7.json index a9caf52a6..bee5a1536 100644 --- a/examples/simplify/qm7.json +++ b/examples/simplify/qm7.json @@ -1,110 +1,110 @@ { - "type_map": [ - "C", - "H", - "N", - "O", - "S" - ], - "mass_map": [ - 12.011, - 1.008, - 14.007, - 15.999, - 32.065 - ], - "pick_data": "/scratch/jz748/simplify/qm7", - "init_data_prefix": "", - "init_data_sys": [], - "sys_configs": [ - null - ], - "sys_batch_size": [ - "auto" - ], - "numb_models": 4, - "default_training_param": { - "model": { - "type_map": [ + "type_map": [ "C", "H", "N", "O", "S" - ], - "descriptor": { - "type": "se_a", - "sel": [ - 7, - 16, - 3, - 3, - 1 - ], - "rcut_smth": 1.0, - "rcut": 6.0, - "neuron": [ - 25, - 50, - 100 - ], - "resnet_dt": false, - "axis_neuron": 12 - }, - "fitting_net": { - "neuron": [ - 240, - 240, - 240 - ], - "resnet_dt": true - } + ], + "mass_map": [ + 12.011, + 1.008, + 14.007, + 15.999, + 32.065 + ], + "pick_data": "/scratch/jz748/simplify/qm7", + "init_data_prefix": "", + "init_data_sys": [], + "sys_configs": [ + null + ], + "sys_batch_size": [ + "auto" + ], + "numb_models": 4, + "default_training_param": { + "model": { + "type_map": [ + "C", + "H", + "N", + "O", + "S" + ], + "descriptor": { + "type": "se_a", + "sel": [ + 7, + 16, + 3, + 3, + 1 + ], + "rcut_smth": 1.0, + "rcut": 6.0, + "neuron": [ + 25, + 50, + 100 + ], + "resnet_dt": false, + "axis_neuron": 12 + }, + "fitting_net": { + "neuron": [ + 240, + 240, + 240 + ], + "resnet_dt": true + } + }, + "learning_rate": { + "type": "exp", + "start_lr": 0.001, + "decay_steps": 10, + "stop_lr": 4.317124741065782e-08 + }, + "loss": { + "start_pref_e": 0.02, + "limit_pref_e": 1, + "start_pref_f": 1000, + "limit_pref_f": 1, + "start_pref_v": 0, + "limit_pref_v": 0, + "start_pref_pf": 0, + "limit_pref_pf": 0 + }, + "training": { + "stop_batch": 10000, + "disp_file": "lcurve.out", + "disp_freq": 1000, + "save_freq": 1000, + "save_ckpt": "model.ckpt", + "disp_training": true, + "time_training": true, + "profiling": false, + "profiling_file": "timeline.json", + "training_data": { + "set_prefix": "set" + } + }, + "_comment1": "that's all" }, - "learning_rate": { - "type": "exp", - "start_lr": 0.001, - "decay_steps": 10, - "stop_lr": 4.317124741065782e-08 + "use_clusters": true, + "fp_style": "gaussian", + "fp_task_max": 1000, + "fp_task_min": 10, + "fp_params": { + "keywords": "mn15/6-31g** force nosymm scf(maxcyc=512)", + "nproc": 28, + "multiplicity": 1, + "_comment2": " that's all " }, - "loss": { - "start_pref_e": 0.02, - "limit_pref_e": 1, - "start_pref_f": 1000, - "limit_pref_f": 1, - "start_pref_v": 0, - "limit_pref_v": 0, - "start_pref_pf": 0, - "limit_pref_pf": 0 - }, - "training": { - "stop_batch": 10000, - "disp_file": "lcurve.out", - "disp_freq": 1000, - "save_freq": 1000, - "save_ckpt": "model.ckpt", - "disp_training": true, - "time_training": true, - "profiling": false, - "profiling_file": "timeline.json", - "training_data": { - "set_prefix": "set" - } - }, - "_comment1": "that's all" - }, - "use_clusters": true, - "fp_style": "gaussian", - "fp_task_max": 1000, - "fp_task_min": 10, - "fp_params": { - "keywords": "mn15/6-31g** force nosymm scf(maxcyc=512)", - "nproc": 28, - "multiplicity": 1, - "_comment2": " that's all " - }, - "init_pick_number": 100, - "iter_pick_number": 100, - "model_devi_f_trust_lo": 0.1, - "model_devi_f_trust_hi": 0.3, - "_comment3": " that's all " + "init_pick_number": 100, + "iter_pick_number": 100, + "model_devi_f_trust_lo": 0.1, + "model_devi_f_trust_hi": 0.3, + "_comment3": " that's all " } diff --git a/examples/test/deepmd_param.json b/examples/test/deepmd_param.json index 75e3da5ad..5d04afc66 100644 --- a/examples/test/deepmd_param.json +++ b/examples/test/deepmd_param.json @@ -1,62 +1,62 @@ { - "_comment1": "models", - "potcar_map": { - "Al": "/somewhere/example/POTCAR" - }, - "conf_dir": "confs/Al/std-fcc", - "key_id": "key id of Material project", - "task_type": "deepmd", - "task": "all", - "vasp_params": { - "ecut": 650, - "ediff": 1e-06, - "kspacing": 0.1, - "kgamma": false, - "npar": 1, - "kpar": 1, - "_comment2": " that's all " - }, - "lammps_params": { - "model_dir": "somewhere/example/Al_model", - "type_map": [ - "Al" + "_comment1": "models", + "potcar_map": { + "Al": "/somewhere/example/POTCAR" + }, + "conf_dir": "confs/Al/std-fcc", + "key_id": "key id of Material project", + "task_type": "deepmd", + "task": "all", + "vasp_params": { + "ecut": 650, + "ediff": 1e-06, + "kspacing": 0.1, + "kgamma": false, + "npar": 1, + "kpar": 1, + "_comment2": " that's all " + }, + "lammps_params": { + "model_dir": "somewhere/example/Al_model", + "type_map": [ + "Al" + ], + "model_name": false, + "model_param_type": false + }, + "_comment3": "00.equi", + "alloy_shift": false, + "_comment4": "01.eos", + "vol_start": 12, + "vol_end": 22, + "vol_step": 0.5, + "_comment5": "02.elastic", + "norm_deform": 0.02, + "shear_deform": 0.05, + "_comment6": "03.vacancy", + "supercell": [ + 3, + 3, + 3 ], - "model_name": false, - "model_param_type": false - }, - "_comment3": "00.equi", - "alloy_shift": false, - "_comment4": "01.eos", - "vol_start": 12, - "vol_end": 22, - "vol_step": 0.5, - "_comment5": "02.elastic", - "norm_deform": 0.02, - "shear_deform": 0.05, - "_comment6": "03.vacancy", - "supercell": [ - 3, - 3, - 3 - ], - "_comment7": "04.interstitial", - "insert_ele": [ - "Al" - ], - "reprod-opt": false, - "_comment8": "05.surface", - "min_slab_size": 10, - "min_vacuum_size": 11, - "_comment9": "pert xz to work around vasp bug...", - "pert_xz": 0.01, - "max_miller": 2, - "relax_box": false, - "_comment10": "06.phonon", - "supercell_matrix": [ - 2, - 2, - 2 - ], - "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", - "_comment11": "that's all" + "_comment7": "04.interstitial", + "insert_ele": [ + "Al" + ], + "reprod-opt": false, + "_comment8": "05.surface", + "min_slab_size": 10, + "min_vacuum_size": 11, + "_comment9": "pert xz to work around vasp bug...", + "pert_xz": 0.01, + "max_miller": 2, + "relax_box": false, + "_comment10": "06.phonon", + "supercell_matrix": [ + 2, + 2, + 2 + ], + "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", + "_comment11": "that's all" } diff --git a/examples/test/meam_param.json b/examples/test/meam_param.json index 29ea4e540..7eeec66d2 100644 --- a/examples/test/meam_param.json +++ b/examples/test/meam_param.json @@ -1,75 +1,75 @@ { - "_comment1": "models", - "potcar_map": { - "Al": "/somewhere/example/POTCAR" - }, - "conf_dir": "confs/Al/std-fcc", - "key_id": "key id of Material project", - "task_type": "meam", - "task": "all", - "vasp_params": { - "ecut": 650, - "ediff": 1e-06, - "kspacing": 0.1, - "kgamma": false, - "npar": 1, - "kpar": 1, - "_comment2": " that's all " - }, - "lammps_params": { - "model_dir": "somewhere/example/meam", - "type_map": [ - "Al", - "Si", - "Mg", - "Cu", - "Fe" + "_comment1": "models", + "potcar_map": { + "Al": "/somewhere/example/POTCAR" + }, + "conf_dir": "confs/Al/std-fcc", + "key_id": "key id of Material project", + "task_type": "meam", + "task": "all", + "vasp_params": { + "ecut": 650, + "ediff": 1e-06, + "kspacing": 0.1, + "kgamma": false, + "npar": 1, + "kpar": 1, + "_comment2": " that's all " + }, + "lammps_params": { + "model_dir": "somewhere/example/meam", + "type_map": [ + "Al", + "Si", + "Mg", + "Cu", + "Fe" + ], + "model_name": [ + "meam.AlSiMgCuFe", + "meam.library" + ], + "model_param_type": [ + "AlS", + "SiS", + "MgS", + "CuS", + "FeS" + ] + }, + "_comment3": "00.equi", + "alloy_shift": false, + "_comment4": "01.eos", + "vol_start": 12, + "vol_end": 22, + "vol_step": 0.5, + "_comment5": "02.elastic", + "norm_deform": 0.02, + "shear_deform": 0.05, + "_comment6": "03.vacancy", + "supercell": [ + 3, + 3, + 3 ], - "model_name": [ - "meam.AlSiMgCuFe", - "meam.library" + "_comment7": "04.interstitial", + "insert_ele": [ + "Al" ], - "model_param_type": [ - "AlS", - "SiS", - "MgS", - "CuS", - "FeS" - ] - }, - "_comment3": "00.equi", - "alloy_shift": false, - "_comment4": "01.eos", - "vol_start": 12, - "vol_end": 22, - "vol_step": 0.5, - "_comment5": "02.elastic", - "norm_deform": 0.02, - "shear_deform": 0.05, - "_comment6": "03.vacancy", - "supercell": [ - 3, - 3, - 3 - ], - "_comment7": "04.interstitial", - "insert_ele": [ - "Al" - ], - "reprod-opt": false, - "_comment8": "05.surface", - "min_slab_size": 10, - "min_vacuum_size": 11, - "_comment9": "pert xz to work around vasp bug...", - "pert_xz": 0.01, - "max_miller": 2, - "relax_box": false, - "_comment10": "06.phonon", - "supercell_matrix": [ - 2, - 2, - 2 - ], - "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", - "_comment11": "that's all" + "reprod-opt": false, + "_comment8": "05.surface", + "min_slab_size": 10, + "min_vacuum_size": 11, + "_comment9": "pert xz to work around vasp bug...", + "pert_xz": 0.01, + "max_miller": 2, + "relax_box": false, + "_comment10": "06.phonon", + "supercell_matrix": [ + 2, + 2, + 2 + ], + "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", + "_comment11": "that's all" } diff --git a/examples/test/vasp_param.json b/examples/test/vasp_param.json index f06060f76..981b78f02 100644 --- a/examples/test/vasp_param.json +++ b/examples/test/vasp_param.json @@ -1,54 +1,54 @@ { - "_comment1": "models", - "potcar_map": { - "Al": "/somewhere/example/POTCAR" - }, - "conf_dir": "confs/Al/std-fcc", - "key_id": "key id of Material project", - "task_type": "vasp", - "task": "all", - "vasp_params": { - "ecut": 650, - "ediff": 1e-06, - "kspacing": 0.1, - "kgamma": false, - "npar": 1, - "kpar": 1, - "_comment2": " that's all " - }, - "_comment3": "00.equi", - "alloy_shift": false, - "_comment4": "01.eos", - "vol_start": 12, - "vol_end": 22, - "vol_step": 0.5, - "_comment5": "02.elastic", - "norm_deform": 0.02, - "shear_deform": 0.05, - "_comment6": "03.vacancy", - "supercell": [ - 3, - 3, - 3 - ], - "_comment7": "04.interstitial", - "insert_ele": [ - "Al" - ], - "reprod-opt": false, - "_comment8": "05.surface", - "min_slab_size": 10, - "min_vacuum_size": 11, - "_comment9": "pert xz to work around vasp bug...", - "pert_xz": 0.01, - "max_miller": 2, - "relax_box": false, - "_comment10": "06.phonon", - "supercell_matrix": [ - 2, - 2, - 2 - ], - "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", - "_comment11": "that's all" + "_comment1": "models", + "potcar_map": { + "Al": "/somewhere/example/POTCAR" + }, + "conf_dir": "confs/Al/std-fcc", + "key_id": "key id of Material project", + "task_type": "vasp", + "task": "all", + "vasp_params": { + "ecut": 650, + "ediff": 1e-06, + "kspacing": 0.1, + "kgamma": false, + "npar": 1, + "kpar": 1, + "_comment2": " that's all " + }, + "_comment3": "00.equi", + "alloy_shift": false, + "_comment4": "01.eos", + "vol_start": 12, + "vol_end": 22, + "vol_step": 0.5, + "_comment5": "02.elastic", + "norm_deform": 0.02, + "shear_deform": 0.05, + "_comment6": "03.vacancy", + "supercell": [ + 3, + 3, + 3 + ], + "_comment7": "04.interstitial", + "insert_ele": [ + "Al" + ], + "reprod-opt": false, + "_comment8": "05.surface", + "min_slab_size": 10, + "min_vacuum_size": 11, + "_comment9": "pert xz to work around vasp bug...", + "pert_xz": 0.01, + "max_miller": 2, + "relax_box": false, + "_comment10": "06.phonon", + "supercell_matrix": [ + 2, + 2, + 2 + ], + "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", + "_comment11": "that's all" } diff --git a/examples/test/vasp_param_from_incar.json b/examples/test/vasp_param_from_incar.json index 77221f2fb..9acf0928e 100644 --- a/examples/test/vasp_param_from_incar.json +++ b/examples/test/vasp_param_from_incar.json @@ -1,47 +1,47 @@ { - "_comment1": "models", - "potcar_map": { - "Al": "/somewhere/example/POTCAR" - }, - "conf_dir": "confs/Al/std-fcc", - "key_id": "key id of Material project", - "task_type": "vasp", - "task": "all", - "relax_incar": "somewhere/relax_incar", - "scf_incar": "somewhere/scf_incar", - "_comment2": "00.equi", - "alloy_shift": false, - "_comment3": "01.eos", - "vol_start": 12, - "vol_end": 22, - "vol_step": 0.5, - "_comment4": "02.elastic", - "norm_deform": 0.02, - "shear_deform": 0.05, - "_comment5": "03.vacancy", - "supercell": [ - 3, - 3, - 3 - ], - "_comment6": "04.interstitial", - "insert_ele": [ - "Al" - ], - "reprod-opt": false, - "_comment7": "05.surface", - "min_slab_size": 10, - "min_vacuum_size": 11, - "_comment8": "pert xz to work around vasp bug...", - "pert_xz": 0.01, - "max_miller": 2, - "relax_box": false, - "_comment9": "06.phonon", - "supercell_matrix": [ - 2, - 2, - 2 - ], - "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", - "_comment10": "that's all" + "_comment1": "models", + "potcar_map": { + "Al": "/somewhere/example/POTCAR" + }, + "conf_dir": "confs/Al/std-fcc", + "key_id": "key id of Material project", + "task_type": "vasp", + "task": "all", + "relax_incar": "somewhere/relax_incar", + "scf_incar": "somewhere/scf_incar", + "_comment2": "00.equi", + "alloy_shift": false, + "_comment3": "01.eos", + "vol_start": 12, + "vol_end": 22, + "vol_step": 0.5, + "_comment4": "02.elastic", + "norm_deform": 0.02, + "shear_deform": 0.05, + "_comment5": "03.vacancy", + "supercell": [ + 3, + 3, + 3 + ], + "_comment6": "04.interstitial", + "insert_ele": [ + "Al" + ], + "reprod-opt": false, + "_comment7": "05.surface", + "min_slab_size": 10, + "min_vacuum_size": 11, + "_comment8": "pert xz to work around vasp bug...", + "pert_xz": 0.01, + "max_miller": 2, + "relax_box": false, + "_comment9": "06.phonon", + "supercell_matrix": [ + 2, + 2, + 2 + ], + "band": "0 1 0 0.5 1 0.5 0.375 0.75 0.375 0 0 0 0.5 0.5 0.5", + "_comment10": "that's all" } diff --git a/tests/auto_test/equi/abacus/cell-relax.json b/tests/auto_test/equi/abacus/cell-relax.json index b8b89fce4..f394f46db 100644 --- a/tests/auto_test/equi/abacus/cell-relax.json +++ b/tests/auto_test/equi/abacus/cell-relax.json @@ -1,4779 +1,4779 @@ { - "@module": "dpdata.system", - "@class": "LabeledSystem", - "data": { - "atom_numbs": [ - 4 - ], - "atom_names": [ - "Al" - ], - "atom_types": { - "@module": "numpy", - "@class": "array", - "dtype": "int64", - "data": [ - 0, - 0, - 0, - 0 - ] - }, - "orig": { - "@module": "numpy", - "@class": "array", - "dtype": "float64", - "data": [ - 0.0, - 0.0, - 0.0 - ] - }, - "cells": { - "@module": "numpy", - "@class": "array", - "dtype": "float64", - "data": [ - [ - [ - 4.05000830557689, - 0.0, - 0.0 - ], - [ - 0.0, - 4.05000830557689, - 0.0 - ], - [ - 0.0, - 0.0, - 4.05000830557689 - ] - ], - [ - [ - 4.046944527057562, - 0.0, - 0.0 - ], - [ - 0.0, - 4.046944527057562, - 0.0 - ], - [ - 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63.55, - 183.8 - ], - "potcars": [ - "abacus.in/Cu_ONCV_PBE-1.0.upf", - "abacus.in/W_ONCV_PBE-1.0.upf" - ], - "relax_incar": "abacus.in/INPUT", - "relax_kpt": "abacus.in/KPT", - "md_kpt": "abacus.in/KPT", - "md_incar": "abacus.in/INPUT.md", - "scale": [ - 0.99 - ], - "skip_relax": true, - "pert_numb": 2, - "md_nstep": 2, - "pert_box": 0.01, - "pert_atom": 0.01, - "coll_ndata": 12, - "type_map": [ - "Cu", - "W" - ], - "_comment1": "that's all" -} \ No newline at end of file + "init_fp_style": "ABACUS", + "stages": [ + 1, + 2, + 3, + 4 + ], + "cell_type": "fcc", + "latt": 3.76, + "super_cell": [ + 1, + 2, + 2 + ], + "elements": [ + "Cu", + "W" + ], + "atom_masses": [ + 63.55, + 183.8 + ], + "potcars": [ + "abacus.in/Cu_ONCV_PBE-1.0.upf", + "abacus.in/W_ONCV_PBE-1.0.upf" + ], + "relax_incar": "abacus.in/INPUT", + "relax_kpt": "abacus.in/KPT", + "md_kpt": "abacus.in/KPT", + "md_incar": "abacus.in/INPUT.md", + "scale": [ + 0.99 + ], + "skip_relax": true, + "pert_numb": 2, + "md_nstep": 2, + "pert_box": 0.01, + "pert_atom": 0.01, + "coll_ndata": 12, + "type_map": [ + "Cu", + "W" + ], + "_comment1": "that's all" +} diff --git a/tests/data/al.json b/tests/data/al.json index c04b95ad9..3c96c484f 100644 --- a/tests/data/al.json +++ b/tests/data/al.json @@ -1,32 +1,32 @@ { - "cell_type": "fcc", - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "Al" - ], - "from_poscar": false, - "from_poscar_path": "example/POSCAR", - "potcars": [ - "example/POTCAR" - ], - "relax_incar": "example/INCAR.rlx", - "md_incar": "example/INCAR.md", - "scale": [ - 1.0 - ], - "skip_relax": false, - "pert_numb": 2, - "md_nstep": 1, - "pert_box": 0.03, - "pert_atom": 0.01, - "coll_ndata": 10, - "type_map": [ - "Mg", - "Al" - ], - "_comment1": "that's all" -} \ No newline at end of file + "cell_type": "fcc", + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al" + ], + "from_poscar": false, + "from_poscar_path": "example/POSCAR", + "potcars": [ + "example/POTCAR" + ], + "relax_incar": "example/INCAR.rlx", + "md_incar": "example/INCAR.md", + "scale": [ + 1.0 + ], + "skip_relax": false, + "pert_numb": 2, + "md_nstep": 1, + "pert_box": 0.03, + "pert_atom": 0.01, + "coll_ndata": 10, + "type_map": [ + "Mg", + "Al" + ], + "_comment1": "that's all" +} diff --git a/tests/data/alloy.json b/tests/data/alloy.json index 04b831215..dd42d585c 100644 --- a/tests/data/alloy.json +++ b/tests/data/alloy.json @@ -1,31 +1,31 @@ { - "cell_type": "fcc", - "latt": 2.4, - "super_cell": [ - 1, - 1, - 1 - ], - "elements": [ - "Al", - "Mg" - ], - "from_poscar": false, - "from_poscar_path": "example/POSCAR", - "potcars": [ - "./POTCAR", - "./POTCAR" - ], - "relax_incar": "./INCAR_metal_rlx_low", - "md_incar": "example/INCAR.md", - "scale": [ - 1.0 - ], - "skip_relax": true, - "pert_numb": 3, - "md_nstep": 1, - "pert_box": 0.03, - "pert_atom": 0.01, - "coll_ndata": 3, - "_comment1": "that's all" -} \ No newline at end of file + "cell_type": "fcc", + "latt": 2.4, + "super_cell": [ + 1, + 1, + 1 + ], + "elements": [ + "Al", + "Mg" + ], + "from_poscar": false, + "from_poscar_path": "example/POSCAR", + "potcars": [ + "./POTCAR", + "./POTCAR" + ], + "relax_incar": "./INCAR_metal_rlx_low", + "md_incar": "example/INCAR.md", + "scale": [ + 1.0 + ], + "skip_relax": true, + "pert_numb": 3, + "md_nstep": 1, + "pert_box": 0.03, + "pert_atom": 0.01, + "coll_ndata": 3, + "_comment1": "that's all" +} diff --git a/tests/data/ch4.json b/tests/data/ch4.json index fe9762bdf..ce67eeb1f 100644 --- a/tests/data/ch4.json +++ b/tests/data/ch4.json @@ -1,46 +1,46 @@ { - "init_fp_style": "ABACUS", - "stages": [ - 1, - 2, - 3, - 4 - ], - "super_cell": [ - 1, - 1, - 1 - ], - "_comment1": "if from_poscar = true, the cell_type and super_cell keys are actually useless", - "cell_type": "fcc", - "elements": [ - "H", - "C" - ], - "atom_masses": [ - 1, - 12 - ], - "_comment2": "if from_poscar = false, you have to set atom_masse.", - "out_dir": "./", - "from_poscar": true, - "from_poscar_path": "./STRU", - "potcars": [ - "./H_ONCV_PBE-1.0.upf", - "./C_ONCV_PBE-1.0.upf" - ], - "relax_incar": "./INPUT", - "relax_kspacing": 10, - "md_incar": "./INPUT.md", - "md_kspacing": 10, - "scale": [ - 0.95 - ], - "skip_relax": false, - "pert_numb": 2, - "md_nstep": 3, - "pert_box": 0.03, - "pert_atom": 0.01, - "coll_ndata": 10, - "_comment3": "that's all" -} \ No newline at end of file + "init_fp_style": "ABACUS", + "stages": [ + 1, + 2, + 3, + 4 + ], + "super_cell": [ + 1, + 1, + 1 + ], + "_comment1": "if from_poscar = true, the cell_type and super_cell keys are actually useless", + "cell_type": "fcc", + "elements": [ + "H", + "C" + ], + "atom_masses": [ + 1, + 12 + ], + "_comment2": "if from_poscar = false, you have to set atom_masse.", + "out_dir": "./", + "from_poscar": true, + "from_poscar_path": "./STRU", + "potcars": [ + "./H_ONCV_PBE-1.0.upf", + "./C_ONCV_PBE-1.0.upf" + ], + "relax_incar": "./INPUT", + "relax_kspacing": 10, + "md_incar": "./INPUT.md", + "md_kspacing": 10, + "scale": [ + 0.95 + ], + "skip_relax": false, + "pert_numb": 2, + "md_nstep": 3, + "pert_box": 0.03, + "pert_atom": 0.01, + "coll_ndata": 10, + "_comment3": "that's all" +} diff --git a/tests/data/surf.json b/tests/data/surf.json index 4131ecf3a..d3f5afee4 100644 --- a/tests/data/surf.json +++ b/tests/data/surf.json @@ -1,46 +1,46 @@ { - "stages": [ - 1, - 2 - ], - "cell_type": "fcc", - "latt": 4.1, - "super_cell": [ - 1, - 1, - 1 - ], - "layer_numb": 3, - "vacuum_max": 9.0, - "vacuum_resol": [ - 0.5, - 1 - ], - "mid_point": 4.0, - "head_ratio": 0.6, - "vacuum_numb": 20, - "millers": [ - [ - 1, - 0, - 0 - ] - ], - "elements": [ - "Al" - ], - "potcars": [ - "./POTCAR" - ], - "relax_incar": "INCAR_metal_rlx_low", - "scale": [ - 0.98, - 1.0 - ], - "skip_relax": true, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "coll_ndata": 5000, - "_comment1": "that's all" -} \ No newline at end of file + "stages": [ + 1, + 2 + ], + "cell_type": "fcc", + "latt": 4.1, + "super_cell": [ + 1, + 1, + 1 + ], + "layer_numb": 3, + "vacuum_max": 9.0, + "vacuum_resol": [ + 0.5, + 1 + ], + "mid_point": 4.0, + "head_ratio": 0.6, + "vacuum_numb": 20, + "millers": [ + [ + 1, + 0, + 0 + ] + ], + "elements": [ + "Al" + ], + "potcars": [ + "./POTCAR" + ], + "relax_incar": "INCAR_metal_rlx_low", + "scale": [ + 0.98, + 1.0 + ], + "skip_relax": true, + "pert_numb": 5, + "pert_box": 0.03, + "pert_atom": 0.01, + "coll_ndata": 5000, + "_comment1": "that's all" +} diff --git a/tests/data/surf_poscar.json b/tests/data/surf_poscar.json index 7e825dda7..2cfbc27a4 100644 --- a/tests/data/surf_poscar.json +++ b/tests/data/surf_poscar.json @@ -1,46 +1,46 @@ { - "stages": [ - 1, - 2 - ], - "cell_type": "fcc", - "from_poscar": true, - "from_poscar_path": "POSCAR", - "super_cell": [ - 1, - 1, - 1 - ], - "layer_numb": 3, - "vacuum_max": 5, - "vacuum_resol": [ - 0.5, - 2 - ], - "mid_point": 2.0, - "_head_ratio": 0.6, - "_vacuum_numb": 20, - "millers": [ - [ - 1, - 0, - 0 - ] - ], - "elements": [ - "Al" - ], - "potcars": [ - "./POTCAR" - ], - "relax_incar": "INCAR_metal_rlx_low", - "scale": [ - 1.0 - ], - "skip_relax": true, - "pert_numb": 5, - "pert_box": 0.03, - "pert_atom": 0.01, - "coll_ndata": 5000, - "_comment1": "that's all" -} \ No newline at end of file + "stages": [ + 1, + 2 + ], + "cell_type": "fcc", + "from_poscar": true, + "from_poscar_path": "POSCAR", + "super_cell": [ + 1, + 1, + 1 + ], + "layer_numb": 3, + "vacuum_max": 5, + "vacuum_resol": [ + 0.5, + 2 + ], + "mid_point": 2.0, + "_head_ratio": 0.6, + "_vacuum_numb": 20, + "millers": [ + [ + 1, + 0, + 0 + ] + ], + "elements": [ + "Al" + ], + "potcars": [ + "./POTCAR" + ], + "relax_incar": "INCAR_metal_rlx_low", + "scale": [ + 1.0 + ], + "skip_relax": true, + "pert_numb": 5, + "pert_box": 0.03, + "pert_atom": 0.01, + "coll_ndata": 5000, + "_comment1": "that's all" +} diff --git a/tests/database/param_Al.json b/tests/database/param_Al.json index 07f7bd305..48f767d30 100644 --- a/tests/database/param_Al.json +++ b/tests/database/param_Al.json @@ -1,100 +1,100 @@ { - "path": "./", - "calculator": "vasp", - "_comment1": "vasp/pwscf/gaussian", - "output": "dpgen_db.json", - "id_prefix": "", - "config_info_dict": { - "fcc-bulk": [ - 0, - 1, - 2, - 3, - 4, - 5, - 6, - 7 - ], - "hcp-bulk": [ - 8, - 9, - 10, - 11, - 12, - 13, - 14, - 15 - ], - "bcc-bulk": [ - 16, - 17, - 18, - 19, - 20, - 21, - 22, - 23 - ], - "fcc-surf-100": [ - 24, - 25, - 26, - 27, - 28, - 29, - 30, - 31 - ], - "fcc-surf-111": [ - 32, - 33, - 34, - 35, - 36, - 37, - 38, - 39 - ], - "fcc-surf-110": [ - 40, - 41, - 42, - 43, - 44, - 45, - 46, - 47 - ], - "hcp-surf-001": [ - 48, - 49, - 50, - 51, - 52, - 53, - 54, - 55 - ], - "hcp-surf-100": [ - 56, - 57, - 58, - 59, - 60, - 61, - 62, - 63 - ], - "hcp-surf-110": [ - 64, - 65, - 66, - 67, - 68, - 69, - 70, - 71 - ] - }, - "skip_init": true -} \ No newline at end of file + "path": "./", + "calculator": "vasp", + "_comment1": "vasp/pwscf/gaussian", + "output": "dpgen_db.json", + "id_prefix": "", + "config_info_dict": { + "fcc-bulk": [ + 0, + 1, + 2, + 3, + 4, + 5, + 6, + 7 + ], + "hcp-bulk": [ + 8, + 9, + 10, + 11, + 12, + 13, + 14, + 15 + ], + "bcc-bulk": [ + 16, + 17, + 18, + 19, + 20, + 21, + 22, + 23 + ], + "fcc-surf-100": [ + 24, + 25, + 26, + 27, + 28, + 29, + 30, + 31 + ], + "fcc-surf-111": [ + 32, + 33, + 34, + 35, + 36, + 37, + 38, + 39 + ], + "fcc-surf-110": [ + 40, + 41, + 42, + 43, + 44, + 45, + 46, + 47 + ], + "hcp-surf-001": [ + 48, + 49, + 50, + 51, + 52, + 53, + 54, + 55 + ], + "hcp-surf-100": [ + 56, + 57, + 58, + 59, + 60, + 61, + 62, + 63 + ], + "hcp-surf-110": [ + 64, + 65, + 66, + 67, + 68, + 69, + 70, + 71 + ] + }, + "skip_init": true +} diff --git a/tests/generator/cluster/cluster1.json b/tests/generator/cluster/cluster1.json index 4818b8401..a7b405d17 100644 --- a/tests/generator/cluster/cluster1.json +++ b/tests/generator/cluster/cluster1.json @@ -1,214 +1,214 @@ { - "@module": "dpdata.system", - "@class": "System", - "data": { - "atom_numbs": [ - 8, - 17 - ], - "atom_names": [ - "C", - "H" - ], - "orig": { - "@module": "numpy", - "@class": "array", - "dtype": "float64", - "data": [ - 0.0, - 0.0, - 0.0 - ] - }, - "cells": { - "@module": "numpy", - "@class": "array", - "dtype": "float64", - "data": [ - [ - [ - 44.8992, - 0.0, - 0.0 - ], - [ - 0.0, - 44.8992, - 0.0 - ], - [ - 0.0, - 0.0, - 44.8992 - ] - ] - ] - }, - "atom_types": { - "@module": "numpy", - "@class": "array", - "dtype": "int64", - "data": [ - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 0, - 1, - 1, - 1, - 1, - 1, - 1, - 1, - 1, - 1, - 1, - 1, - 1, - 1, - 1, - 1, - 1, - 1 - ] - }, - "coords": { - "@module": "numpy", - "@class": "array", - "dtype": "float64", - "data": [ - [ - [ - 40.92869999999999, - 21.974000000000004, - 38.42430000000001 - ], - [ - 39.6113, - 21.946500000000004, - 39.4466 - ], - [ - 39.5837, - 21.935900000000004, - 41.0881 - ], - [ - 40.5351, - 20.8477, - 41.019200000000005 - ], - [ - 41.6708, - 21.2669, - 42.0895 - ], - [ - 41.5102, - 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46.882529999999996 - ], - [ - 39.9996, - 22.2298, - 45.363275 - ] - ] - ] + "@module": "dpdata.system", + "@class": "System", + "data": { + "atom_numbs": [ + 8, + 17 + ], + "atom_names": [ + "C", + "H" + ], + "orig": { + "@module": "numpy", + "@class": "array", + "dtype": "float64", + "data": [ + 0.0, + 0.0, + 0.0 + ] + }, + "cells": { + "@module": "numpy", + "@class": "array", + "dtype": "float64", + "data": [ + [ + [ + 44.8992, + 0.0, + 0.0 + ], + [ + 0.0, + 44.8992, + 0.0 + ], + [ + 0.0, + 0.0, + 44.8992 + ] + ] + ] + }, + "atom_types": { + "@module": "numpy", + "@class": "array", + "dtype": "int64", + "data": [ + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1, + 1 + ] + }, + "coords": { + "@module": "numpy", + "@class": "array", + "dtype": "float64", + "data": [ + [ + [ + 40.92869999999999, + 21.974000000000004, + 38.42430000000001 + ], + [ + 39.6113, + 21.946500000000004, + 39.4466 + ], + [ + 39.5837, + 21.935900000000004, + 41.0881 + ], + [ + 40.5351, + 20.8477, + 41.019200000000005 + ], + [ + 41.6708, + 21.2669, + 42.0895 + ], + [ + 41.5102, + 21.450400000000002, + 43.6033 + ], + [ + 42.093700000000005, + 22.467100000000002, + 44.6771 + ], + [ + 40.8365, + 22.764600000000005, + 45.76440099999999 + ], + [ + 40.72740000000001, + 22.0739, + 37.4974 + ], + [ + 41.67810000000001, + 22.7849, + 38.7914 + ], + [ + 39.0785, + 20.9028, + 38.9622 + ], + [ + 39.16049999999999, + 22.868500000000004, + 39.1868 + ], + [ + 38.575900000000004, + 21.682100000000002, + 41.1571 + ], + [ + 39.73299999999999, + 22.959200000000003, + 41.3309 + ], + [ + 40.9748, + 20.9371, + 40.015100000000004 + ], + [ + 39.7529, + 20.0048, + 40.8674 + ], + [ + 42.1817, + 22.268500000000003, + 41.9158 + ], + [ + 42.6849, + 20.325400000000002, + 41.9751 + ], + [ + 41.66340000000001, + 20.5363, + 43.7852 + ], + [ + 40.412, + 21.2711, + 43.57180000000001 + ], + [ + 42.8889, + 23.378400000000006, + 44.3826 + ], + [ + 42.841899999999995, + 22.1742, + 45.512007000000004 + ], + [ + 40.5156, + 23.777600000000007, + 45.97272 + ], + [ + 41.3013, + 22.319600000000005, + 46.882529999999996 + ], + [ + 39.9996, + 22.2298, + 45.363275 + ] + ] + ] + } } - } -} \ No newline at end of file +} diff --git a/tests/generator/gromacs/model_devi_case/input.json b/tests/generator/gromacs/model_devi_case/input.json index d2fbd8262..bd68970d2 100644 --- a/tests/generator/gromacs/model_devi_case/input.json +++ b/tests/generator/gromacs/model_devi_case/input.json @@ -1,7 +1,7 @@ { - "graph_file": "/data1/anguse/yuzhi/fep/20210520_gromacs_dpgen/iter.000000/00.train/graph.000.pb", - "box_file": "/data1/anguse/yingze/fep/deepmd/input/box.raw", - "type_file": "/data1/anguse/yuzhi/fep/DP_FF/tyk2/init_data/lig_ejm_31/type.raw", - "index_file": "index.raw", - "lambda": 1.0 -} \ No newline at end of file + "graph_file": "/data1/anguse/yuzhi/fep/20210520_gromacs_dpgen/iter.000000/00.train/graph.000.pb", + "box_file": "/data1/anguse/yingze/fep/deepmd/input/box.raw", + "type_file": "/data1/anguse/yuzhi/fep/DP_FF/tyk2/init_data/lig_ejm_31/type.raw", + "index_file": "index.raw", + "lambda": 1.0 +} diff --git a/tests/generator/machine-local-v1.json b/tests/generator/machine-local-v1.json index 81f0ce0ea..6ffac93a7 100644 --- a/tests/generator/machine-local-v1.json +++ b/tests/generator/machine-local-v1.json @@ -1,52 +1,52 @@ { - "train_machine": { - "machine_type": "shell", - "lazy_local": true - }, - "train_resources": { - "numb_node": 1, - "numb_gpu": 0, - "task_per_node": 4, - "exclude_list": [], - "source_list": [ - "/home/wanghan/study/deep.md/venvs/py3.6-tf1.8/bin/active" - ], - "envs": {}, - "_comment1": "that's All" - }, - "python_path": "/home/wanghan/study/deep.md/venvs/py3.6-tf1.8/bin/python", - "model_devi_machine": { - "machine_type": "shell", - "work_path": "/home/wanghan/study/deep.md/dpgen/almg/tmp" - }, - "model_devi_resources": { - "numb_node": 1, - "task_per_node": 4, - "with_mpi": true, - "module_list": [ - "mpi" - ], - "exclude_list": [], - "source_list": [], - "_comment2": "that's All" - }, - "model_devi_command": "/home/wanghan/local/bin/lmp_mpi_1_1_0", - "model_devi_group_size": 10, - "fp_machine": { - "machine_type": "shell", - "work_path": "/home/wanghan/study/deep.md/dpgen/almg/tmp" - }, - "fp_resources": { - "cvasp": false, - "task_per_node": 4, - "exclude_list": [], - "with_mpi": true, - "module_list": [ - "mpi" - ], - "source_list": [], - "_comment3": "that's All" - }, - "fp_command": "/home/wanghan/local/bin/vasp_std", - "fp_group_size": 5 -} \ No newline at end of file + "train_machine": { + "machine_type": "shell", + "lazy_local": true + }, + "train_resources": { + "numb_node": 1, + "numb_gpu": 0, + "task_per_node": 4, + "exclude_list": [], + "source_list": [ + "/home/wanghan/study/deep.md/venvs/py3.6-tf1.8/bin/active" + ], + "envs": {}, + "_comment1": "that's All" + }, + "python_path": "/home/wanghan/study/deep.md/venvs/py3.6-tf1.8/bin/python", + "model_devi_machine": { + "machine_type": "shell", + "work_path": "/home/wanghan/study/deep.md/dpgen/almg/tmp" + }, + "model_devi_resources": { + "numb_node": 1, + "task_per_node": 4, + "with_mpi": true, + "module_list": [ + "mpi" + ], + "exclude_list": [], + "source_list": [], + "_comment2": "that's All" + }, + "model_devi_command": "/home/wanghan/local/bin/lmp_mpi_1_1_0", + "model_devi_group_size": 10, + "fp_machine": { + "machine_type": "shell", + "work_path": "/home/wanghan/study/deep.md/dpgen/almg/tmp" + }, + "fp_resources": { + "cvasp": false, + "task_per_node": 4, + "exclude_list": [], + "with_mpi": true, + "module_list": [ + "mpi" + ], + "source_list": [], + "_comment3": "that's All" + }, + "fp_command": "/home/wanghan/local/bin/vasp_std", + "fp_group_size": 5 +} diff --git a/tests/generator/machine-local.json b/tests/generator/machine-local.json index 8404bd2ab..fb2d47073 100644 --- a/tests/generator/machine-local.json +++ b/tests/generator/machine-local.json @@ -1,55 +1,55 @@ { - "_comment1": "training on localhost ", - "deepmd_path": "/home/wanghan/local/deepmd/0.10.1/", - "train_machine": { - "machine_type": "local", - "hostname": "127.0.0.1", - "port": 22, - "username": "wanghan", - "work_path": "/home/wanghan/tmp/subs/", - "_comment2": "that's all" - }, - "train_resources": { - "envs": { - "PYTHONPATH": "/home/wanghan/local/tensorflow/1.8.py/lib/python3.6/site-packages/" + "_comment1": "training on localhost ", + "deepmd_path": "/home/wanghan/local/deepmd/0.10.1/", + "train_machine": { + "machine_type": "local", + "hostname": "127.0.0.1", + "port": 22, + "username": "wanghan", + "work_path": "/home/wanghan/tmp/subs/", + "_comment2": "that's all" }, - "_comment3": "that's all" - }, - "_comment4": "model_devi on localhost ", - "model_devi_command": "/home/wanghan/local/bin/lmp_mpi_010", - "model_devi_group_size": 5, - "model_devi_machine": { - "machine_type": "local", - "hostname": "127.0.0.1", - "port": 22, - "username": "wanghan", - "work_path": "/home/wanghan/tmp/subs/", - "_comment5": "that's all" - }, - "model_devi_resources": { - "_comment6": "that's all" - }, - "_comment7": "fp on localhost ", - "fp_command": "/home/wanghan/local/bin/vasp_std", - "fp_group_size": 2, - "fp_machine": { - "machine_type": "local", - "hostname": "127.0.0.1", - "port": 22, - "username": "wanghan", - "work_path": "/home/wanghan/tmp/subs/", - "_comment8": "that's all" - }, - "fp_resources": { - "module_list": [ - "mpi" + "train_resources": { + "envs": { + "PYTHONPATH": "/home/wanghan/local/tensorflow/1.8.py/lib/python3.6/site-packages/" + }, + "_comment3": "that's all" + }, + "_comment4": "model_devi on localhost ", + "model_devi_command": "/home/wanghan/local/bin/lmp_mpi_010", + "model_devi_group_size": 5, + "model_devi_machine": { + "machine_type": "local", + "hostname": "127.0.0.1", + "port": 22, + "username": "wanghan", + "work_path": "/home/wanghan/tmp/subs/", + "_comment5": "that's all" + }, + "model_devi_resources": { + "_comment6": "that's all" + }, + "_comment7": "fp on localhost ", + "fp_command": "/home/wanghan/local/bin/vasp_std", + "fp_group_size": 2, + "fp_machine": { + "machine_type": "local", + "hostname": "127.0.0.1", + "port": 22, + "username": "wanghan", + "work_path": "/home/wanghan/tmp/subs/", + "_comment8": "that's all" + }, + "fp_resources": { + "module_list": [ + "mpi" + ], + "task_per_node": 4, + "with_mpi": true, + "_comment9": "that's all" + }, + "fp_user_forward_files": [ + "vdw_kernel.bindat" ], - "task_per_node": 4, - "with_mpi": true, - "_comment9": "that's all" - }, - "fp_user_forward_files": [ - "vdw_kernel.bindat" - ], - "_comment10": " that's all " -} \ No newline at end of file + "_comment10": " that's all " +} diff --git a/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000000/job.json b/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000000/job.json index 9047111dd..660b8b34d 100644 --- a/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000000/job.json +++ b/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000000/job.json @@ -1,3 +1,3 @@ { - "ele_temp": 0 -} \ No newline at end of file + "ele_temp": 0 +} diff --git a/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000001/job.json b/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000001/job.json index 11836af6a..4d97f09db 100644 --- a/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000001/job.json +++ b/tests/generator/out_data_post_fp_vasp/02.fp/task.000.000001/job.json @@ -1,3 +1,3 @@ { - "ele_temp": 1 -} \ No newline at end of file + "ele_temp": 1 +} diff --git a/tests/generator/out_data_post_fp_vasp/02.fp/task.001.000000/job.json b/tests/generator/out_data_post_fp_vasp/02.fp/task.001.000000/job.json index 174650337..75362c521 100644 --- a/tests/generator/out_data_post_fp_vasp/02.fp/task.001.000000/job.json +++ b/tests/generator/out_data_post_fp_vasp/02.fp/task.001.000000/job.json @@ -1,3 +1,3 @@ { - "ele_temp": 100000 -} \ No newline at end of file + "ele_temp": 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of file + "_comment12": " that's all " +} diff --git a/tests/sample.json b/tests/sample.json index 1d24fd344..603a4ea06 100644 --- a/tests/sample.json +++ b/tests/sample.json @@ -1,3 +1,3 @@ { - "aa": "bb" -} \ No newline at end of file + "aa": "bb" +} diff --git a/tests/tools/machine_fp_single.json b/tests/tools/machine_fp_single.json index 9169f709c..bb828fc32 100644 --- a/tests/tools/machine_fp_single.json +++ b/tests/tools/machine_fp_single.json @@ -1,17 +1,17 @@ { - "fp": [ - { - "command": "vasp_std", - "machine": { - "batch_type": "PBS" - }, - "resources": { - "group_size": 8 - }, - "_comments": "In user_forward_files, define input files to be uploaded.", - "user_forward_files": [ - "vdw_kernel.bindat" - ] - } - ] -} \ No newline at end of file + "fp": [ + { + "command": "vasp_std", + "machine": { + "batch_type": "PBS" + }, + "resources": { + "group_size": 8 + }, + "_comments": "In user_forward_files, define input files to be uploaded.", + "user_forward_files": [ + "vdw_kernel.bindat" + ] + } + ] +} diff --git a/tests/tools/machine_fp_single2.json b/tests/tools/machine_fp_single2.json index 302a02d74..772f655ca 100644 --- a/tests/tools/machine_fp_single2.json +++ b/tests/tools/machine_fp_single2.json @@ -1,15 +1,15 @@ { - "fp": { - "command": "vasp_std", - "machine": { - "batch_type": "PBS" - }, - "resources": { - "group_size": 8 - }, - "_comments": "In user_forward_files, define input files to be uploaded.", - "user_forward_files": [ - "vdw_kernel.bindat" - ] - } -} \ No newline at end of file + "fp": { + "command": "vasp_std", + "machine": { + "batch_type": "PBS" + }, + "resources": { + "group_size": 8 + }, + "_comments": "In user_forward_files, define input files to be uploaded.", + "user_forward_files": [ + "vdw_kernel.bindat" + ] + } +} diff --git a/tests/tools/run_report_test_output/param.json b/tests/tools/run_report_test_output/param.json index ce637c424..397a785df 100644 --- a/tests/tools/run_report_test_output/param.json +++ 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