Nexus: Add Lowdin example to nexus/examples

nexus/examples/qmcpack/rsqmc_misc/diamond_lowdin/diamond.py

@@ -0,0 +1,144 @@
+#! /usr/bin/env python
+
+from nexus import settings
+from nexus import job
+from nexus import run_project
+from nexus import generate_physical_system
+from nexus import generate_pwscf
+from nexus import generate_projwfc
+from nexus import generate_pw2qmcpack
+from nexus import generate_qmcpack
+from nexus import vmc
+
+from structure import *
+
+from qmcpack_input import dm1b
+from qmcpack_input import sposet
+
+settings(
+    pseudo_dir    = '../../pseudopotentials',
+    results       = '',
+    status_only   = 0,
+    generate_only = 0,
+    skip_submit   = 0,
+    sleep         = 3,
+    machine       = 'ws4'
+    )
+
+dia16 = generate_physical_system(
+    units  = 'A',
+    axes   = [[ 1.785,  1.785,  0.   ],
+              [ 0.   ,  1.785,  1.785],
+              [ 1.785,  0.   ,  1.785]],
+    elem   = ['C','C'],
+    pos    = [[ 0.    ,  0.    ,  0.    ],
+              [ 0.8925,  0.8925,  0.8925]],
+    tiling = (1,1,1),
+    C      = 4
+    )
+
+# k-mesh used for density
+scf_kg = dia16.structure.kgrid_from_kspacing(0.5) # Get SCF kmesh from k-spacing
+
+# twist-mesh used for qmc
+dia16.structure.add_symmetrized_kmesh(kgrid=(2,2,2),kshift=(0,0,0))
+
+
+number_of_ks_orbs = 11
+
+scf = generate_pwscf(
+    identifier   = 'scf',
+    path         = 'scf',
+    job          = job(nodes=1,app='pw.x',hours=1),
+    input_type   = 'generic',
+    calculation  = 'scf',
+    nspin        = 1,
+    nbnd         = number_of_ks_orbs,
+    input_dft    = 'lda',
+    ecutwfc      = 200,
+    conv_thr     = 1e-8,
+    nosym        = False,
+    wf_collect   = False,
+    system       = dia16,
+    kgrid        = scf_kg,
+    kshift       = (0,0,0),
+    pseudos      = ['C.BFD.upf'],
+    )
+
+nscf = generate_pwscf(
+    identifier   = 'nscf',
+    path         = 'nscf',
+    job          = job(nodes=1,app='pw.x',hours=1),
+    input_type   = 'generic',
+    calculation  = 'nscf',
+    input_dft    = 'lda',
+    ecutwfc      = 200,
+    nspin        = 1,
+    conv_thr     = 1e-8,
+    nosym        = True,
+    wf_collect   = True,
+    system       = dia16,
+    nbnd         = number_of_ks_orbs,
+    verbosity    = 'high', #verbosity must be set to high
+    pseudos      = ['C.BFD.upf'],
+    dependencies = (scf,'charge_density'),
+    )
+
+# To obtain the overlaps between the Bloch states and atomic orbitals,
+# projwfc.x needs to be run. The overlaps will be stored in:
+# pwscf_output/pwscf.save/atomic_proj.xml
+# WARNING: Always check the the <OVERLAPS> element is written to atomic_proj.xml
+#          Sometimes QE will not write <OVERLAPS> if running on >1 core.
+pwf = generate_projwfc(
+    identifier      = 'pwf',
+    path            = 'nscf',
+    job             = job(nodes=1,app='projwfc.x',hours=1),
+    lwrite_overlaps = True,
+    lsym            = False,
+    dependencies    = (nscf,'other')
+    )
+
+# Generate orbital h5 file
+conv = generate_pw2qmcpack(
+    identifier   = 'conv',
+    path         = 'nscf',
+    job          = job(cores=1,app='pw2qmcpack.x',hours=1),
+    write_psir   = False,
+    dependencies = (nscf,'orbitals'),
+    )
+
+# Define 1RDM Parameters
+dm_estimator = dm1b(
+        energy_matrix = False,
+        integrator    = 'uniform_grid',
+        points        = 6,
+        scale         = 1.0,
+        basis         = sposet(type='bspline',size=number_of_ks_orbs,spindataset=0),
+        evaluator     = 'matrix',
+        center        = (0,0,0),
+        check_overlap = False,
+        )
+
+qmc = generate_qmcpack(
+    identifier   = 'vmc_1rdm_noJ',
+    path         = 'vmc_1rdm_noJ',
+    job          = job(cores=3,app='qmcpack_complex',hours=1),
+    input_type   = 'basic',
+    system       = dia16,
+    pseudos      = ['C.BFD.xml'],
+    estimators   = [dm_estimator],
+    jastrows     = [],
+    calculations = [
+        vmc(
+            walkers     =   1,
+            warmupsteps =  20,
+            blocks      = 200,
+            steps       =  10,
+            substeps    =   2,
+            timestep    =  .4
+            )
+        ],
+    dependencies = (conv,'orbitals'),
+    )
+
+run_project()

nexus/examples/qmcpack/rsqmc_misc/diamond_lowdin/diamond_spin.py

@@ -0,0 +1,181 @@
+#! /usr/bin/env python
+
+from nexus import settings
+from nexus import job
+from nexus import run_project
+from nexus import generate_physical_system
+from nexus import generate_pwscf
+from nexus import generate_projwfc
+from nexus import generate_pw2qmcpack
+from nexus import generate_qmcpack
+from nexus import vmc
+
+from structure import *
+
+from qmcpack_input import dm1b
+from qmcpack_input import sposet
+
+settings(
+    pseudo_dir    = '../../pseudopotentials',
+    runs          = 'runs_spin',
+    results       = '',
+    status_only   = 0,
+    generate_only = 0,
+    skip_submit   = 0,
+    sleep         = 3,
+    machine       = 'ws4'
+    )
+
+dia16 = generate_physical_system(
+    units  = 'A',
+    axes   = [[ 1.785,  1.785,  0.   ],
+              [ 0.   ,  1.785,  1.785],
+              [ 1.785,  0.   ,  1.785]],
+    elem   = ['C','C'],
+    pos    = [[ 0.    ,  0.    ,  0.    ],
+              [ 0.8925,  0.8925,  0.8925]],
+    tiling = (1,1,1),
+    C      = 4
+    )
+
+# k-mesh used for density
+scf_kg = dia16.structure.kgrid_from_kspacing(0.5) # Get SCF kmesh from k-spacing
+
+# twist-mesh used for qmc
+dia16.structure.add_symmetrized_kmesh(kgrid=(2,2,2),kshift=(0,0,0))
+
+
+number_of_ks_orbs = 11
+
+scf = generate_pwscf(
+    identifier   = 'scf',
+    path         = 'scf',
+    job          = job(cores=1,app='pw.x',hours=1),
+    input_type   = 'generic',
+    calculation  = 'scf',
+    nspin        = 2,
+    tot_magnetization = 0,
+    nbnd         = number_of_ks_orbs,
+    input_dft    = 'lda',
+    ecutwfc      = 200,
+    conv_thr     = 1e-8,
+    nosym        = False,
+    wf_collect   = False,
+    system       = dia16,
+    kgrid        = scf_kg,
+    kshift       = (0,0,0),
+    pseudos      = ['C.BFD.upf'],
+    )
+
+nscf = generate_pwscf(
+    identifier   = 'nscf',
+    path         = 'nscf',
+    job          = job(cores=1,app='pw.x',hours=1),
+    input_type   = 'generic',
+    calculation  = 'nscf',
+    input_dft    = 'lda',
+    ecutwfc      = 200,
+    nspin        = 2,
+    tot_magnetization = 0,
+    conv_thr     = 1e-8,
+    nosym        = True,
+    wf_collect   = True,
+    system       = dia16,
+    nbnd         = number_of_ks_orbs,
+    verbosity    = 'high', #verbosity must be set to high
+    pseudos      = ['C.BFD.upf'],
+    dependencies = (scf,'charge_density'),
+    )
+
+# To obtain the overlaps between the Bloch states and atomic orbitals,
+# projwfc.x needs to be run. The overlaps will be stored in:
+# pwscf_output/pwscf.save/atomic_proj.xml
+# WARNING: Always check the the <OVERLAPS> element is written to atomic_proj.xml
+#          Sometimes QE will not write <OVERLAPS> if running on >1 core.
+pwf = generate_projwfc(
+    identifier      = 'pwf',
+    path            = 'nscf',
+    job             = job(cores=1,app='projwfc.x',hours=1),
+    lwrite_overlaps = True,
+    lsym            = False,
+    dependencies    = (nscf,'other')
+    )
+
+# Generate orbital h5 file
+conv = generate_pw2qmcpack(
+    identifier   = 'conv',
+    path         = 'nscf',
+    job          = job(cores=1,app='pw2qmcpack.x',hours=1),
+    write_psir   = False,
+    dependencies = (nscf,'orbitals'),
+    )
+
+# Define 1RDM Parameters
+dm_estimator = dm1b(
+        energy_matrix = False,
+        integrator    = 'uniform_grid',
+        points        = 6,
+        scale         = 1.0,
+        basis         = sposet(type='bspline',size=number_of_ks_orbs,spindataset=0),
+        evaluator     = 'matrix',
+        center        = (0,0,0),
+        check_overlap = False,
+        )
+
+down_dm_estimator = dm1b(
+        energy_matrix = False,
+        integrator    = 'uniform_grid',
+        points        = 6,
+        scale         = 1.0,
+        basis         = sposet(type='bspline',size=number_of_ks_orbs,spindataset=1),
+        evaluator     = 'matrix',
+        center        = (0,0,0),
+        check_overlap = False,
+        )
+
+
+qmc = generate_qmcpack(
+    identifier   = 'vmc_1rdm_noJ',
+    path         = 'vmc_1rdm_noJ',
+    job          = job(cores=3,app='qmcpack_complex',hours=1),
+    input_type   = 'basic',
+    system       = dia16,
+    pseudos      = ['C.BFD.xml'],
+    estimators   = [dm_estimator],
+    jastrows     = [],
+    calculations = [
+        vmc(
+            walkers     =   1,
+            warmupsteps =  20,
+            blocks      = 200,
+            steps       =  10,
+            substeps    =   2,
+            timestep    =  .4
+            )
+        ],
+    dependencies = (conv,'orbitals'),
+    )
+
+qmc = generate_qmcpack(
+    identifier   = 'vmc_1rdm_down_noJ',
+    path         = 'vmc_1rdm_down_noJ',
+    job          = job(cores=3,app='qmcpack_complex',hours=1),
+    input_type   = 'basic',
+    system       = dia16,
+    pseudos      = ['C.BFD.xml'],
+    estimators   = [down_dm_estimator],
+    jastrows     = [],
+    calculations = [
+        vmc(
+            walkers     =   1,
+            warmupsteps =  20,
+            blocks      = 200,
+            steps       =  10,
+            substeps    =   2,
+            timestep    =  .4
+            )
+        ],
+    dependencies = (conv,'orbitals'),
+    )
+run_project()
+