Merge recent development on devel into master #216

amcadmus · 2021-11-13T02:11:48Z

No description provided.

Sync devel with master

enable unittests of ase and pymatgen

fix two bugs that implemented in deepmodeling#168

* Update dump.py * Create test_lammps_dump_unfold.py * Create conf_unfold.dump * Update dump.py * Create conf_s_su.dump * Create test_lammps_dump_s_su.py * Update dump.py * Update conf_unfold.dump * Update dump.py

…#184) * if cp2k output is not converged, return the sys len = 0 * modify the cp2k output code 1. use fp.seek(0) to avoid open file twice 2. add 'scf run' line in cp2k_output to read the output content, just to test the parser. * add cp2k non converge output unittest * add unittest for noncon output * modify the unittest name

* add BondOrderSystem * add BondOrderSystem * add BondOrderSystem * add BondOrderSystem * add BondOrderSystem * Update BondOrderSystem * solve oveall dependency on rdkit * Add dpdata/rdkit package * Add information on functions * Spelling correction * Add bond order assignment * Add test cases for bond order assignment * Add support for AmberTools sqm/out * Add bond order assignment * Add support for AmberTools sqm/out * Creat __init__.py * Add rdkit & openbabel environment * Update README.md * Update test.yml * Remove non user-friendly warnings * Update dpdata/rdkit/sanitize.py Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> * Use obabel python interface * Update README.md * Remove dependency on data for MolFormat & SdfFormat * Support dump multiple conformers for sdf file * Fix bug of SetFormalCharge type error RDKit cannot automatically transfer np.int32 to int * Add ut for to_sdf_file * Bug fix of dump to deepmd/raw file Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

* add .github/workflows/mirror_gitee.yml * add env: ORGANIZATION in mirror_gitee.yml * Update mirror_gitee.yml

* automatically generate API docs * Update copyright Co-authored-by: Han Wang <amcadmus@gmail.com> Co-authored-by: Han Wang <amcadmus@gmail.com>

…eepmodeling#190) * add MultiSystem for ASE traj(or any other format can be read by ASE) fix bug(?) for ASE 'to_labeled_system' * add unittest add error type of exception

* add BondOrderSystem * add BondOrderSystem * add BondOrderSystem * add BondOrderSystem * add BondOrderSystem * Update BondOrderSystem * solve oveall dependency on rdkit * Add dpdata/rdkit package * Add information on functions * Spelling correction * Add bond order assignment * Add test cases for bond order assignment * Add support for AmberTools sqm/out * Add bond order assignment * Add support for AmberTools sqm/out * Creat __init__.py * Add rdkit & openbabel environment * Update README.md * Update test.yml * Remove non user-friendly warnings * Update dpdata/rdkit/sanitize.py Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> * Use obabel python interface * Update README.md * Remove dependency on data for MolFormat & SdfFormat * Support dump multiple conformers for sdf file * Fix bug of SetFormalCharge type error RDKit cannot automatically transfer np.int32 to int * Add ut for to_sdf_file * Bug fix of dump to deepmd/raw file * More flexibility to control writing to gro file Support control resname / add atom index shift when dumping to .gro file * Support parse sqm.out to LabeledSystem & prepare sqm.in file Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

…eling#201)

* add deepmd/hdf5 format To support deepmodeling/deepmd-kit#1163. * bugfix * add an example

fix deepmodeling#206.

* add .github/workflows/mirror_gitee.yml * implement support for pymatgen.core.Molecule * implement support for pymatgen.core.Molecule * Change atom_types in dpdata/pymatgen/molecule.py * Change doc string in dpdata/plugins/pymatgen.py * add dpdata/pymatgin to setup.py * modify molecule.py * modify molecule.py * modify molecule.py * Support of pymatgen.Molecule in dpdata * Update tests/test_pymatgen_molecule.py * Moved "remove_pbc" from pymatgen/molecule.py to system.py

* add ABACUS MD interface. * Update system.py * Add files via upload

* add ABACUS MD interface. * Update system.py * Add files via upload * Update md.py * Update md.py

codecov-commenter · 2021-11-13T02:15:14Z

Codecov Report

Merging #216 (f1859eb) into master (ea32d45) will increase coverage by 1.97%.
The diff coverage is 87.89%.

@@            Coverage Diff             @@
##           master     #216      +/-   ##
==========================================
+ Coverage   80.07%   82.05%   +1.97%     
==========================================
  Files          54       58       +4     
  Lines        4553     5027     +474     
==========================================
+ Hits         3646     4125     +479     
+ Misses        907      902       -5

Impacted Files	Coverage Δ
dpdata/system.py	`80.90% <44.73%> (-0.74%)`	⬇️
dpdata/rdkit/utils.py	`61.79% <50.00%> (-1.00%)`	⬇️
dpdata/plugins/rdkit.py	`80.64% <66.66%> (+16.12%)`	⬆️
dpdata/plugins/ase.py	`65.45% <77.41%> (+46.22%)`	⬆️
dpdata/deepmd/hdf5.py	`82.66% <82.66%> (ø)`
dpdata/plugins/pymatgen.py	`85.71% <84.61%> (+59.90%)`	⬆️
dpdata/lammps/dump.py	`89.83% <87.50%> (-0.39%)`	⬇️
dpdata/unit.py	`88.15% <88.15%> (ø)`
dpdata/bond_order_system.py	`64.78% <88.88%> (+3.49%)`	⬆️
dpdata/plugins/deepmd.py	`93.87% <88.88%> (-6.13%)`	⬇️
... and 24 more

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amcadmus and others added 24 commits July 7, 2021 07:29

Merge pull request deepmodeling#169 from deepmodeling/master

f0273f7

Sync devel with master

enable unittests of ase and pymatgen

89b0596

support pymatgen v2022

cbf3ed8

fix two bugs that implemented in deepmodeling#168

1f10a5c

add unittests

e24e467

Merge pull request deepmodeling#171 from njzjz/ut-ase-pymatgen

d238c6a

enable unittests of ase and pymatgen

Merge pull request deepmodeling#172 from njzjz/bugfix

6000e31

fix two bugs that implemented in deepmodeling#168

catch rdkit ModuleNotFoundError (deepmodeling#176)

980f297

Support of all lammps dump coordinate style (deepmodeling#179)

73ad164

* Update dump.py * Create test_lammps_dump_unfold.py * Create conf_unfold.dump * Update dump.py * Create conf_s_su.dump * Create test_lammps_dump_s_su.py * Update dump.py * Update conf_unfold.dump * Update dump.py

fix a bug in AmberMDFormat (deepmodeling#186)

fbf5bd7

add .github/workflows/mirror_gitee.yml (deepmodeling#187)

1a62714

* add .github/workflows/mirror_gitee.yml * add env: ORGANIZATION in mirror_gitee.yml * Update mirror_gitee.yml

automatically generate API docs (deepmodeling#189)

243c563

* automatically generate API docs * Update copyright Co-authored-by: Han Wang <amcadmus@gmail.com> Co-authored-by: Han Wang <amcadmus@gmail.com>

add MultiSystem for ASE traj(or any other format can be read by ASE) (d…

f594787

…eepmodeling#190) * add MultiSystem for ASE traj(or any other format can be read by ASE) fix bug(?) for ASE 'to_labeled_system' * add unittest add error type of exception

use np.testing.assert_almost_equal to compare numpy arrays (deepmod…

3c595ca

…eling#201)

Add unit.py to manage unit conversions (deepmodeling#202)

23e9f3b

add deepmd/hdf5 format (deepmodeling#203)

b58aa63

* add deepmd/hdf5 format To support deepmodeling/deepmd-kit#1163. * bugfix * add an example

fix support for deepmd-kit 2.0.2 (deepmodeling#207)

3e96c2c

fix deepmodeling#206.

Added ABACUS MD interface (deepmodeling#208)

f864b36

* add ABACUS MD interface. * Update system.py * Add files via upload

Update README.md (deepmodeling#209)

5990c78

Fix bug in abacus MD support (deepmodeling#214)

f1859eb

* add ABACUS MD interface. * Update system.py * Add files via upload * Update md.py * Update md.py

amcadmus requested review from njzjz and AnguseZhang November 13, 2021 02:11

AnguseZhang approved these changes Nov 14, 2021

View reviewed changes

njzjz approved these changes Nov 14, 2021

View reviewed changes

wanghan-iapcm merged commit 1d1084d into deepmodeling:master Nov 14, 2021

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Merge recent development on devel into master #216

Merge recent development on devel into master #216

amcadmus commented Nov 13, 2021

codecov-commenter commented Nov 13, 2021 •

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Merge recent development on devel into master #216

Merge recent development on devel into master #216

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amcadmus commented Nov 13, 2021

codecov-commenter commented Nov 13, 2021 • edited Loading

Codecov Report

codecov-commenter commented Nov 13, 2021 •

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