Merge recent development on devel into master#216
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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>
* add deepmd/hdf5 format To support deepmodeling/deepmd-kit#1163. * bugfix * add an example
* 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 ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #216 +/- ##
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+ Coverage 80.07% 82.05% +1.97%
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Files 54 58 +4
Lines 4553 5027 +474
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+ Hits 3646 4125 +479
+ Misses 907 902 -5 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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AnguseZhang
approved these changes
Nov 14, 2021
njzjz
approved these changes
Nov 14, 2021
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