├── .git-blame-ignore-revs ├── .git_archival.txt ├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ ├── feature_request.yml │ └── generic-issue.yml ├── dependabot.yml └── workflows │ ├── benchmark.yml │ ├── mirror_gitee.yml │ ├── pub-pypi.yml │ ├── pyright.yml │ ├── test.yml │ └── test_import.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── AGENTS.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── benchmark ├── __init__.py └── test_import.py ├── docs ├── Makefile ├── cli.rst ├── conf.py ├── credits.rst ├── drivers.rst ├── environment.yml ├── formats.rst ├── index.rst ├── installation.md ├── make_format.py ├── minimizers.rst ├── nb │ ├── OUTCAR │ └── try_dpdata.ipynb ├── plugin.md ├── requirements.txt ├── rtd_environment.yml ├── systems │ ├── bond_order_system.md │ ├── index.rst │ ├── mixed.md │ ├── multi.md │ └── system.md └── try_dpdata.rst ├── dpdata ├── __about__.py ├── __init__.py ├── __main__.py ├── abacus │ ├── __init__.py │ ├── md.py │ ├── relax.py │ ├── scf.py │ └── stru.py ├── amber │ ├── __init__.py │ ├── mask.py │ ├── md.py │ └── sqm.py ├── ase_calculator.py ├── bond_order_system.py ├── cli.py ├── cp2k │ ├── __init__.py │ ├── cell.py │ └── output.py ├── data_type.py ├── deepmd │ ├── __init__.py │ ├── comp.py │ ├── hdf5.py │ ├── mixed.py │ └── raw.py ├── dftbplus │ ├── __init__.py │ └── output.py ├── driver.py ├── fhi_aims │ ├── __init__.py │ └── output.py ├── format.py ├── gaussian │ ├── __init__.py │ ├── fchk.py │ ├── gjf.py │ └── log.py ├── gromacs │ ├── __init__.py │ └── gro.py ├── lammps │ ├── __init__.py │ ├── dump.py │ └── lmp.py ├── md │ ├── __init__.py │ ├── msd.py │ ├── pbc.py │ ├── rdf.py │ └── water.py ├── openmx │ ├── __init__.py │ └── omx.py ├── orca │ ├── __init__.py │ └── output.py ├── periodic_table.json ├── periodic_table.py ├── plugin.py ├── plugins │ ├── 3dmol.py │ ├── __init__.py │ ├── abacus.py │ ├── amber.py │ ├── ase.py │ ├── cp2k.py │ ├── deepmd.py │ ├── dftbplus.py │ ├── fhi_aims.py │ ├── gaussian.py │ ├── gromacs.py │ ├── lammps.py │ ├── list.py │ ├── n2p2.py │ ├── openmx.py │ ├── orca.py │ ├── psi4.py │ ├── pwmat.py │ ├── pymatgen.py │ ├── qe.py │ ├── rdkit.py │ ├── siesta.py │ ├── vasp.py │ └── xyz.py ├── psi4 │ ├── __init__.py │ ├── input.py │ └── output.py ├── pwmat │ ├── __init__.py │ ├── atomconfig.py │ └── movement.py ├── py.typed ├── pymatgen │ ├── __init__.py │ ├── molecule.py │ └── structure.py ├── qe │ ├── __init__.py │ ├── scf.py │ └── traj.py ├── rdkit │ ├── __init__.py │ ├── sanitize.py │ └── utils.py ├── siesta │ ├── __init__.py │ ├── aiMD_output.py │ └── output.py ├── stat.py ├── system.py ├── unit.py ├── utils.py ├── vasp │ ├── __init__.py │ ├── outcar.py │ ├── poscar.py │ └── xml.py └── xyz │ ├── __init__.py │ ├── quip_gap_xyz.py │ └── xyz.py ├── plugin_example ├── README.md ├── dpdata_random │ └── __init__.py └── pyproject.toml ├── pyproject.toml └── tests ├── POSCAR ├── abacus.md.newversion ├── INPUT ├── OUT.Sn_nve │ ├── MD_dump │ └── running_md.log ├── STRU ├── coord.ref ├── force.ref └── virial.ref ├── abacus.md.nostress ├── INPUT ├── OUT.autotest │ ├── MD_dump │ └── running_md.log ├── STRU ├── Si_coord └── Si_force ├── abacus.md.unconv ├── INPUT ├── OUT.ABACUS │ ├── MD_dump │ └── running_md.log ├── STRU ├── water_coord ├── water_force └── water_virial ├── abacus.md ├── INPUT ├── OUT.abacus │ ├── MD_dump │ └── running_md.log ├── STRU ├── water_coord ├── water_force └── water_virial ├── abacus.relax ├── INPUT ├── INPUT.spin ├── KPT ├── OUT.abacus │ ├── INPUT │ ├── STRU_ION_D │ ├── STRU_READIN_ADJUST.cif │ ├── running_cell-relax.log.abnormal │ ├── running_cell-relax.log.normal │ ├── running_cell-relax.log.nostress │ └── running_cell-relax.log.v341 ├── STRU.Si ├── STRU.h2o ├── STRU.spin ├── coord.ref ├── force.ref ├── force.v341.ref ├── stress.ref ├── stress.v341.ref └── virial.ref ├── abacus.scf ├── C.orb ├── C.upf ├── H.orb ├── H.upf ├── INPUT.ch4-noforcestress ├── INPUT.fail ├── INPUT.ok ├── OUT.ch4-noForceStress │ └── running_scf.log ├── OUT.ch4 │ └── running_scf.log ├── OUT.ch4fail │ └── running_scf.log ├── STRU.ch4 ├── ch4_coord ├── ch4_force ├── ch4_virial ├── jle.orb ├── stru.ref └── stru_test ├── abacus.spin ├── INPUT.md ├── INPUT.relax ├── INPUT.scf ├── INPUT.scf.nspin2 ├── OUT.ABACUS-nspin2 │ └── running_scf.log ├── OUT.ABACUS │ ├── MD_dump │ ├── running_md.log │ ├── running_relax.log │ └── running_scf.log ├── STRU └── STRU.spin ├── amber ├── 02_Heat.mden ├── 02_Heat.mdfrc ├── 02_Heat.nc ├── 02_Heat.parm7 ├── corr │ ├── dataset │ │ └── C6H11HW192O6OW96P1 │ │ │ ├── nopbc │ │ │ ├── set.000 │ │ │ ├── box.npy │ │ │ ├── coord.npy │ │ │ ├── energy.npy │ │ │ └── force.npy │ │ │ ├── type.raw │ │ │ └── type_map.raw │ ├── dp_amber_mask │ │ └── C6EP0H11HW192O6OW96P1 │ │ │ ├── nopbc │ │ │ ├── set.000 │ │ │ ├── box.npy │ │ │ ├── coord.npy │ │ │ ├── energy.npy │ │ │ └── force.npy │ │ │ ├── type.raw │ │ │ └── type_map.raw │ ├── dp_corr │ │ ├── set.000 │ │ │ ├── box.npy │ │ │ ├── coord.npy │ │ │ ├── energy.npy │ │ │ └── force.npy │ │ ├── type.raw │ │ └── type_map.raw │ ├── dp_hl │ │ ├── set.000 │ │ │ ├── box.npy │ │ │ ├── coord.npy │ │ │ ├── energy.npy │ │ │ └── force.npy │ │ ├── type.raw │ │ └── type_map.raw │ ├── dp_ll │ │ ├── set.000 │ │ │ ├── box.npy │ │ │ ├── coord.npy │ │ │ ├── energy.npy │ │ │ └── force.npy │ │ ├── type.raw │ │ └── type_map.raw │ ├── high_level.mdfrc │ ├── high_level.mdout │ ├── low_level.mdfrc │ ├── low_level.mdout │ ├── qmmm.parm7 │ └── rc.nc ├── methane.mol ├── sqm.in ├── sqm_forces.out ├── sqm_no_forces.out └── sqm_opt.out ├── ase_traj ├── Al0He4O0 │ ├── box.raw │ ├── coord.raw │ ├── energy.raw │ ├── force.raw │ ├── type.raw │ ├── type_map.raw │ └── virial.raw ├── Al2He1O3 │ ├── box.raw │ ├── coord.raw │ ├── energy.raw │ ├── force.raw │ ├── type.raw │ ├── type_map.raw │ └── virial.raw ├── Al2He2O3 │ ├── box.raw │ ├── coord.raw │ ├── energy.raw │ ├── force.raw │ ├── type.raw │ ├── type_map.raw │ └── virial.raw ├── Al4He0O6 │ ├── box.raw │ ├── coord.raw │ ├── energy.raw │ ├── force.raw │ ├── type.raw │ ├── type_map.raw │ └── virial.raw ├── Al4He2O6 │ ├── box.raw │ ├── coord.raw │ ├── energy.raw │ ├── force.raw │ ├── type.raw │ ├── type_map.raw │ └── virial.raw ├── Al4He4O6 │ ├── box.raw │ ├── coord.raw │ ├── energy.raw │ ├── force.raw │ ├── type.raw │ ├── type_map.raw │ └── virial.raw ├── Al8He0O12 │ ├── box.raw │ ├── coord.raw │ ├── energy.raw │ ├── force.raw │ ├── type.raw │ ├── type_map.raw │ └── virial.raw ├── Al8He4O12 │ ├── box.raw │ ├── coord.raw │ ├── energy.raw │ ├── force.raw │ ├── type.raw │ ├── type_map.raw │ └── virial.raw ├── Al8He8O12 │ ├── box.raw │ ├── coord.raw │ ├── energy.raw │ ├── force.raw │ ├── type.raw │ ├── type_map.raw │ └── virial.raw ├── HeAlO.traj ├── MoS2.traj └── MoS2 │ ├── box.raw │ ├── coord.raw │ ├── energy.raw │ ├── force.raw │ ├── type.raw │ ├── type_map.raw │ └── virial.raw ├── bond_order ├── BOH4-.mol ├── C5H5-.mol ├── CH3CC-.mol ├── CH3NC.mol ├── CH3NH3+.mol ├── CH3NO2.mol ├── CH3OAsO3_2-.mol ├── CH3OH.mol ├── CH3OPO3_2-.mol ├── CH3PH3+.mol ├── CH3SH.mol ├── CH3SO3-.mol ├── CH3_2SO.mol ├── CH3_2SO2.mol ├── OCH3+.mol ├── arg.mol ├── formal_charge.mol ├── gly.mol ├── methane.sdf ├── methane_ethane.sdf ├── oxpy.mol └── refined-set-ligands │ ├── obabel │ ├── 1a4r_ligand_obabel.sdf │ ├── 1ai5_ligand_obabel.sdf │ ├── 1f5l_ligand_obabel.sdf │ ├── 1m1b_ligand_obabel.sdf │ ├── 1mue_ligand_obabel.sdf │ ├── 1w4q_ligand_obabel.sdf │ ├── 2e94_ligand_obabel.sdf │ ├── 4xaq_ligand_obabel.sdf │ └── 4xtw_ligand_obabel.sdf │ └── origin │ ├── 1a4r_ligand.sdf │ ├── 1ai5_ligand.sdf │ ├── 1f5l_ligand.sdf │ ├── 1m1b_ligand.sdf │ ├── 1mue_ligand.sdf │ ├── 1w4q_ligand.sdf │ ├── 2e94_ligand.sdf │ ├── 4xaq_ligand.sdf │ └── 4xtw_ligand.sdf ├── comp_sys.py ├── computed_structure_entry.json ├── context.py ├── cp2k ├── aimd │ ├── DPGEN-1.ener │ ├── DPGEN-frc-1.xyz │ ├── DPGEN-pos-1.xyz │ ├── cp2k.log │ ├── deepmd │ │ ├── set.000 │ │ │ ├── box.npy │ │ │ ├── coord.npy │ │ │ ├── energy.npy │ │ │ └── force.npy │ │ ├── type.raw │ │ └── type_map.raw │ └── input.inp ├── aimd_stress │ ├── DPGEN-pos-1.xyz │ ├── cp2k.log │ ├── deepmd │ │ ├── set.000 │ │ │ ├── box.npy │ │ │ ├── coord.npy │ │ │ ├── energy.npy │ │ │ ├── force.npy │ │ │ └── virial.npy │ │ ├── type.raw │ │ └── type_map.raw │ └── input.inp ├── cp2k_duplicate_header │ ├── cp2k_output_duplicate_header │ └── deepmd │ │ ├── set.000 │ │ ├── box.npy │ │ ├── coord.npy │ │ ├── energy.npy │ │ ├── force.npy │ │ └── virial.npy │ │ ├── type.raw │ │ └── type_map.raw ├── cp2k_element_replace │ ├── cp2k_output_element_replace │ └── deepmd │ │ ├── set.000 │ │ ├── box.npy │ │ ├── coord.npy │ │ ├── energy.npy │ │ ├── force.npy │ │ └── virial.npy │ │ ├── type.raw │ │ └── type_map.raw ├── cp2k_nocon_output └── cp2k_normal_output │ ├── cp2k_output │ └── deepmd │ ├── set.000 │ ├── box.npy │ ├── coord.npy │ ├── energy.npy │ ├── force.npy │ └── virial.npy │ ├── type.raw │ └── type_map.raw ├── dftbplus ├── detailed.out └── dftb_pin.hsd ├── fhi_aims ├── out_md ├── out_scf ├── output_multi_elements ├── ref_cell.txt ├── ref_cell_md.txt ├── ref_cell_md_m.txt ├── ref_coord.txt ├── ref_coord_md.txt ├── ref_coord_md_m.txt ├── ref_energy_md.txt ├── ref_energy_md_m.txt ├── ref_force.txt ├── ref_force_md.txt └── ref_force_md_m.txt ├── gaussian ├── aimd_gaussian_CH4_output ├── h2pbc.gaussianlog ├── largeforce.gaussianlog ├── methane.gaussianlog ├── methane_reordered.gaussianlog ├── methane_sub.gaussianlog ├── no_input_orient.gaussianlog ├── noncoveraged.gaussianlog ├── oxygen.gaussianlog ├── waterfreq.gaussianfchk └── waterfreq.gaussianlog ├── gromacs ├── 1h.gro ├── 1h.tri.gro ├── case_for_format_atom_name.gro └── multi_frames.gro ├── lammps ├── in.lmp ├── spin.lmp ├── traj.dump ├── traj_partial_spin.dump └── traj_with_random_type_id.dump ├── n2p2 └── input.data ├── openmx ├── Methane.dat ├── Methane.md ├── Methane2.dat └── Methane2.md ├── orca └── orca.spout ├── plugin ├── dpdata_plugin_test │ └── __init__.py └── pyproject.toml ├── poscars ├── 6362_OUTCAR ├── CONTCAR.h2o.md ├── OUTCAR.Ge.vdw ├── OUTCAR.ch4.1step ├── OUTCAR.ch4.ml ├── OUTCAR.ch4.unconverged ├── OUTCAR.h2o.md ├── OUTCAR.h2o.md.10 ├── POSCAR.P42nmc ├── POSCAR.P42nmc.replace ├── POSCAR.SiC ├── POSCAR.SiC.const ├── POSCAR.SiC.normal ├── POSCAR.SiC.partpert ├── POSCAR.SiC.replicate123 ├── POSCAR.SiC.uniform ├── POSCAR.h2o.md ├── POSCAR.h4o3 ├── POSCAR.oh.c ├── POSCAR.oh.d ├── POSCAR.oh.d.dup ├── POSCAR.oh.err1 ├── POSCAR.oh.err2 ├── Ti-O-Ti-v6 │ ├── OUTCAR │ └── vasprun.xml ├── Ti-aimd-nwrite0 │ ├── OUTCAR │ └── vasprun.xml ├── conf.5.dump ├── conf.dump ├── conf.lmp ├── conf.waterion.lmp ├── conf2.dump ├── conf_s_su.dump ├── conf_unfold.dump ├── deepmd.h2o.md │ ├── box.raw │ ├── coord.raw │ ├── energy.raw │ ├── force.raw │ ├── type.raw │ └── virial.raw ├── h2o.md.json ├── outcar.longit │ └── OUTCAR ├── poscar_ref_oh.py ├── shift_origin.dump ├── test_lammps_dump_s_su.py ├── vasprun.Ge.vdw.xml ├── vasprun.h2o.md.10.xml ├── vasprun.h2o.md.conv.xml ├── vasprun.h2o.md.duplicate.xml ├── vasprun.h2o.md.novirial.xml ├── vasprun.h2o.md.tribox.lower.xml ├── vasprun.h2o.md.tribox.xml └── vasprun.h2o.md.xml ├── psi4 └── psi4.out ├── pwmat ├── MOVEMENT ├── MOVEMENT_1 ├── OUT.MLMD ├── atom.config ├── atom.config.oh ├── conf.lmp ├── config_ref_ch4.py ├── config_ref_oh.py ├── mlmd_cell ├── mlmd_coord ├── mlmd_force ├── ref_cell ├── ref_cell_1 ├── ref_coord ├── ref_coord_1 ├── ref_force └── ref_force_1 ├── pymatgen_data ├── FA-001.vasp ├── FA-001.xyz ├── deepmd │ ├── set.000 │ │ ├── box.npy │ │ ├── coord.npy │ │ ├── energy.npy │ │ ├── force.npy │ │ └── virial.npy │ ├── type.raw │ └── type_map.raw ├── mol2-new.vasp └── mol2.vasp ├── qe.scf ├── 01.in ├── 01.out ├── 02.in ├── 02.out ├── 03.in ├── 03.out ├── Al.in ├── Al.out ├── ch4_coord ├── ch4_force ├── ch4_force_2 ├── ch4_virial ├── h2o_cell ├── h2o_coord ├── h2o_force ├── h2o_virial ├── na.in └── na.out ├── qe.traj ├── oh-md.evp ├── oh-md.for ├── oh-md.in ├── oh-md.pos ├── si.wrongstr │ ├── si.cel │ ├── si.evp │ ├── si.for │ ├── si.in │ ├── si.pos │ └── si.str ├── si │ ├── si.cel │ ├── si.evp │ ├── si.for │ ├── si.in │ ├── si.pos │ └── si.str ├── traj6.cel ├── traj6.evp ├── traj6.for ├── traj6.in └── traj6.pos ├── siesta ├── aimd │ ├── cell │ ├── coord │ ├── energy │ ├── force │ ├── output │ └── virial └── scf │ ├── ref_cell │ ├── ref_coord │ ├── ref_energy │ ├── ref_force │ ├── ref_virial │ └── siesta_output ├── test_abacus_md.py ├── test_abacus_pw_scf.py ├── test_abacus_relax.py ├── test_abacus_spin.py ├── test_abacus_stru_dump.py ├── test_amber_md.py ├── test_amber_sqm.py ├── test_ase_traj.py ├── test_bond_order_system.py ├── test_cell_to_low_triangle.py ├── test_cli.py ├── test_corr.py ├── test_cp2k_aimd_output.py ├── test_cp2k_output.py ├── test_custom_data_type.py ├── test_deepmd_comp.py ├── test_deepmd_hdf5.py ├── test_deepmd_mixed.py ├── test_deepmd_raw.py ├── test_deepmd_spin.py ├── test_dftbplus.py ├── test_elements_index.py ├── test_empty.py ├── test_fhi_md_multi_elem_output.py ├── test_fhi_md_output.py ├── test_fhi_output.py ├── test_gaussian_driver.py ├── test_gaussian_fchk.py ├── test_gaussian_gjf.py ├── test_gaussian_log.py ├── test_gromacs_gro.py ├── test_json.py ├── test_lammps_atom_styles.py ├── test_lammps_dump_idx.py ├── test_lammps_dump_shift_origin.py ├── test_lammps_dump_skipload.py ├── test_lammps_dump_to_system.py ├── test_lammps_dump_unfold.py ├── test_lammps_lmp_dump.py ├── test_lammps_lmp_to_system.py ├── test_lammps_read_from_trajs.py ├── test_lammps_spin.py ├── test_msd.py ├── test_multisystems.py ├── test_n2p2.py ├── test_openmx.py ├── test_openmx_check_convergence.py ├── test_orca_spout.py ├── test_periodic_table.py ├── test_perturb.py ├── test_pick_atom_idx.py ├── test_predict.py ├── test_psi4.py ├── test_pwmat_config_dump.py ├── test_pwmat_config_to_system.py ├── test_pwmat_mlmd.py ├── test_pwmat_movement.py ├── test_pymatgen_molecule.py ├── test_pymatgen_structure.py ├── test_qe_cp_traj.py ├── test_qe_cp_traj_skipload.py ├── test_qe_pw_scf.py ├── test_qe_pw_scf_crystal_atomic_positions.py ├── test_qe_pw_scf_energy_bug.py ├── test_qe_single_line_evp.py ├── test_quip_gap_xyz.py ├── test_quip_gap_xyz_to_methods.py ├── test_read_file.py ├── test_remove_atom_names.py ├── test_remove_outlier.py ├── test_remove_pbc.py ├── test_replace.py ├── test_replicate.py ├── test_shuffle.py ├── test_siesta_aiMD_output.py ├── test_siesta_output.py ├── test_split_dataset.py ├── test_sqm_driver.py ├── test_stat.py ├── test_system_append.py ├── test_system_apply_pbc.py ├── test_system_set_type.py ├── test_to_ase.py ├── test_to_list.py ├── test_to_pymatgen.py ├── test_to_pymatgen_entry.py ├── test_type_map.py ├── test_vasp_outcar.py ├── test_vasp_poscar_dump.py ├── test_vasp_poscar_to_system.py ├── test_vasp_unconverged_outcar.py ├── test_vasp_xml.py ├── test_water_ions.py ├── test_xyz.py ├── tmp.deepmd.spin ├── Fe16-npy │ ├── set.000 │ │ ├── box.npy │ │ ├── coord.npy │ │ ├── energy.npy │ │ ├── force.npy │ │ ├── force_mag.npy │ │ ├── spin.npy │ │ └── virial.npy │ ├── type.raw │ └── type_map.raw └── Fe16-raw │ ├── box.raw │ ├── coord.raw │ ├── energy.raw │ ├── force.raw │ ├── force_mag.raw │ ├── spin.raw │ ├── type.raw │ ├── type_map.raw │ └── virial.raw └── xyz ├── B1C9 ├── box.raw ├── coord.raw ├── energy.raw ├── force.raw ├── type.raw ├── type_map.raw └── virial.raw ├── B5C7 ├── box.raw ├── coord.raw ├── energy.raw ├── force.raw ├── type.raw ├── type_map.raw └── virial.raw ├── B5C7_novirials ├── box.raw ├── coord.raw ├── energy.raw ├── force.raw ├── type.raw └── type_map.raw ├── xyz_B5C7_novirials.xyz ├── xyz_unittest.field.xyz ├── xyz_unittest.sort.xyz └── xyz_unittest.xyz /.git-blame-ignore-revs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/deepmodeling/dpdata/HEAD/.git-blame-ignore-revs -------------------------------------------------------------------------------- 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