dpgen package

dpgen.info()

Subpackages

• dpgen.auto_test package
  • Subpackages
    • dpgen.auto_test.lib package
      • Submodules
      • dpgen.auto_test.lib.abacus module
      • dpgen.auto_test.lib.crys module
      • dpgen.auto_test.lib.lammps module
      • dpgen.auto_test.lib.lmp module
      • dpgen.auto_test.lib.mfp_eosfit module
      • dpgen.auto_test.lib.pwscf module
      • dpgen.auto_test.lib.siesta module
      • dpgen.auto_test.lib.util module
      • dpgen.auto_test.lib.utils module
      • dpgen.auto_test.lib.vasp module
  • Submodules
  • dpgen.auto_test.ABACUS module
    • ABACUS
      • ABACUS.backward_files()
      • ABACUS.compute()
      • ABACUS.forward_common_files()
      • ABACUS.forward_files()
      • ABACUS.make_input_file()
      • ABACUS.make_potential_files()
      • ABACUS.modify_input()
  • dpgen.auto_test.EOS module
    • EOS
      • EOS.make_confs()
      • EOS.post_process()
      • EOS.task_param()
      • EOS.task_type()
  • dpgen.auto_test.Elastic module
    • Elastic
      • Elastic.make_confs()
      • Elastic.post_process()
      • Elastic.task_param()
      • Elastic.task_type()
  • dpgen.auto_test.Gamma module
    • Gamma
      • Gamma.centralize_slab()
      • Gamma.make_confs()
      • Gamma.post_process()
      • Gamma.return_direction()
      • Gamma.task_param()
      • Gamma.task_type()
  • dpgen.auto_test.Interstitial module
    • Interstitial
      • Interstitial.make_confs()
      • Interstitial.post_process()
      • Interstitial.task_param()
      • Interstitial.task_type()
  • dpgen.auto_test.Lammps module
    • Lammps
      • Lammps.backward_files()
      • Lammps.compute()
      • Lammps.forward_common_files()
      • Lammps.forward_files()
      • Lammps.make_input_file()
      • Lammps.make_potential_files()
      • Lammps.set_inter_type_func()
      • Lammps.set_model_param()
  • dpgen.auto_test.Property module
    • Property
      • Property.compute()
      • Property.make_confs()
      • Property.post_process()
      • Property.task_param
      • Property.task_type
  • dpgen.auto_test.Surface module
    • Surface
      • Surface.make_confs()
      • Surface.post_process()
      • Surface.task_param()
      • Surface.task_type()
  • dpgen.auto_test.Task module
    • Task
      • Task.backward_files
      • Task.compute()
      • Task.forward_common_files
      • Task.forward_files
      • Task.make_input_file()
      • Task.make_potential_files()
  • dpgen.auto_test.VASP module
    • VASP
      • VASP.backward_files()
      • VASP.compute()
      • VASP.forward_common_files()
      • VASP.forward_files()
      • VASP.make_input_file()
      • VASP.make_potential_files()
  • dpgen.auto_test.Vacancy module
    • Vacancy
      • Vacancy.make_confs()
      • Vacancy.post_process()
      • Vacancy.task_param()
      • Vacancy.task_type()
  • dpgen.auto_test.calculator module
    • make_calculator()
  • dpgen.auto_test.common_equi module
    • make_equi()
    • post_equi()
    • run_equi()
  • dpgen.auto_test.common_prop module
    • make_property()
    • make_property_instance()
    • post_property()
    • run_property()
    • worker()
  • dpgen.auto_test.gen_confs module
    • gen_alloy()
    • gen_ele_std()
    • gen_element()
    • gen_element_std()
    • make_path_mp()
    • test_fit()
  • dpgen.auto_test.mpdb module
    • check_apikey()
    • get_structure()
  • dpgen.auto_test.refine module
    • make_refine()
  • dpgen.auto_test.reproduce module
    • make_repro()
    • post_repro()
  • dpgen.auto_test.run module
    • gen_test()
    • run_task()
• dpgen.collect package
  • Submodules
  • dpgen.collect.collect module
    • collect_data()
    • gen_collect()
• dpgen.data package
  • Subpackages
    • dpgen.data.tools package
      • Submodules
      • dpgen.data.tools.bcc module
      • dpgen.data.tools.cessp2force_lin module
      • dpgen.data.tools.create_random_disturb module
      • dpgen.data.tools.diamond module
      • dpgen.data.tools.fcc module
      • dpgen.data.tools.hcp module
      • dpgen.data.tools.io_lammps module
      • dpgen.data.tools.ovito_file_convert module
      • dpgen.data.tools.poscar_copy module
      • dpgen.data.tools.sc module
  • Submodules
  • dpgen.data.arginfo module
    • init_bulk_abacus_args()
    • init_bulk_jdata_arginfo()
    • init_bulk_mdata_arginfo()
    • init_bulk_variant_type_args()
    • init_bulk_vasp_args()
    • init_reaction_jdata_arginfo()
    • init_reaction_mdata_arginfo()
    • init_surf_jdata_arginfo()
    • init_surf_mdata_arginfo()
  • dpgen.data.gen module
    • class_cell_type()
    • coll_abacus_md()
    • coll_vasp_md()
    • create_path()
    • gen_init_bulk()
    • make_abacus_md()
    • make_abacus_relax()
    • make_combines()
    • make_scale()
    • make_scale_ABACUS()
    • make_super_cell()
    • make_super_cell_ABACUS()
    • make_super_cell_STRU()
    • make_super_cell_poscar()
    • make_unit_cell()
    • make_unit_cell_ABACUS()
    • make_vasp_md()
    • make_vasp_relax()
    • out_dir_name()
    • pert_scaled()
    • place_element()
    • place_element_ABACUS()
    • poscar_ele()
    • poscar_natoms()
    • poscar_scale()
    • poscar_scale_abacus()
    • poscar_scale_cartesian()
    • poscar_scale_direct()
    • poscar_shuffle()
    • replace()
    • run_abacus_md()
    • run_abacus_relax()
    • run_vasp_md()
    • run_vasp_relax()
    • shuffle_stru_data()
    • stru_ele()
  • dpgen.data.reaction module
    • convert_data()
    • gen_init_reaction()
    • link_fp_input()
    • link_reaxff()
    • link_trj()
    • make_lmp()
    • run_build_dataset()
    • run_fp()
    • run_reaxff()
  • dpgen.data.surf module
    • class_cell_type()
    • create_path()
    • gen_init_surf()
    • make_combines()
    • make_scale()
    • make_super_cell_pymatgen()
    • make_unit_cell()
    • make_vasp_relax()
    • out_dir_name()
    • pert_scaled()
    • place_element()
    • poscar_ele()
    • poscar_elong()
    • poscar_natoms()
    • poscar_scale()
    • poscar_scale_cartesian()
    • poscar_scale_direct()
    • poscar_shuffle()
    • replace()
    • run_vasp_relax()
• dpgen.database package
  • DPPotcar
    • DPPotcar.as_dict()
    • DPPotcar.from_dict()
    • DPPotcar.from_file()
    • DPPotcar.write_file()
  • Entry
    • Entry.as_dict()
    • Entry.from_dict()
    • Entry.number_element
  • VaspInput
    • VaspInput.as_dict()
    • VaspInput.from_dict()
    • VaspInput.from_directory()
    • VaspInput.write_input()
  • Submodules
  • dpgen.database.entry module
    • Entry
      • Entry.as_dict()
      • Entry.from_dict()
      • Entry.number_element
  • dpgen.database.run module
    • db_run()
    • parsing_gaussian()
    • parsing_pwscf()
    • parsing_vasp()
  • dpgen.database.vasp module
    • DPPotcar
      • DPPotcar.as_dict()
      • DPPotcar.from_dict()
      • DPPotcar.from_file()
      • DPPotcar.write_file()
    • VaspInput
      • VaspInput.as_dict()
      • VaspInput.from_dict()
      • VaspInput.from_directory()
      • VaspInput.write_input()
• dpgen.dispatcher package
  • Submodules
  • dpgen.dispatcher.Dispatcher module
    • make_submission()
    • make_submission_compat()
    • mdata_arginfo()
• dpgen.generator package
  • Subpackages
    • dpgen.generator.lib package
      • Submodules
      • dpgen.generator.lib.abacus_scf module
      • dpgen.generator.lib.calypso_check_outcar module
      • dpgen.generator.lib.calypso_run_model_devi module
      • dpgen.generator.lib.calypso_run_opt module
      • dpgen.generator.lib.cp2k module
      • dpgen.generator.lib.cvasp module
      • dpgen.generator.lib.ele_temp module
      • dpgen.generator.lib.gaussian module
      • dpgen.generator.lib.lammps module
      • dpgen.generator.lib.make_calypso module
      • dpgen.generator.lib.parse_calypso module
      • dpgen.generator.lib.pwmat module
      • dpgen.generator.lib.pwscf module
      • dpgen.generator.lib.run_calypso module
      • dpgen.generator.lib.siesta module
      • dpgen.generator.lib.utils module
      • dpgen.generator.lib.vasp module
  • Submodules
  • dpgen.generator.arginfo module
    • basic_args()
    • data_args()
    • fp_args()
    • fp_style_abacus_args()
    • fp_style_amber_diff_args()
    • fp_style_cp2k_args()
    • fp_style_cpx_args()
    • fp_style_custom_args()
    • fp_style_gaussian_args()
    • fp_style_pwscf_args()
    • fp_style_siesta_args()
    • fp_style_variant_type_args()
    • fp_style_vasp_args()
    • model_devi_amber_args()
    • model_devi_args()
    • model_devi_jobs_args()
    • model_devi_jobs_rev_mat_args()
    • model_devi_jobs_template_args()
    • model_devi_lmp_args()
    • run_jdata_arginfo()
    • run_mdata_arginfo()
    • training_args()
    • training_args_common()
    • training_args_dp()
  • dpgen.generator.run module
    • check_bad_box()
    • check_cluster()
    • copy_model()
    • detect_batch_size()
    • dump_to_deepmd_raw()
    • expand_idx()
    • expand_matrix_values()
    • find_only_one_key()
    • gen_run()
    • get_atomic_masses()
    • get_job_names()
    • get_nframes()
    • get_sys_index()
    • make_fp()
    • make_fp_abacus_scf()
    • make_fp_amber_diff()
    • make_fp_calculation()
    • make_fp_cp2k()
    • make_fp_cpx()
    • make_fp_custom()
    • make_fp_gaussian()
    • make_fp_pwmat()
    • make_fp_pwscf()
    • make_fp_siesta()
    • make_fp_task_name()
    • make_fp_vasp()
    • make_fp_vasp_cp_cvasp()
    • make_fp_vasp_incar()
    • make_fp_vasp_kp()
    • make_model_devi()
    • make_model_devi_conf_name()
    • make_model_devi_task_name()
    • make_pwmat_input()
    • make_train()
    • make_train_dp()
    • make_vasp_incar()
    • make_vasp_incar_ele_temp()
    • parse_cur_job()
    • parse_cur_job_revmat()
    • parse_cur_job_sys_revmat()
    • poscar_natoms()
    • poscar_to_conf()
    • post_fp()
    • post_fp_abacus_scf()
    • post_fp_amber_diff()
    • post_fp_check_fail()
    • post_fp_cp2k()
    • post_fp_cpx()
    • post_fp_custom()
    • post_fp_gaussian()
    • post_fp_pwmat()
    • post_fp_pwscf()
    • post_fp_siesta()
    • post_fp_vasp()
    • post_model_devi()
    • post_train()
    • post_train_dp()
    • revise_by_keys()
    • revise_lmp_input_dump()
    • revise_lmp_input_model()
    • revise_lmp_input_neigh_modify()
    • revise_lmp_input_pair_coeff()
    • revise_lmp_input_plm()
    • run_fp()
    • run_fp_inner()
    • run_iter()
    • run_md_model_devi()
    • run_model_devi()
    • run_train()
    • run_train_dp()
    • set_version()
    • sys_link_fp_vasp_pp()
    • update_mass_map()
• dpgen.remote package
  • Submodules
  • dpgen.remote.decide_machine module
    • convert_mdata()
• dpgen.simplify package
  • Submodules
  • dpgen.simplify.arginfo module
    • fp_args()
    • fp_style_variant_type_args()
    • general_simplify_arginfo()
    • simplify_jdata_arginfo()
    • simplify_mdata_arginfo()
  • dpgen.simplify.simplify module
    • gen_simplify()
    • get_multi_system()
    • get_system_cls()
    • init_model()
    • init_model_dp()
    • init_pick()
    • make_fp()
    • make_fp_configs()
    • make_fp_labeled()
    • make_model_devi()
    • post_model_devi()
    • run_iter()
    • run_model_devi()
• dpgen.tools package
  • Submodules
  • dpgen.tools.auto_gen_param module
    • Iteration
      • Iteration.current_num_of_itearation
      • Iteration.current_num_of_sub_itearation
      • Iteration.gen_sub_iter()
      • Iteration.index_iteration
      • Iteration.register_iteration()
      • Iteration.register_sub_iteartion()
    • System
      • System.add_sub_system()
      • System.current_num_of_sub_systems
      • System.current_num_of_system
      • System.get_sub_system()
      • System.index_system
      • System.register_sub_system()
      • System.register_system()
    • auto_gen_param()
    • default_map_generator()
    • default_temps_generator()
    • get_basic_param_json()
    • get_init_data_sys()
    • get_model_devi_jobs()
    • get_sys_configs()
    • get_system_list()
    • scan_files()
  • dpgen.tools.collect_data module
    • collect_data()
    • file_len()
  • dpgen.tools.relabel module
    • copy_pp_files()
    • create_init_tasks()
    • create_tasks()
    • get_lmp_info()
    • link_pp_files()
    • make_pwscf()
    • make_siesta()
    • make_vasp()
    • make_vasp_incar()
  • dpgen.tools.run_report module
    • run_report()
  • dpgen.tools.stat_iter module
    • stat_iter()
  • dpgen.tools.stat_sys module
    • ascii_hist()
    • run_report()
    • stat_sys()
  • dpgen.tools.stat_time module
    • stat_time()

Submodules

dpgen.arginfo module

dpgen.arginfo.general_mdata_arginfo(name: str, tasks: tuple[str]) → Argument

Generate arginfo for general mdata.

Parameters:

namestr

mdata name

taskstuple[str]

tuple of task keys, e.g. (“train”, “model_devi”, “fp”)

Returns:

Argument

arginfo

dpgen.gui module

DP-GUI entrypoint.

dpgen.gui.start_dpgui(args: Namespace)

Host DP-GUI server.

Parameters:

argsargparse.Namespace

Arguments from argparse.

Raises:

ModuleNotFoundError

The dpgui package is not installed

dpgen.main module

dpgen.main.main()

dpgen.main.main_parser() → ArgumentParser

Returns parser for dpgen command.

Returns:

argparse.ArgumentParser

parser for dpgen command

dpgen.util module

dpgen.util.box_center(ch='', fill=' ', sp='|')

Put the string at the center of | |.

dpgen.util.convert_training_data_to_hdf5(input_files: list[str], h5_file: str)

Convert training data to HDF5 format and update the input files.

Parameters:

input_fileslist of str

DeePMD-kit input file names

h5_filestr

HDF5 file name

dpgen.util.expand_sys_str(root_dir: str | Path) → list[str]

Recursively iterate over directories taking those that contain type.raw file.

If root_dir is a file but not a directory, it will be assumed as an HDF5 file.

Parameters:

root_dirUnion[str, Path]

starting directory

Returns:

List[str]

list of string pointing to system directories

Raises:

RuntimeError

No system was found in the directory

dpgen.util.load_file(filename: str | PathLike) → dict

Load data from a JSON or YAML file.

Parameters:

filenamestr or os.PathLike

The filename to load data from, whose suffix should be .json, .yaml, or .yml

Returns:

dict

The data loaded from the file

Raises:

ValueError

If the file format is not supported

dpgen.util.normalize(arginfo: Argument, data: dict, strict_check: bool = True) → dict

Normalize and check input data.

Parameters:

arginfodargs.Argument

argument information

datadict

input data

strict_checkbool, default=True

strict check data or not

Returns:

dict

normalized data

dpgen.util.sepline(ch='-', sp='-', screen=False)

Seperate the output by ‘-‘.

dpgen.util.set_directory(path: Path)

Sets the current working path within the context.

Parameters:

pathPath

The path to the cwd

Yields:

None

Examples

>>> with set_directory("some_path"):
...    do_something()

dpgen.util.setup_ele_temp(atomic: bool)

Set electronic temperature as required input data.

Parameters:

atomicbool

Whether to use atomic temperature or frame temperature