dpgen.generator package

Subpackages

• dpgen.generator.lib package
  • Submodules
  • dpgen.generator.lib.abacus_scf module
    • get_abacus_STRU()
    • get_abacus_input_parameters()
    • get_additional_from_STRU()
    • get_mass_from_STRU()
    • get_natoms_from_stru()
    • make_abacus_scf_input()
    • make_abacus_scf_kpt()
    • make_abacus_scf_stru()
    • make_kspacing_kpoints_stru()
    • make_supercell_abacus()
  • 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
    • iterdict()
    • make_cp2k_input()
    • make_cp2k_input_from_external()
    • make_cp2k_xyz()
    • update_dict()
  • dpgen.generator.lib.cvasp module
    • runvasp()
  • dpgen.generator.lib.ele_temp module
    • NBandsEsti
      • NBandsEsti.predict()
      • NBandsEsti.save()
  • dpgen.generator.lib.gaussian module
    • detect_multiplicity()
    • make_gaussian_input()
    • take_cluster()
  • dpgen.generator.lib.lammps module
    • get_all_dumped_forces()
    • get_dumped_forces()
    • make_lammps_input()
  • dpgen.generator.lib.make_calypso module
    • make_calypso_input()
    • write_model_devi_out()
  • dpgen.generator.lib.parse_calypso module
  • dpgen.generator.lib.pwmat module
    • input_upper()
    • make_pwmat_input_dict()
    • make_pwmat_input_user_dict()
    • write_input_dict()
  • dpgen.generator.lib.pwscf module
    • cvt_1frame()
    • get_atom_types()
    • get_block()
    • get_cell()
    • get_coords()
    • get_energy()
    • get_force()
    • get_natoms()
    • get_stress()
    • get_types()
    • make_pwscf_01_runctrl_dict()
    • make_pwscf_input()
  • dpgen.generator.lib.run_calypso module
    • analysis()
    • gen_main()
    • gen_structures()
    • run_calypso_model_devi()
  • dpgen.generator.lib.siesta module
    • make_siesta_input()
  • dpgen.generator.lib.utils module
    • cmd_append_log()
    • copy_file_list()
    • create_path()
    • log_iter()
    • log_task()
    • make_iter_name()
    • record_iter()
    • repeat_to_length()
    • replace()
    • symlink_user_forward_files()
  • dpgen.generator.lib.vasp module
    • incar_upper()
    • make_vasp_incar_user_dict()
    • write_incar_dict()

Submodules

dpgen.generator.arginfo module

dpgen.generator.arginfo.basic_args() → list[Argument]

dpgen.generator.arginfo.data_args() → list[Argument]

dpgen.generator.arginfo.fp_args() → list[Argument]

dpgen.generator.arginfo.fp_style_abacus_args() → list[Argument]

dpgen.generator.arginfo.fp_style_amber_diff_args() → list[Argument]

Arguments for FP style amber/diff.

Returns:

list[dargs.Argument]

list of amber/diff fp style arguments

dpgen.generator.arginfo.fp_style_cp2k_args() → list[Argument]

dpgen.generator.arginfo.fp_style_custom_args() → list[Argument]

Arguments for FP style custom.

Returns:

list[dargs.Argument]

list of custom fp style arguments

dpgen.generator.arginfo.fp_style_gaussian_args() → list[Argument]

Gaussian fp style arguments.

Returns:

list[dargs.Argument]

list of Gaussian fp style arguments

dpgen.generator.arginfo.fp_style_pwscf_args() → list[Argument]

Arguments for FP style pwscf (Quantum Espresso).

Returns:

list[dargs.Argument]

list of pwscf fp style arguments

dpgen.generator.arginfo.fp_style_siesta_args() → list[Argument]

dpgen.generator.arginfo.fp_style_variant_type_args() → Variant

dpgen.generator.arginfo.fp_style_vasp_args() → list[Argument]

dpgen.generator.arginfo.model_devi_amber_args() → list[Argument]

Amber engine arguments.

dpgen.generator.arginfo.model_devi_args() → list[Variant]

dpgen.generator.arginfo.model_devi_jobs_args() → list[Argument]

dpgen.generator.arginfo.model_devi_jobs_rev_mat_args() → Argument

dpgen.generator.arginfo.model_devi_jobs_template_args() → Argument

dpgen.generator.arginfo.model_devi_lmp_args() → list[Argument]

dpgen.generator.arginfo.run_jdata_arginfo() → Argument

Argument information for dpgen run mdata.

Returns:

Argument

argument information

dpgen.generator.arginfo.run_mdata_arginfo() → Argument

Generate arginfo for dpgen run mdata.

Returns:

Argument

arginfo

dpgen.generator.arginfo.training_args() → list[Argument]

Traning arguments.

Returns:

list[dargs.Argument]

List of training arguments.

dpgen.generator.run module

init: data iter:

00.train 01.model_devi 02.vasp 03.data.

dpgen.generator.run.check_bad_box(conf_name, criteria, fmt='lammps/dump')

dpgen.generator.run.check_cluster(conf_name, fp_cluster_vacuum, fmt='lammps/dump')

dpgen.generator.run.copy_model(numb_model, prv_iter_index, cur_iter_index)

dpgen.generator.run.detect_batch_size(batch_size, system=None)

dpgen.generator.run.dump_to_deepmd_raw(dump, deepmd_raw, type_map, fmt='gromacs/gro', charge=None)

dpgen.generator.run.expand_idx(in_list)

dpgen.generator.run.expand_matrix_values(target_list, cur_idx=0)

dpgen.generator.run.find_only_one_key(lmp_lines, key)

dpgen.generator.run.gen_run(args)

dpgen.generator.run.get_atomic_masses(atom)

dpgen.generator.run.get_job_names(jdata)

dpgen.generator.run.get_nframes(system)

dpgen.generator.run.get_sys_index(task)

dpgen.generator.run.make_fp(iter_index, jdata, mdata)

Select the candidate strutures and make the input file of FP calculation.

Parameters:

iter_indexint

iter index

jdatadict

Run parameters.

mdatadict

Machine parameters.

dpgen.generator.run.make_fp_abacus_scf(iter_index, jdata)

dpgen.generator.run.make_fp_amber_diff(iter_index: int, jdata: dict)

Run amber twice to calculate high-level and low-level potential, and then generate difference between them.

Besides AMBER, one needs to install dpamber package, which is avaiable at https://github.com/njzjz/dpamber

Currently, it should be used with the AMBER model_devi driver.

Parameters:

iter_indexint

iter index

jdatadict

Run parameters. The following parameters are used in this method:

mdin_prefixstr

The path prefix to AMBER mdin files

qm_regionlist[str]

AMBER mask of the QM region. Each mask maps to a system.

qm_chargelist[int]

Charge of the QM region. Each charge maps to a system.

high_levelstr

high level method

low_levelstr

low level method

fp_paramsdict

This parameters includes:

high_level_mdinstr

High-level AMBER mdin file. %qm_theory%, %qm_region%, and %qm_charge% will be replace.

low_level_mdinstr

Low-level AMBER mdin file. %qm_theory%, %qm_region%, and %qm_charge% will be replace.

parm7_prefixstr

The path prefix to AMBER PARM7 files

parm7list[str]

List of paths to AMBER PARM7 files. Each file maps to a system.

References

[1]

Development of Range-Corrected Deep Learning Potentials for Fast, Accurate Quantum Mechanical/Molecular Mechanical Simulations of Chemical Reactions in Solution, Jinzhe Zeng, Timothy J. Giese, Şölen Ekesan, and Darrin M. York, Journal of Chemical Theory and Computation 2021 17 (11), 6993-7009

dpgen.generator.run.make_fp_calculation(iter_index, jdata, mdata)

Make the input file of FP calculation.

Parameters:

iter_indexint

iter index

jdatadict

Run parameters.

mdatadict

Machine parameters.

dpgen.generator.run.make_fp_cp2k(iter_index, jdata)

dpgen.generator.run.make_fp_custom(iter_index, jdata)

Make input file for customized FP style.

Convert the POSCAR file to custom format.

Parameters:

iter_indexint

iter index

jdatadict

Run parameters.

dpgen.generator.run.make_fp_gaussian(iter_index, jdata)

dpgen.generator.run.make_fp_pwmat(iter_index, jdata)

dpgen.generator.run.make_fp_pwscf(iter_index, jdata)

dpgen.generator.run.make_fp_siesta(iter_index, jdata)

dpgen.generator.run.make_fp_task_name(sys_idx, counter)

dpgen.generator.run.make_fp_vasp(iter_index, jdata)

dpgen.generator.run.make_fp_vasp_cp_cvasp(iter_index, jdata)

dpgen.generator.run.make_fp_vasp_incar(iter_index, jdata, nbands_esti=None)

dpgen.generator.run.make_fp_vasp_kp(iter_index, jdata)

dpgen.generator.run.make_model_devi(iter_index, jdata, mdata)

dpgen.generator.run.make_model_devi_conf_name(sys_idx, conf_idx)

dpgen.generator.run.make_model_devi_task_name(sys_idx, task_idx)

dpgen.generator.run.make_pwmat_input(jdata, filename)

dpgen.generator.run.make_train(iter_index, jdata, mdata)

dpgen.generator.run.make_vasp_incar(jdata, filename)

dpgen.generator.run.make_vasp_incar_ele_temp(jdata, filename, ele_temp, nbands_esti=None)

dpgen.generator.run.parse_cur_job(cur_job)

dpgen.generator.run.parse_cur_job_revmat(cur_job, use_plm=False)

dpgen.generator.run.parse_cur_job_sys_revmat(cur_job, sys_idx, use_plm=False)

dpgen.generator.run.poscar_natoms(lines)

dpgen.generator.run.poscar_shuffle(poscar_in, poscar_out)

dpgen.generator.run.poscar_to_conf(poscar, conf)

dpgen.generator.run.post_fp(iter_index, jdata)

dpgen.generator.run.post_fp_abacus_scf(iter_index, jdata)

dpgen.generator.run.post_fp_amber_diff(iter_index, jdata)

dpgen.generator.run.post_fp_check_fail(iter_index, jdata, rfailed=None)

dpgen.generator.run.post_fp_cp2k(iter_index, jdata, rfailed=None)

dpgen.generator.run.post_fp_custom(iter_index, jdata)

Post fp for custom fp. Collect data from user-defined output_fn.

Parameters:

iter_indexint

The index of the current iteration.

jdatadict

The parameter data.

dpgen.generator.run.post_fp_gaussian(iter_index, jdata)

dpgen.generator.run.post_fp_pwmat(iter_index, jdata, rfailed=None)

dpgen.generator.run.post_fp_pwscf(iter_index, jdata)

dpgen.generator.run.post_fp_siesta(iter_index, jdata)

dpgen.generator.run.post_fp_vasp(iter_index, jdata, rfailed=None)

dpgen.generator.run.post_model_devi(iter_index, jdata, mdata)

dpgen.generator.run.post_train(iter_index, jdata, mdata)

dpgen.generator.run.revise_by_keys(lmp_lines, keys, values)

dpgen.generator.run.revise_lmp_input_dump(lmp_lines, trj_freq, model_devi_merge_traj=False)

dpgen.generator.run.revise_lmp_input_model(lmp_lines, task_model_list, trj_freq, deepmd_version='1')

dpgen.generator.run.revise_lmp_input_plm(lmp_lines, in_plm, out_plm='output.plumed')

dpgen.generator.run.run_fp(iter_index, jdata, mdata)

dpgen.generator.run.run_fp_inner(iter_index, jdata, mdata, forward_files, backward_files, check_fin, log_file='fp.log', forward_common_files=[])

dpgen.generator.run.run_iter(param_file, machine_file)

dpgen.generator.run.run_md_model_devi(iter_index, jdata, mdata)

dpgen.generator.run.run_model_devi(iter_index, jdata, mdata)

dpgen.generator.run.run_train(iter_index, jdata, mdata)

dpgen.generator.run.set_version(mdata)

dpgen.generator.run.sys_link_fp_vasp_pp(iter_index, jdata)

dpgen.generator.run.update_mass_map(jdata)