dpgen.auto_test package

Subpackages

• dpgen.auto_test.lib package
  • Submodules
  • dpgen.auto_test.lib.abacus module
    • check_finished()
    • check_stru_fixed()
    • final_stru()
    • make_kspacing_kpt()
    • modify_stru_path()
    • poscar2stru()
    • stru2Structure()
    • stru_fix_atom()
    • stru_scale()
    • write_input()
    • write_kpt()
  • dpgen.auto_test.lib.crys module
    • bcc()
    • dhcp()
    • diamond()
    • fcc()
    • fcc1()
    • hcp()
    • sc()
  • dpgen.auto_test.lib.lammps module
    • apply_type_map()
    • check_finished()
    • check_finished_new()
    • cvt_lammps_conf()
    • element_list()
    • get_base_area()
    • get_nev()
    • get_stress()
    • inter_deepmd()
    • inter_eam_alloy()
    • inter_eam_fs()
    • inter_meam()
    • make_lammps_elastic()
    • make_lammps_equi()
    • make_lammps_eval()
    • make_lammps_phonon()
    • make_lammps_press_relax()
    • poscar_from_last_dump()
  • dpgen.auto_test.lib.lmp module
    • box2lmpbox()
    • from_system_data()
    • get_atoms()
    • get_atype()
    • get_lmpbox()
    • get_natoms()
    • get_natoms_vec()
    • get_natomtypes()
    • get_posi()
    • lmpbox2box()
    • system_data()
    • to_system_data()
  • dpgen.auto_test.lib.mfp_eosfit module
    • BM4()
    • BM5()
    • LOG4()
    • LOG5()
    • Li4p()
    • SJX_5p()
    • SJX_v2()
    • TEOS()
    • birch()
    • calc_props_BM4()
    • calc_props_LOG4()
    • calc_props_SJX_5p()
    • calc_props_mBM4()
    • calc_props_mBM4poly()
    • calc_props_mBM5poly()
    • calc_props_morse()
    • calc_props_morse_6p()
    • calc_props_vinet()
    • calc_v0_mBM4poly()
    • calc_v0_mBM5poly()
    • ext_splint()
    • ext_vec()
    • ext_velp()
    • get_eos_list()
    • get_eos_list_3p()
    • get_eos_list_4p()
    • get_eos_list_5p()
    • get_eos_list_6p()
    • init_guess()
    • lsqfit_eos()
    • mBM4()
    • mBM4poly()
    • mBM5()
    • mBM5poly()
    • mie()
    • mie_simple()
    • morse()
    • morse_3p()
    • morse_6p()
    • morse_AB()
    • murnaghan()
    • parse_argument()
    • rBM4()
    • rBM4_pv()
    • rBM5()
    • rBM5_pv()
    • rPT4()
    • rPT4_pv()
    • rPT5()
    • rPT5_pv()
    • read_ve()
    • read_velp()
    • read_vlp()
    • repro_ve()
    • repro_vp()
    • res_BM4()
    • res_BM5()
    • res_LOG4()
    • res_LOG5()
    • res_Li4p()
    • res_SJX_5p()
    • res_SJX_v2()
    • res_TEOS()
    • res_birch()
    • res_mBM4()
    • res_mBM4poly()
    • res_mBM5()
    • res_mBM5poly()
    • res_mie()
    • res_mie_simple()
    • res_morse()
    • res_morse_3p()
    • res_morse_6p()
    • res_morse_AB()
    • res_murnaghan()
    • res_rBM4()
    • res_rBM4_pv()
    • res_rBM5()
    • res_rBM5_pv()
    • res_rPT4()
    • res_rPT4_pv()
    • res_rPT5()
    • res_rPT5_pv()
    • res_universal()
    • res_vinet()
    • res_vinet_pv()
    • universal()
    • vinet()
    • vinet_pv()
  • dpgen.auto_test.lib.pwscf module
    • make_pwscf_input()
  • dpgen.auto_test.lib.siesta module
    • make_siesta_input()
  • dpgen.auto_test.lib.util module
    • collect_task()
    • get_machine_info()
    • insert_data()
    • make_work_path()
    • voigt_to_stress()
  • dpgen.auto_test.lib.utils module
    • cmd_append_log()
    • copy_file_list()
    • create_path()
    • log_iter()
    • log_task()
    • make_iter_name()
    • record_iter()
    • repeat_to_length()
    • replace()
  • dpgen.auto_test.lib.vasp module
    • OutcarItemError
    • check_finished()
    • get_boxes()
    • get_energies()
    • get_nev()
    • get_poscar_natoms()
    • get_poscar_types()
    • get_stress()
    • make_kspacing_kpoints()
    • make_vasp_kpoints()
    • make_vasp_kpoints_from_incar()
    • make_vasp_phonon_incar()
    • make_vasp_relax_incar()
    • make_vasp_static_incar()
    • perturb_xz()
    • poscar_natoms()
    • poscar_scale()
    • poscar_vol()
    • reciprocal_box()
    • regulate_poscar()
    • sort_poscar()

Submodules

dpgen.auto_test.ABACUS module

class dpgen.auto_test.ABACUS.ABACUS(inter_parameter, path_to_poscar)

Bases: Task

Methods

backward_files([property_type])	Return backward files.
compute(output_dir)	Compute output of the task.
forward_common_files([property_type])	Return forward common files.
forward_files([property_type])	Return forward files.
make_input_file(output_dir, task_type, ...)	Prepare input files for a computational task For example, the VASP prepares INCAR.
make_potential_files(output_dir)	Prepare potential files for a computational task.

modify_input

backward_files(property_type='relaxation')

Return backward files.

compute(output_dir)

Compute output of the task. IMPORTANT: The output configuration should be converted and stored in a CONTCAR file.

Parameters:

output_dirstr

The directory storing the input and output files.

Returns:

result_dict: dict

A dict that storing the result. For example: { “energy”: xxx, “force”: [xxx] }

Notes

The following files are generated: CONTCAR: output file

The output configuration is converted to CONTCAR and stored in the output_dir

forward_common_files(property_type='relaxation')

Return forward common files.

forward_files(property_type='relaxation')

Return forward files.

make_input_file(output_dir, task_type, task_param)

Prepare input files for a computational task For example, the VASP prepares INCAR. LAMMPS (including DeePMD, MEAM…) prepares in.lammps.

Parameters:

output_dirstr

The directory storing the input files.

task_typestr

Can be - “relaxation:”: structure relaxation - “static”: static computation calculates the energy, force… of a strcture

task_paramdict

The parameters of the task. For example the VASP interaction can be provided with { “ediff”: 1e-6, “ediffg”: 1e-5 }

make_potential_files(output_dir)

Prepare potential files for a computational task. For example, the VASP prepares POTCAR. DeePMD prepares frozen model(s). IMPORTANT: Interaction should be stored in output_dir/inter.json.

Parameters:

output_dirstr

The directory storing the potential files.

Notes

The following files are generated:

inter.json: output file

The task information is stored in output_dir/inter.json

modify_input(incar, x, y)

dpgen.auto_test.EOS module

class dpgen.auto_test.EOS.EOS(parameter, inter_param=None)

Bases: Property

Methods

compute(output_file, print_file, path_to_work)	Postprocess the finished tasks to compute the property.
make_confs(path_to_work, path_to_equi[, refine])	Make configurations needed to compute the property.
post_process(task_list)	post_process the KPOINTS file in elastic.
task_param()	Return the parameter of each computational task, for example, {'ediffg': 1e-4}.
task_type()	Return the type of each computational task, for example, 'relaxation', 'static'....

make_confs(path_to_work, path_to_equi, refine=False)

Make configurations needed to compute the property. The tasks directory will be named as path_to_work/task.xxxxxx IMPORTANT: handel the case when the directory exists.

Parameters:

path_to_workstr

The path where the tasks for the property are located

path_to_equistr

-refine == False: The path to the directory that equilibrated the configuration. -refine == True: The path to the directory that has property confs.

refinestr

To refine existing property confs or generate property confs from a equilibrated conf

Returns:

task_list: list of str

The list of task directories.

post_process(task_list)

post_process the KPOINTS file in elastic.

task_param()

Return the parameter of each computational task, for example, {‘ediffg’: 1e-4}.

task_type()

Return the type of each computational task, for example, ‘relaxation’, ‘static’….

dpgen.auto_test.Elastic module

class dpgen.auto_test.Elastic.Elastic(parameter, inter_param=None)

Bases: Property

Methods

compute(output_file, print_file, path_to_work)	Postprocess the finished tasks to compute the property.
make_confs(path_to_work, path_to_equi[, refine])	Make configurations needed to compute the property.
post_process(task_list)	post_process the KPOINTS file in elastic.
task_param()	Return the parameter of each computational task, for example, {'ediffg': 1e-4}.
task_type()	Return the type of each computational task, for example, 'relaxation', 'static'....

make_confs(path_to_work, path_to_equi, refine=False)

Make configurations needed to compute the property. The tasks directory will be named as path_to_work/task.xxxxxx IMPORTANT: handel the case when the directory exists.

Parameters:

path_to_workstr

The path where the tasks for the property are located

path_to_equistr

-refine == False: The path to the directory that equilibrated the configuration. -refine == True: The path to the directory that has property confs.

refinestr

To refine existing property confs or generate property confs from a equilibrated conf

Returns:

task_list: list of str

The list of task directories.

post_process(task_list)

post_process the KPOINTS file in elastic.

task_param()

Return the parameter of each computational task, for example, {‘ediffg’: 1e-4}.

task_type()

Return the type of each computational task, for example, ‘relaxation’, ‘static’….

dpgen.auto_test.Gamma module

class dpgen.auto_test.Gamma.Gamma(parameter, inter_param=None)

Bases: Property

Calculation of common gamma lines for bcc and fcc.

Methods

compute(output_file, print_file, path_to_work)	Postprocess the finished tasks to compute the property.
make_confs(path_to_work, path_to_equi[, refine])	Make configurations needed to compute the property.
post_process(task_list)	post_process the KPOINTS file in elastic.
task_param()	Return the parameter of each computational task, for example, {'ediffg': 1e-4}.
task_type()	Return the type of each computational task, for example, 'relaxation', 'static'....

centralize_slab
return_direction

static centralize_slab(slab) → None

make_confs(path_to_work, path_to_equi, refine=False)

Make configurations needed to compute the property. The tasks directory will be named as path_to_work/task.xxxxxx IMPORTANT: handel the case when the directory exists.

Parameters:

path_to_workstr

The path where the tasks for the property are located

path_to_equistr

-refine == False: The path to the directory that equilibrated the configuration. -refine == True: The path to the directory that has property confs.

refinestr

To refine existing property confs or generate property confs from a equilibrated conf

Returns:

task_list: list of str

The list of task directories.

post_process(task_list)

post_process the KPOINTS file in elastic.

return_direction()

task_param()

Return the parameter of each computational task, for example, {‘ediffg’: 1e-4}.

task_type()

Return the type of each computational task, for example, ‘relaxation’, ‘static’….

dpgen.auto_test.Interstitial module

class dpgen.auto_test.Interstitial.Interstitial(parameter, inter_param=None)

Bases: Property

Methods

compute(output_file, print_file, path_to_work)	Postprocess the finished tasks to compute the property.
make_confs(path_to_work, path_to_equi[, refine])	Make configurations needed to compute the property.
post_process(task_list)	post_process the KPOINTS file in elastic.
task_param()	Return the parameter of each computational task, for example, {'ediffg': 1e-4}.
task_type()	Return the type of each computational task, for example, 'relaxation', 'static'....

make_confs(path_to_work, path_to_equi, refine=False)

Make configurations needed to compute the property. The tasks directory will be named as path_to_work/task.xxxxxx IMPORTANT: handel the case when the directory exists.

Parameters:

path_to_workstr

The path where the tasks for the property are located

path_to_equistr

-refine == False: The path to the directory that equilibrated the configuration. -refine == True: The path to the directory that has property confs.

refinestr

To refine existing property confs or generate property confs from a equilibrated conf

Returns:

task_list: list of str

The list of task directories.

post_process(task_list)

post_process the KPOINTS file in elastic.

task_param()

Return the parameter of each computational task, for example, {‘ediffg’: 1e-4}.

task_type()

Return the type of each computational task, for example, ‘relaxation’, ‘static’….

dpgen.auto_test.Lammps module

class dpgen.auto_test.Lammps.Lammps(inter_parameter, path_to_poscar)

Bases: Task

Methods

backward_files([property_type])	Return backward files.
compute(output_dir)	Compute output of the task.
forward_common_files([property_type])	Return forward common files.
forward_files([property_type])	Return forward files.
make_input_file(output_dir, task_type, ...)	Prepare input files for a computational task For example, the VASP prepares INCAR.
make_potential_files(output_dir)	Prepare potential files for a computational task.

set_inter_type_func
set_model_param

backward_files(property_type='relaxation')

Return backward files.

compute(output_dir)

Compute output of the task. IMPORTANT: The output configuration should be converted and stored in a CONTCAR file.

Parameters:

output_dirstr

The directory storing the input and output files.

Returns:

result_dict: dict

A dict that storing the result. For example: { “energy”: xxx, “force”: [xxx] }

Notes

The following files are generated: CONTCAR: output file

The output configuration is converted to CONTCAR and stored in the output_dir

forward_common_files(property_type='relaxation')

Return forward common files.

forward_files(property_type='relaxation')

Return forward files.

make_input_file(output_dir, task_type, task_param)

Prepare input files for a computational task For example, the VASP prepares INCAR. LAMMPS (including DeePMD, MEAM…) prepares in.lammps.

Parameters:

output_dirstr

The directory storing the input files.

task_typestr

Can be - “relaxation:”: structure relaxation - “static”: static computation calculates the energy, force… of a strcture

task_paramdict

The parameters of the task. For example the VASP interaction can be provided with { “ediff”: 1e-6, “ediffg”: 1e-5 }

make_potential_files(output_dir)

Prepare potential files for a computational task. For example, the VASP prepares POTCAR. DeePMD prepares frozen model(s). IMPORTANT: Interaction should be stored in output_dir/inter.json.

Parameters:

output_dirstr

The directory storing the potential files.

Notes

The following files are generated:

inter.json: output file

The task information is stored in output_dir/inter.json

set_inter_type_func()

set_model_param()

dpgen.auto_test.Property module

class dpgen.auto_test.Property.Property(parameter)

Bases: ABC

Attributes:

task_param

Return the parameter of each computational task, for example, {‘ediffg’: 1e-4}.

task_type

Return the type of each computational task, for example, ‘relaxation’, ‘static’….

Methods

compute(output_file, print_file, path_to_work)	Postprocess the finished tasks to compute the property.
make_confs(path_to_work, path_to_equi[, refine])	Make configurations needed to compute the property.
post_process(task_list)	post_process the KPOINTS file in elastic.

compute(output_file, print_file, path_to_work)

Postprocess the finished tasks to compute the property. Output the result to a json database.

Parameters:

output_file:

The file to output the property in json format

print_file:

The file to output the property in txt format

path_to_work:

The working directory where the computational tasks locate.

abstract make_confs(path_to_work, path_to_equi, refine=False)

Make configurations needed to compute the property. The tasks directory will be named as path_to_work/task.xxxxxx IMPORTANT: handel the case when the directory exists.

Parameters:

path_to_workstr

The path where the tasks for the property are located

path_to_equistr

-refine == False: The path to the directory that equilibrated the configuration. -refine == True: The path to the directory that has property confs.

refinestr

To refine existing property confs or generate property confs from a equilibrated conf

Returns:

task_list: list of str

The list of task directories.

abstract post_process(task_list)

post_process the KPOINTS file in elastic.

abstract property task_param

Return the parameter of each computational task, for example, {‘ediffg’: 1e-4}.

abstract property task_type

Return the type of each computational task, for example, ‘relaxation’, ‘static’….

dpgen.auto_test.Surface module

class dpgen.auto_test.Surface.Surface(parameter, inter_param=None)

Bases: Property

Methods

compute(output_file, print_file, path_to_work)	Postprocess the finished tasks to compute the property.
make_confs(path_to_work, path_to_equi[, refine])	Make configurations needed to compute the property.
post_process(task_list)	post_process the KPOINTS file in elastic.
task_param()	Return the parameter of each computational task, for example, {'ediffg': 1e-4}.
task_type()	Return the type of each computational task, for example, 'relaxation', 'static'....

make_confs(path_to_work, path_to_equi, refine=False)

Make configurations needed to compute the property. The tasks directory will be named as path_to_work/task.xxxxxx IMPORTANT: handel the case when the directory exists.

Parameters:

path_to_workstr

The path where the tasks for the property are located

path_to_equistr

-refine == False: The path to the directory that equilibrated the configuration. -refine == True: The path to the directory that has property confs.

refinestr

To refine existing property confs or generate property confs from a equilibrated conf

Returns:

task_list: list of str

The list of task directories.

post_process(task_list)

post_process the KPOINTS file in elastic.

task_param()

Return the parameter of each computational task, for example, {‘ediffg’: 1e-4}.

task_type()

Return the type of each computational task, for example, ‘relaxation’, ‘static’….

dpgen.auto_test.Task module

class dpgen.auto_test.Task.Task(inter_parameter, path_to_poscar)

Bases: ABC

Attributes:

backward_files

Return backward files.

forward_common_files

Return forward common files.

forward_files

Return forward files.

Methods

compute(output_dir)	Compute output of the task.
make_input_file(output_dir, task_type, ...)	Prepare input files for a computational task For example, the VASP prepares INCAR.
make_potential_files(output_dir)	Prepare potential files for a computational task.

abstract property backward_files

Return backward files.

abstract compute(output_dir)

Compute output of the task. IMPORTANT: The output configuration should be converted and stored in a CONTCAR file.

Parameters:

output_dirstr

The directory storing the input and output files.

Returns:

result_dict: dict

A dict that storing the result. For example: { “energy”: xxx, “force”: [xxx] }

Notes

The following files are generated: CONTCAR: output file

The output configuration is converted to CONTCAR and stored in the output_dir

abstract property forward_common_files

Return forward common files.

abstract property forward_files

Return forward files.

abstract make_input_file(output_dir, task_type, task_param)

Prepare input files for a computational task For example, the VASP prepares INCAR. LAMMPS (including DeePMD, MEAM…) prepares in.lammps.

Parameters:

output_dirstr

The directory storing the input files.

task_typestr

Can be - “relaxation:”: structure relaxation - “static”: static computation calculates the energy, force… of a strcture

task_paramdict

The parameters of the task. For example the VASP interaction can be provided with { “ediff”: 1e-6, “ediffg”: 1e-5 }

abstract make_potential_files(output_dir)

Prepare potential files for a computational task. For example, the VASP prepares POTCAR. DeePMD prepares frozen model(s). IMPORTANT: Interaction should be stored in output_dir/inter.json.

Parameters:

output_dirstr

The directory storing the potential files.

Notes

The following files are generated:

inter.json: output file

The task information is stored in output_dir/inter.json

dpgen.auto_test.VASP module

class dpgen.auto_test.VASP.VASP(inter_parameter, path_to_poscar)

Bases: Task

Methods

backward_files([property_type])	Return backward files.
compute(output_dir)	Compute output of the task.
forward_common_files([property_type])	Return forward common files.
forward_files([property_type])	Return forward files.
make_input_file(output_dir, task_type, ...)	Prepare input files for a computational task For example, the VASP prepares INCAR.
make_potential_files(output_dir)	Prepare potential files for a computational task.

backward_files(property_type='relaxation')

Return backward files.

compute(output_dir)

Compute output of the task. IMPORTANT: The output configuration should be converted and stored in a CONTCAR file.

Parameters:

output_dirstr

The directory storing the input and output files.

Returns:

result_dict: dict

A dict that storing the result. For example: { “energy”: xxx, “force”: [xxx] }

Notes

The following files are generated: CONTCAR: output file

The output configuration is converted to CONTCAR and stored in the output_dir

forward_common_files(property_type='relaxation')

Return forward common files.

forward_files(property_type='relaxation')

Return forward files.

make_input_file(output_dir, task_type, task_param)

Prepare input files for a computational task For example, the VASP prepares INCAR. LAMMPS (including DeePMD, MEAM…) prepares in.lammps.

Parameters:

output_dirstr

The directory storing the input files.

task_typestr

Can be - “relaxation:”: structure relaxation - “static”: static computation calculates the energy, force… of a strcture

task_paramdict

The parameters of the task. For example the VASP interaction can be provided with { “ediff”: 1e-6, “ediffg”: 1e-5 }

make_potential_files(output_dir)

Prepare potential files for a computational task. For example, the VASP prepares POTCAR. DeePMD prepares frozen model(s). IMPORTANT: Interaction should be stored in output_dir/inter.json.

Parameters:

output_dirstr

The directory storing the potential files.

Notes

The following files are generated:

inter.json: output file

The task information is stored in output_dir/inter.json

dpgen.auto_test.Vacancy module

class dpgen.auto_test.Vacancy.Vacancy(parameter, inter_param=None)

Bases: Property

Methods

compute(output_file, print_file, path_to_work)	Postprocess the finished tasks to compute the property.
make_confs(path_to_work, path_to_equi[, refine])	Make configurations needed to compute the property.
post_process(task_list)	post_process the KPOINTS file in elastic.
task_param()	Return the parameter of each computational task, for example, {'ediffg': 1e-4}.
task_type()	Return the type of each computational task, for example, 'relaxation', 'static'....

make_confs(path_to_work, path_to_equi, refine=False)

Make configurations needed to compute the property. The tasks directory will be named as path_to_work/task.xxxxxx IMPORTANT: handel the case when the directory exists.

Parameters:

path_to_workstr

The path where the tasks for the property are located

path_to_equistr

-refine == False: The path to the directory that equilibrated the configuration. -refine == True: The path to the directory that has property confs.

refinestr

To refine existing property confs or generate property confs from a equilibrated conf

Returns:

task_list: list of str

The list of task directories.

post_process(task_list)

post_process the KPOINTS file in elastic.

task_param()

Return the parameter of each computational task, for example, {‘ediffg’: 1e-4}.

task_type()

Return the type of each computational task, for example, ‘relaxation’, ‘static’….

dpgen.auto_test.calculator module

dpgen.auto_test.calculator.make_calculator(inter_parameter, path_to_poscar)

Make an instance of Task.

dpgen.auto_test.common_equi module

dpgen.auto_test.common_equi.make_equi(confs, inter_param, relax_param)

dpgen.auto_test.common_equi.post_equi(confs, inter_param)

dpgen.auto_test.common_equi.run_equi(confs, inter_param, mdata)

dpgen.auto_test.common_prop module

dpgen.auto_test.common_prop.make_property(confs, inter_param, property_list)

dpgen.auto_test.common_prop.make_property_instance(parameters, inter_param)

Make an instance of Property.

dpgen.auto_test.common_prop.post_property(confs, inter_param, property_list)

dpgen.auto_test.common_prop.run_property(confs, inter_param, property_list, mdata)

dpgen.auto_test.common_prop.worker(work_path, all_task, forward_common_files, forward_files, backward_files, mdata, inter_type)

dpgen.auto_test.gen_confs module

dpgen.auto_test.gen_confs.gen_alloy(eles, key)

dpgen.auto_test.gen_confs.gen_ele_std(ele_name, ctype)

dpgen.auto_test.gen_confs.gen_element(ele_name, key)

dpgen.auto_test.gen_confs.gen_element_std(ele_name)

dpgen.auto_test.gen_confs.make_path_mp(ii)

dpgen.auto_test.gen_confs.test_fit(struct, data)

dpgen.auto_test.mpdb module

dpgen.auto_test.mpdb.check_apikey()

dpgen.auto_test.mpdb.get_structure(mp_id)

dpgen.auto_test.refine module

dpgen.auto_test.refine.make_refine(init_from_suffix, output_suffix, path_to_work)

dpgen.auto_test.reproduce module

dpgen.auto_test.reproduce.make_repro(inter_param, init_data_path, init_from_suffix, path_to_work, reprod_last_frame=True)

dpgen.auto_test.reproduce.post_repro(init_data_path, init_from_suffix, all_tasks, ptr_data, reprod_last_frame=True)

dpgen.auto_test.run module

dpgen.auto_test.run.gen_test(args)

dpgen.auto_test.run.run_task(step, param_file, machine_file=None)