dpgen.auto_test package

Subpackages

Submodules

dpgen.auto_test.ABACUS module

class dpgen.auto_test.ABACUS.ABACUS(inter_parameter, path_to_poscar)[source]

Bases: Task

Methods

backward_files([property_type])

staticmethod(function) -> method

compute(output_dir)

Compute output of the task.

forward_common_files([property_type])

staticmethod(function) -> method

forward_files([property_type])

staticmethod(function) -> method

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')[source]

staticmethod(function) -> method

Convert a function to be a static method.

A static method does not receive an implicit first argument. To declare a static method, use this idiom:

class C:

@staticmethod def f(arg1, arg2, …):

…

It can be called either on the class (e.g. C.f()) or on an instance (e.g. C().f()). The instance is ignored except for its class.

Static methods in Python are similar to those found in Java or C++. For a more advanced concept, see the classmethod builtin.

compute(output_dir)[source]

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] }

forward_common_files(property_type='relaxation')[source]

staticmethod(function) -> method

Convert a function to be a static method.

A static method does not receive an implicit first argument. To declare a static method, use this idiom:

class C:

@staticmethod def f(arg1, arg2, …):

…

It can be called either on the class (e.g. C.f()) or on an instance (e.g. C().f()). The instance is ignored except for its class.

Static methods in Python are similar to those found in Java or C++. For a more advanced concept, see the classmethod builtin.

forward_files(property_type='relaxation')[source]

staticmethod(function) -> method

Convert a function to be a static method.

A static method does not receive an implicit first argument. To declare a static method, use this idiom:

class C:

@staticmethod def f(arg1, arg2, …):

…

It can be called either on the class (e.g. C.f()) or on an instance (e.g. C().f()). The instance is ignored except for its class.

Static methods in Python are similar to those found in Java or C++. For a more advanced concept, see the classmethod builtin.

make_input_file(output_dir, task_type, task_param)[source]

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_parame: dict

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)[source]

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.

Outputs
——-
inter.json: output file

The task information is stored in output_dir/inter.json

modify_input(incar, x, y)[source]

dpgen.auto_test.EOS module

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

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)[source]

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.

refine: str

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)[source]

post_process the KPOINTS file in elastic.

task_param()[source]

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

task_type()[source]

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)[source]

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)[source]

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.

refine: str

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)[source]

post_process the KPOINTS file in elastic.

task_param()[source]

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

task_type()[source]

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)[source]

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[source]
make_confs(path_to_work, path_to_equi, refine=False)[source]

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.

refine: str

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)[source]

post_process the KPOINTS file in elastic.

return_direction()[source]
task_param()[source]

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

task_type()[source]

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)[source]

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)[source]

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.

refine: str

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)[source]

post_process the KPOINTS file in elastic.

task_param()[source]

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

task_type()[source]

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)[source]

Bases: Task

Methods

backward_files([property_type])

staticmethod(function) -> method

compute(output_dir)

Compute output of the task.

forward_common_files([property_type])

staticmethod(function) -> method

forward_files([property_type])

staticmethod(function) -> method

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')[source]

staticmethod(function) -> method

Convert a function to be a static method.

A static method does not receive an implicit first argument. To declare a static method, use this idiom:

class C:

@staticmethod def f(arg1, arg2, …):

…

It can be called either on the class (e.g. C.f()) or on an instance (e.g. C().f()). The instance is ignored except for its class.

Static methods in Python are similar to those found in Java or C++. For a more advanced concept, see the classmethod builtin.

compute(output_dir)[source]

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] }

forward_common_files(property_type='relaxation')[source]

staticmethod(function) -> method

Convert a function to be a static method.

A static method does not receive an implicit first argument. To declare a static method, use this idiom:

class C:

@staticmethod def f(arg1, arg2, …):

…

It can be called either on the class (e.g. C.f()) or on an instance (e.g. C().f()). The instance is ignored except for its class.

Static methods in Python are similar to those found in Java or C++. For a more advanced concept, see the classmethod builtin.

forward_files(property_type='relaxation')[source]

staticmethod(function) -> method

Convert a function to be a static method.

A static method does not receive an implicit first argument. To declare a static method, use this idiom:

class C:

@staticmethod def f(arg1, arg2, …):

…

It can be called either on the class (e.g. C.f()) or on an instance (e.g. C().f()). The instance is ignored except for its class.

Static methods in Python are similar to those found in Java or C++. For a more advanced concept, see the classmethod builtin.

make_input_file(output_dir, task_type, task_param)[source]

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_parame: dict

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)[source]

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.

Outputs
——-
inter.json: output file

The task information is stored in output_dir/inter.json

set_inter_type_func()[source]
set_model_param()[source]

dpgen.auto_test.Property module

class dpgen.auto_test.Property.Property(parameter)[source]

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)[source]

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)[source]

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.

refine: str

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)[source]

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)[source]

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)[source]

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.

refine: str

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)[source]

post_process the KPOINTS file in elastic.

task_param()[source]

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

task_type()[source]

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)[source]

Bases: ABC

Attributes
backward_files

staticmethod(function) -> method

forward_common_files

staticmethod(function) -> method

forward_files

staticmethod(function) -> method

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

staticmethod(function) -> method

Convert a function to be a static method.

A static method does not receive an implicit first argument. To declare a static method, use this idiom:

class C:

@staticmethod def f(arg1, arg2, …):

…

It can be called either on the class (e.g. C.f()) or on an instance (e.g. C().f()). The instance is ignored except for its class.

Static methods in Python are similar to those found in Java or C++. For a more advanced concept, see the classmethod builtin.

abstract compute(output_dir)[source]

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] }

abstract property forward_common_files

staticmethod(function) -> method

Convert a function to be a static method.

A static method does not receive an implicit first argument. To declare a static method, use this idiom:

class C:

@staticmethod def f(arg1, arg2, …):

…

It can be called either on the class (e.g. C.f()) or on an instance (e.g. C().f()). The instance is ignored except for its class.

Static methods in Python are similar to those found in Java or C++. For a more advanced concept, see the classmethod builtin.

abstract property forward_files

staticmethod(function) -> method

Convert a function to be a static method.

A static method does not receive an implicit first argument. To declare a static method, use this idiom:

class C:

@staticmethod def f(arg1, arg2, …):

…

It can be called either on the class (e.g. C.f()) or on an instance (e.g. C().f()). The instance is ignored except for its class.

Static methods in Python are similar to those found in Java or C++. For a more advanced concept, see the classmethod builtin.

abstract make_input_file(output_dir, task_type, task_param)[source]

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_parame: dict

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)[source]

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.

Outputs
——-
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)[source]

Bases: Task

Methods

backward_files([property_type])

staticmethod(function) -> method

compute(output_dir)

Compute output of the task.

forward_common_files([property_type])

staticmethod(function) -> method

forward_files([property_type])

staticmethod(function) -> method

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')[source]

staticmethod(function) -> method

Convert a function to be a static method.

A static method does not receive an implicit first argument. To declare a static method, use this idiom:

class C:

@staticmethod def f(arg1, arg2, …):

…

It can be called either on the class (e.g. C.f()) or on an instance (e.g. C().f()). The instance is ignored except for its class.

Static methods in Python are similar to those found in Java or C++. For a more advanced concept, see the classmethod builtin.

compute(output_dir)[source]

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] }

forward_common_files(property_type='relaxation')[source]

staticmethod(function) -> method

Convert a function to be a static method.

A static method does not receive an implicit first argument. To declare a static method, use this idiom:

class C:

@staticmethod def f(arg1, arg2, …):

…

It can be called either on the class (e.g. C.f()) or on an instance (e.g. C().f()). The instance is ignored except for its class.

Static methods in Python are similar to those found in Java or C++. For a more advanced concept, see the classmethod builtin.

forward_files(property_type='relaxation')[source]

staticmethod(function) -> method

Convert a function to be a static method.

A static method does not receive an implicit first argument. To declare a static method, use this idiom:

class C:

@staticmethod def f(arg1, arg2, …):

…

It can be called either on the class (e.g. C.f()) or on an instance (e.g. C().f()). The instance is ignored except for its class.

Static methods in Python are similar to those found in Java or C++. For a more advanced concept, see the classmethod builtin.

make_input_file(output_dir, task_type, task_param)[source]

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_parame: dict

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)[source]

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.

Outputs
——-
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)[source]

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)[source]

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.

refine: str

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)[source]

post_process the KPOINTS file in elastic.

task_param()[source]

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

task_type()[source]

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)[source]

Make an instance of Task

dpgen.auto_test.common_equi module

dpgen.auto_test.common_equi.make_equi(confs, inter_param, relax_param)[source]
dpgen.auto_test.common_equi.post_equi(confs, inter_param)[source]
dpgen.auto_test.common_equi.run_equi(confs, inter_param, mdata)[source]

dpgen.auto_test.common_prop module

dpgen.auto_test.common_prop.make_property(confs, inter_param, property_list)[source]
dpgen.auto_test.common_prop.make_property_instance(parameters, inter_param)[source]

Make an instance of Property

dpgen.auto_test.common_prop.post_property(confs, inter_param, property_list)[source]
dpgen.auto_test.common_prop.run_property(confs, inter_param, property_list, mdata)[source]
dpgen.auto_test.common_prop.worker(work_path, all_task, forward_common_files, forward_files, backward_files, mdata, inter_type)[source]

dpgen.auto_test.gen_confs module

dpgen.auto_test.gen_confs.gen_alloy(eles, key)[source]
dpgen.auto_test.gen_confs.gen_ele_std(ele_name, ctype)[source]
dpgen.auto_test.gen_confs.gen_element(ele_name, key)[source]
dpgen.auto_test.gen_confs.gen_element_std(ele_name)[source]
dpgen.auto_test.gen_confs.make_path_mp(ii)[source]
dpgen.auto_test.gen_confs.test_fit(struct, data)[source]

dpgen.auto_test.mpdb module

dpgen.auto_test.mpdb.check_apikey()[source]
dpgen.auto_test.mpdb.get_structure(mp_id)[source]

dpgen.auto_test.refine module

dpgen.auto_test.refine.make_refine(init_from_suffix, output_suffix, path_to_work)[source]

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

dpgen.auto_test.run module

dpgen.auto_test.run.gen_test(args)[source]
dpgen.auto_test.run.run_task(step, param_file, machine_file=None)[source]