dpgen2.exploration.task package

Subpackages

Submodules

dpgen2.exploration.task.caly_task_group module

class dpgen2.exploration.task.caly_task_group.CalyTaskGroup[source]

Bases: ExplorationTaskGroup

Attributes:
task_list

Get the list of ExplorationTask

Methods

add_group(group)

Add another group to the group.

add_task(task)

Add one task to the group.

count(value)

index(value, [start, [stop]])

Raises ValueError if the value is not present.

make_task()

Make the CALYPSO task group.

set_params(numb_of_species, name_of_atoms, ...)

Set calypso parameters

clear
make_task() → ExplorationTaskGroup[source]

Make the CALYPSO task group.

Returns:
task_grp: ExplorationTaskGroup

Return one calypso task group.

set_params(numb_of_species, name_of_atoms, atomic_number, numb_of_atoms, distance_of_ions, pop_size: int = 30, max_step: int = 5, system_name: str = 'CALYPSO', numb_of_formula: List[int] = [1, 1], pressure: float = 0.001, fmax: float = 0.01, volume: float = 0, ialgo: int = 2, pso_ratio: float = 0.6, icode: int = 15, numb_of_lbest: int = 4, numb_of_local_optim: int = 4, command: str = 'sh submit.sh', max_time: int = 9000, gen_type: int = 1, pick_up: bool = False, pick_step: int = 1, parallel: bool = False, split: bool = True, spec_space_group: List[int] = [2, 230], vsc: bool = True, ctrl_range: List[List[int]] = [[1, 10]], max_numb_atoms: int = 100)[source]

Set calypso parameters

dpgen2.exploration.task.conf_sampling_task_group module

class dpgen2.exploration.task.conf_sampling_task_group.ConfSamplingTaskGroup[source]

Bases: ExplorationTaskGroup

Attributes:
task_list

Get the list of ExplorationTask

Methods

add_group(group)

Add another group to the group.

add_task(task)

Add one task to the group.

count(value)

index(value, [start, [stop]])

Raises ValueError if the value is not present.

make_task()

Make the task group.

set_conf(conf_list[, n_sample, random_sample])

Set the configurations of exploration

clear
set_conf(conf_list: List[str], n_sample: int | None = None, random_sample: bool = False)[source]

Set the configurations of exploration

Parameters:
conf_list str

A list of file contents

n_sample int

Number of samples drawn from the conf list each time make_task is called. If set to None, n_sample is set to length of the conf_list.

random_sample bool

If true the confs are randomly sampled, otherwise are consecutively sampled from the conf_list

dpgen2.exploration.task.customized_lmp_template_task_group module

class dpgen2.exploration.task.customized_lmp_template_task_group.CustomizedLmpTemplateTaskGroup[source]

Bases: ConfSamplingTaskGroup

Attributes:
task_list

Get the list of ExplorationTask

Methods

add_group(group)

Add another group to the group.

add_task(task)

Add one task to the group.

count(value)

index(value, [start, [stop]])

Raises ValueError if the value is not present.

make_task()

Make the task group.

set_conf(conf_list[, n_sample, random_sample])

Set the configurations of exploration

set_lmp(numb_models, custom_shell_commands)

Set lammps task.

clear
make_task() → CustomizedLmpTemplateTaskGroup[source]

Make the task group.

set_lmp(numb_models: int, custom_shell_commands: List[str], revisions: dict = {}, traj_freq: int = 10, input_lmp_conf_name: str = 'conf.lmp', input_lmp_tmpl_name: str = 'in.lammps', input_plm_tmpl_name: str | None = None, input_extra_files: List[str] = [], output_dir_pattern: str | List[str] = '*', output_lmp_conf_name: str = 'conf.lmp', output_lmp_tmpl_name: str = 'in.lammps', output_plm_tmpl_name: str | None = None) → None[source]

Set lammps task.

Parameters:
numb_modelsint

Number of models

custom_shell_commandsstr

Customized shell commands to be run for each configuration. The commands require input_lmp_conf_name as input conf file, input_lmp_tmpl_name and input_plm_tmpl_name as templates, and input_extra_files as extra input files. By running the commands a series folders in pattern output_dir_pattern are supposed to be generated, and each folder is supposed to contain a configuration file output_lmp_conf_name, a lammps template file output_lmp_tmpl_name and a plumed template file output_plm_tmpl_name.

revisionsdict

Revision dictionary. Provided in {key: [enumerated values]} format

traj_freqint

Frequency along trajectory of checking model deviation

input_lmp_conf_namestr

Input conf file name for the shell commands.

input_lmp_tmpl_namestr

Template file name of lammps input

input_plm_tmpl_namestr

Template file name of the plumed input

input_extra_filesList[str]

Extra files that may be needed to execute the shell commands

output_dir_patternUnion[str, List[str]]

Pattern of resultant folders generated by the shell commands.

output_lmp_conf_namestr

Generated conf file name.

output_lmp_tmpl_namestr

Generated lmp input file name.

output_plm_tmpl_namestr

Generated plm input file name.

dpgen2.exploration.task.lmp_template_task_group module

class dpgen2.exploration.task.lmp_template_task_group.LmpTemplateTaskGroup[source]

Bases: ConfSamplingTaskGroup

Attributes:
task_list

Get the list of ExplorationTask

Methods

add_group(group)

Add another group to the group.

add_task(task)

Add one task to the group.

count(value)

index(value, [start, [stop]])

Raises ValueError if the value is not present.

make_task()

Make the task group.

set_conf(conf_list[, n_sample, random_sample])

Set the configurations of exploration

clear

make_cont

set_lmp
make_cont(templates: list, revisions: dict)[source]
make_task() → LmpTemplateTaskGroup[source]

Make the task group.

set_lmp(numb_models: int, lmp_template_fname: str, plm_template_fname: str | None = None, revisions: dict = {}, traj_freq: int = 10) → None[source]
dpgen2.exploration.task.lmp_template_task_group.find_only_one_key(lmp_lines, key)[source]
dpgen2.exploration.task.lmp_template_task_group.revise_by_keys(lmp_lines, keys, values)[source]
dpgen2.exploration.task.lmp_template_task_group.revise_lmp_input_dump(lmp_lines, trj_freq)[source]
dpgen2.exploration.task.lmp_template_task_group.revise_lmp_input_model(lmp_lines, task_model_list, trj_freq, deepmd_version='1')[source]
dpgen2.exploration.task.lmp_template_task_group.revise_lmp_input_plm(lmp_lines, in_plm, out_plm='output.plumed')[source]

dpgen2.exploration.task.make_task_group_from_config module

dpgen2.exploration.task.make_task_group_from_config.caly_normalize(data)[source]
dpgen2.exploration.task.make_task_group_from_config.caly_task_group_args()[source]
dpgen2.exploration.task.make_task_group_from_config.caly_task_grp_args()[source]
dpgen2.exploration.task.make_task_group_from_config.config_strip_confidx(config)[source]
dpgen2.exploration.task.make_task_group_from_config.customized_lmp_template_task_group_args()[source]
dpgen2.exploration.task.make_task_group_from_config.lmp_normalize(data)[source]
dpgen2.exploration.task.make_task_group_from_config.lmp_task_group_args()[source]
dpgen2.exploration.task.make_task_group_from_config.lmp_template_task_group_args()[source]
dpgen2.exploration.task.make_task_group_from_config.make_calypso_task_group_from_config(config)[source]
dpgen2.exploration.task.make_task_group_from_config.make_lmp_task_group_from_config(numb_models, mass_map, config)[source]
dpgen2.exploration.task.make_task_group_from_config.make_task_group_from_config(numb_models, mass_map, config)[source]
dpgen2.exploration.task.make_task_group_from_config.npt_task_group_args()[source]
dpgen2.exploration.task.make_task_group_from_config.variant_task_group()[source]

dpgen2.exploration.task.npt_task_group module

class dpgen2.exploration.task.npt_task_group.NPTTaskGroup[source]

Bases: ConfSamplingTaskGroup

Attributes:
task_list

Get the list of ExplorationTask

Methods

add_group(group)

Add another group to the group.

add_task(task)

Add one task to the group.

count(value)

index(value, [start, [stop]])

Raises ValueError if the value is not present.

make_task()

Make the LAMMPS task group.

set_conf(conf_list[, n_sample, random_sample])

Set the configurations of exploration

set_md(numb_models, mass_map, temps[, ...])

Set MD parameters

clear
make_task() → NPTTaskGroup[source]

Make the LAMMPS task group.

Returns:
task_grp: ExplorationTaskGroup

The returned lammps task group. The number of tasks is nconf*nT*nP. nconf is set by n_sample parameter of set_conf. nT and nP are lengths of the temps and press parameters of set_md.

set_md(numb_models, mass_map, temps: List[float], press: List[float] | None = None, ens: str = 'npt', dt: float = 0.001, nsteps: int = 1000, trj_freq: int = 10, tau_t: float = 0.1, tau_p: float = 0.5, pka_e: float | None = None, neidelay: int | None = None, no_pbc: bool = False, use_clusters: bool = False, relative_f_epsilon: float | None = None, relative_v_epsilon: float | None = None, ele_temp_f: float | None = None, ele_temp_a: float | None = None)[source]

Set MD parameters

dpgen2.exploration.task.stage module

class dpgen2.exploration.task.stage.ExplorationStage[source]

Bases: object

The exploration stage.

Methods

add_task_group(grp)

Add an exploration group

clear()

Clear all exploration group.

make_task()

Make the LAMMPS task group.
add_task_group(grp: ExplorationTaskGroup)[source]

Add an exploration group

Parameters:
grpExplorationTaskGroup

The added exploration task group

clear()[source]

Clear all exploration group.

make_task() → BaseExplorationTaskGroup[source]

Make the LAMMPS task group.

Returns:
task_grp: BaseExplorationTaskGroup

The returned lammps task group. The number of tasks is equal to the summation of task groups defined by all the exploration groups added to the stage.

dpgen2.exploration.task.task module

class dpgen2.exploration.task.task.ExplorationTask[source]

Bases: object

Define the files needed by an exploration task.

Examples

>>> # this example dumps all files needed by the task.
>>> files = exploration_task.files()
... for file_name, file_content in files.items():
...     with open(file_name, 'w') as fp:
...         fp.write(file_content)

Methods

add_file(fname, fcont)

Add file to the task

files()

Get all files for the task.
add_file(fname: str, fcont: str)[source]

Add file to the task

Parameters:
fnamestr

The name of the file

fcontstr

The content of the file.

files() → Dict[source]

Get all files for the task.

Returns:
filesdict

The dict storing all files for the task. The file name is a key of the dict, and the file content is the corresponding value.

dpgen2.exploration.task.task_group module

class dpgen2.exploration.task.task_group.BaseExplorationTaskGroup[source]

Bases: Sequence

A group of exploration tasks. Implemented as a list of ExplorationTask.

Attributes:
task_list

Get the list of ExplorationTask

Methods

add_group(group)

Add another group to the group.

add_task(task)

Add one task to the group.

count(value)

index(value, [start, [stop]])

Raises ValueError if the value is not present.

clear
add_group(group: ExplorationTaskGroup)[source]

Add another group to the group.

add_task(task: ExplorationTask)[source]

Add one task to the group.

clear() → None[source]
property task_list: List[ExplorationTask]

Get the list of ExplorationTask

class dpgen2.exploration.task.task_group.ExplorationTaskGroup[source]

Bases: ABC, BaseExplorationTaskGroup

Attributes:
task_list

Get the list of ExplorationTask

Methods

add_group(group)

Add another group to the group.

add_task(task)

Add one task to the group.

count(value)

index(value, [start, [stop]])

Raises ValueError if the value is not present.

make_task()

Make the task group.

clear
abstract make_task() → ExplorationTaskGroup[source]

Make the task group.

class dpgen2.exploration.task.task_group.FooTask(conf_name='conf.lmp', conf_cont='', inpu_name='in.lammps', inpu_cont='')[source]

Bases: ExplorationTask

Methods

add_file(fname, fcont)

Add file to the task

files()

Get all files for the task.
class dpgen2.exploration.task.task_group.FooTaskGroup(numb_task)[source]

Bases: BaseExplorationTaskGroup

Attributes:
task_list

Get the list of ExplorationTask

Methods

add_group(group)

Add another group to the group.

add_task(task)

Add one task to the group.

count(value)

index(value, [start, [stop]])

Raises ValueError if the value is not present.

clear
property task_list

Get the list of ExplorationTask