ai2_kit.domain.cp2k module

class ai2_kit.domain.cp2k.CllCp2kContext(path_prefix: str, resource_manager: ai2_kit.core.resource_manager.ResourceManager, config: ai2_kit.domain.cp2k.CllCp2kContextConfig)

Bases: BaseCllContext

config: CllCp2kContextConfig

class ai2_kit.domain.cp2k.CllCp2kContextConfig(*, script_template: BashTemplate, cp2k_cmd: str = 'cp2k', post_cp2k_cmd: str = 'echo "no post_cp2k_cmd"', concurrency: int = 5)

Bases: BaseModel

concurrency: int

cp2k_cmd: str

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {'extra': 'forbid'}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'concurrency': FieldInfo(annotation=int, required=False, default=5), 'cp2k_cmd': FieldInfo(annotation=str, required=False, default='cp2k'), 'post_cp2k_cmd': FieldInfo(annotation=str, required=False, default='echo "no post_cp2k_cmd"'), 'script_template': FieldInfo(annotation=BashTemplate, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

post_cp2k_cmd: str

script_template: BashTemplate

class ai2_kit.domain.cp2k.CllCp2kInput(config: ai2_kit.domain.cp2k.CllCp2kInputConfig, mode: Literal['default', 'dpff', 'fep-redox', 'fep-pka'], system_files: List[ai2_kit.core.artifact.Artifact], type_map: List[str], initiated: bool = False)

Bases: object

config: CllCp2kInputConfig

initiated: bool = False

mode: Literal['default', 'dpff', 'fep-redox', 'fep-pka']

system_files: List[Artifact]

type_map: List[str]

class ai2_kit.domain.cp2k.CllCp2kInputConfig(*, init_system_files: List[str] = [], wfn_warmup_template: Optional[str] = None, input_template: Optional[str] = None, template_vars: Mapping[str, Any] = {}, limit: int = 50, limit_method: Literal['even', 'random', 'truncate'] = 'even', ignore_error: bool = False)

Bases: BaseModel

ignore_error: bool

Ignore error when running cp2k.

init_system_files: List[str]

input_template: Optional[str]

Input template for cp2k. Could be a dict or content of a cp2k input file.

limit: int

Limit of the number of systems to be labeled.

limit_method: Literal['even', 'random', 'truncate']

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {'extra': 'forbid'}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'ignore_error': FieldInfo(annotation=bool, required=False, default=False), 'init_system_files': FieldInfo(annotation=List[str], required=False, default=[]), 'input_template': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'limit': FieldInfo(annotation=int, required=False, default=50), 'limit_method': FieldInfo(annotation=Literal['even', 'random', 'truncate'], required=False, default='even'), 'template_vars': FieldInfo(annotation=Mapping[str, Any], required=False, default={}), 'wfn_warmup_template': FieldInfo(annotation=Union[str, NoneType], required=False, default=None)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

template_vars: Mapping[str, Any]

Template variables for input_template and wfn_warmup_template.

Those vars can be referenced in the LAMMPS input template as $$VAR_NAME.

wfn_warmup_template: Optional[str]

Warmup template for cp2k. Could be a dict or content of a cp2k input file. This template will be used to generate input files for warmup runs. The warmup runs can be used to generate wave function files for the main runs.

class ai2_kit.domain.cp2k.Cp2kInputTemplate(template)

Bases: Template

delimiter = '$$'

pattern = re.compile('\n            \\$\\$(?:\n              (?P<escaped>\\$\\$)  |   # Escape sequence of two delimiters\n              (?P<named>(?a:[_a-z][_a-z0-9]*))       |   # delimiter and a Python identifier\n    , re.IGNORECASE|re.VERBOSE)

class ai2_kit.domain.cp2k.GenericCp2kOutput(cp2k_outputs: List[ai2_kit.core.artifact.Artifact])

Bases: ICllLabelOutput

cp2k_outputs: List[Artifact]

get_labeled_system_dataset()

async ai2_kit.domain.cp2k.cll_cp2k(input: CllCp2kInput, ctx: CllCp2kContext) → GenericCp2kOutput

ai2_kit.domain.cp2k.dump_coord_n_cell(fp, atoms: Atoms)

ai2_kit.domain.cp2k.lammps_efield_to_cp2k(efield: Iterable[float])

IN CP2K, the efield is defined as INTENSITY and POLARIZATION (direction of the electric field)

Parameters:

efield – list of 3 floats, the electric field in lammps unit

Returns:

intensity, polarization

ai2_kit.domain.cp2k.make_cp2k_task_dirs(system_files: List[ArtifactDict], type_map: List[str], input_template: Optional[str], template_vars: Mapping[str, Any], base_dir: str, mode: Literal['default', 'dpff', 'fep-redox', 'fep-pka'], limit: int = 0, wfn_warmup_template: Optional[str] = None, limit_method: Literal['even', 'random', 'truncate'] = 'even', input_file_name: str = 'input.inp', warmup_file_name: str = 'wfn_warmup.inp') → List[ArtifactDict]

Generate CP2K input files from LAMMPS dump files or XYZ files.