Estimator

Bases: object

Core class of PFP. Estimator calculates the energy and related values (e.g. atomic forces) of given atomic structure. A single Estimator instance can only be used by at most
one ASECalculator instance.

Acceptable PFP model versions are:

• v7.0.0: latest version, supporting 24 additional elements, for a total of 96 elements.

• v6.0.0: improving the reproducibility of sparse environments
  (e.g. molecules in vacuum) and high-density structures.

• v5.0.0: improving the reproducibility of physical properties
  for partially element-substituted structures, liquid, and organic crystals.

• v4.0.0: improving the reproducibility of the energy order
  and the density of bulk structures of crystals, and intermolecular interactions.

• v3.0.0: supporting 17 additional elements, for a total of 72 elements.

• v2.0.0: model version with support for D3 correction and zero Hubbard U parameter.

• v1.1.0: the same model as v1.0.0 with D3 correction support.

• v1.0.0: initial stable version, does not support D3.

• v0.0.0: PFP paper version, does not support D3.

• latest: alias for v7.0.0.

property application_context: Optional[str]#

attach_to_calculator(_: Calculator) → None#

property available_models: Sequence[str]#

property calc_mode: Optional[EstimatorCalcMode]#

estimate(args: EstimatorSystem) → Dict[str, Union[List[MessageEnum], ndarray]]#

This function receives atomic system information and returns energy, forces and related values.

Parameters:

args (EstimatorSystem) – For details, see the document for EstimatorSystem.

Returns:

results – Dictionary which contains various calculated properties

Return type:

Dict[str, any]

get_shift_energy_table(calc_mode: Optional[Union[EstimatorCalcMode, str]] = None, model_version: Optional[str] = None) → Dict[int, float]#

Return the table of shift energies of input atoms.

Parameters:

calc_mode (str, EstimatorCalcMode, or None) – Calculation mode. If not specified, calc_mode set in the estimator will be used.

Returns:

shift_energies_table – Table of shift energies.

Return type:

Dict[int, float]

property method_type: EstimatorMethodType#

property model_version: str#

property priority: int#

set_calc_mode(calc_mode: Union[EstimatorCalcMode, str]) → None#

Set estimator calculation mode.

Parameters:

calc_mode (Union[EstimatorCalcMode, str]) – The calculation mode to be set.

set_message_status(message: MessageEnum, message_enable: bool) → None#

Toggle whether to show individual messages in estimate().

Parameters:

• message (MessageEnum) – Message to toggle.

• message_enable (bool) – True/False correspond to enabling/disabling the message.

set_method_type(method_type: Union[EstimatorMethodType, str]) → None#

Set estimator method type.

Parameters:

method_type (Union[EstimatorMethodType, str]) – The inference method type to be set.

set_model_version(model_version: str) → None#

Set model version.

Parameters:

model_version (str) – The model version to be set.

set_priority(priority: int) → None#

supported_elements(model_version: Optional[str] = None, status: Union[EstimatorElementStatus, Tuple[EstimatorElementStatus, …]] = EstimatorElementStatus.Expected, calc_mode: Optional[Union[EstimatorCalcMode, str]] = None) → List[str]#

Return list of implemented elements in specified model version.

Parameters:

• model_version (str, optional) – Model version to be specified.

• status (EstimatorElementStatus or tuple of EstimatorElementStatus, optional) – Target support status to return. Multiple keywords can be specified.

• calc_mode (EstimatorCalcMode, or str, optional) – Calculation mode. If not specified, calc_mode set in the estimator will be used.

Returns:

elements – List which contains implemented elements.

Return type:

List[str]

Bases: Enum

Enum class which is used to determine calc_mode in Estimator.

Variables:

• CRYSTAL – Crystal mode. This mode corresponds to DFT calculations with plane wave basis sets.

• CRYSTAL_PLUS_D3 – Crystal mode with D3 correction enabled. This mode corresponds to DFT calculations with plane wave basis sets, plus a D3 dispersion correction.

• CRYSTAL_U0 – Crystal mode with Hubbard U parameter switched off. This mode corresponds to DFT calculations with plane wave basis sets.

• CRYSTAL_U0_PLUS_D3 – Crystal mode with Hubbard U parameter switched off and D3 correction enabled. This mode corresponds to DFT calculations with plane wave basis sets, plus a D3 dispersion correction.

• MOLECULE – Molecule mode. This mode corresponds to DFT calculations with local basis sets.

CRYSTAL = ‘crystal’#

CRYSTAL_PLUS_D3 = ‘crystal_plus_d3’#

CRYSTAL_U0 = ‘crystal_u0’#

CRYSTAL_U0_PLUS_D3 = ‘crystal_u0_plus_d3’#

MOLECULE = ‘molecule’#

PBE = ‘pbe’#

PBE_PLUS_D3 = ‘pbe_plus_d3’#

PBE_U = ‘pbe_u’#

PBE_U_PLUS_D3 = ‘pbe_u_plus_d3’#

R2SCAN = ‘r2scan’#

R2SCAN_PLUS_D3 = ‘r2scan_plus_d3’#

WB97XD = ‘wb97xd’#

static from_str(label: str) → EstimatorCalcMode#

Bases: Enum

Enum class which is used to determine element_status in Estimator.

Variables:

• Expected – Fully supported elements.

• Experimental – Experimentally supported elements.

• Unexpected – Unsopported elements.

Expected = ‘EstimatorElementStatus.Expected’#

Experimental = ‘EstimatorElementStatus.Experimental’#

Bases: Enum

Enum class which is used to determine method_type in Estimator.

Variables:

• PFVM – Inference is performed in pfvm mode. Inference of dftd3 is performed in torch mode.

• MNCORE_ACCURATE – Inference is performed in accurate mode on MN-Core.

• MNCORE_FAST – Inference is performed in fast mode on MN-Core.

• PFVM_D3_PFVM – Inferences of pfp and dftd3 are performed in pfvm mode.

MNCORE = ‘mncore’#

MNCORE_ACCURATE = ‘mncore_accurate’#

MNCORE_FAST = ‘mncore_fast’#

PFVM = ‘pfvm’#

PFVM_D3_PFVM = ‘pfvm_d3_pfvm’#

static from_str(label: str) → EstimatorMethodType#

Bases: object

Input argument of Estimator.estimate function.

Parameters:

• properties (List[str]) – What properties should be calculated. Current implemented properties are “energy”, “forces”, “charges”, and “virial”. If gradient-based parameters (forces, virial) are not requested, the estimator does not calculate them.

• coordinates (np.ndarray (dtype=np.float32 or np.float64)) – Coordination of atoms. The shape is (n_atoms, 3).

• cell (np.ndarray (dtype=np.float32 or np.float64)) – Simulation cell of the system. The shape is (3, 3)

• species (Optional[np.ndarray] (dtype=”)) – Element list of atoms as string. Either species or atomic_numbers should be provided. The shape is (n_atoms, )

• atomic_numbers (Optional[np.ndarray] (dtype=np.uint8)) – Element list of atoms as atomic number. Either species or atomic_numbers should be provided. The shape is (n_atoms, )

• pbc (Optional[np.ndarray] (dtype=np.uint8)) – Whether periodic boundary conditions are applied (1) or not (0) for each axis. The shape is (3, )

• calc_mode (Optional[EstimatorCalcMode]) – Calculate results with given calculation mode.