espei.error_functions package

Submodules

espei.error_functions.activity_error module

Calculate error due to measured activities.

espei.error_functions.activity_error.calculate_activity_error(dbf, comps, phases, datasets, parameters=None, phase_models=None, callables=None, data_weight=1.0)

Return the sum of square error from activity data

Parameters
  • dbf (pycalphad.Database) – Database to consider

  • comps (list) – List of active component names

  • phases (list) – List of phases to consider

  • datasets (espei.utils.PickleableTinyDB) – Datasets that contain single phase data

  • parameters (dict) – Dictionary of symbols that will be overridden in pycalphad.equilibrium

  • phase_models (dict) – Phase models to pass to pycalphad calculations

  • callables (dict) – Callables to pass to pycalphad

  • data_weight (float) – Weight for standard deviation of activity measurements, dimensionless. Corresponds to the standard deviation of differences in chemical potential in typical measurements of activity, in J/mol.

Returns

A single float of the sum of square errors

Return type

float

Notes

General procedure: 1. Get the datasets 2. For each dataset

  1. Calculate reference state equilibrium

  2. Calculate current chemical potentials

  3. Find the target chemical potentials

  4. Calculate error due to chemical potentials

espei.error_functions.activity_error.chempot_error(sample_chempots, target_chempots, std_dev=10.0)

Return the sum of square error from chemical potentials

sample_chempotsnumpy.ndarray

Calculated chemical potentials

target_activitynumpy.ndarray

Chemical potentials to target

std_devfloat

Standard deviation of activity measurements in J/mol. Corresponds to the standard deviation of differences in chemical potential in typical measurements of activity.

Returns

Error due to chemical potentials

Return type

float

espei.error_functions.activity_error.target_chempots_from_activity(component, target_activity, temperatures, reference_result)

Return an array of experimental chemical potentials for the component

Parameters
  • component (str) – Name of the component

  • target_activity (numpy.ndarray) – Array of experimental activities

  • temperatures (numpy.ndarray) – Ravelled array of temperatures (of same size as exp_activity).

  • reference_result (xarray.Dataset) – Dataset of the equilibrium reference state. Should contain a singe point calculation.

Returns

Array of experimental chemical potentials

Return type

numpy.ndarray

espei.error_functions.context module

Convenience function to create a context for the built in error functions

espei.error_functions.context.setup_context(dbf, datasets, symbols_to_fit=None, data_weights=None, make_callables=True)

Set up a context dictionary for calculating error.

Parameters
  • dbf (Database) – A pycalphad Database that will be fit

  • datasets (PickleableTinyDB) – A database of single- and multi-phase data to fit

  • symbols_to_fit (list of str) – List of symbols in the Database that will be fit. If None (default) are passed, then all parameters prefixed with VV followed by a number, e.g. VV0001 will be fit.

Notes

A copy of the Database is made and used in the context. To commit changes back to the original database, the dbf.symbols.update method should be used.

espei.error_functions.equilibrium_thermochemical_error module

Calculate error due to equilibrium thermochemical properties.

class espei.error_functions.equilibrium_thermochemical_error.EqPropData(dbf, species, phases, potential_conds, composition_conds, models, params_keys, phase_records, output, samples, weight, reference)

Bases: tuple

property composition_conds

Alias for field number 4

property dbf

Alias for field number 0

property models

Alias for field number 5

property output

Alias for field number 8

property params_keys

Alias for field number 6

property phase_records

Alias for field number 7

property phases

Alias for field number 2

property potential_conds

Alias for field number 3

property reference

Alias for field number 11

property samples

Alias for field number 9

property species

Alias for field number 1

property weight

Alias for field number 10

espei.error_functions.equilibrium_thermochemical_error.build_eqpropdata(data: tinydb.table.Document, dbf: pycalphad.io.database.Database, parameters: Optional[Dict[str, float]] = None, data_weight_dict: Optional[Dict[str, float]] = None)espei.error_functions.equilibrium_thermochemical_error.EqPropData

Build EqPropData for the calculations corresponding to a single dataset.

Parameters
  • data (tinydb.database.Document) – Document corresponding to a single ESPEI dataset.

  • dbf (Database) – Database that should be used to construct the Model and PhaseRecord objects.

  • parameters (Optional[Dict[str, float]]) – Mapping of parameter symbols to values.

  • data_weight_dict (Optional[Dict[str, float]]) – Mapping of a data type (e.g. HM or SM) to a weight.

Returns

Return type

EqPropData

espei.error_functions.equilibrium_thermochemical_error.calc_prop_differences(eqpropdata: espei.error_functions.equilibrium_thermochemical_error.EqPropData, parameters: numpy.ndarray, approximate_equilibrium: Optional[bool] = False)Tuple[numpy.ndarray, numpy.ndarray]

Calculate differences between the expected and calculated values for a property

Parameters
  • eqpropdata (EqPropData) – Data corresponding to equilibrium calculations for a single datasets.

  • parameters (np.ndarray) – Array of parameters to fit. Must be sorted in the same symbol sorted order used to create the PhaseRecords.

  • approximate_equilibrium (Optional[bool]) – Whether or not to use an approximate version of equilibrium that does not refine the solution and uses starting_point instead.

Returns

Pair of * differences between the calculated property and expected property * weights for this dataset

Return type

Tuple[np.ndarray, np.ndarray]

espei.error_functions.equilibrium_thermochemical_error.calculate_equilibrium_thermochemical_probability(eq_thermochemical_data: Sequence[espei.error_functions.equilibrium_thermochemical_error.EqPropData], parameters: numpy.ndarray, approximate_equilibrium: Optional[bool] = False)float

Calculate the total equilibrium thermochemical probability for all EqPropData

Parameters
  • eq_thermochemical_data (Sequence[EqPropData]) – List of equilibrium thermochemical data corresponding to the datasets.

  • parameters (np.ndarray) – Values of parameters for this iteration to be updated in PhaseRecords.

  • approximate_equilibrium (Optional[bool], optional) –

  • eq_thermochemical_data

Returns

Sum of log-probability for all thermochemical data.

Return type

float

espei.error_functions.equilibrium_thermochemical_error.get_equilibrium_thermochemical_data(dbf: pycalphad.io.database.Database, comps: Sequence[str], phases: Sequence[str], datasets: espei.utils.PickleableTinyDB, parameters: Optional[Dict[str, float]] = None, data_weight_dict: Optional[Dict[str, float]] = None)Sequence[espei.error_functions.equilibrium_thermochemical_error.EqPropData]

Get all the EqPropData for each matching equilibrium thermochemical dataset in the datasets

Parameters
  • dbf (Database) – Database with parameters to fit

  • comps (Sequence[str]) – List of pure element components used to find matching datasets.

  • phases (Sequence[str]) – List of phases used to search for matching datasets.

  • datasets (PickleableTinyDB) – Datasets that contain single phase data

  • parameters (Optional[Dict[str, float]]) – Mapping of parameter symbols to values.

  • data_weight_dict (Optional[Dict[str, float]]) – Mapping of a data type (e.g. HM or SM) to a weight.

Notes

Found datasets will be subsets of the components and phases. Equilibrium thermochemical data is assumed to be any data that does not have the solver key, and does not have an output of ZPF or ACR (which correspond to different data types than can be calculated here.)

Returns

Return type

Sequence[EqPropData]

espei.error_functions.non_equilibrium_thermochemical_error module

Calculate error due to thermochemical quantities: heat capacity, entropy, enthalpy.

espei.error_functions.non_equilibrium_thermochemical_error.calculate_non_equilibrium_thermochemical_probability(thermochemical_data, parameters=None)

Calculate the weighted single phase error in the Database

Parameters
  • thermochemical_data (list) – List of thermochemical data dicts

  • parameters (np.ndarray) – Array of parameters to calculate the error with.

Returns

A single float of the residual sum of square errors

Return type

float

espei.error_functions.non_equilibrium_thermochemical_error.calculate_points_array(phase_constituents, configuration, occupancies=None)

Calculate the points array to use in pycalphad calculate calls.

Converts the configuration data (and occupancies for mixing data) into the points array by looking up the indices in the active phase constituents.

Parameters
  • phase_constituents (list) – List of active constituents in a phase

  • configuration (list) – List of the sublattice configuration

  • occupancies (list) – List of sublattice occupancies. Required for mixing sublattices, otherwise takes no effect.

Returns

Return type

numpy.ndarray

Notes

Errors will be raised if components in the configuration are not in the corresponding phase constituents sublattice.

espei.error_functions.non_equilibrium_thermochemical_error.get_prop_samples(desired_data, constituents)

Return data values and the conditions to calculate them using pycalphad.calculate

Parameters
  • desired_data (List[Dict[str, Any]]) – List of dataset dictionaries that contain the values to sample

  • constituents (List[List[str]]) – Names of constituents in each sublattice.

Returns

Dictionary of condition kwargs for pycalphad’s calculate and the expected values

Return type

Dict[str, Union[float, ArrayLike, List[float]]]

espei.error_functions.non_equilibrium_thermochemical_error.get_thermochemical_data(dbf, comps, phases, datasets, weight_dict=None, symbols_to_fit=None)
Parameters
  • dbf (pycalphad.Database) – Database to consider

  • comps (list) – List of active component names

  • phases (list) – List of phases to consider

  • datasets (espei.utils.PickleableTinyDB) – Datasets that contain single phase data

  • weight_dict (dict) – Dictionary of weights for each data type, e.g. {‘HM’: 200, ‘SM’: 2}

  • symbols_to_fit (list) – Parameters to fit. Used to build the models and PhaseRecords.

Returns

List of data dictionaries to iterate over

Return type

list

espei.error_functions.zpf_error module

Calculate driving_force due to ZPF tielines.

The general approach is similar to the PanOptimizer rough search method.

  1. With all phases active, calculate the chemical potentials of the tieline endpoints via equilibrium calls. Done in estimate_hyperplane.

  2. Calculate the target chemical potentials, which are the average chemical potentials of all of the current chemical potentials at the tieline endpoints.

  3. Calculate the current chemical potentials of the desired single phases

  4. The error is the difference between these chemical potentials

There’s some special handling for tieline endpoints where we do not know the composition conditions to calculate chemical potentials at.

class espei.error_functions.zpf_error.PhaseRegion(vertices: Sequence[espei.error_functions.zpf_error.RegionVertex], potential_conds: Dict[pycalphad.variables.StateVariable, float], species: Sequence[pycalphad.variables.Species], phases: Sequence[str], models: Dict[str, pycalphad.model.Model])

Bases: object

eq_str()
models: Dict[str, pycalphad.model.Model]
phases: Sequence[str]
potential_conds: Dict[pycalphad.variables.StateVariable, float]
species: Sequence[pycalphad.variables.Species]
vertices: Sequence[espei.error_functions.zpf_error.RegionVertex]
class espei.error_functions.zpf_error.RegionVertex(phase_name: str, composition: Union[int, float, complex, str, bytes, numpy.generic, Sequence[Union[int, float, complex, str, bytes, numpy.generic]], Sequence[Sequence[Any]], numpy._array_like._SupportsArray], comp_conds: Dict[pycalphad.variables.MoleFraction, float], points: Union[int, float, complex, str, bytes, numpy.generic, Sequence[Union[int, float, complex, str, bytes, numpy.generic]], Sequence[Sequence[Any]], numpy._array_like._SupportsArray], phase_records: Dict[str, pycalphad.core.phase_rec.PhaseRecord], is_disordered: bool, has_missing_comp_cond: bool)

Bases: object

comp_conds: Dict[pycalphad.variables.MoleFraction, float]
composition: Union[int, float, complex, str, bytes, numpy.generic, Sequence[Union[int, float, complex, str, bytes, numpy.generic]], Sequence[Sequence[Any]], numpy.typing._array_like._SupportsArray]
has_missing_comp_cond: bool
is_disordered: bool
phase_name: str
phase_records: Dict[str, pycalphad.core.phase_rec.PhaseRecord]
points: Union[int, float, complex, str, bytes, numpy.generic, Sequence[Union[int, float, complex, str, bytes, numpy.generic]], Sequence[Sequence[Any]], numpy.typing._array_like._SupportsArray]
espei.error_functions.zpf_error.calculate_zpf_driving_forces(zpf_data: Sequence[Dict[str, Any]], parameters: Optional[Union[int, float, complex, str, bytes, numpy.generic, Sequence[Union[int, float, complex, str, bytes, numpy.generic]], Sequence[Sequence[Any]], numpy.typing._array_like._SupportsArray]] = None, approximate_equilibrium: bool = False, short_circuit: bool = False)Tuple[List[List[float]], List[List[float]]]

Calculate error due to phase equilibria data

zpf_dataSequence[Dict[str, Any]]

Datasets that contain single phase data

parametersArrayLike

Array of parameters to calculate the error with.

approximate_equilibriumbool

Whether or not to use an approximate version of equilibrium that does not refine the solution and uses starting_point instead.

short_circuit: bool

If True, immediately return a size 1 array with a driving force of np.nan (failed hyperplane) or np.inf (failed driving force). Can save computational time if the caller will aggregate driving forces.

Returns

Driving forces and weights as ragged 2D arrays with shape (len(zpf_data), len(vertices in each zpf_data))

Return type

Tuple[List[List[float]], List[List[float]]]

Notes

The physical picture of the standard deviation is that we’ve measured a ZPF line. That line corresponds to some equilibrium chemical potentials. The standard deviation is the standard deviation of those ‘measured’ chemical potentials.

espei.error_functions.zpf_error.calculate_zpf_error(zpf_data: Sequence[Dict[str, Any]], parameters: Optional[numpy.ndarray] = None, data_weight: int = 1.0, approximate_equilibrium: bool = False)float

Calculate the likelihood due to phase equilibria data.

For detailed documentation, see calculate_zpf_driving_forces

Returns

Log probability of ZPF driving forces

Return type

float

espei.error_functions.zpf_error.driving_force_to_hyperplane(target_hyperplane_chempots: numpy.ndarray, phase_region: espei.error_functions.zpf_error.PhaseRegion, vertex: espei.error_functions.zpf_error.RegionVertex, parameters: numpy.ndarray, approximate_equilibrium: bool = False)float

Calculate the integrated driving force between the current hyperplane and target hyperplane.

espei.error_functions.zpf_error.estimate_hyperplane(phase_region: espei.error_functions.zpf_error.PhaseRegion, parameters: numpy.ndarray, approximate_equilibrium: bool = False)numpy.ndarray

Calculate the chemical potentials for the target hyperplane, one vertex at a time

Notes

This takes just one set of phase equilibria, a phase region, e.g. a dataset point of [[‘FCC_A1’, [‘CU’], [0.1]], [‘LAVES_C15’, [‘CU’], [0.3]]] and calculates the chemical potentials given all the phases possible at the given compositions. Then the average chemical potentials of each end point are taken as the target hyperplane for the given equilibria.

espei.error_functions.zpf_error.get_zpf_data(dbf: pycalphad.io.database.Database, comps: Sequence[str], phases: Sequence[str], datasets: espei.utils.PickleableTinyDB, parameters: Dict[str, float])

Return the ZPF data used in the calculation of ZPF error

Parameters
  • comps (list) – List of active component names

  • phases (list) – List of phases to consider

  • datasets (espei.utils.PickleableTinyDB) – Datasets that contain single phase data

  • parameters (dict) – Dictionary mapping symbols to optimize to their initial values

Returns

List of data dictionaries with keys weight, phase_regions and dataset_references.

Return type

list

Module contents

Functions for calculating error.