Phases Module#

class thermoengine.phases.base_phase.Phase(abbrev: str, phs_calc: PhaseCalculator, XTOL=1e-12)#

Abstract parent class defining generic phase properties.

The user must use a subclass, like PurePhase or SolutionPhase, which implements the Phase interface.

Parameters:

phase_classnmstr

Official class name for phase (implemented in src code). String has the form classname if source is objc, else:

if !calib [‘cy’, ‘phase name’, ‘module name’, ‘’]

if calib [‘cy’, ‘phase name’, ‘module name’, ‘calib’, ‘’]

abbrevstr

Official abbreviation of phase (regardless of implementation).

calibbool, default True

Indicates whether sample phase should be calibration ready.

sourcestr

Code source for phase implementation. Default is ‘objc’ (code in objective-C that is part of the original code base). Alternative is ‘coder’ (code generated by the coder module).

coder_modulestr

Name of the coder module that contains the phase classes. See documentation for model.Database for additional information and examples.

Attributes:

abbrev: Official unique abbreviation for phase
calib: Indicates whether phase calibration is enabled
class_name
endmember_ids: ID number of each endmember in phase
endmember_names: Name of each endmember
endmember_num: Number of endmembers in phase
formula: Array of formulas for each endmember of phase
identifier: Identifier of phase
module
MOLWTS: Array of molecular weights of oxides
OXIDES: Array of oxide names
param_names: Array of parameter names
param_props: Dictionary of phase model parameters
phase_name: Name of phase
phase_obj: Instance of the phase object
phase_type: Phase type
props: Dictionary of phase properties
source

Methods

`activity`(T, P[, mol, V, deriv, deriv_param, ...])	Calculate activity (or derivatives) for phase.
`bulk_mod`(T, P[, mol, V, const, deriv, ...])	Calculate bulk modulus (or derivatives) for phase.
`check_missing_components`([mol])	Check whether a composition contains missing components.
`chem_potential`(T, P[, mol, V, deriv, ...])	Calculate chemical potential (or derivatives) for phase.
`compressibility`(T, P[, mol, V, const, ...])	Calculate compressibility (or derivatives) for phase.
`density`(T, P[, mol, V, deriv, deriv_param, ...])	Calculate density (or derivatives) for phase.
`disable_gibbs_energy_reference_state`()	Unset Gibbs energy of the reference state.
`enable_gibbs_energy_reference_state`()	Set Gibbs energy of the reference state.
`enthalpy`(T, P[, mol, V, deriv, deriv_param, ...])	Calculate enthalpy (or derivatives) for phase.
`entropy`(T, P[, mol, V, deriv, deriv_param, ...])	Calculate entropy (or derivatives) for phase.
`fugacity`(T, P[, mol, V, deriv, deriv_param, ...])	Calculate activity (or derivatives) for phase.
`gamma`(T, P[, mol, V, deriv, deriv_param, ...])	Calculate grüneisen parameter (or derivatives) for phase.
`get_param_values`([param_names, all_params])	Get current values for listed parameters.
`get_phase_amount_from_elements`(elements[, kind])	Convert list of elements to quantity of phase.
`gibbs_energy`(T, P[, mol, V, deriv, ...])	Calculate Gibbs energy (or derivatives) for phase.
`heat_capacity`(T, P[, mol, V, const, deriv, ...])	Calculate heat capacity (or derivatives) for phase.
`helmholtz_energy`(T, P[, mol, V, deriv, ...])	Calculate helmholtz energy (or derivatives) for phase.
`internal_energy`(T, P[, mol, V, deriv, ...])	Calculate internal energy (or derivatives) for phase.
`param_units`([param_names, all_params])	Get units for listed parameters.
`set_param_values`([param_names, param_values])	Set new values for listed parameters.
`set_ref_state`([Tr, Pr, Trl])	Set reference state P/T conditions.
`thermal_exp`(T, P[, mol, V, deriv, ...])	Calculate heat capacity (or derivatives) for phase.
`validate`()
`volume`(T, P[, mol, V, deriv, deriv_param, ...])	Calculate volume (or derivatives) for phase.

affinity_and_comp
affinity_and_comp_legacy

Notes

This code is highly dependent on implementation and is likely to change dramatically with changes in the underlying code that calculates phase properties.
The pure water phase, “H2O”, is very complex and thus not available for calibration. The water phase will force its calib flag to False, regardless of input value.

property MOLWTS#

Array of molecular weights of oxides

Returns:

Numpy array of molecular weights, (nparray)

property OXIDES#

Array of oxide names

Returns:

Array of oxide names, [str,…]

property abbrev: str#

Official unique abbreviation for phase

Returns:

Abbreviation (str)

activity(T, P, mol=None, V=None, deriv=None, deriv_param=None, mol_deriv_qty=True, endmember=None, const=None, species=None)#

Calculate activity (or derivatives) for phase.

Parameters:

Tarray-like: Temperature in Kelvin.
Parray-like: Pressure in bars.
molarray-like, optional: Composition in terms of mols of endmembers (unneeded for pure phases).
Varray-like, optional (default None): Volume in J/bar. Overrides pressure if not None.
derivdict of ints: Derivative order for each parameter (default is zero for all params).
endmemberNone or int scalar or int array: If None, retrieve an array of chemical potentials; else chemical potential for endmber index or index set in array

Returns:

valuearray-like: Activity (or derivatives in deriv units).

bulk_mod(T, P, mol=None, V=None, const='T', deriv=None, deriv_param=None, mol_deriv_qty=True, endmember=None, species=None)#

Calculate bulk modulus (or derivatives) for phase.

Parameters:

Tarray-like: Temperature in Kelvin.
Parray-like: Pressure in bars.
molarray-like, optional: Composition in terms of mols of endmembers (unneeded for pure phases).
const[‘T’, ‘S’], optional: Defines constant path for derivative (yielding K_T vs K_S)
Varray-like, optional (default None): Volume in J/bar. Overrides pressure if not None.
derivdict of ints: Derivative order for each parameter (default is zero for all params).

Returns:

valuearray-like: Bulk modulus in bars (or derivatives in deriv units).

property calculator#

Python module attribute for coder generated functions

Returns:

module: Module attribute returned from importlib.import_module, else None if source is ‘objc’

property calib#

Indicates whether phase calibration is enabled

Returns:

valuebool: True or False, for whether calibration is enabled

check_missing_components(mol: ndarray[Any, dtype[float64]] | None = None) → ndarray[Any, dtype[bool_]]#

Check whether a composition contains missing components.

Parameters:

molNDArray, default: None: The mol composition of the phase

Returns:

NDArray[bool]: Whether each component is missing or not (True = missing)

chem_potential(T, P, mol=None, V=None, deriv=None, deriv_param=None, mol_deriv_qty=True, endmember=None, species=False, const=None)#

Calculate chemical potential (or derivatives) for phase.

Parameters:

Tarray-like: Temperature in Kelvin.
Parray-like: Pressure in bars.
molarray-like, optional: Composition in terms of mols of endmembers (unneeded for pure phases).
Varray-like, optional (default None): Volume in J/bar. Overrides pressure if not None.
derivdict of ints: Derivative order for each parameter (default is zero for all params).
endmemberNone or int scalar or int array: If None, retrieve an array of chemical potentials, else chemical potential for endmember index or index set in array
speciesboolean: If False, returned value is for components of the solution. If True, returned value is for species in the solution.

Returns:

valuearray-like: Chemical potential in J (or derivative in deriv units).

compressibility(T, P, mol=None, V=None, const='T', deriv=None, deriv_param=None, mol_deriv_qty=True, endmember=None, species=None)#

Calculate compressibility (or derivatives) for phase.

Parameters:

Tarray-like: Temperature in Kelvin.
Parray-like: Pressure in bars.
molarray-like, optional: Composition in terms of mols of endmembers (unneeded for pure phases).
const[‘T’, ‘S’], optional: Defines constant path for derivative (yielding Beta_T vs Beta_S)
Varray-like, optional (default None): Volume in J/bar. Overrides pressure if not None.
derivdict of ints: Derivative order for each parameter (default is zero for all params).

Returns:

valuearray-like: Bulk modulus in 1/bars (or derivatives in deriv units).

density(T, P, mol=None, V=None, deriv=None, deriv_param=None, mol_deriv_qty=None, endmember=None, const=None, species=None)#

Calculate density (or derivatives) for phase.

Parameters:

Tarray-like: Temperature in Kelvin.
Parray-like: Pressure in bars.
molarray-like, optional: Composition in terms of mols of endmembers (unneeded for pure phases).
Varray-like, optional (default None): Volume in J/bar. Overrides pressure if not None.
derivdict of ints: Derivative order for each parameter (default is zero for all params).

Returns:

valuearray-like: Density in g*bar/J (or derivative in deriv units).

disable_gibbs_energy_reference_state()#

Unset Gibbs energy of the reference state.

Notes

Call method on any phase class, and it automatically applies to all.

enable_gibbs_energy_reference_state()#

Set Gibbs energy of the reference state.

Notes

Call method on any phase class, and it automatically applies to all.

property endmember_elem_comp#

Endmember elemental composition (compact)

Returns:

Dataframe (or matrix) with elemental composition (cols)
for each endmember (rows). Only includes elements that are part of the
solution phase.

property endmember_element_comps: ndarray[Any, dtype[int64]]#

Array of element comps for each endmember of phase

Returns:

Element comps for phase endmembers (Array[float])

property endmember_formulas: ndarray[Any, dtype[str_]]#

Array of formulas for each endmember of phase

Returns:

Formulas of phase endmembers (Array[str])

property endmember_ids#

ID number of each endmember in phase

Returns:

Array of ids, [int,…]

property endmember_mol_oxide_comps: ndarray[Any, dtype[float64]]#

Array of mol oxides for each endmember of phase

Returns:

Number of moles of oxides for phase endmembers (Array[float])

property endmember_molwts: ndarray[Any, dtype[float64]]#

Array of mol-weights for each endmember of phase

Returns:

Mol-wts for phase endmembers (Array[float])

Name of each endmember

Returns:

List of endmember names for this solution phase, [str,…]

property endmember_num: int#

Number of endmembers in phase

Returns:

Number of endmembers in phase (int)

property endmember_number_of_atoms: ndarray[Any, dtype[int64]]#

Array of number of atoms for each endmember of phase

Returns:

Number of atoms for phase endmembers (Array[float])

enthalpy(T, P, mol=None, V=None, deriv=None, deriv_param=None, mol_deriv_qty=None, endmember=None, const=None, species=None)#

Calculate enthalpy (or derivatives) for phase.

Parameters:

Tarray-like: Temperature in Kelvin
Parray-like: Pressure in bars
molarray-like, optional: Composition in terms of mols of endmembers (unneeded for pure phases).
Varray-like, optional (default None): Volume in J/bar. Overrides pressure if not None.
derivdict of ints: Derivative order for each parameter (default is zero for all params).

Returns:

valuearray-like: Enthalpy in J (or derivative in deriv units).

entropy(T, P, mol=None, V=None, deriv=None, deriv_param=None, mol_deriv_qty=None, endmember=None, const=None, species=None)#

Calculate entropy (or derivatives) for phase.

Parameters:

Tarray-like: Temperature in Kelvin.
Parray-like: Pressure in bars.
molarray-like, optional: Composition in terms of mols of endmembers (unneeded for pure phases).
Varray-like, optional (default None): Volume in J/bar. Overrides pressure if not None.
derivdict of ints: Derivative order for each parameter (default is zero for all params).

Returns:

valuearray-like: Entropy in J/K (or derivative in deriv units).

property exchange_equil#

Exchange equilibrium object responsible for calculating metastable equilibrium properties of the phase

Returns:

Exchange Equilibrium object

property formula: ndarray[Any, dtype[str_]]#

Array of formulas for each endmember of phase

NOTE: To be deprecated

Returns:

Formulas of phase endmembers (Array[str])

fugacity(T, P, mol=None, V=None, deriv=None, deriv_param=None, mol_deriv_qty=True, endmember=None, const=None, species=None)#

Calculate activity (or derivatives) for phase.

Parameters:

Tarray-like: Temperature in Kelvin.
Parray-like: Pressure in bars.
molarray-like, optional: Composition in terms of mols of endmembers (unneeded for pure phases).
Varray-like, optional (default None): Volume in J/bar. Overrides pressure if not None.
derivdict of ints: Derivative order for each parameter (default is zero for all params).

Returns:

valuearray-like: Fugacity in bars (or derivatives in deriv units).

gamma(T, P, mol=None, V=None, deriv=None, deriv_param=None, mol_deriv_qty=True, endmember=None, const=None, species=None)#

Calculate grüneisen parameter (or derivatives) for phase.

NOT IMPLEMENTED

get_param_values(param_names=[], all_params=False)#

Get current values for listed parameters.

Parameters:

param_namesstr array: List of parameter names
all_paramsbool, default False: If true, returns units for all parameters

Returns:

valuesdouble array: List of values for selected parameters

get_phase_amount_from_elements(elements, kind='mass')#

Convert list of elements to quantity of phase.

Parameters:

elementsdouble array: Number of each element
kind{‘mass’,’moles’}: Determines how phase amount is determined (mass vs. moles)

Returns:

amountdouble: Amount of phase (expressed according to kind)

gibbs_energy(T, P, mol=None, V=None, deriv=None, deriv_param=None, mol_deriv_qty=None, endmember=None, const=None, species=None)#

Calculate Gibbs energy (or derivatives) for phase.

Parameters:

Tarray-like: Temperature in Kelvin
Parray-like: Pressure in bars
molarray-like, optional: Composition in terms of mols of endmembers (unneeded for pure phases)
Varray-like, optional (default None): Volume in J/bar. Overrides pressure if not None.
derivdict of ints: Derivative order for each parameter (Default is zero for all params.)
deriv_paramarray of strs: Parameter names that identify returned derivatives (Default is None.)

Returns:

valuearray-like: Gibbs energy in J (or derivative in deriv units)

heat_capacity(T, P, mol=None, V=None, const='P', deriv=None, deriv_param=None, mol_deriv_qty=True, endmember=None, species=None)#

Calculate heat capacity (or derivatives) for phase.

Parameters:

Tarray-like: Temperature in Kelvin.
Parray-like: Pressure in bars.
molarray-like, optional: Composition in terms of mols of endmembers (unneeded for pure phases).
const[‘P’, ‘V’], optional: Defines constant path for derivative (yielding C_P vs C_V)
Varray-like, optional (default None): Volume in J/bar. Overrides pressure if not None.
derivdict of ints: Derivative order for each parameter (default is zero for all params).

Returns:

valuearray-like: Thermal expansion in J/K (or derivatives in deriv units).

helmholtz_energy(T, P, mol=None, V=None, deriv=None, deriv_param=None, mol_deriv_qty=None, endmember=None, const=None, species=None)#

Calculate helmholtz energy (or derivatives) for phase.

Parameters:

Tarray-like: Temperature in Kelvin.
Parray-like: Pressure in bars.
molarray-like, optional: Composition in terms of mols of endmembers (unneeded for pure phases).
Varray-like, optional (default None): Volume in J/bar. Overrides pressure if not None.
derivdict of ints: Derivative order for each parameter (default is zero for all params).

Returns:

valuearray-like: Helmholtz energy in J (or derivative in deriv units).

property identifier#

Identifier of phase

Returns:

Identifier of phase (str)

internal_energy(T, P, mol=None, V=None, deriv=None, deriv_param=None, mol_deriv_qty=None, endmember=None, const=None, species=None)#

Calculate internal energy (or derivatives) for phase.

Parameters:

Tarray-like: Temperature in Kelvin.
Parray-like: Pressure in bars.
molarray-like, optional: Composition in terms of mols of endmembers (unneeded for pure phases).
Varray-like, optional (default None): Volume in J/bar. Overrides pressure if not None.
derivdict of ints: Derivative order for each parameter (default is zero for all params).

Returns:

valuearray-like: Internal energy in J (or derivative in deriv units).

property oxide_space: ndarray[Any, dtype[bool_]]#

Array of bools indicating if phase can contain each oxide

Returns:

Whether each oxide is in the phase or not

property param_names#

Array of parameter names

Returns:

Array of names for each parameter of the phase model, [str,…]

property param_props#

Dictionary of phase model parameters

This dictionary defines parameter properties for the phase, using these keys:

supports_calibbool: Flag indicating whether phase allows calibration
param_numint: Number of parameters
param_namesstr array: Name of each parameter
param_unitsstr array: Units for each parameter
param0double array: Initial parameter values

Returns:

Dictionary of phase model parametersdict: A dictionary of phase model parameters

param_units(param_names=[], all_params=False)#

Get units for listed parameters.

Parameters:

param_namesstr array: List of parameter names
all_paramsbool, default False: If true, returns units for all parameters

Returns:

unitsdouble array: List of units for selected parameters

property phase_name: str#

Name of phase

Returns:

Name of phase (str)

property phase_obj#

Instance of the phase object

Returns:

Object instance

property phase_type#

Phase type

Returns:

Phase type (str): Permissible values are ‘pure’ or ‘solution’.

property props#

Dictionary of phase properties

The dictionary defines phase properties with these keys:

abbrevstr: Official unique phase abbreviation
namestr: Name of phase (implementation dependent)
class_namestr: Official class name for phase (implemented in src code)
formulastr: Formula of phase
natomint: Number of atoms in formula unit
molwtdouble: Molecular weight of phase (in g/mol-formula-unit)
elemental_entropydouble: Estimated entropy from elemental formula (from Robie et al. 1979)
element_symbolsstr array: Symbol array string
element_compint array: Phase formula in terms of number of each element

Returns:

A Python dictionarydict: A dictionary of phase properties

Notes

Need to update these dictionary values to be vectors for solution phases

set_param_values(param_names=[], param_values=[])#

Set new values for listed parameters.

Parameters:

param_namesstr array: List of parameter names
param_valuesdouble array: List of parameter values

set_ref_state(Tr=298.15, Pr=1.0, Trl=298.15)#

Set reference state P/T conditions.

Parameters:

Trdouble, default 298.15: Reference temperature in Kelvin
Prdouble, default 1.0: Reference pressure in bars
Trldouble, default 298.15: Reference temperature for lambda heat capacity correction in Kelvin

property species_elem_comp#

Species elemental composition (compact)

Returns:

Dataframe (or matrix) with elemental composition (cols)
for each species(rows). Only includes elements that are part of the
solution phase.

property species_element_comps: ndarray[Any, dtype[float64]]#

Array of element comps for each species in phase

Returns:

Element comps for phase species (Array[float])

property species_names: ndarray[Any, dtype[str_]]#

Names of the species in phase

Returns:

Names of species in phase (Array[str])

property species_num: int#

Number of species in phase

Returns:

Number of species in phase (int)

property species_stoic#

Species Stoichiometry

Returns:

Dataframe (or matrix) with molar endmember stoichiometry (cols)
for each species (rows). Expresses species in terms of independent
endmembers.

property species_stoic_T#

Species Stoichiometry Transpose

Returns:

Dataframe (or matrix) with molar endmember stoichiometry (rows)
for each species (cols). Expresses species in terms of independent
endmembers.

thermal_exp(T, P, mol=None, V=None, deriv=None, deriv_param=None, mol_deriv_qty=True, endmember=None, const=None, species=None)#

Calculate heat capacity (or derivatives) for phase.

Parameters:

Tarray-like: Temperature in Kelvin.
Parray-like: Pressure in bars.
molarray-like, optional: Composition in terms of mols of endmembers (unneeded for pure phases).
Varray-like, optional (default None): Volume in J/bar. Overrides pressure if not None.
derivdict of ints: Derivative order for each parameter (default is zero for all params).

Returns:

valuearray-like: Thermal expansion in 1/K (or derivatives in deriv units).

volume(T, P, mol=None, V=None, deriv=None, deriv_param=None, mol_deriv_qty=None, endmember=None, const=None, species=None)#

Calculate volume (or derivatives) for phase.

Parameters:

Tarray-like: Temperature in Kelvin.
Parray-like: Pressure in bars.
molarray-like, optional: Composition in terms of mols of endmembers (unneeded for pure phases).
Varray-like, optional (default None): Volume in J/bar. Overrides pressure if not None.
derivdict of ints: Derivative order for each parameter (default is zero for all params).

Returns:

valuearray-like: Volume in J/bar (or derivative in deriv units).

class thermoengine.phases.pure_phase.PurePhase(abbrev, phs_calc: PhaseCalculator, XTOL=1e-12)#

Pure stoichiometric phases.

Implements the Phase interface.

Parameters:

phase_classnmstr: Official class name for phase (implemented in src code)
abbrevstr: Official abbreviation of phase (regardless of implementation)
calibbool, default True: Indicates whether sample phase should be calibration ready

Attributes:

Berman_formula: Representation of formula using Berman format

Methods

`activity`(T, P[, mol, V, deriv, deriv_param, ...])	Calculate activity (or derivatives) for phase.
`bulk_mod`(T, P[, mol, V, const, deriv, ...])	Calculate bulk modulus (or derivatives) for phase.
`check_missing_components`([mol])	Check whether a composition contains missing components.
`chem_potential`(T, P[, mol, V, deriv, ...])	Calculate chemical potential (or derivatives) for phase.
`compressibility`(T, P[, mol, V, const, ...])	Calculate compressibility (or derivatives) for phase.
`density`(T, P[, mol, V, deriv, deriv_param, ...])	Calculate density (or derivatives) for phase.
`disable_gibbs_energy_reference_state`()	Unset Gibbs energy of the reference state.
`enable_gibbs_energy_reference_state`()	Set Gibbs energy of the reference state.
`enthalpy`(T, P[, mol, V, deriv, deriv_param, ...])	Calculate enthalpy (or derivatives) for phase.
`entropy`(T, P[, mol, V, deriv, deriv_param, ...])	Calculate entropy (or derivatives) for phase.
`fugacity`(T, P[, mol, V, deriv, deriv_param, ...])	Calculate activity (or derivatives) for phase.
`gamma`(T, P[, mol, V, deriv, deriv_param, ...])	Calculate grüneisen parameter (or derivatives) for phase.
`get_param_values`([param_names, all_params])	Get current values for listed parameters.
`get_phase_amount_from_elements`(elements[, kind])	Convert list of elements to quantity of phase.
`gibbs_energy`(T, P[, mol, V, deriv, ...])	Calculate Gibbs energy (or derivatives) for phase.
`heat_capacity`(T, P[, mol, V, const, deriv, ...])	Calculate heat capacity (or derivatives) for phase.
`helmholtz_energy`(T, P[, mol, V, deriv, ...])	Calculate helmholtz energy (or derivatives) for phase.
`internal_energy`(T, P[, mol, V, deriv, ...])	Calculate internal energy (or derivatives) for phase.
`param_units`([param_names, all_params])	Get units for listed parameters.
`set_param_values`([param_names, param_values])	Set new values for listed parameters.
`set_ref_state`([Tr, Pr, Trl])	Set reference state P/T conditions.
`thermal_exp`(T, P[, mol, V, deriv, ...])	Calculate heat capacity (or derivatives) for phase.
`validate`()
`volume`(T, P[, mol, V, deriv, deriv_param, ...])	Calculate volume (or derivatives) for phase.

affinity_and_comp
affinity_and_comp_legacy
not_coded

Notes

This code is highly dependent on implementation and is likely to change dramatically with changes in the underlying code that calculates phase properties.
The pure water phase, “H2O”, is very complex and thus not available for calibration. The water phase will force its calib flag to False, regardless of input value.
In addition to the attributes listed, this class inherits the Phase class attributes.

property Berman_formula#

Representation of formula using Berman format

Returns:

Chemical formula of phase (str)

class thermoengine.phases.solution_phase.SolutionPhase(abbrev, phs_calc, XTOL=1e-12)#

Solid solution phases.

Implements the Phase interface.

Parameters:

phase_classnmstr: Official class name for phase (implemented in src code).
abbrevstr: Official abbreviation of phase (regardless of implementation).
calibbool, default True: Indicates whether sample phase should be calibration ready.

Attributes:

Attributes for this class are inherited from the Phase class.

Methods

`activity`(T, P[, mol, V, deriv, deriv_param, ...])	Calculate activity (or derivatives) for phase.
`bulk_mod`(T, P[, mol, V, const, deriv, ...])	Calculate bulk modulus (or derivatives) for phase.
`calc_endmember_comp`(mol_oxide_comp[, ...])	Get fraction of each endmember given the composition.
`check_missing_components`([mol])	Check whether a composition contains missing components.
`chem_potential`(T, P[, mol, V, deriv, ...])	Calculate chemical potential (or derivatives) for phase.
`compressibility`(T, P[, mol, V, const, ...])	Calculate compressibility (or derivatives) for phase.
`compute_formula`(T, P, mol_comp)	Converts an input array of moles of endmember components to the chemical formula of the phase
`convert_elements`(mol_elm[, output])	Converts an array of mole numbers of elements (in the standard order) to the specified output quantity
`convert_endmember_comp`(mol_comp[, output])	Converts an input array of moles of endmember components to the specified quantity
`convert_species_to_comp`(mol_species[, method])	Converts an input array of moles of species to moles of endmember components
`covert_endmember_comp`(mol_comp[, output])
`density`(T, P[, mol, V, deriv, deriv_param, ...])	Calculate density (or derivatives) for phase.
`disable_gibbs_energy_reference_state`()	Unset Gibbs energy of the reference state.
`enable_gibbs_energy_reference_state`()	Set Gibbs energy of the reference state.
`enthalpy`(T, P[, mol, V, deriv, deriv_param, ...])	Calculate enthalpy (or derivatives) for phase.
`entropy`(T, P[, mol, V, deriv, deriv_param, ...])	Calculate entropy (or derivatives) for phase.
`fugacity`(T, P[, mol, V, deriv, deriv_param, ...])	Calculate activity (or derivatives) for phase.
`gamma`(T, P[, mol, V, deriv, deriv_param, ...])	Calculate grüneisen parameter (or derivatives) for phase.
`get_endmember_ind`(mol_oxide_comp[, ...])	Get index of endmember that best matches composition.
`get_param_values`([param_names, all_params])	Get current values for listed parameters.
`get_phase_amount_from_elements`(elements[, kind])	Convert list of elements to quantity of phase.
`gibbs_energy`(T, P[, mol, V, deriv, ...])	Calculate Gibbs energy (or derivatives) for phase.
`heat_capacity`(T, P[, mol, V, const, deriv, ...])	Calculate heat capacity (or derivatives) for phase.
`helmholtz_energy`(T, P[, mol, V, deriv, ...])	Calculate helmholtz energy (or derivatives) for phase.
`internal_energy`(T, P[, mol, V, deriv, ...])	Calculate internal energy (or derivatives) for phase.
`param_units`([param_names, all_params])	Get units for listed parameters.
`set_param_values`([param_names, param_values])	Set new values for listed parameters.
`set_ref_state`([Tr, Pr, Trl])	Set reference state P/T conditions.
`test_endmember_comp`(mol_comp)	Tests validity of endmember component moles array
`thermal_exp`(T, P[, mol, V, deriv, ...])	Calculate heat capacity (or derivatives) for phase.
`validate`()
`volume`(T, P[, mol, V, deriv, deriv_param, ...])	Calculate volume (or derivatives) for phase.

affinity_and_comp
affinity_and_comp_legacy
not_coded

Notes

This code is highly dependent on implementation and is likely to change dramatically with changes in the underlying code that calculates phase properties.
The pure water phase, “H2O”, is very complex and thus not available for calibration. The water phase will force its calib flag to False, regardless of input value.

calc_endmember_comp(mol_oxide_comp, method='least_squares', output_residual=False, normalize=False, decimals=10)#

Get fraction of each endmember given the composition.

Parameters:

mol_oxide_compdouble array: Amounts of each oxide in standard order (defined in OXIDES)
decimalsint, default 10: Number of decimals to round result to
methodstr, default ‘least_squares’: Method used to convert oxide composition (in moles) to moles of endmembers ‘intrinsic’ is alternate method, hardcoded by the solution implementation

Returns:

endmember_compdouble array: Best-fit molar composition in terms of endmembers
mol_oxide_comp_residualdouble array: Residual molar oxide composition

Notes

Eventually, we may want the ability to calculate endmember comp. using a variety of methods for inputing composition:
- kind[‘wt_oxide’, ‘mol_oxide’, ‘element’]
  Identifies how composition is defined.

compute_formula(T, P, mol_comp)#

Converts an input array of moles of endmember components to the chemical formula of the phase

Parameters:

Tdouble: Temperature in Kelvins
Pdouble: Pressure in bars
mol_compdouble array: Mole numbers of each component in the solution

Returns:

formulastr: A string with the formula of the phase

convert_elements(mol_elm, output='moles_end')#

Converts an array of mole numbers of elements (in the standard order) to the specified output quantity

Parameters:

mole_elmdouble array

Mole numbers of elements in the standard order

outputstr, default = ‘moles_end’

Output quantity:

‘moles_end’ - double array of moles of endmembers
‘total_moles’ - double, sum of moles of endmembers
‘total_grams’ - double, sum of grams of solution

Returns:

resultdouble or double array: The computed quantity as double or double array

convert_endmember_comp(mol_comp, output='total_moles')#

Converts an input array of moles of endmember components to the specified quantity

Parameters:

mol_compdouble array

Mole numbers of each component in the solution

outputstr, default = ‘total_moles’

Output quantity:

‘total_moles’ - double
‘moles_elements’ - double array (standard order and length)
‘mole_fraction’ - double array (same order and length as input)
‘moles_species’ - pandas series or array w/ accepted order

Returns:

resultdouble or double array/pandas series: The computed quantity as double or double array (or series)

convert_species_to_comp(mol_species, method='linear')#

Converts an input array of moles of species to moles of endmember components

Parameters:

mol_speciesdouble array: Mole numbers of each species in the solution
method{‘linear’, ‘source’}: Default is ‘linear’, using basic dot-product. Otherwise, optimized methods can be used from source code by selecting ‘source’.

Returns:

resultdouble array: Moles of endmember components

covert_endmember_comp(mol_comp, output='total_moles')#: Deprecated since version 1.0: This will be removed in 2.0. This legacy function name has a typo. Use convert_endmember_comp instead.

get_endmember_ind(mol_oxide_comp, get_endmember_comp=False, TOL=1e-06)#

Get index of endmember that best matches composition.

Parameters:

mol_oxide_compdouble array: Amounts of each oxide in standard order (defined in OXIDES)
TOLdouble, default 1e-6: Allowed tolerance for mismatch to defined composition
get_endmember_compbool, default False: If true, also return endmember composition array.

Returns:

endmember_indint

Index of best-fit endmember

endmember_compdouble array, optional

Composition array in terms of endmembers.

Return if get_endmember_comp==True

test_endmember_comp(mol_comp)#

Tests validity of endmember component moles array

Parameters:

mol_compdouble array: Mole numbers of each component in the solution

Returns:

flagboolean: True is composition is valid, otherwise False.

Phases Module#

This Page