pymatgen.analysis.elasticity.elastic module

This module provides a class used to describe the elastic tensor, including methods used to fit the elastic tensor from linear response stress-strain data

class ComplianceTensor(s_array)

Bases: Tensor

This class represents the compliance tensor, and exists primarily to keep the voigt-conversion scheme consistent since the compliance tensor has a unique vscale

Parameters:

() (s_array) –

class ElasticTensor(input_array, tol: float = 0.0001)

Bases: NthOrderElasticTensor

This class extends Tensor to describe the 3x3x3x3 second-order elastic tensor, C_{ijkl}, with various methods for estimating other properties derived from the second order elastic tensor

Create an ElasticTensor object. The constructor throws an error if the shape of the input_matrix argument is not 3x3x3x3, i. e. in true tensor notation. Issues a warning if the input_matrix argument does not satisfy standard symmetries. Note that the constructor uses __new__ rather than __init__ according to the standard method of subclassing numpy ndarrays.

Parameters:

• input_array (3x3x3x3 array-like) – the 3x3x3x3 array-like representing the elastic tensor

• tol (float) – tolerance for initial symmetry test of tensor

cahill_thermalcond(*args, **kwargs)

Parameters:

• () (**kwargs) –

• () –

• () –

Returns:

clarke_thermalcond(*args, **kwargs)

Parameters:

• () (**kwargs) –

• () –

• () –

Returns:

property compliance_tensor

Returns the Voigt-notation compliance tensor, which is the matrix inverse of the Voigt-notation elastic tensor

debye_temperature(*args, **kwargs)

Parameters:

• () (**kwargs) –

• () –

• () –

Returns:

directional_elastic_mod(n)

Calculates directional elastic modulus for a specific vector

directional_poisson_ratio(n, m, tol: float = 1e-08)

Calculates the poisson ratio for a specific direction relative to a second, orthogonal direction

Parameters:

• n (3-d vector) – principal direction

• m (3-d vector) – secondary direction orthogonal to n

• tol (float) – tolerance for testing of orthogonality

classmethod from_independent_strains(strains, stresses, eq_stress=None, vasp=False, tol: float = 1e-10)

Constructs the elastic tensor least-squares fit of independent strains :param strains: list of strain objects to fit :type strains: list of Strains :param stresses: list of stress objects to use in fit

corresponding to the list of strains

Parameters:

• eq_stress (Stress) – equilibrium stress to use in fitting

• vasp (bool) – flag for whether the stress tensor should be converted based on vasp units/convention for stress

• tol (float) – tolerance for removing near-zero elements of the resulting tensor

classmethod from_pseudoinverse(strains, stresses)

Class method to fit an elastic tensor from stress/strain data. Method uses Moore-Penrose pseudoinverse to invert the s = C*e equation with elastic tensor, stress, and strain in voigt notation

Parameters:

• stresses (Nx3x3 array-like) – list or array of stresses

• strains (Nx3x3 array-like) – list or array of strains

property g_reuss

Returns the G_r shear modulus

property g_voigt

Returns the G_v shear modulus

property g_vrh

Returns the G_vrh (Voigt-Reuss-Hill) average shear modulus

get_structure_property_dict(structure: Structure, include_base_props: bool = True, ignore_errors: bool = False) → dict[str, float | Structure | None]

Returns a dictionary of properties derived from the elastic tensor and an associated structure

Parameters:

• structure (Structure) – structure object for which to calculate associated properties

• include_base_props (bool) – whether to include base properties, like k_vrh, etc.

• ignore_errors (bool) – if set to true, will set problem properties that depend on a physical tensor to None, defaults to False

green_kristoffel(u)

Returns the Green-Kristoffel tensor for a second-order tensor

property homogeneous_poisson

Returns the homogeneous poisson ratio

property k_reuss

Returns the K_r bulk modulus

property k_voigt

Returns the K_v bulk modulus

property k_vrh

Returns the K_vrh (Voigt-Reuss-Hill) average bulk modulus

long_v(*args, **kwargs)

Parameters:

• () (**kwargs) –

• () –

• () –

Returns:

property property_dict

Returns a dictionary of properties derived from the elastic tensor

snyder_ac(*args, **kwargs)

Parameters:

• () (**kwargs) –

• () –

• () –

Returns:

snyder_opt(*args, **kwargs)

Parameters:

• () (**kwargs) –

• () –

• () –

Returns:

snyder_total(*args, **kwargs)

Parameters:

• () (**kwargs) –

• () –

• () –

Returns:

trans_v(*args, **kwargs)

Parameters:

• () (**kwargs) –

• () –

• () –

Returns:

property universal_anisotropy

Returns the universal anisotropy value

property y_mod

Calculates Young’s modulus (in SI units) using the Voigt-Reuss-Hill averages of bulk and shear moduli

class ElasticTensorExpansion(c_list)

Bases: TensorCollection

This class is a sequence of elastic tensors corresponding to an elastic tensor expansion, which can be used to calculate stress and energy density and inherits all of the list-based properties of TensorCollection (e. g. symmetrization, voigt conversion, etc.)

Initialization method for ElasticTensorExpansion

Parameters:

c_list (list or tuple) – sequence of Tensor inputs or tensors from which the elastic tensor expansion is constructed.

calculate_stress(strain)

Calculate’s a given elastic tensor’s contribution to the stress using Einstein summation

energy_density(strain, convert_GPa_to_eV=True)

Calculates the elastic energy density due to a strain

classmethod from_diff_fit(strains, stresses, eq_stress=None, tol: float = 1e-10, order=3)

Generates an elastic tensor expansion via the fitting function defined below in diff_fit

get_compliance_expansion()

Gets a compliance tensor expansion from the elastic tensor expansion.

get_effective_ecs(strain, order=2)

Returns the effective elastic constants from the elastic tensor expansion.

Parameters:

• strain (Strain or 3x3 array-like) – strain condition under which to calculate the effective constants

• order (int) – order of the ecs to be returned

get_ggt(n, u)

Gets the Generalized Gruneisen tensor for a given third-order elastic tensor expansion.

Parameters:

• n (3x1 array-like) – normal mode direction

• u (3x1 array-like) – polarization direction

get_gruneisen_parameter(temperature=None, structure=None, quad=None)

Gets the single average gruneisen parameter from the TGT.

Parameters:

• temperature (float) – Temperature in kelvin, if not specified will return non-cv-normalized value

• structure (float) – Structure to be used in directional heat capacity determination, only necessary if temperature is specified

• quad (dict) – quadrature for integration, should be dictionary with “points” and “weights” keys defaults to quadpy.sphere.Lebedev(19) as read from file

get_heat_capacity(temperature, structure: Structure, n, u, cutoff=100.0)

Gets the directional heat capacity for a higher order tensor expansion as a function of direction and polarization.

Parameters:

• temperature (float) – Temperature in kelvin

• structure (float) – Structure to be used in directional heat capacity determination

• n (3x1 array-like) – direction for Cv determination

• u (3x1 array-like) – polarization direction, note that no attempt for verification of eigenvectors is made

• cutoff (float) – cutoff for scale of kt / (hbar * omega) if lower than this value, returns 0

get_stability_criteria(s, n)

Gets the stability criteria from the symmetric Wallace tensor from an input vector and stress value.

Parameters:

• s (float) – Stress value at which to evaluate the stability criteria

• n (3x1 array-like) – direction of the applied stress

get_strain_from_stress(stress)

Gets the strain from a stress state according to the compliance expansion corresponding to the tensor expansion.

get_symmetric_wallace_tensor(tau)

Gets the symmetrized wallace tensor for determining yield strength criteria.

Parameters:

tau (3x3 array-like) – stress at which to evaluate the wallace tensor.

get_tgt(temperature=None, structure=None, quad=None)

Gets the thermodynamic Gruneisen tensor (TGT) by via an integration of the GGT weighted by the directional heat capacity.

See refs:

R. N. Thurston and K. Brugger, Phys. Rev. 113, A1604 (1964). K. Brugger Phys. Rev. 137, A1826 (1965).

Parameters:

• temperature (float) – Temperature in kelvin, if not specified will return non-cv-normalized value

• structure (float) – Structure to be used in directional heat capacity determination, only necessary if temperature is specified

• quad (dict) – quadrature for integration, should be dictionary with “points” and “weights” keys defaults to quadpy.sphere.Lebedev(19) as read from file

get_wallace_tensor(tau)

Gets the Wallace Tensor for determining yield strength criteria.

Parameters:

tau (3x3 array-like) – stress at which to evaluate the wallace tensor

get_yield_stress(n)

Gets the yield stress for a given direction

Parameters:

n (3x1 array-like) – direction for which to find the yield stress

omega(structure: Structure, n, u)

Finds directional frequency contribution to the heat capacity from direction and polarization

Parameters:

• structure (Structure) – Structure to be used in directional heat capacity determination

• n (3x1 array-like) – direction for Cv determination

• u (3x1 array-like) – polarization direction, note that no attempt for verification of eigenvectors is made

property order

Order of the elastic tensor expansion, i. e. the order of the highest included set of elastic constants

thermal_expansion_coeff(structure: Structure, temperature, mode='debye')

Gets thermal expansion coefficient from third-order constants.

Parameters:

• temperature (float) – Temperature in kelvin, if not specified will return non-cv-normalized value

• structure (Structure) – Structure to be used in directional heat capacity determination, only necessary if temperature is specified

• mode (str) – mode for finding average heat-capacity, current supported modes are ‘debye’ and ‘dulong-petit’

class NthOrderElasticTensor(input_array, check_rank=None, tol: float = 0.0001)

Bases: Tensor

An object representing an nth-order tensor expansion of the stress-strain constitutive equations

Parameters:

• () (tol) –

• () –

• () –

GPa_to_eV_A3 = 0.006241509074460764

calculate_stress(strain)

Calculate’s a given elastic tensor’s contribution to the stress using Einstein summation

Parameters:

strain (3x3 array-like) – matrix corresponding to strain

energy_density(strain, convert_GPa_to_eV=True)

Calculates the elastic energy density due to a strain

classmethod from_diff_fit(strains, stresses, eq_stress=None, order=2, tol: float = 1e-10)

Takes a list of strains and stresses, and returns a list of coefficients for a polynomial fit of the given order.

Parameters:

• strains – a list of strain values

• stresses – the stress values

• eq_stress – The stress at which the material is assumed to be elastic.

• order – The order of the polynomial to fit. Defaults to 2

• tol (float) – tolerance for the fit.

Returns:

the fitted elastic tensor

Return type:

NthOrderElasticTensor

property order

Order of the elastic tensor

symbol = 'C'

diff_fit(strains, stresses, eq_stress=None, order=2, tol: float = 1e-10)

nth order elastic constant fitting function based on central-difference derivatives with respect to distinct strain states. The algorithm is summarized as follows:

1. Identify distinct strain states as sets of indices for which nonzero strain values exist, typically [(0), (1), (2), (3), (4), (5), (0, 1) etc.]

2. For each strain state, find and sort strains and stresses by strain value.

3. Find first, second .. nth derivatives of each stress with respect to scalar variable corresponding to the smallest perturbation in the strain.

4. Use the pseudoinverse of a matrix-vector expression corresponding to the parameterized stress-strain relationship and multiply that matrix by the respective calculated first or second derivatives from the previous step.

5. Place the calculated nth-order elastic constants appropriately.

Parameters:

• order (int) – order of the elastic tensor set to return

• strains (nx3x3 array-like) – Array of 3x3 strains to use in fitting of ECs

• stresses (nx3x3 array-like) – Array of 3x3 stresses to use in fitting ECs. These should be PK2 stresses.

• eq_stress (3x3 array-like) – stress corresponding to equilibrium strain (i. e. “0” strain state). If not specified, function will try to find the state in the list of provided stresses and strains. If not found, defaults to 0.

• tol (float) – value for which strains below are ignored in identifying strain states.

Returns:

Set of tensors corresponding to nth order expansion of the stress/strain relation

find_eq_stress(strains, stresses, tol: float = 1e-10)

Finds stress corresponding to zero strain state in stress-strain list

Parameters:

• strains (Nx3x3 array-like) – array corresponding to strains

• stresses (Nx3x3 array-like) – array corresponding to stresses

• tol (float) – tolerance to find zero strain state

generate_pseudo(strain_states, order=3)

Generates the pseudoinverse for a given set of strains.

Parameters:

• strain_states (6xN array like) – a list of voigt-notation “strain-states”, i. e. perturbed indices of the strain as a function of the smallest strain e. g. (0, 1, 0, 0, 1, 0)

• order (int) – order of pseudoinverse to calculate

Returns:

pseudo inverses for each order tensor, these can

be multiplied by the central difference derivative of the stress with respect to the strain state

absent_syms: symbols of the tensor absent from the PI

expression

Return type:

mis

get_diff_coeff(hvec, n=1)

Helper function to find difference coefficients of an derivative on an arbitrary mesh.

Parameters:

• hvec (1D array-like) – sampling stencil

• n (int) – degree of derivative to find

get_strain_state_dict(strains, stresses, eq_stress=None, tol: float = 1e-10, add_eq=True, sort=True)

Creates a dictionary of voigt-notation stress-strain sets keyed by “strain state”, i. e. a tuple corresponding to the non-zero entries in ratios to the lowest nonzero value, e.g. [0, 0.1, 0, 0.2, 0, 0] -> (0,1,0,2,0,0) This allows strains to be collected in stencils as to evaluate parameterized finite difference derivatives

Parameters:

• strains (Nx3x3 array-like) – strain matrices

• stresses (Nx3x3 array-like) – stress matrices

• eq_stress (Nx3x3 array-like) – equilibrium stress

• tol (float) – tolerance for sorting strain states

• add_eq (bool) – flag for whether to add eq_strain to stress-strain sets for each strain state

• sort (bool) – flag for whether to sort strain states

Returns:

strain state keys and dictionaries with stress-strain data corresponding to strain state

Return type:

dict

get_symbol_list(rank, dim=6)

Returns a symbolic representation of the voigt-notation tensor that places identical symbols for entries related by index transposition, i. e. C_1121 = C_1211 etc.

Parameters:

• dim (int) – dimension of matrix/tensor, e. g. 6 for voigt notation and 3 for standard

• rank (int) – rank of tensor, e. g. 3 for third-order ECs

Returns:

array representing distinct indices c_arr (array): array representing tensor with equivalent

indices assigned as above

Return type:

c_vec (array)

raise_error_if_unphysical(f)

Wrapper for functions or properties that should raise an error if tensor is unphysical.

subs(entry, cmap)

Sympy substitution function, primarily for the purposes of numpy vectorization

Parameters:

• entry (symbol or exp) – sympy expr to undergo subs

• cmap (dict) – map for symbols to values to use in subs

Returns:

Evaluated expression with substitution