schrodinger.application.matsci.elasticity.strain module¶

This module provides classes and methods used to describe deformations and strains, including applying those deformations to structure objects and generating deformed structure sets for further calculations.

class schrodinger.application.matsci.elasticity.strain.Deformation(deformation_gradient)¶

Bases: schrodinger.application.matsci.elasticity.tensors.SquareTensor

Subclass of SquareTensor that describes the deformation gradient tensor

is_independent(tol=1e-08)¶: checks to determine whether the deformation is independent

get_perturbed_indices(tol=1e-08)¶: Gets indices of perturbed elements of the deformation gradient, i. e. those that differ from the identity

property green_lagrange_strain¶: calculates the euler-lagrange strain from the deformation gradient

apply_to_structure(structure)¶

Apply the deformation gradient to a structure.

Args:

structure (Structure object): the structure object to: be modified by the deformation

classmethod from_index_amount(matrixpos, amt)¶

Factory method for constructing a Deformation object from a matrix position and amount

Args:

matrixpos (tuple): tuple corresponding the matrix position to: have a perturbation added
amt (float): amount to add to the identity matrix at position: matrixpos

class schrodinger.application.matsci.elasticity.strain.DeformedStructureSet(structure, norm_strains=None, shear_strains=None, symmetry=False)¶

Bases: collections.abc.Sequence

class that generates a set of independently deformed structures that can be used to calculate linear stress-strain response

NORM_INDICES = [(0, 0), (1, 1), (2, 2)]¶

NORM_STRAINS = [-0.01, -0.005, 0.005, 0.01]¶

SHEAR_INDICES = [(0, 1), (0, 2), (1, 2)]¶

SHEAR_STRAINS = [-0.06, -0.03, 0.03, 0.06]¶

__init__(structure, norm_strains=None, shear_strains=None, symmetry=False)¶

constructs the deformed geometries of a structure. Generates m + n deformed structures according to the supplied parameters.

Parameters

structure (Structure) – structure to undergo deformation
shear_strains (list[float]) – strain values to apply to each shear mode.
symmetry (bool) – whether or not to use symmetry reduction.

Param

norm_strains: strain values to apply to each normal mode.

__len__()¶

class schrodinger.application.matsci.elasticity.strain.Strain(strain_matrix, dfm=None, dfm_shape='upper')¶

Bases: schrodinger.application.matsci.elasticity.tensors.SquareTensor

Subclass of SquareTensor that describes the Green-Lagrange strain tensor.

classmethod from_deformation(deformation)¶

Factory method that returns a Strain object from a deformation gradient

Args:: deformation (3x3 array-like):

classmethod from_index_amount(idx, amount)¶

Like Deformation.from_index_amount, except generates a strain from the zero 3x3 tensor or voigt vector with the amount specified in the index location. Ensures symmetric strain.

Parameters

idx (tuple or integer) – index to be perturbed, can be voigt or full-tensor notation
amount (float) – amount to perturb selected index

property deformation_matrix¶: returns the deformation matrix

property von_mises_strain¶: Equivalent strain to Von Mises Stress

schrodinger.application.matsci.elasticity.strain.convert_strain_to_deformation(strain, shape='upper')¶

This function converts a strain to a deformation gradient that will produce that strain. Supports three methods:

Parameters

strain – (3x3 array-like) strain matrix
shape (str) – method for determining deformation, supports: - “upper” produces an upper triangular defo - “lower” produces a lower triangular defo - “symmetric” produces a symmetric defo