pymatgen.analysis.piezo_sensitivity module

Piezo sensitivity analysis module.

class BornEffectiveCharge(structure, bec, pointops, tol=0.001)[source]

Bases: object

This class describes the Nx3x3 born effective charge tensor

Create an BornEffectiveChargeTensor object defined by a structure, point operations of the structure’s atomic sites. Note that the constructor uses __new__ rather than __init__ according to the standard method ofsubclassing numpy ndarrays.

Parameters

input_matrix (Nx3x3 array-like) – the Nx3x3 array-like representing the born effective charge tensor

get_BEC_operations(eigtol=1e-05, opstol=0.001)[source]

Returns the symmetry operations which maps the tensors belonging to equivalent sites onto each other in the form [site index 1, site index 2, [Symmops mapping from site index 1 to site index 2]]

Parameters
  • eigtol (float) – tolerance for determining if two sites are

  • by symmetry (related) –

  • opstol (float) – tolerance for determining if a symmetry

  • relates two sites (operation) –

Returns

list of symmetry operations mapping equivalent sites and the indexes of those sites.

get_rand_BEC(max_charge=1)[source]

Generate a random born effective charge tensor which obeys a structure’s symmetry and the acoustic sum rule

Parameters

max_charge (float) – maximum born effective charge value

Returns

np.array Born effective charge tensor

class ForceConstantMatrix(structure, fcm, pointops, sharedops, tol=0.001)[source]

Bases: object

This class describes the NxNx3x3 force constant matrix defined by a structure, point operations of the structure’s atomic sites, and the shared symmetry operations between pairs of atomic sites.

Create an ForceConstantMatrix object.

Parameters

input_matrix (NxNx3x3 array-like) – the NxNx3x3 array-like representing the force constant matrix

get_FCM_operations(eigtol=1e-05, opstol=1e-05)[source]

Returns the symmetry operations which maps the tensors belonging to equivalent sites onto each other in the form [site index 1a, site index 1b, site index 2a, site index 2b, [Symmops mapping from site index 1a, 1b to site index 2a, 2b]]

Parameters
  • eigtol (float) – tolerance for determining if two sites are

  • by symmetry (related) –

  • opstol (float) – tolerance for determining if a symmetry

  • relates two sites (operation) –

Returns

list of symmetry operations mapping equivalent sites and the indexes of those sites.

get_asum_FCM(fcm, numiter=15)[source]

Generate a symmeterized force constant matrix that obeys the objects symmetry constraints and obeys the acoustic sum rule through an iterative procedure

Parameters
  • fcm (numpy array) – 3Nx3N unsymmeterized force constant matrix

  • numiter (int) – number of iterations to attempt to obey the acoustic sum rule

Returns

numpy array representing the force constant matrix

get_rand_FCM(asum=15, force=10)[source]

Generate a symmeterized force constant matrix from an unsymmeterized matrix that has no unstable modes and also obeys the acoustic sum rule through an iterative procedure

Parameters
  • force (float) – maximum force constant

  • asum (int) – number of iterations to attempt to obey the acoustic sum rule

Returns

NxNx3x3 np.array representing the force constant matrix

get_stable_FCM(fcm, fcmasum=10)[source]

Generate a symmeterized force constant matrix that obeys the objects symmetry constraints, has no unstable modes and also obeys the acoustic sum rule through an iterative procedure

Parameters
  • fcm (numpy array) – unsymmeterized force constant matrix

  • fcmasum (int) – number of iterations to attempt to obey the acoustic sum rule

Returns

3Nx3N numpy array representing the force constant matrix

get_symmetrized_FCM(unsymmetrized_fcm, max_force=1)[source]

Generate a symmeterized force constant matrix from an unsymmeterized matrix

Parameters
  • unsymmetrized_fcm (numpy array) – unsymmeterized force constant matrix

  • max_charge (float) – maximum born effective charge value

Returns

3Nx3N numpy array representing the force constant matrix

get_unstable_FCM(max_force=1)[source]

Generate an unsymmeterized force constant matrix

Parameters

max_charge (float) – maximum born effective charge value

Returns

numpy array representing the force constant matrix

class InternalStrainTensor(structure, ist, pointops, tol=0.001)[source]

Bases: object

This class describes the Nx3x3x3 internal tensor defined by a structure, point operations of the structure’s atomic sites.

Create an InternalStrainTensor object.

Parameters

input_matrix (Nx3x3x3 array-like) – the Nx3x3x3 array-like representing the internal strain tensor

get_IST_operations(opstol=0.001)[source]

Returns the symmetry operations which maps the tensors belonging to equivalent sites onto each other in the form [site index 1, site index 2, [Symmops mapping from site index 1 to site index 2]]

Parameters
  • opstol (float) – tolerance for determining if a symmetry

  • relates two sites (operation) –

Returns

list of symmetry operations mapping equivalent sites and the indexes of those sites.

get_rand_IST(max_force=1)[source]

Generate a random internal strain tensor which obeys a structure’s symmetry and the acoustic sum rule

Parameters

max_force (float) – maximum born effective charge value

Returns

InternalStrainTensor object

get_piezo(BEC, IST, FCM, rcond=0.0001)[source]

Generate a random piezoelectric tensor based on a structure and corresponding symmetry

Parameters
  • BEC (numpy array) – Nx3x3 array representing the born effective charge tensor

  • IST (numpy array) – Nx3x3x3 array representing the internal strain tensor

  • FCM (numpy array) – NxNx3x3 array representing the born effective charge tensor

  • rcondy (float) – condition for excluding eigenvalues in the pseudoinverse

Returns

3x3x3 calculated Piezo tensor

rand_piezo(struc, pointops, sharedops, BEC, IST, FCM, anumiter=10)[source]

Generate a random piezoelectric tensor based on a structure and corresponding symmetry

Parameters
  • struc (pymatgen structure) – structure whose symmetry operations the piezo tensor must obey

  • pointops – list of point operations obeyed by a single atomic site

  • sharedops – list of point operations shared by a pair of atomic sites

  • BEC (numpy array) – Nx3x3 array representing the born effective charge tensor

  • IST (numpy array) – Nx3x3x3 array representing the internal strain tensor

  • FCM (numpy array) – NxNx3x3 array representing the born effective charge tensor

  • anumiter (int) – number of iterations for acoustic sum rule convergence

Returns

list in the form of [Nx3x3 random born effective charge tenosr, Nx3x3x3 random internal strain tensor, NxNx3x3 random force constant matrix, 3x3x3 piezo tensor]