INSTRUCTION stringlengths 1 8.43k | RESPONSE stringlengths 75 104k |
|---|---|
Open the SIGRES file located in the in self. outdir. Returns: class: ScrFile object None if file could not be found or file is not readable. | def open_scr(self):
"""
Open the SIGRES file located in the in self.outdir.
Returns :class:`ScrFile` object, None if file could not be found or file is not readable.
"""
scr_path = self.scr_path
if not scr_path:
logger.critical("%s didn't produce a SCR.nc fil... |
Absolute path of the SIGRES file. Empty string if file is not present. | def sigres_path(self):
"""Absolute path of the SIGRES file. Empty string if file is not present."""
# Lazy property to avoid multiple calls to has_abiext.
try:
return self._sigres_path
except AttributeError:
path = self.outdir.has_abiext("SIGRES")
if p... |
Open the SIGRES file located in the in self. outdir. Returns: class: SigresFile object None if file could not be found or file is not readable. | def open_sigres(self):
"""
Open the SIGRES file located in the in self.outdir.
Returns :class:`SigresFile` object, None if file could not be found or file is not readable.
"""
sigres_path = self.sigres_path
if not sigres_path:
logger.critical("%s didn't produ... |
Returns an instance of: class: ScissorsBuilder from the SIGRES file. | def get_scissors_builder(self):
"""
Returns an instance of :class:`ScissorsBuilder` from the SIGRES file.
Raise:
`RuntimeError` if SIGRES file is not found.
"""
from abipy.electrons.scissors import ScissorsBuilder
if self.sigres_path:
return Sciss... |
BSE calculations with Haydock can be restarted only if we have the excitonic Hamiltonian and the HAYDR_SAVE file. | def restart(self):
"""
BSE calculations with Haydock can be restarted only if we have the
excitonic Hamiltonian and the HAYDR_SAVE file.
"""
# TODO: This version seems to work but the main output file is truncated
# TODO: Handle restart if CG method is used
# TODO... |
Absolute path of the MDF file. Empty string if file is not present. | def mdf_path(self):
"""Absolute path of the MDF file. Empty string if file is not present."""
# Lazy property to avoid multiple calls to has_abiext.
try:
return self._mdf_path
except AttributeError:
path = self.outdir.has_abiext("MDF.nc")
if path: self... |
Open the MDF file located in the in self. outdir. Returns: class: MdfFile object None if file could not be found or file is not readable. | def open_mdf(self):
"""
Open the MDF file located in the in self.outdir.
Returns :class:`MdfFile` object, None if file could not be found or file is not readable.
"""
mdf_path = self.mdf_path
if not mdf_path:
logger.critical("%s didn't produce a MDF file in %s... |
Set the working directory of the task. | def set_workdir(self, workdir, chroot=False):
"""Set the working directory of the task."""
super().set_workdir(workdir, chroot=chroot)
# Small hack: the log file of optics is actually the main output file.
self.output_file = self.log_file |
Optic does not use get or ird variables hence we should never try to change the input when we connect this task | def set_vars(self, *args, **kwargs):
"""
Optic does not use `get` or `ird` variables hence we should never try
to change the input when we connect this task
"""
kwargs.update(dict(*args))
self.history.info("OpticTask intercepted set_vars with args %s" % kwargs)
i... |
String with the list of files and prefixes needed to execute ABINIT. | def filesfile_string(self):
"""String with the list of files and prefixes needed to execute ABINIT."""
lines = []
app = lines.append
#optic.in ! Name of input file
#optic.out ! Unused
#optic ! Root name for all files that will be produced
app(self.i... |
Returns ( at runtime ) the absolute path of the DDK files produced by the DDK runs. | def ddk_filepaths(self):
"""Returns (at runtime) the absolute path of the DDK files produced by the DDK runs."""
# This to support new version of optic that used DDK.nc
paths = [ddk_task.outdir.has_abiext("DDK.nc") for ddk_task in self.ddk_nodes]
if all(p for p in paths):
ret... |
Construct and write the input file of the calculation. | def make_input(self):
"""Construct and write the input file of the calculation."""
# Set the file paths.
all_files ={"ddkfile_" + str(n + 1): ddk for n, ddk in enumerate(self.ddk_filepaths)}
all_files.update({"wfkfile": self.wfk_filepath})
files_nml = {"FILES": all_files}
... |
restart from scratch this is to be used if a job is restarted with more resources after a crash | def reset_from_scratch(self):
"""
restart from scratch, this is to be used if a job is restarted with more resources after a crash
"""
# Move output files produced in workdir to _reset otherwise check_status continues
# to see the task as crashed even if the job did not run
... |
Build a: class: AnaddbTask with a temporary workdir. The task is executed via the shell with 1 MPI proc. Mainly used for post - processing the DDB files. | def temp_shell_task(cls, inp, ddb_node, mpi_procs=1,
gkk_node=None, md_node=None, ddk_node=None, workdir=None, manager=None):
"""
Build a :class:`AnaddbTask` with a temporary workdir. The task is executed via
the shell with 1 MPI proc. Mainly used for post-processing the ... |
String with the list of files and prefixes needed to execute ABINIT. | def filesfile_string(self):
"""String with the list of files and prefixes needed to execute ABINIT."""
lines = []
app = lines.append
app(self.input_file.path) # 1) Path of the input file
app(self.output_file.path) # 2) Path of the output file
app(self.dd... |
Returns ( at runtime ) the absolute path of the input DDB file. | def ddb_filepath(self):
"""Returns (at runtime) the absolute path of the input DDB file."""
# This is not very elegant! A possible approach could to be path self.ddb_node.outdir!
if isinstance(self.ddb_node, FileNode): return self.ddb_node.filepath
path = self.ddb_node.outdir.has_abiext(... |
Returns ( at runtime ) the absolute path of the input MD file. | def md_filepath(self):
"""Returns (at runtime) the absolute path of the input MD file."""
if self.md_node is None: return "MD_FILE_DOES_NOT_EXIST"
if isinstance(self.md_node, FileNode): return self.md_node.filepath
path = self.md_node.outdir.has_abiext("MD")
return path if path ... |
Returns ( at runtime ) the absolute path of the input GKK file. | def gkk_filepath(self):
"""Returns (at runtime) the absolute path of the input GKK file."""
if self.gkk_node is None: return "GKK_FILE_DOES_NOT_EXIST"
if isinstance(self.gkk_node, FileNode): return self.gkk_node.filepath
path = self.gkk_node.outdir.has_abiext("GKK")
return path ... |
Returns ( at runtime ) the absolute path of the input DKK file. | def ddk_filepath(self):
"""Returns (at runtime) the absolute path of the input DKK file."""
if self.ddk_node is None: return "DDK_FILE_DOES_NOT_EXIST"
if isinstance(self.ddk_node, FileNode): return self.ddk_node.filepath
path = self.ddk_node.outdir.has_abiext("DDK")
return path ... |
Open PHBST file produced by Anaddb and returns: class: PhbstFile object. | def open_phbst(self):
"""Open PHBST file produced by Anaddb and returns :class:`PhbstFile` object."""
from abipy.dfpt.phonons import PhbstFile
phbst_path = os.path.join(self.workdir, "run.abo_PHBST.nc")
if not phbst_path:
if self.status == self.S_OK:
logger.cr... |
Open PHDOS file produced by Anaddb and returns: class: PhdosFile object. | def open_phdos(self):
"""Open PHDOS file produced by Anaddb and returns :class:`PhdosFile` object."""
from abipy.dfpt.phonons import PhdosFile
phdos_path = os.path.join(self.workdir, "run.abo_PHDOS.nc")
if not phdos_path:
if self.status == self.S_OK:
logger.cr... |
Reads and returns a pymatgen structure from a NetCDF file containing crystallographic data in the ETSF - IO format. | def structure_from_ncdata(ncdata, site_properties=None, cls=Structure):
"""
Reads and returns a pymatgen structure from a NetCDF file
containing crystallographic data in the ETSF-IO format.
Args:
ncdata: filename or NetcdfReader instance.
site_properties: Dictionary with site properties... |
Navigate all the groups in the file starting from top. If top is None the root group is used. | def walk_tree(self, top=None):
"""
Navigate all the groups in the file starting from top.
If top is None, the root group is used.
"""
if top is None:
top = self.rootgrp
values = top.groups.values()
yield values
for value in top.groups.values()... |
Returns the value of a dimension. | def read_dimvalue(self, dimname, path="/", default=NO_DEFAULT):
"""
Returns the value of a dimension.
Args:
dimname: Name of the variable
path: path to the group.
default: return `default` if `dimname` is not present and
`default` is not `NO_D... |
List of variable names stored in the group specified by path. | def read_varnames(self, path="/"):
"""List of variable names stored in the group specified by path."""
if path == "/":
return self.rootgrp.variables.keys()
else:
group = self.path2group[path]
return group.variables.keys() |
Returns the values of variable with name varname in the group specified by path. | def read_value(self, varname, path="/", cmode=None, default=NO_DEFAULT):
"""
Returns the values of variable with name varname in the group specified by path.
Args:
varname: Name of the variable
path: path to the group.
cmode: if cmode=="c", a complex ndarrays... |
Read a list of variables/ dimensions from file. If a key is not present the corresponding entry in the output dictionary is set to None. | def read_keys(self, keys, dict_cls=AttrDict, path="/"):
"""
Read a list of variables/dimensions from file. If a key is not present the corresponding
entry in the output dictionary is set to None.
"""
od = dict_cls()
for k in keys:
try:
# Try to... |
Chemical symbols char [ number of atom species ] [ symbol length ]. | def chemical_symbols(self):
"""Chemical symbols char [number of atom species][symbol length]."""
charr = self.read_value("chemical_symbols")
symbols = []
for v in charr:
s = "".join(c.decode("utf-8") for c in v)
symbols.append(s.strip())
return symbols |
Returns the crystalline structure. | def read_structure(self, cls=Structure):
"""Returns the crystalline structure."""
if self.ngroups != 1:
raise NotImplementedError("In file %s: ngroups != 1" % self.path)
return structure_from_ncdata(self, cls=cls) |
Read the variables associated to the Abinit header. | def read_abinit_hdr(self):
"""
Read the variables associated to the Abinit header.
Return :class:`AbinitHeader`
"""
d = {}
for hvar in _HDR_VARIABLES.values():
ncname = hvar.etsf_name if hvar.etsf_name is not None else hvar.name
if ncname in self.... |
String representation. kwargs are passed to pprint. pformat. | def to_string(self, verbose=0, title=None, **kwargs):
"""
String representation. kwargs are passed to `pprint.pformat`.
Args:
verbose: Verbosity level
title: Title string.
"""
from pprint import pformat
s = pformat(self, **kwargs)
if title... |
Add an electrode to the plot. | def add_electrode(self, electrode, label=None):
"""
Add an electrode to the plot.
Args:
electrode: An electrode. All electrodes satisfying the
AbstractElectrode interface should work.
label: A label for the electrode. If None, defaults to a counting
... |
Returns a plot object. | def get_plot(self, width=8, height=8):
"""
Returns a plot object.
Args:
width: Width of the plot. Defaults to 8 in.
height: Height of the plot. Defaults to 6 in.
Returns:
A matplotlib plot object.
"""
plt = pretty_plot(width, height)
... |
Save the plot to an image file. | def save(self, filename, image_format="eps", width=8, height=6):
"""
Save the plot to an image file.
Args:
filename: Filename to save to.
image_format: Format to save to. Defaults to eps.
"""
self.get_plot(width, height).savefig(filename, format=image_for... |
Process structure from previous run. | def get_structure_from_prev_run(vasprun, outcar=None, sym_prec=0.1,
international_monoclinic=True):
"""
Process structure from previous run.
Args:
vasprun (Vasprun): Vasprun that contains the final structure
from previous run.
outcar (Outcar): Out... |
Batch write vasp input for a sequence of structures to output_dir following the format output_dir/ { group }/ { formula } _ { number }. | def batch_write_input(structures, vasp_input_set=MPRelaxSet, output_dir=".",
make_dir_if_not_present=True, subfolder=None,
sanitize=False, include_cif=False, **kwargs):
"""
Batch write vasp input for a sequence of structures to
output_dir, following the format out... |
List of POTCAR symbols. | def potcar_symbols(self):
"""
List of POTCAR symbols.
"""
elements = self.poscar.site_symbols
potcar_symbols = []
settings = self._config_dict["POTCAR"]
if isinstance(settings[elements[-1]], dict):
for el in elements:
potcar_symbols.ap... |
Returns all input files as a dict of { filename: vasp object } | def all_input(self):
"""
Returns all input files as a dict of {filename: vasp object}
Returns:
dict of {filename: object}, e.g., {'INCAR': Incar object, ...}
"""
return {'INCAR': self.incar,
'KPOINTS': self.kpoints,
'POSCAR': self.posc... |
Writes a set of VASP input to a directory. | def write_input(self, output_dir,
make_dir_if_not_present=True, include_cif=False):
"""
Writes a set of VASP input to a directory.
Args:
output_dir (str): Directory to output the VASP input files
make_dir_if_not_present (bool): Set to True if you want... |
Gets the default number of electrons for a given structure. | def nelect(self):
"""
Gets the default number of electrons for a given structure.
"""
# if structure is not sorted this can cause problems, so must take
# care to remove redundant symbols when counting electrons
site_symbols = list(set(self.poscar.site_symbols))
n... |
Writes out a KPOINTS file using the fully automated grid method. Uses Gamma centered meshes for hexagonal cells and Monk grids otherwise. | def kpoints(self):
"""
Writes out a KPOINTS file using the fully automated grid method. Uses
Gamma centered meshes for hexagonal cells and Monk grids otherwise.
Algorithm:
Uses a simple approach scaling the number of divisions along each
reciprocal lattice vector... |
Generate a set of Vasp input files for static calculations from a directory of previous Vasp run. | def from_prev_calc(cls, prev_calc_dir, standardize=False, sym_prec=0.1,
international_monoclinic=True, reciprocal_density=100,
small_gap_multiply=None, **kwargs):
"""
Generate a set of Vasp input files for static calculations from a
directory of prev... |
Generate a set of Vasp input files for HSE calculations from a directory of previous Vasp run. if mode == gap it explicitly adds VBM and CBM of the prev run to the k - point list of this run. | def from_prev_calc(cls, prev_calc_dir, mode="gap",
reciprocal_density=50, copy_chgcar=True, **kwargs):
"""
Generate a set of Vasp input files for HSE calculations from a
directory of previous Vasp run. if mode=="gap", it explicitly adds VBM
and CBM of the prev run ... |
Generate a set of Vasp input files for NonSCF calculations from a directory of previous static Vasp run. | def from_prev_calc(cls, prev_calc_dir, copy_chgcar=True,
nbands_factor=1.2, standardize=False, sym_prec=0.1,
international_monoclinic=True, reciprocal_density=100,
kpoints_line_density=20, small_gap_multiply=None,
**kwargs):
... |
Generate a set of Vasp input files for SOC calculations from a directory of previous static Vasp run. SOC calc requires all 3 components for MAGMOM for each atom in the structure. | def from_prev_calc(cls, prev_calc_dir, copy_chgcar=True,
nbands_factor=1.2, standardize=False, sym_prec=0.1,
international_monoclinic=True, reciprocal_density=100,
small_gap_multiply=None, **kwargs):
"""
Generate a set of Vasp input fi... |
Generate gamma center k - points mesh grid for GW calc which is requested by GW calculation. | def kpoints(self):
"""
Generate gamma center k-points mesh grid for GW calc,
which is requested by GW calculation.
"""
return Kpoints.automatic_density_by_vol(self.structure,
self.reciprocal_density,
... |
Generate a set of Vasp input files for GW or BSE calculations from a directory of previous Exact Diag Vasp run. | def from_prev_calc(cls, prev_calc_dir, copy_wavecar=True, mode="DIAG",
nbands_factor=5, ncores=16, **kwargs):
"""
Generate a set of Vasp input files for GW or BSE calculations from a
directory of previous Exact Diag Vasp run.
Args:
prev_calc_dir (str):... |
k_product default to 50 is kpoint number * length for a & b directions also for c direction in bulk calculations Automatic mesh & Gamma is the default setting. | def kpoints(self):
"""
k_product, default to 50, is kpoint number * length for a & b
directions, also for c direction in bulk calculations
Automatic mesh & Gamma is the default setting.
"""
# To get input sets, the input structure has to has the same number
#... |
k_product default to 40 is kpoint number * length for a & b directions also for c direction in bulk calculations Automatic mesh & Gamma is the default setting. | def kpoints(self):
"""
k_product, default to 40, is kpoint number * length for a & b
directions, also for c direction in bulk calculations
Automatic mesh & Gamma is the default setting.
"""
# To get input sets, the input structure has to has the same number
# of ... |
Remove any atom jumps across the cell | def _process_structures(structures):
"""
Remove any atom jumps across the cell
"""
input_structures = structures
structures = [input_structures[0]]
for s in input_structures[1:]:
prev = structures[-1]
for i in range(len(s)):
t = np.... |
NEB inputs has a special directory structure where inputs are in 00 01 02.... | def write_input(self, output_dir, make_dir_if_not_present=True,
write_cif=False, write_path_cif=False,
write_endpoint_inputs=False):
"""
NEB inputs has a special directory structure where inputs are in 00,
01, 02, ....
Args:
output_dir... |
Gets a unit vector parallel to input vector | def get_uvec(vec):
""" Gets a unit vector parallel to input vector"""
l = np.linalg.norm(vec)
if l < 1e-8:
return vec
return vec / l |
Function that converts a list of tensors corresponding to a structure and returns a dictionary consisting of unique tensor keys with symmop values corresponding to transformations that will result in derivative tensors from the original list | def symmetry_reduce(tensors, structure, tol=1e-8, **kwargs):
"""
Function that converts a list of tensors corresponding to a structure
and returns a dictionary consisting of unique tensor keys with symmop
values corresponding to transformations that will result in derivative
tensors from the origina... |
Helper function to find a value in a tensor - keyed - dictionary using an approximation to the key. This is useful if rounding errors in construction occur or hashing issues arise in tensor - keyed - dictionaries ( e. g. from symmetry_reduce ). Resolves most hashing issues and is preferable to redefining eq methods in ... | def get_tkd_value(tensor_keyed_dict, tensor, allclose_kwargs=None):
"""
Helper function to find a value in a tensor-keyed-
dictionary using an approximation to the key. This
is useful if rounding errors in construction occur
or hashing issues arise in tensor-keyed-dictionaries
(e. g. from symme... |
returns the matrix with all entries below a certain threshold ( i. e. tol ) set to zero | def zeroed(self, tol=1e-3):
"""
returns the matrix with all entries below a certain threshold
(i.e. tol) set to zero
"""
new_tensor = self.copy()
new_tensor[abs(new_tensor) < tol] = 0
return new_tensor |
Applies a rotation directly and tests input matrix to ensure a valid rotation. | def rotate(self, matrix, tol=1e-3):
"""
Applies a rotation directly, and tests input matrix to ensure a valid
rotation.
Args:
matrix (3x3 array-like): rotation matrix to be applied to tensor
tol (float): tolerance for testing rotation matrix validity
"""
... |
Calculates the result of an einstein summation expression | def einsum_sequence(self, other_arrays, einsum_string=None):
"""
Calculates the result of an einstein summation expression
"""
if not isinstance(other_arrays, list):
raise ValueError("other tensors must be list of "
"tensors or tensor input")
... |
Convenience method for projection of a tensor into a vector. Returns the tensor dotted into a unit vector along the input n. | def project(self, n):
"""
Convenience method for projection of a tensor into a
vector. Returns the tensor dotted into a unit vector
along the input n.
Args:
n (3x1 array-like): direction to project onto
Returns (float):
scalar value correspondin... |
Method for averaging the tensor projection over the unit with option for custom quadrature. | def average_over_unit_sphere(self, quad=None):
"""
Method for averaging the tensor projection over the unit
with option for custom quadrature.
Args:
quad (dict): quadrature for integration, should be
dictionary with "points" and "weights" keys defaults
... |
Gets index sets for equivalent tensor values | def get_grouped_indices(self, voigt=False, **kwargs):
"""
Gets index sets for equivalent tensor values
Args:
voigt (bool): whether to get grouped indices
of voigt or full notation tensor, defaults
to false
**kwargs: keyword args for np.isc... |
Creates a summary dict for tensor with associated symbol | def get_symbol_dict(self, voigt=True, zero_index=False, **kwargs):
"""
Creates a summary dict for tensor with associated symbol
Args:
voigt (bool): whether to get symbol dict for voigt
notation tensor, as opposed to full notation,
defaults to true
... |
Wrapper around numpy. round to ensure object of same type is returned | def round(self, decimals=0):
"""
Wrapper around numpy.round to ensure object
of same type is returned
Args:
decimals :Number of decimal places to round to (default: 0).
If decimals is negative, it specifies the number of
positions to the left ... |
Returns a generally symmetrized tensor calculated by taking the sum of the tensor and its transpose with respect to all possible permutations of indices | def symmetrized(self):
"""
Returns a generally symmetrized tensor, calculated by taking
the sum of the tensor and its transpose with respect to all
possible permutations of indices
"""
perms = list(itertools.permutations(range(self.rank)))
return sum([np.transpose... |
Returns a voigt - symmetrized tensor i. e. a voigt - notation tensor such that it is invariant wrt permutation of indices | def voigt_symmetrized(self):
"""
Returns a "voigt"-symmetrized tensor, i. e. a voigt-notation
tensor such that it is invariant wrt permutation of indices
"""
if not (self.rank % 2 == 0 and self.rank >= 2):
raise ValueError("V-symmetrization requires rank even and >= 2... |
Returns a tensor that is invariant with respect to symmetry operations corresponding to a structure | def fit_to_structure(self, structure, symprec=0.1):
"""
Returns a tensor that is invariant with respect to symmetry
operations corresponding to a structure
Args:
structure (Structure): structure from which to generate
symmetry operations
symprec (... |
Tests whether a tensor is invariant with respect to the symmetry operations of a particular structure by testing whether the residual of the symmetric portion is below a tolerance | def is_fit_to_structure(self, structure, tol=1e-2):
"""
Tests whether a tensor is invariant with respect to the
symmetry operations of a particular structure by testing
whether the residual of the symmetric portion is below a
tolerance
Args:
structure (Struct... |
Returns the tensor in Voigt notation | def voigt(self):
"""
Returns the tensor in Voigt notation
"""
v_matrix = np.zeros(self._vscale.shape, dtype=self.dtype)
this_voigt_map = self.get_voigt_dict(self.rank)
for ind in this_voigt_map:
v_matrix[this_voigt_map[ind]] = self[ind]
if not self.is_... |
Tests symmetry of tensor to that necessary for voigt - conversion by grouping indices into pairs and constructing a sequence of possible permutations to be used in a tensor transpose | def is_voigt_symmetric(self, tol=1e-6):
"""
Tests symmetry of tensor to that necessary for voigt-conversion
by grouping indices into pairs and constructing a sequence of
possible permutations to be used in a tensor transpose
"""
transpose_pieces = [[[0 for i in range(self... |
Returns a dictionary that maps indices in the tensor to those in a voigt representation based on input rank | def get_voigt_dict(rank):
"""
Returns a dictionary that maps indices in the tensor to those
in a voigt representation based on input rank
Args:
rank (int): Tensor rank to generate the voigt map
"""
vdict = {}
for ind in itertools.product(*[range(3)] *... |
Constructor based on the voigt notation vector or matrix. | def from_voigt(cls, voigt_input):
"""
Constructor based on the voigt notation vector or matrix.
Args:
voigt_input (array-like): voigt input for a given tensor
"""
voigt_input = np.array(voigt_input)
rank = sum(voigt_input.shape) // 3
t = cls(np.zeros(... |
Given a structure associated with a tensor determines the rotation matrix for IEEE conversion according to the 1987 IEEE standards. | def get_ieee_rotation(structure, refine_rotation=True):
"""
Given a structure associated with a tensor, determines
the rotation matrix for IEEE conversion according to
the 1987 IEEE standards.
Args:
structure (Structure): a structure associated with the
... |
Given a structure associated with a tensor attempts a calculation of the tensor in IEEE format according to the 1987 IEEE standards. | def convert_to_ieee(self, structure, initial_fit=True,
refine_rotation=True):
"""
Given a structure associated with a tensor, attempts a
calculation of the tensor in IEEE format according to
the 1987 IEEE standards.
Args:
structure (Structure)... |
Transforms a tensor from one basis for an original structure into a new basis defined by a new structure. | def structure_transform(self, original_structure, new_structure,
refine_rotation=True):
"""
Transforms a tensor from one basis for an original structure
into a new basis defined by a new structure.
Args:
original_structure (Structure): structure c... |
Creates a tensor from values and indices with options for populating the remainder of the tensor. | def from_values_indices(cls, values, indices, populate=False,
structure=None, voigt_rank=None,
vsym=True, verbose=False):
"""
Creates a tensor from values and indices, with options
for populating the remainder of the tensor.
Args:
... |
Takes a partially populated tensor and populates the non - zero entries according to the following procedure iterated until the desired convergence ( specified via prec ) is achieved. | def populate(self, structure, prec=1e-5, maxiter=200, verbose=False,
precond=True, vsym=True):
"""
Takes a partially populated tensor, and populates the non-zero
entries according to the following procedure, iterated until
the desired convergence (specified via prec) is ... |
Serializes the tensor object | def as_dict(self, voigt=False):
"""
Serializes the tensor object
Args:
voigt (bool): flag for whether to store entries in
voigt-notation. Defaults to false, as information
may be lost in conversion.
Returns (Dict):
serialized for... |
shorthand for matrix inverse on SquareTensor | def inv(self):
"""
shorthand for matrix inverse on SquareTensor
"""
if self.det == 0:
raise ValueError("SquareTensor is non-invertible")
return SquareTensor(np.linalg.inv(self)) |
Test to see if tensor is a valid rotation matrix performs a test to check whether the inverse is equal to the transpose and if the determinant is equal to one within the specified tolerance | def is_rotation(self, tol=1e-3, include_improper=True):
"""
Test to see if tensor is a valid rotation matrix, performs a
test to check whether the inverse is equal to the transpose
and if the determinant is equal to one within the specified
tolerance
Args:
to... |
Helper method for refining rotation matrix by ensuring that second and third rows are perpindicular to the first. Gets new y vector from an orthogonal projection of x onto y and the new z vector from a cross product of the new x and y | def refine_rotation(self):
"""
Helper method for refining rotation matrix by ensuring
that second and third rows are perpindicular to the first.
Gets new y vector from an orthogonal projection of x onto y
and the new z vector from a cross product of the new x and y
Args:... |
Calculates the average oxidation state of a site | def compute_average_oxidation_state(site):
"""
Calculates the average oxidation state of a site
Args:
site: Site to compute average oxidation state
Returns:
Average oxidation state of site.
"""
try:
avg_oxi = sum([sp.oxi_state * occu
for sp, occu ... |
Gives total ewald energy for certain sites being removed i. e. zeroed out. | def compute_partial_energy(self, removed_indices):
"""
Gives total ewald energy for certain sites being removed, i.e. zeroed
out.
"""
total_energy_matrix = self.total_energy_matrix.copy()
for i in removed_indices:
total_energy_matrix[i, :] = 0
tota... |
Gives total ewald energy for an sub structure in the same lattice. The sub_structure must be a subset of the original structure with possible different charges. | def compute_sub_structure(self, sub_structure, tol=1e-3):
"""
Gives total ewald energy for an sub structure in the same
lattice. The sub_structure must be a subset of the original
structure, with possible different charges.
Args:
substructure (Structure): Substructur... |
The total energy. | def total_energy(self):
"""
The total energy.
"""
return sum(sum(self._recip)) + sum(sum(self._real)) + sum(self._point) + self._charged_cell_energy |
The total energy matrix. Each matrix element ( i j ) corresponds to the total interaction energy between site i and site j. | def total_energy_matrix(self):
"""
The total energy matrix. Each matrix element (i, j) corresponds to the
total interaction energy between site i and site j.
Note that this does not include the charged-cell energy, which is only important
when the simulation cell is not charge b... |
Compute the energy for a single site in the structure Args: site_index ( int ): Index of site ReturnS: ( float ) - Energy of that site | def get_site_energy(self, site_index):
"""Compute the energy for a single site in the structure
Args:
site_index (int): Index of site
ReturnS:
(float) - Energy of that site"""
if self._charged:
warn('Per atom energies for charged structures no... |
Perform the reciprocal space summation. Calculates the quantity E_recip = 1/ ( 2PiV ) sum_ { G < Gmax } exp ( - ( G. G/ 4/ eta ))/ ( G. G ) S ( G ) S ( - G ) where S ( G ) = sum_ { k = 1 N } q_k exp ( - i G. r_k ) S ( G ) S ( - G ) = |S ( G ) | ** 2 | def _calc_recip(self):
"""
Perform the reciprocal space summation. Calculates the quantity
E_recip = 1/(2PiV) sum_{G < Gmax} exp(-(G.G/4/eta))/(G.G) S(G)S(-G)
where
S(G) = sum_{k=1,N} q_k exp(-i G.r_k)
S(G)S(-G) = |S(G)|**2
This method is heavily vectorized to ut... |
Determines the self energy - ( eta/ pi ) ** ( 1/ 2 ) * sum_ { i = 1 } ^ { N } q_i ** 2 | def _calc_real_and_point(self):
"""
Determines the self energy -(eta/pi)**(1/2) * sum_{i=1}^{N} q_i**2
"""
fcoords = self._s.frac_coords
forcepf = 2.0 * self._sqrt_eta / sqrt(pi)
coords = self._coords
numsites = self._s.num_sites
ereal = np.empty((numsites... |
This method finds and returns the permutations that produce the lowest ewald sum calls recursive function to iterate through permutations | def minimize_matrix(self):
"""
This method finds and returns the permutations that produce the lowest
ewald sum calls recursive function to iterate through permutations
"""
if self._algo == EwaldMinimizer.ALGO_FAST or \
self._algo == EwaldMinimizer.ALGO_BE... |
This adds an m_list to the output_lists and updates the current minimum if the list is full. | def add_m_list(self, matrix_sum, m_list):
"""
This adds an m_list to the output_lists and updates the current
minimum if the list is full.
"""
if self._output_lists is None:
self._output_lists = [[matrix_sum, m_list]]
else:
bisect.insort(self._outp... |
Computes a best case given a matrix and manipulation list. | def best_case(self, matrix, m_list, indices_left):
"""
Computes a best case given a matrix and manipulation list.
Args:
matrix: the current matrix (with some permutations already
performed)
m_list: [(multiplication fraction, number_of_indices, indices,
... |
Returns an index that should have the most negative effect on the matrix sum | def get_next_index(self, matrix, manipulation, indices_left):
"""
Returns an index that should have the most negative effect on the
matrix sum
"""
f = manipulation[0]
indices = list(indices_left.intersection(manipulation[2]))
sums = np.sum(matrix[indices], axis=1)... |
This method recursively finds the minimal permutations using a binary tree search strategy. | def _recurse(self, matrix, m_list, indices, output_m_list=[]):
"""
This method recursively finds the minimal permutations using a binary
tree search strategy.
Args:
matrix: The current matrix (with some permutations already
performed).
m_list: The... |
Calculates the ensemble averaged Voronoi coordination numbers of a list of Structures using VoronoiNN. Typically used for analyzing the output of a Molecular Dynamics run. Args: structures ( list ): list of Structures. freq ( int ): sampling frequency of coordination number [ every freq steps ]. Returns: Dictionary of ... | def average_coordination_number(structures, freq=10):
"""
Calculates the ensemble averaged Voronoi coordination numbers
of a list of Structures using VoronoiNN.
Typically used for analyzing the output of a Molecular Dynamics run.
Args:
structures (list): list of Structures.
freq (int... |
Helper method to calculate the solid angle of a set of coords from the center. | def solid_angle(center, coords):
"""
Helper method to calculate the solid angle of a set of coords from the
center.
Args:
center (3x1 array): Center to measure solid angle from.
coords (Nx3 array): List of coords to determine solid angle.
Returns:
The solid angle.
"""
... |
Provides max bond length estimates for a structure based on the JMol table and algorithms. Args: structure: ( structure ) el_radius_updates: ( dict ) symbol - > float to update atomic radii Returns: ( dict ) - ( Element1 Element2 ) - > float. The two elements are ordered by Z. | def get_max_bond_lengths(structure, el_radius_updates=None):
"""
Provides max bond length estimates for a structure based on the JMol
table and algorithms.
Args:
structure: (structure)
el_radius_updates: (dict) symbol->float to update atomic radii
Returns: (dict) - (Element... |
This method returns whether a structure is 3D 2D ( layered ) or 1D ( linear chains or molecules ) according to the algorithm published in Gorai P. Toberer E. & Stevanovic V. Computational Identification of Promising Thermoelectric Materials Among Known Quasi - 2D Binary Compounds. J. Mater. Chem. A 2 4136 ( 2016 ). | def get_dimensionality(structure, max_hkl=2, el_radius_updates=None,
min_slab_size=5, min_vacuum_size=5,
standardize=True, bonds=None):
"""
This method returns whether a structure is 3D, 2D (layered), or 1D (linear
chains or molecules) according to the algorithm... |
Determines if a structure contains peroxide anions. | def contains_peroxide(structure, relative_cutoff=1.1):
"""
Determines if a structure contains peroxide anions.
Args:
structure (Structure): Input structure.
relative_cutoff: The peroxide bond distance is 1.49 Angstrom.
Relative_cutoff * 1.49 stipulates the maximum distance two O... |
Determines if an oxide is a peroxide/ superoxide/ ozonide/ normal oxide | def oxide_type(structure, relative_cutoff=1.1, return_nbonds=False):
"""
Determines if an oxide is a peroxide/superoxide/ozonide/normal oxide
Args:
structure (Structure): Input structure.
relative_cutoff (float): Relative_cutoff * act. cutoff stipulates the
max distance two O at... |
Determines if a structure is a sulfide/ polysulfide | def sulfide_type(structure):
"""
Determines if a structure is a sulfide/polysulfide
Args:
structure (Structure): Input structure.
Returns:
(str) sulfide/polysulfide/sulfate
"""
structure = structure.copy()
structure.remove_oxidation_states()
s = Element("S")
comp = ... |
Performs Voronoi analysis and returns the polyhedra around atom n in Schlaefli notation. | def analyze(self, structure, n=0):
"""
Performs Voronoi analysis and returns the polyhedra around atom n
in Schlaefli notation.
Args:
structure (Structure): structure to analyze
n (int): index of the center atom in structure
Returns:
voronoi ... |
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