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A complete dos object which incorporates the total dos and all
projected dos.
def complete_dos(self):
"""
A complete dos object which incorporates the total dos and all
projected dos.
"""
final_struct = self.final_structure
pdoss = {final_struct[i]: pdos for i, p... |
Hubbard U values used if a vasprun is a GGA+U run. {} otherwise.
def hubbards(self):
"""
Hubbard U values used if a vasprun is a GGA+U run. {} otherwise.
"""
symbols = [s.split()[1] for s in self.potcar_symbols]
symbols = [re.split(r"_", s)[0] for s in symbols]
if not se... |
Returns the run type. Currently supports LDA, GGA, vdW-DF and HF calcs.
TODO: Fix for other functional types like PW91, other vdW types, etc.
def run_type(self):
"""
Returns the run type. Currently supports LDA, GGA, vdW-DF and HF calcs.
TODO: Fix for other functional types like PW91,... |
True if run is a DFT+U run.
def is_hubbard(self):
"""
True if run is a DFT+U run.
"""
if len(self.hubbards) == 0:
return False
return sum(self.hubbards.values()) > 1e-8 |
Returns a ComputedStructureEntry from the vasprun.
Args:
inc_structure (bool): Set to True if you want
ComputedStructureEntries to be returned instead of
ComputedEntries.
parameters (list): Input parameters to include. It has to be one of
... |
Returns the band structure as a BandStructure object
Args:
kpoints_filename (str): Full path of the KPOINTS file from which
the band structure is generated.
If none is provided, the code will try to intelligently
determine the appropriate KPOINTS file... |
Band properties from the eigenvalues as a tuple,
(band gap, cbm, vbm, is_band_gap_direct).
def eigenvalue_band_properties(self):
"""
Band properties from the eigenvalues as a tuple,
(band gap, cbm, vbm, is_band_gap_direct).
"""
vbm = -float("inf")
vbm_kpoint = No... |
Json-serializable dict representation.
def as_dict(self):
"""
Json-serializable dict representation.
"""
d = {"vasp_version": self.vasp_version,
"has_vasp_completed": self.converged,
"nsites": len(self.final_structure)}
comp = self.final_structure.compo... |
Json-serializable dict representation.
def as_dict(self):
"""
Json-serializable dict representation.
"""
d = {"vasp_version": self.vasp_version,
"has_vasp_completed": True,
"nsites": len(self.final_structure)}
comp = self.final_structure.composition
... |
General pattern reading. Uses monty's regrep method. Takes the same
arguments.
Args:
patterns (dict): A dict of patterns, e.g.,
{"energy": r"energy\\(sigma->0\\)\\s+=\\s+([\\d\\-.]+)"}.
reverse (bool): Read files in reverse. Defaults to false. Useful for
... |
Parse table-like data. A table composes of three parts: header,
main body, footer. All the data matches "row pattern" in the main body
will be returned.
Args:
header_pattern (str): The regular expression pattern matches the
table header. This pattern should match all... |
Parses the eletrostatic potential for the last ionic step
def read_electrostatic_potential(self):
"""
Parses the eletrostatic potential for the last ionic step
"""
pattern = {"ngf": r"\s+dimension x,y,z NGXF=\s+([\.\-\d]+)\sNGYF=\s+([\.\-\d]+)\sNGZF=\s+([\.\-\d]+)"}
self.read_pa... |
Parses the frequency dependent dielectric function (obtained with
LOPTICS). Frequencies (in eV) are in self.frequencies, and dielectric
tensor function is given as self.dielectric_tensor_function.
def read_freq_dielectric(self):
"""
Parses the frequency dependent dielectric function (ob... |
Parse the NMR chemical shieldings data. Only the second part "absolute, valence and core"
will be parsed. And only the three right most field (ISO_SHIELDING, SPAN, SKEW) will be retrieved.
Returns:
List of chemical shieldings in the order of atoms from the OUTCAR. Maryland notation is adopt... |
Parse the G0 contribution of NMR chemical shielding.
Returns:
G0 contribution matrix as list of list.
def read_cs_g0_contribution(self):
"""
Parse the G0 contribution of NMR chemical shielding.
Returns:
G0 contribution matrix as list of list.
... |
Parse the core contribution of NMR chemical shielding.
Returns:
G0 contribution matrix as list of list.
def read_cs_core_contribution(self):
"""
Parse the core contribution of NMR chemical shielding.
Returns:
G0 contribution matrix as list of list.
... |
Parse the matrix form of NMR tensor before corrected to table.
Returns:
nsymmetrized tensors list in the order of atoms.
def read_cs_raw_symmetrized_tensors(self):
"""
Parse the matrix form of NMR tensor before corrected to table.
Returns:
nsymmetrized tensors list in ... |
Parses the NMR Electric Field Gradient Raw Tensors
Returns:
A list of Electric Field Gradient Tensors in the order of Atoms from OUTCAR
def read_nmr_efg_tensor(self):
"""
Parses the NMR Electric Field Gradient Raw Tensors
Returns:
A list of Electric Field Gradi... |
Parse the NMR Electric Field Gradient interpretted values.
Returns:
Electric Field Gradient tensors as a list of dict in the order of atoms from OUTCAR.
Each dict key/value pair corresponds to a component of the tensors.
def read_nmr_efg(self):
"""
Parse the NMR Electri... |
Parse the elastic tensor data.
Returns:
6x6 array corresponding to the elastic tensor from the OUTCAR.
def read_elastic_tensor(self):
"""
Parse the elastic tensor data.
Returns:
6x6 array corresponding to the elastic tensor from the OUTCAR.
"""
... |
Parse the piezo tensor data
def read_piezo_tensor(self):
"""
Parse the piezo tensor data
"""
header_pattern = r"PIEZOELECTRIC TENSOR for field in x, y, " \
r"z\s+\(C/m\^2\)\s+([X-Z][X-Z]\s+)+\-+"
row_pattern = r"[x-z]\s+" + r"\s+".join([r"(\-*[\.\d]+)"]... |
Reads NEB data. This only works with OUTCARs from both normal
VASP NEB calculations or from the CI NEB method implemented by
Henkelman et al.
Args:
reverse (bool): Read files in reverse. Defaults to false. Useful for
large files, esp OUTCARs, especially when used wit... |
Renders accessible:
er_ev = e<r>_ev (dictionary with Spin.up/Spin.down as keys)
er_bp = e<r>_bp (dictionary with Spin.up/Spin.down as keys)
er_ev_tot = spin up + spin down summed
er_bp_tot = spin up + spin down summed
p_elc = spin up + spin down summed
... |
Reads the internal strain tensor and populates self.internal_strain_tensor with an array of voigt notation
tensors for each site.
def read_internal_strain_tensor(self):
"""
Reads the internal strain tensor and populates self.internal_strain_tensor with an array of voigt notation
... |
Create pseudopotential ZVAL dictionary.
def read_pseudo_zval(self):
"""
Create pseudopotential ZVAL dictionary.
"""
try:
def poscar_line(results, match):
poscar_line = match.group(1)
results.poscar_line = re.findall(r'[A-Z][a-z]?', poscar_line... |
Read the core state eigenenergies at each ionic step.
Returns:
A list of dict over the atom such as [{"AO":[core state eig]}].
The core state eigenenergie list for each AO is over all ionic
step.
Example:
The core state eigenenergie of the 2s AO of the 6... |
Read the core potential at each ionic step.
Returns:
A list for each ionic step containing a list of the average core
potentials for each atom: [[avg core pot]].
Example:
The average core potential of the 2nd atom of the structure at the
last ionic step ... |
output example:
Fermi contact (isotropic) hyperfine coupling parameter (MHz)
-------------------------------------------------------------
ion A_pw A_1PS A_1AE A_1c A_tot
-------------------------------------------------------------
1 -0.002 -0.002... |
The data decomposed into actual spin data as {spin: data}.
Essentially, this provides the actual Spin.up and Spin.down data
instead of the total and diff. Note that by definition, a
non-spin-polarized run would have Spin.up data == Spin.down data.
def spin_data(self):
"""
The d... |
Returns the grid for a particular axis.
Args:
ind (int): Axis index.
def get_axis_grid(self, ind):
"""
Returns the grid for a particular axis.
Args:
ind (int): Axis index.
"""
ng = self.dim
num_pts = ng[ind]
lengths = self.struct... |
Method to do a linear sum of volumetric objects. Used by + and -
operators as well. Returns a VolumetricData object containing the
linear sum.
Args:
other (VolumetricData): Another VolumetricData object
scale_factor (float): Factor to scale the other data by.
Re... |
Convenience method to parse a generic volumetric data file in the vasp
like format. Used by subclasses for parsing file.
Args:
filename (str): Path of file to parse
Returns:
(poscar, data)
def parse_file(filename):
"""
Convenience method to parse a gene... |
Write the VolumetricData object to a vasp compatible file.
Args:
file_name (str): Path to a file
vasp4_compatible (bool): True if the format is vasp4 compatible
def write_file(self, file_name, vasp4_compatible=False):
"""
Write the VolumetricData object to a vasp compat... |
Get integrated difference of atom index ind up to radius. This can be
an extremely computationally intensive process, depending on how many
grid points are in the VolumetricData.
Args:
ind (int): Index of atom.
radius (float): Radius of integration.
nbins (in... |
Get the averaged total of the volumetric data a certain axis direction.
For example, useful for visualizing Hartree Potentials from a LOCPOT
file.
Args:
ind (int): Index of axis.
Returns:
Average total along axis
def get_average_along_axis(self, ind):
"... |
Writes the VolumetricData to a HDF5 format, which is a highly optimized
format for reading storing large data. The mapping of the VolumetricData
to this file format is as follows:
VolumetricData.data -> f["vdata"]
VolumetricData.structure ->
f["Z"]: Sequence of atomic number... |
Method returning a dictionary of projections on elements.
Args:
structure (Structure): Input structure.
Returns:
a dictionary in the {Spin.up:[k index][b index][{Element:values}]]
def get_projection_on_elements(self, structure):
"""
Method returning a dictionar... |
Returns the occupation for a particular orbital of a particular atom.
Args:
atom_num (int): Index of atom in the PROCAR. It should be noted
that VASP uses 1-based indexing for atoms, but this is
converted to 0-based indexing in this parser to be
consi... |
Compilation of all energies from all electronic steps and ionic steps
as a tuple of list of energies, e.g.,
((4507.24605593, 143.824705755, -512.073149912, ...), ...)
def all_energies(self):
"""
Compilation of all energies from all electronic steps and ionic steps
as a tuple of ... |
Sequence of symbols associated with the Xdatcar. Similar to 6th line in
vasp 5+ Xdatcar.
def site_symbols(self):
"""
Sequence of symbols associated with the Xdatcar. Similar to 6th line in
vasp 5+ Xdatcar.
"""
syms = [site.specie.symbol for site in self.structures[0]]
... |
Sequence of number of sites of each type associated with the Poscar.
Similar to 7th line in vasp 5+ Xdatcar.
def natoms(self):
"""
Sequence of number of sites of each type associated with the Poscar.
Similar to 7th line in vasp 5+ Xdatcar.
"""
syms = [site.specie.symbol ... |
Write Xdatcar class into a file
Args:
filename (str): Filename of output XDATCAR file.
ionicstep_start (int): Starting number of ionic step.
ionicstep_end (int): Ending number of ionic step.
def get_string(self, ionicstep_start=1,
ionicstep_end=None,
... |
calculate phonon frequencies
def get_phonon_frequencies(self):
"""calculate phonon frequencies"""
# TODO: the following is most likely not correct or suboptimal
# hence for demonstration purposes only
frequencies = []
for k, v0 in self.data.iteritems():
for v1 in v0.... |
Helper function that determines maximum number of b vectors for
each direction.
This algorithm is adapted from WaveTrans (see Class docstring). There
should be no reason for this function to be called outside of
initialization.
def _generate_nbmax(self):
"""
Helper func... |
Helper function to generate G-points based on nbmax.
This function iterates over possible G-point values and determines
if the energy is less than G_{cut}. Valid values are appended to
the output array. This function should not be called outside of
initialization.
Args:
... |
r"""
Evaluates the wavefunction for a given position, r.
The wavefunction is given by the k-point and band. It is evaluated
at the given position by summing over the components. Formally,
\psi_n^k (r) = \sum_{i=1}^N c_i^{n,k} \exp (i (k + G_i^{n,k}) \cdot r)
where \psi_n^k is ... |
Places the coefficients of a wavefunction onto an fft mesh.
Once the mesh has been obtained, a discrete fourier transform can be
used to obtain real-space evaluation of the wavefunction. The output
of this function can be passed directly to numpy's fft function. For
example:
... |
Generates a Chgcar object, which is the charge density of the specified
wavefunction.
This function generates a Chgcar object with the charge density of the
wavefunction specified by band and kpoint (and spin, if the WAVECAR
corresponds to a spin-polarized calculation). The phase tag is... |
Method returning a numpy array with elements
[cdum_x_real, cdum_x_imag, cdum_y_real, cdum_y_imag, cdum_z_real, cdum_z_imag]
between bands band_i and band_j (vasp 1-based indexing) for all kpoints.
Args:
band_i (Integer): Index of band i
band_j (Integer): Index of band ... |
Method returning a value
between bands band_i and band_j for k-point index, spin-channel and cartesian direction.
Args:
band_i (Integer): Index of band i
band_j (Integer): Index of band j
kpoint (Integer): Index of k-point
spin (Integer): Index of spin-c... |
Creates a symmetry operation from a rotation matrix and a translation
vector.
Args:
rotation_matrix (3x3 array): Rotation matrix.
translation_vec (3x1 array): Translation vector.
tol (float): Tolerance to determine if rotation matrix is valid.
Returns:
... |
Apply the operation on a point.
Args:
point: Cartesian coordinate.
Returns:
Coordinates of point after operation.
def operate(self, point):
"""
Apply the operation on a point.
Args:
point: Cartesian coordinate.
Returns:
... |
Apply the operation on a list of points.
Args:
points: List of Cartesian coordinates
Returns:
Numpy array of coordinates after operation
def operate_multi(self, points):
"""
Apply the operation on a list of points.
Args:
points: List of Car... |
Applies rotation portion to a tensor. Note that tensor has to be in
full form, not the Voigt form.
Args:
tensor (numpy array): a rank n tensor
Returns:
Transformed tensor.
def transform_tensor(self, tensor):
"""
Applies rotation portion to a tensor. Not... |
Checks if two points are symmetrically related.
Args:
point_a (3x1 array): First point.
point_b (3x1 array): Second point.
tol (float): Absolute tolerance for checking distance.
Returns:
True if self.operate(point_a) == point_b or vice versa.
def are_sy... |
Returns inverse of transformation.
def inverse(self):
"""
Returns inverse of transformation.
"""
invr = np.linalg.inv(self.affine_matrix)
return SymmOp(invr) |
Generates a SymmOp for a rotation about a given axis plus translation.
Args:
axis: The axis of rotation in cartesian space. For example,
[1, 0, 0]indicates rotation about x-axis.
angle (float): Angle of rotation.
angle_in_radians (bool): Set to True if angles... |
Generates a SymmOp for a rotation about a given axis through an
origin.
Args:
origin (3x1 array): The origin which the axis passes through.
axis (3x1 array): The axis of rotation in cartesian space. For
example, [1, 0, 0]indicates rotation about x-axis.
... |
Returns reflection symmetry operation.
Args:
normal (3x1 array): Vector of the normal to the plane of
reflection.
origin (3x1 array): A point in which the mirror plane passes
through.
Returns:
SymmOp for the reflection about the plane... |
Inversion symmetry operation about axis.
Args:
origin (3x1 array): Origin of the inversion operation. Defaults
to [0, 0, 0].
Returns:
SymmOp representing an inversion operation about the origin.
def inversion(origin=(0, 0, 0)):
"""
Inversion sym... |
Returns a roto-reflection symmetry operation
Args:
axis (3x1 array): Axis of rotation / mirror normal
angle (float): Angle in degrees
origin (3x1 array): Point left invariant by roto-reflection.
Defaults to (0, 0, 0).
Return:
Roto-reflect... |
Returns a string of the form 'x, y, z', '-x, -y, z',
'-y+1/2, x+1/2, z+1/2', etc. Only works for integer rotation matrices
def as_xyz_string(self):
"""
Returns a string of the form 'x, y, z', '-x, -y, z',
'-y+1/2, x+1/2, z+1/2', etc. Only works for integer rotation matrices
"""
... |
Args:
xyz_string: string of the form 'x, y, z', '-x, -y, z',
'-2y+1/2, 3x+1/2, z-y+1/2', etc.
Returns:
SymmOp
def from_xyz_string(xyz_string):
"""
Args:
xyz_string: string of the form 'x, y, z', '-x, -y, z',
'-2y+1/2, 3x+1/2, z... |
Apply time reversal operator on the magnetic moment. Note that
magnetic moments transform as axial vectors, not polar vectors.
See 'Symmetry and magnetic structures', Rodríguez-Carvajal and
Bourée for a good discussion. DOI: 10.1051/epjconf/20122200010
Args:
magmom: Magnet... |
Initialize a MagSymmOp from a SymmOp and time reversal operator.
Args:
symmop (SymmOp): SymmOp
time_reversal (int): Time reversal operator, +1 or -1.
Returns:
MagSymmOp object
def from_symmop(cls, symmop, time_reversal):
"""
Initiali... |
Creates a symmetry operation from a rotation matrix, translation
vector and time reversal operator.
Args:
rotation_matrix (3x3 array): Rotation matrix.
translation_vec (3x1 array): Translation vector.
time_reversal (int): Time reversal operator, +1 or -1.
... |
Args:
xyz_string: string of the form 'x, y, z, +1', '-x, -y, z, -1',
'-2y+1/2, 3x+1/2, z-y+1/2, +1', etc.
Returns:
MagSymmOp object
def from_xyzt_string(xyzt_string):
"""
Args:
xyz_string: string of the form 'x, y, z, +1', '-x, -y, z, -1',
... |
Returns a string of the form 'x, y, z, +1', '-x, -y, z, -1',
'-y+1/2, x+1/2, z+1/2, +1', etc. Only works for integer rotation matrices
def as_xyzt_string(self):
"""
Returns a string of the form 'x, y, z, +1', '-x, -y, z, -1',
'-y+1/2, x+1/2, z+1/2, +1', etc. Only works for integer rotat... |
Very flexible arguments to support many types of potential setups.
Users should use more friendly static methods unless they need the
flexibility.
Args:
mol: Input molecule
charge: Charge of the molecule. If None, charge on molecule is
used. Defaults to N... |
A class method for quickly creating DFT tasks with optional
cosmo parameter .
Args:
mol: Input molecule
xc: Exchange correlation to use.
\\*\\*kwargs: Any of the other kwargs supported by NwTask. Note the
theory is always "dft" for a dft task.
def df... |
Read an NwInput from a string. Currently tested to work with
files generated from this class itself.
Args:
string_input: string_input to parse.
Returns:
NwInput object
def from_string(cls, string_input):
"""
Read an NwInput from a string. Currently test... |
Parses TDDFT roots. Adapted from nw_spectrum.py script.
Returns:
{
"singlet": [
{
"energy": float,
"osc_strength: float
}
],
"triplet": [
{
... |
Generate an excitation spectra from the singlet roots of TDDFT
calculations.
Args:
width (float): Width for Gaussian smearing.
npoints (int): Number of energy points. More points => smoother
curve.
Returns:
(ExcitationSpectrum) which can be p... |
Returns a formula string, with elements sorted by electronegativity,
e.g., Li4 Fe4 P4 O16.
def formula(self):
"""
Returns a formula string, with elements sorted by electronegativity,
e.g., Li4 Fe4 P4 O16.
"""
formula = super().formula
chg_str = ""
if self... |
An anonymized formula. Appends charge to the end
of anonymized composition
def anonymized_formula(self):
"""
An anonymized formula. Appends charge to the end
of anonymized composition
"""
anon_formula = super().anonymized_formula
chg = self._charge
chg_st... |
Returns a reduced formula string with appended charge.
def reduced_formula(self):
"""
Returns a reduced formula string with appended charge.
"""
reduced_formula = super().reduced_formula
charge = self._charge / self.get_reduced_composition_and_factor()[1]
if charge > 0:
... |
Returns a reduced formula string with appended charge
def alphabetical_formula(self):
"""
Returns a reduced formula string with appended charge
"""
alph_formula = super().alphabetical_formula
chg_str = ""
if self.charge > 0:
chg_str = " +" + formula_double_fo... |
Generates an ion object from a dict created by as_dict().
Args:
d:
{symbol: amount} dict.
def from_dict(cls, d):
"""
Generates an ion object from a dict created by as_dict().
Args:
d:
{symbol: amount} dict.
"""
ch... |
Returns:
dict with element symbol and reduced amount e.g.,
{"Fe": 2.0, "O":3.0}.
def to_reduced_dict(self):
"""
Returns:
dict with element symbol and reduced amount e.g.,
{"Fe": 2.0, "O":3.0}.
"""
d = self.composition.to_reduced_dict
... |
Returns the cost of the best assignment
def min_cost(self):
"""
Returns the cost of the best assignment
"""
if self._min_cost:
return self._min_cost
self._min_cost = np.sum(self.c[np.arange(self.nx), self.solution])
return self._min_cost |
Column reduction and reduction transfer steps from LAPJV algorithm
def _column_reduction(self):
"""
Column reduction and reduction transfer steps from LAPJV algorithm
"""
#assign each column to its lowest cost row, ensuring that only row
#or column is assigned once
i1, j... |
Augmenting row reduction step from LAPJV algorithm
def _augmenting_row_reduction(self):
"""
Augmenting row reduction step from LAPJV algorithm
"""
unassigned = np.where(self._x == -1)[0]
for i in unassigned:
for _ in range(self.c.size):
# Time in this... |
Updates the reduced costs with the values from the
dual solution
def _update_cred(self):
"""
Updates the reduced costs with the values from the
dual solution
"""
ui = self.c[self._inds, self._x] - self._v[self._x]
self.cred = self.c - ui[:, None] - self._v[None, ... |
Finds a minimum cost path and adds it to the matching
def _augment(self):
"""
Finds a minimum cost path and adds it to the matching
"""
#build a minimum cost tree
_pred, _ready, istar, j, mu = self._build_tree()
#update prices
self._v[_ready] += self._d[_ready] ... |
Builds the tree finding an augmenting path. Alternates along
matched and unmatched edges between X and Y. The paths are
stored in _pred (new predecessor of nodes in Y), and
self._x and self._y
def _build_tree(self):
"""
Builds the tree finding an augmenting path. Alternates alon... |
Decorator for methods that add MSON serializations keys
to the dictionary. See documentation of MSON for more details
def pmg_serialize(method):
"""
Decorator for methods that add MSON serializations keys
to the dictionary. See documentation of MSON for more details
"""
@functools.wraps(method... |
Serialize obj as a JSON formatted stream to the given filename (
pretty printing version)
def json_pretty_dump(obj, filename):
"""
Serialize obj as a JSON formatted stream to the given filename (
pretty printing version)
"""
with open(filename, "wt") as fh:
json.dump(obj, fh, indent=4, ... |
Instead of pickling as a regular class instance, we emit a
persistent ID.
def persistent_id(self, obj):
"""Instead of pickling as a regular class instance, we emit a
persistent ID."""
if isinstance(obj, Element):
# Here, our persistent ID is simply a tuple, containing a tag ... |
This method is invoked whenever a persistent ID is encountered.
Here, pid is the tuple returned by PmgPickler.
def persistent_load(self, pid):
"""
This method is invoked whenever a persistent ID is encountered.
Here, pid is the tuple returned by PmgPickler.
"""
try:
... |
Get value from dict using MongoDB dot-separated path semantics.
For example:
>>> assert mongo_getattr({'a': {'b': 1}, 'x': 2}, 'a.b') == 1
>>> assert mongo_getattr({'a': {'b': 1}, 'x': 2}, 'x') == 2
>>> assert mongo_getattr({'a': {'b': 1}, 'x': 2}, 'a.b.c') is None
:param rec: mongodb document
... |
Scan a nested dict d, and return the first value associated to the given key.
Returns None if key is not found.
>>> d = {0: 1, 1: {"hello": {"world": {None: [1,2,3]}}}, "foo": [{"bar": 1}, {"color": "red"}]}
>>> assert scan_nestdict(d, 1) == {"hello": {"world": {None: [1,2,3]}}}
>>> assert scan_nestdic... |
Set the name of the collection, return old value
def set_collection_name(self, value):
"""Set the name of the collection, return old value"""
old = self.collection
self.collection = str(value)
return old |
Establish a connection with the database.
Returns MongoDb collection
def get_collection(self, **kwargs):
"""
Establish a connection with the database.
Returns MongoDb collection
"""
from pymongo import MongoClient
if self.host and self.port:
client... |
Checks for a transformations.json* file and returns the history.
def _get_transformation_history(path):
"""
Checks for a transformations.json* file and returns the history.
"""
trans_json = glob.glob(os.path.join(path, "transformations.json*"))
if trans_json:
try:
with zopen(tra... |
Obtains a SpaceGroup name from its international number.
Args:
int_number (int): International number.
hexagonal (bool): For rhombohedral groups, whether to return the
hexagonal setting (default) or rhombohedral setting.
Returns:
(str) Spacegroup symbol
def sg_symbol_from_... |
Extremely efficient nd-array comparison using numpy's broadcasting. This
function checks if a particular array a, is present in a list of arrays.
It works for arrays of any size, e.g., even matrix searches.
Args:
array_list ([array]): A list of arrays to compare to.
a (array): The test arra... |
True if this group is a subgroup of the supplied group.
Args:
supergroup (SymmetryGroup): Supergroup to test.
Returns:
True if this group is a subgroup of the supplied group.
def is_subgroup(self, supergroup):
"""
True if this group is a subgroup of the supplie... |
True if this group is a supergroup of the supplied group.
Args:
subgroup (SymmetryGroup): Subgroup to test.
Returns:
True if this group is a supergroup of the supplied group.
def is_supergroup(self, subgroup):
"""
True if this group is a supergroup of the suppl... |
Strips whitespace, carriage returns and empty lines from a list of strings.
Args:
string_list: List of strings
remove_empty_lines: Set to True to skip lines which are empty after
stripping.
Returns:
List of clean strings with no whitespaces.
def clean_lines(string_list, re... |
Small awk-mimicking search routine.
'file' is file to search through.
'search' is the "search program", a list of lists/tuples with 3 elements;
i.e. [[regex,test,run],[regex,test,run],...]
'results' is a an object that your search program will have access to for
storing results.
Here regex is ... |
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