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train | FermiDos.get_fermi | Finds the fermi level at which the doping concentration at the given
temperature (T) is equal to c. A greedy algorithm is used where the
relative error is minimized by calculating the doping at a grid which
is continuously become finer.
Args:
c (float): doping concentration.... | pymatgen/electronic_structure/dos.py | def get_fermi(self, c, T, rtol=0.01, nstep=50, step=0.1, precision=8):
"""
Finds the fermi level at which the doping concentration at the given
temperature (T) is equal to c. A greedy algorithm is used where the
relative error is minimized by calculating the doping at a grid which
... | def get_fermi(self, c, T, rtol=0.01, nstep=50, step=0.1, precision=8):
"""
Finds the fermi level at which the doping concentration at the given
temperature (T) is equal to c. A greedy algorithm is used where the
relative error is minimized by calculating the doping at a grid which
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train | CompleteDos.get_site_orbital_dos | Get the Dos for a particular orbital of a particular site.
Args:
site: Site in Structure associated with CompleteDos.
orbital: Orbital in the site.
Returns:
Dos containing densities for orbital of site. | pymatgen/electronic_structure/dos.py | def get_site_orbital_dos(self, site, orbital):
"""
Get the Dos for a particular orbital of a particular site.
Args:
site: Site in Structure associated with CompleteDos.
orbital: Orbital in the site.
Returns:
Dos containing densities for orbital of si... | def get_site_orbital_dos(self, site, orbital):
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Get the Dos for a particular orbital of a particular site.
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site: Site in Structure associated with CompleteDos.
orbital: Orbital in the site.
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train | CompleteDos.get_site_dos | Get the total Dos for a site (all orbitals).
Args:
site: Site in Structure associated with CompleteDos.
Returns:
Dos containing summed orbital densities for site. | pymatgen/electronic_structure/dos.py | def get_site_dos(self, site):
"""
Get the total Dos for a site (all orbitals).
Args:
site: Site in Structure associated with CompleteDos.
Returns:
Dos containing summed orbital densities for site.
"""
site_dos = functools.reduce(add_densities, se... | def get_site_dos(self, site):
"""
Get the total Dos for a site (all orbitals).
Args:
site: Site in Structure associated with CompleteDos.
Returns:
Dos containing summed orbital densities for site.
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train | CompleteDos.get_site_spd_dos | Get orbital projected Dos of a particular site
Args:
site: Site in Structure associated with CompleteDos.
Returns:
dict of {orbital: Dos}, e.g. {"s": Dos object, ...} | pymatgen/electronic_structure/dos.py | def get_site_spd_dos(self, site):
"""
Get orbital projected Dos of a particular site
Args:
site: Site in Structure associated with CompleteDos.
Returns:
dict of {orbital: Dos}, e.g. {"s": Dos object, ...}
"""
spd_dos = dict()
for orb, pdo... | def get_site_spd_dos(self, site):
"""
Get orbital projected Dos of a particular site
Args:
site: Site in Structure associated with CompleteDos.
Returns:
dict of {orbital: Dos}, e.g. {"s": Dos object, ...}
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spd_dos = dict()
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train | CompleteDos.get_site_t2g_eg_resolved_dos | Get the t2g, eg projected DOS for a particular site.
Args:
site: Site in Structure associated with CompleteDos.
Returns:
A dict {"e_g": Dos, "t2g": Dos} containing summed e_g and t2g DOS
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"""
Get the t2g, eg projected DOS for a particular site.
Args:
site: Site in Structure associated with CompleteDos.
Returns:
A dict {"e_g": Dos, "t2g": Dos} containing summed e_g and t2g DOS
for the site.... | def get_site_t2g_eg_resolved_dos(self, site):
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Get the t2g, eg projected DOS for a particular site.
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site: Site in Structure associated with CompleteDos.
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train | CompleteDos.get_spd_dos | Get orbital projected Dos.
Returns:
dict of {orbital: Dos}, e.g. {"s": Dos object, ...} | pymatgen/electronic_structure/dos.py | def get_spd_dos(self):
"""
Get orbital projected Dos.
Returns:
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"""
spd_dos = {}
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orbital_type = _get_orb_type... | def get_spd_dos(self):
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Get orbital projected Dos.
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"""
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train | CompleteDos.get_element_dos | Get element projected Dos.
Returns:
dict of {Element: Dos} | pymatgen/electronic_structure/dos.py | def get_element_dos(self):
"""
Get element projected Dos.
Returns:
dict of {Element: Dos}
"""
el_dos = {}
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el = site.specie
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... | def get_element_dos(self):
"""
Get element projected Dos.
Returns:
dict of {Element: Dos}
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el_dos = {}
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train | CompleteDos.spin_polarization | Calculates spin polarization at Fermi level.
See Sanvito et al., doi: 10.1126/sciadv.1602241 for
an example usage.
:return (float): spin polarization in range [0, 1],
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"""
Calculates spin polarization at Fermi level.
See Sanvito et al., doi: 10.1126/sciadv.1602241 for
an example usage.
:return (float): spin polarization in range [0, 1],
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"""
Calculates spin polarization at Fermi level.
See Sanvito et al., doi: 10.1126/sciadv.1602241 for
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train | CompleteDos.as_dict | Json-serializable dict representation of CompleteDos. | pymatgen/electronic_structure/dos.py | def as_dict(self):
"""
Json-serializable dict representation of CompleteDos.
"""
d = {"@module": self.__class__.__module__,
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Json-serializable dict representation of CompleteDos.
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train | LobsterCompleteDos.get_element_spd_dos | Get element and spd projected Dos
Args:
el: Element in Structure.composition associated with LobsterCompleteDos
Returns:
dict of {Element: {"S": densities, "P": densities, "D": densities}} | pymatgen/electronic_structure/dos.py | def get_element_spd_dos(self, el):
"""
Get element and spd projected Dos
Args:
el: Element in Structure.composition associated with LobsterCompleteDos
Returns:
dict of {Element: {"S": densities, "P": densities, "D": densities}}
"""
el = get_el_s... | def get_element_spd_dos(self, el):
"""
Get element and spd projected Dos
Args:
el: Element in Structure.composition associated with LobsterCompleteDos
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dict of {Element: {"S": densities, "P": densities, "D": densities}}
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train | LobsterCompleteDos.from_dict | Returns: CompleteDos object from dict representation. | pymatgen/electronic_structure/dos.py | def from_dict(cls, d):
"""
Returns: CompleteDos object from dict representation.
"""
tdos = Dos.from_dict(d)
struct = Structure.from_dict(d["structure"])
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for i in range(len(d["pdos"])):
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orb_dos = {}
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"""
Returns: CompleteDos object from dict representation.
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tdos = Dos.from_dict(d)
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train | AflowPrototypeMatcher.get_prototypes | Get prototype(s) structures for a given
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Get prototype(s) structures for a given
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your work, please cite the appropriate
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Mehl, M. J., Hicks, D., Toher, C., Levy, O.,
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Get prototype(s) structures for a given
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train | read_pattern | General pattern reading on an input string
Args:
text_str (str): the input string to search for patterns
patterns (dict): A dict of patterns, e.g.,
{"energy": r"energy\\(sigma->0\\)\\s+=\\s+([\\d\\-.]+)"}.
terminate_on_match (bool): Whether to terminate when ... | pymatgen/io/qchem/utils.py | def read_pattern(text_str, patterns, terminate_on_match=False,
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"""
General pattern reading on an input string
Args:
text_str (str): the input string to search for patterns
patterns (dict): A dict of patterns, e.g.,
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"""
General pattern reading on an input string
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text_str (str): the input string to search for patterns
patterns (dict): A dict of patterns, e.g.,
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train | read_table_pattern | Parse table-like data. A table composes of three parts: header,
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Args:
text_str (str): the input string to search for patterns
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Parse table-like data. A table c... | def read_table_pattern(text_str,
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train | process_parsed_coords | Takes a set of parsed coordinates, which come as an array of strings,
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"""
Generates the transformation matricies that convert a set of 2D
vectors into a super lattice of integer area multiple as proven
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Cassels, John William Scott. An introduction to the geometry of
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train | vec_angle | Calculate angle between two vectors | pymatgen/analysis/substrate_analyzer.py | def vec_angle(a, b):
"""
Calculate angle between two vectors
"""
cosang = np.dot(a, b)
sinang = fast_norm(np.cross(a, b))
return np.arctan2(sinang, cosang) | def vec_angle(a, b):
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Calculate angle between two vectors
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train | reduce_vectors | Generate independent and unique basis vectors based on the
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"""
Generate independent and unique basis vectors based on the
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"""
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if fast_norm(a) > fast_norm(b):
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Generate independent and unique basis vectors based on the
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train | ZSLGenerator.is_same_vectors | Determine if two sets of vectors are the same within length and angle
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Args:
vec_set1(array[array]): an array of two vectors
vec_set2(array[array]): second array of two vectors | pymatgen/analysis/substrate_analyzer.py | def is_same_vectors(self, vec_set1, vec_set2):
"""
Determine if two sets of vectors are the same within length and angle
tolerances
Args:
vec_set1(array[array]): an array of two vectors
vec_set2(array[array]): second array of two vectors
"""
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"""
Determine if two sets of vectors are the same within length and angle
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vec_set1(array[array]): an array of two vectors
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train | ZSLGenerator.generate_sl_transformation_sets | Generates transformation sets for film/substrate pair given the
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Args:
film_area(int): the unit cell area for the film
... | pymatgen/analysis/substrate_analyzer.py | def generate_sl_transformation_sets(self, film_area, substrate_area):
"""
Generates transformation sets for film/substrate pair given the
area of the unit cell area for the film and substrate. The
transformation sets map the film and substrate unit cells to super
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"""
Applies the transformation_sets to the film and substrate vectors
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Applies the transformation_sets to the film and substrate vectors
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train | ZSLGenerator.match_as_dict | Returns dict which contains ZSL match
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film_miller(array)
substrate_miller(array) | pymatgen/analysis/substrate_analyzer.py | def match_as_dict(self, film_sl_vectors, substrate_sl_vectors, film_vectors, substrate_vectors, match_area):
"""
Returns dict which contains ZSL match
Args:
film_miller(array)
substrate_miller(array)
"""
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d["film_sl_vecs"] = np.asarray(film_... | def match_as_dict(self, film_sl_vectors, substrate_sl_vectors, film_vectors, substrate_vectors, match_area):
"""
Returns dict which contains ZSL match
Args:
film_miller(array)
substrate_miller(array)
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train | SubstrateAnalyzer.generate_surface_vectors | Generates the film/substrate slab combinations for a set of given
miller indicies
Args:
film_millers(array): all miller indices to generate slabs for
film
substrate_millers(array): all miller indicies to generate slabs
for substrate | pymatgen/analysis/substrate_analyzer.py | def generate_surface_vectors(self, film_millers, substrate_millers):
"""
Generates the film/substrate slab combinations for a set of given
miller indicies
Args:
film_millers(array): all miller indices to generate slabs for
film
substrate_millers(a... | def generate_surface_vectors(self, film_millers, substrate_millers):
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Generates the film/substrate slab combinations for a set of given
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film_millers(array): all miller indices to generate slabs for
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train | SubstrateAnalyzer.calculate | Finds all topological matches for the substrate and calculates elastic
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Args:
film(Structure): conventional standard structure for the film
substrate(Structure): convent... | pymatgen/analysis/substrate_analyzer.py | def calculate(self, film, substrate, elasticity_tensor=None,
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"""
Finds all topological matches for the substrate and calculates elastic
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Finds all topological matches for the substrate and calculates elastic
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train | SubstrateAnalyzer.calculate_3D_elastic_energy | Calculates the multi-plane elastic energy. Returns 999 if no elastic
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Args:
film(Structure): conventional standard structure for the film
match(dictionary) : match dictionary from substrate analyzer
elasticity_tensor(ElasticTensor): elasticity... | pymatgen/analysis/substrate_analyzer.py | def calculate_3D_elastic_energy(self, film, match, elasticity_tensor=None,
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"""
Calculates the multi-plane elastic energy. Returns 999 if no elastic
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Args:
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Calculates the multi-plane elastic energy. Returns 999 if no elastic
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train | XYZ._from_frame_string | Convert a single frame XYZ string to a molecule | pymatgen/io/xyz.py | def _from_frame_string(contents):
"""
Convert a single frame XYZ string to a molecule
"""
lines = contents.split("\n")
num_sites = int(lines[0])
coords = []
sp = []
coord_patt = re.compile(
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Convert a single frame XYZ string to a molecule
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train | XYZ.from_string | Creates XYZ object from a string.
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contents: String representing an XYZ file.
Returns:
XYZ object | pymatgen/io/xyz.py | def from_string(contents):
"""
Creates XYZ object from a string.
Args:
contents: String representing an XYZ file.
Returns:
XYZ object
"""
if contents[-1] != "\n":
contents += "\n"
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Creates XYZ object from a string.
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contents: String representing an XYZ file.
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train | ChemicalShielding.principal_axis_system | Returns a chemical shielding tensor aligned to the principle axis system
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"""
Returns a chemical shielding tensor aligned to the principle axis system
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train | ChemicalShielding.haeberlen_values | Returns: the Chemical shielding tensor in Haeberlen Notation | pymatgen/analysis/nmr.py | def haeberlen_values(self):
"""
Returns: the Chemical shielding tensor in Haeberlen Notation
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pas=self.principal_axis_system
sigma_iso=pas.trace() / 3
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sigmas=sorted(sigmas, key=lambda x: np.abs(x - sigma_iso))
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Returns: the Chemical shielding tensor in Haeberlen Notation
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pas=self.principal_axis_system
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train | ChemicalShielding.mehring_values | Returns: the Chemical shielding tensor in Mehring Notation | pymatgen/analysis/nmr.py | def mehring_values(self):
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Returns: the Chemical shielding tensor in Mehring Notation
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train | ChemicalShielding.maryland_values | Returns: the Chemical shielding tensor in Maryland Notation | pymatgen/analysis/nmr.py | def maryland_values(self):
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Returns: the Chemical shielding tensor in Maryland Notation
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Returns: the Chemical shielding tensor in Maryland Notation
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train | ElectricFieldGradient.principal_axis_system | Returns a electric field gradient tensor aligned to the principle axis system so that only the 3 diagnol components are non-zero | pymatgen/analysis/nmr.py | def principal_axis_system(self):
"""
Returns a electric field gradient tensor aligned to the principle axis system so that only the 3 diagnol components are non-zero
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train | ElectricFieldGradient.asymmetry | Asymmetry of the electric field tensor defined as:
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Asymmetry of the electric field tensor defined as:
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"""
diags=np.diag(self.principal_axis_system)
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train | ElectricFieldGradient.coupling_constant | Computes the couplling constant C_q as defined in:
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"""
Computes the couplling constant C_q as defined in:
Wasylishen R E, Ashbrook S E, Wimperis S. NMR of quadrupolar nuclei
in solid materials[M]. John Wiley & Sons, 2012. (Chapter 3.2)
C_q for a specific atom type for this electric fi... | def coupling_constant(self, specie):
"""
Computes the couplling constant C_q as defined in:
Wasylishen R E, Ashbrook S E, Wimperis S. NMR of quadrupolar nuclei
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train | JahnTellerAnalyzer.get_analysis_and_structure | Obtain an analysis of a given structure and if it may be Jahn-Teller
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false negatives (false positives are preferred).
:param structure: input structure
:param calculate_valences (bool): whether to attempt to calculate ... | pymatgen/analysis/magnetism/jahnteller.py | def get_analysis_and_structure(self,
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guesstimate_spin=False,
op_threshold=0.1):
"""
Obtain an analysis of a given structure and ... | def get_analysis_and_structure(self,
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train | JahnTellerAnalyzer.get_magnitude_of_effect_from_species | Get magnitude of Jahn-Teller effect from provided species, spin state and motife.
:param species: e.g. Fe2+
:param spin_state (str): "high" or "low"
:param motif (str): "oct" or "tet"
:return (str): | pymatgen/analysis/magnetism/jahnteller.py | def get_magnitude_of_effect_from_species(self, species, spin_state, motif):
"""
Get magnitude of Jahn-Teller effect from provided species, spin state and motife.
:param species: e.g. Fe2+
:param spin_state (str): "high" or "low"
:param motif (str): "oct" or "tet"
:retur... | def get_magnitude_of_effect_from_species(self, species, spin_state, motif):
"""
Get magnitude of Jahn-Teller effect from provided species, spin state and motife.
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train | JahnTellerAnalyzer.get_magnitude_of_effect_from_spin_config | Roughly, the magnitude of Jahn-Teller distortion will be:
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* in tetrahedral environments always weaker
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"""
Roughly, the magnitude of Jahn-Teller distortion will be:
* in octahedral environments, strong if e_g orbitals
unevenly occupied but weak if t_2g orbitals unevenly
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"""
Roughly, the magnitude of Jahn-Teller distortion will be:
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train | JahnTellerAnalyzer._estimate_spin_state | Simple heuristic to estimate spin state. If magnetic moment
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we assign it that state. If we only have data for one spin
state then that's the one we use (e.g. we assume all tetrahedral
complexes are high-spin, since this is t... | pymatgen/analysis/magnetism/jahnteller.py | def _estimate_spin_state(species, motif, known_magmom):
"""
Simple heuristic to estimate spin state. If magnetic moment
is sufficiently close to that predicted for a given spin state,
we assign it that state. If we only have data for one spin
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"""
Simple heuristic to estimate spin state. If magnetic moment
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train | JahnTellerAnalyzer.mu_so | Calculates the spin-only magnetic moment for a
given species. Only supports transition metals.
:param species: str or Species
:param motif: "oct" or "tet"
:param spin_state: "high" or "low"
:return: spin-only magnetic moment in Bohr magnetons | pymatgen/analysis/magnetism/jahnteller.py | def mu_so(species, motif, spin_state):
"""
Calculates the spin-only magnetic moment for a
given species. Only supports transition metals.
:param species: str or Species
:param motif: "oct" or "tet"
:param spin_state: "high" or "low"
:return: spin-only magnetic mo... | def mu_so(species, motif, spin_state):
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Calculates the spin-only magnetic moment for a
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train | get_conversion_factor | Conversion factor to convert between cm^2/s diffusivity measurements and
mS/cm conductivity measurements based on number of atoms of diffusing
species. Note that the charge is based on the oxidation state of the
species (where available), or else the number of valence electrons
(usually a good guess, es... | pymatgen/analysis/diffusion_analyzer.py | def get_conversion_factor(structure, species, temperature):
"""
Conversion factor to convert between cm^2/s diffusivity measurements and
mS/cm conductivity measurements based on number of atoms of diffusing
species. Note that the charge is based on the oxidation state of the
species (where available... | def get_conversion_factor(structure, species, temperature):
"""
Conversion factor to convert between cm^2/s diffusivity measurements and
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species. Note that the charge is based on the oxidation state of the
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train | fit_arrhenius | Returns Ea, c, standard error of Ea from the Arrhenius fit:
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Args:
temps ([float]): A sequence of temperatures. units: K
diffusivities ([float]): A sequence of diffusivities (e.g.,
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"""
Returns Ea, c, standard error of Ea from the Arrhenius fit:
D = c * exp(-Ea/kT)
Args:
temps ([float]): A sequence of temperatures. units: K
diffusivities ([float]): A sequence of diffusivities (e.g.,
from DiffusionAnalyzer.dif... | def fit_arrhenius(temps, diffusivities):
"""
Returns Ea, c, standard error of Ea from the Arrhenius fit:
D = c * exp(-Ea/kT)
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temps ([float]): A sequence of temperatures. units: K
diffusivities ([float]): A sequence of diffusivities (e.g.,
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train | get_extrapolated_diffusivity | Returns (Arrhenius) extrapolated diffusivity at new_temp
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temps ([float]): A sequence of temperatures. units: K
diffusivities ([float]): A sequence of diffusivities (e.g.,
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Returns (Arrhenius) extrapolated diffusivity at new_temp
Args:
temps ([float]): A sequence of temperatures. units: K
diffusivities ([float]): A sequence of diffusivities (e.g.,
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Returns (Arrhenius) extrapolated diffusivity at new_temp
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temps ([float]): A sequence of temperatures. units: K
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train | get_extrapolated_conductivity | Returns extrapolated mS/cm conductivity.
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diffusivities ([float]): A sequence of diffusivities (e.g.,
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Returns extrapolated mS/cm conductivity.
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temps ([float]): A sequence of temperatures. units: K
diffusivities ([float]): A sequence of diffusivities (e.g.,
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temps ([float]): A sequence of temperatures. units: K
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train | get_arrhenius_plot | Returns an Arrhenius plot.
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diffusivity_errors ([float]): A sequence of errors for the
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"""
Returns an Arrhenius plot.
Args:
temps ([float]): A sequence of temperatures.
diffusivities ([float]): A sequence of diffusivities (e.g.,
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temps ([float]): A sequence of temperatures.
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train | DiffusionAnalyzer.get_drift_corrected_structures | Returns an iterator for the drift-corrected structures. Use of
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Args:
start, stop, step (int): applies a start/stop/step to the iterator.
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Returns an iterator for the drift-corrected structures. Use of
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Returns an iterator for the drift-corrected structures. Use of
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train | DiffusionAnalyzer.get_summary_dict | Provides a summary of diffusion information.
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include_msd_t (bool): Whether to include mean square displace and
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include_msd_t (bool): Whether to include mean square charge displace and
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"""
Provides a summary of diffusion information.
Args:
include_msd_t (bool): Whether to include mean square displace and
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Provides a summary of diffusion information.
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include_msd_t (bool): Whether to include mean square displace and
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train | DiffusionAnalyzer.get_framework_rms_plot | Get the plot of rms framework displacement vs time. Useful for checking
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plt (matplotlib.pyplot)... | pymatgen/analysis/diffusion_analyzer.py | def get_framework_rms_plot(self, plt=None, granularity=200,
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"""
Get the plot of rms framework displacement vs time. Useful for checking
for melting, especially if framework atoms can move via paddle-wheel
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train | DiffusionAnalyzer.get_msd_plot | Get the plot of the smoothed msd vs time graph. Useful for
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plt: A plot object. Defaults to None, which means one will be
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mode (str): Determines type of msd plot. By "species", "sites",
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plt: A plot object. Defaults to None, which means one will be
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plt: A plot object. Defaults to None, which means one will be
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train | DiffusionAnalyzer.export_msdt | Writes MSD data to a csv file that can be easily plotted in other
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Args:
filename (str): Filename. Supported formats are csv and dat. If
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"""
Writes MSD data to a csv file that can be easily plotted in other
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Args:
filename (str): Filename. Supported formats are csv and dat. If
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train | DiffusionAnalyzer.from_structures | Convenient constructor that takes in a list of Structure objects to
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structures ([Structure]): list of Structure objects (must be
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"""
Convenient constructor that takes in a list of Structure objects to
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train | DiffusionAnalyzer.from_vaspruns | Convenient constructor that takes in a list of Vasprun objects to
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train | DiffusionAnalyzer.from_files | Convenient constructor that takes in a list of vasprun.xml paths to
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you may have done sequential VAS... | pymatgen/analysis/diffusion_analyzer.py | def from_files(cls, filepaths, specie, step_skip=10, ncores=None,
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Convenient constructor that takes in a list of vasprun.xml paths to
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train | CoordinationGeometry.pauling_stability_ratio | Returns the theoretical Pauling stability ratio (rC/rA) for this environment. | pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py | def pauling_stability_ratio(self):
"""
Returns the theoretical Pauling stability ratio (rC/rA) for this environment.
"""
if self._pauling_stability_ratio is None:
if self.ce_symbol in ['S:1', 'L:2']:
self._pauling_stability_ratio = 0.0
else:
... | def pauling_stability_ratio(self):
"""
Returns the theoretical Pauling stability ratio (rC/rA) for this environment.
"""
if self._pauling_stability_ratio is None:
if self.ce_symbol in ['S:1', 'L:2']:
self._pauling_stability_ratio = 0.0
else:
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train | CoordinationGeometry.number_of_permutations | Returns the number of permutations of this coordination geometry. | pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py | def number_of_permutations(self):
"""
Returns the number of permutations of this coordination geometry.
"""
if self.permutations_safe_override:
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Returns the number of permutations of this coordination geometry.
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train | CoordinationGeometry.faces | Returns the list of faces of this coordination geometry. Each face is given as a
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Returns the list of faces of this coordination geometry. Each face is given as a
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if permutation is None:
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Returns the list of faces of this coordination geometry. Each face is given as a
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train | CoordinationGeometry.edges | Returns the list of edges of this coordination geometry. Each edge is given as a
list of its end vertices coordinates. | pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py | def edges(self, sites, permutation=None, input='sites'):
"""
Returns the list of edges of this coordination geometry. Each edge is given as a
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"""
if input == 'sites':
coords = [site.coords for site in sites]
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Returns the list of edges of this coordination geometry. Each edge is given as a
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train | CoordinationGeometry.solid_angles | Returns the list of "perfect" solid angles Each edge is given as a
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"""
Returns the list of "perfect" solid angles Each edge is given as a
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"""
if permutation is None:
return self._solid_angles
else:
return [self._solid_angles[ii] for ii... | def solid_angles(self, permutation=None):
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Returns the list of "perfect" solid angles Each edge is given as a
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train | CoordinationGeometry.get_pmeshes | Returns the pmesh strings used for jmol to show this geometry. | pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py | def get_pmeshes(self, sites, permutation=None):
"""
Returns the pmesh strings used for jmol to show this geometry.
"""
pmeshes = []
# _vertices = [site.coords for site in sites]
if permutation is None:
_vertices = [site.coords for site in sites]
else:
... | def get_pmeshes(self, sites, permutation=None):
"""
Returns the pmesh strings used for jmol to show this geometry.
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pmeshes = []
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if permutation is None:
_vertices = [site.coords for site in sites]
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train | AllCoordinationGeometries.get_geometries | Returns a list of coordination geometries with the given coordination number.
:param coordination: The coordination number of which the list of coordination geometries are returned. | pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py | def get_geometries(self, coordination=None, returned='cg'):
"""
Returns a list of coordination geometries with the given coordination number.
:param coordination: The coordination number of which the list of coordination geometries are returned.
"""
geom = list()
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Returns a list of coordination geometries with the given coordination number.
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train | AllCoordinationGeometries.get_implemented_geometries | Returns a list of the implemented coordination geometries with the given coordination number.
:param coordination: The coordination number of which the list of implemented coordination geometries
are returned. | pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py | def get_implemented_geometries(self, coordination=None, returned='cg',
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"""
Returns a list of the implemented coordination geometries with the given coordination number.
:param coordination: The coordination number of which the list o... | def get_implemented_geometries(self, coordination=None, returned='cg',
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Returns a list of the implemented coordination geometries with the given coordination number.
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train | AllCoordinationGeometries.get_not_implemented_geometries | Returns a list of the implemented coordination geometries with the given coordination number.
:param coordination: The coordination number of which the list of implemented coordination geometries
are returned. | pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py | def get_not_implemented_geometries(self, coordination=None,
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"""
Returns a list of the implemented coordination geometries with the given coordination number.
:param coordination: The coordination number of which the list of implemente... | def get_not_implemented_geometries(self, coordination=None,
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train | AllCoordinationGeometries.get_geometry_from_name | Returns the coordination geometry of the given name.
:param name: The name of the coordination geometry. | pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py | def get_geometry_from_name(self, name):
"""
Returns the coordination geometry of the given name.
:param name: The name of the coordination geometry.
"""
for gg in self.cg_list:
if gg.name == name or name in gg.alternative_names:
return gg
raise... | def get_geometry_from_name(self, name):
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train | AllCoordinationGeometries.get_geometry_from_IUPAC_symbol | Returns the coordination geometry of the given IUPAC symbol.
:param IUPAC_symbol: The IUPAC symbol of the coordination geometry. | pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py | def get_geometry_from_IUPAC_symbol(self, IUPAC_symbol):
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Returns the coordination geometry of the given IUPAC symbol.
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"""
for gg in self.cg_list:
if gg.IUPAC_symbol == IUPAC_symbol:
... | def get_geometry_from_IUPAC_symbol(self, IUPAC_symbol):
"""
Returns the coordination geometry of the given IUPAC symbol.
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for gg in self.cg_list:
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train | AllCoordinationGeometries.get_geometry_from_IUCr_symbol | Returns the coordination geometry of the given IUCr symbol.
:param IUCr_symbol: The IUCr symbol of the coordination geometry. | pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py | def get_geometry_from_IUCr_symbol(self, IUCr_symbol):
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for gg in self.cg_list:
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train | AllCoordinationGeometries.get_geometry_from_mp_symbol | Returns the coordination geometry of the given mp_symbol.
:param mp_symbol: The mp_symbol of the coordination geometry. | pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py | def get_geometry_from_mp_symbol(self, mp_symbol):
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for gg in self.cg_list:
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ra... | def get_geometry_from_mp_symbol(self, mp_symbol):
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"""
for gg in self.cg_list:
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train | AllCoordinationGeometries.is_a_valid_coordination_geometry | Checks whether a given coordination geometry is valid (exists) and whether the parameters are coherent with
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:param IUPAC_symbol:
:param IUCr_symbol:
:param name:
:param cn:
:param mp_symbol: The mp_symbol of the coordination geometry. | pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py | def is_a_valid_coordination_geometry(self, mp_symbol=None,
IUPAC_symbol=None, IUCr_symbol=None,
name=None, cn=None):
"""
Checks whether a given coordination geometry is valid (exists) and whether the parameters are coheren... | def is_a_valid_coordination_geometry(self, mp_symbol=None,
IUPAC_symbol=None, IUCr_symbol=None,
name=None, cn=None):
"""
Checks whether a given coordination geometry is valid (exists) and whether the parameters are coheren... | [
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sp2: Second species. A dict of {specie/element: amt} as per the
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sp2: Second species. A dict of {specie/element: amt} as per the
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train | StructureMatcher._get_supercell_size | Returns the supercell size, and whether the supercell should
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true, to avoid ambiguity. | pymatgen/analysis/structure_matcher.py | def _get_supercell_size(self, s1, s2):
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train | StructureMatcher._get_lattices | Yields lattices for s with lengths and angles close to the
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returned lattice will have that number of primitive cells
in it
Args:
s, target_s: Structure objects | pymatgen/analysis/structure_matcher.py | def _get_lattices(self, target_lattice, s, supercell_size=1):
"""
Yields lattices for s with lengths and angles close to the
lattice of target_s. If supercell_size is specified, the
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Yields lattices for s with lengths and angles close to the
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train | StructureMatcher._get_supercells | Computes all supercells of one structure close to the lattice of the
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yields: s1, s2, supercell_matrix, average_lattice, supercell_matrix | pymatgen/analysis/structure_matcher.py | def _get_supercells(self, struct1, struct2, fu, s1_supercell):
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yields: s1, s2, supercell_matrix, aver... | def _get_supercells(self, struct1, struct2, fu, s1_supercell):
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train | StructureMatcher._cmp_fstruct | Returns true if a matching exists between s2 and s2
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train | StructureMatcher._cart_dists | Finds a matching in cartesian space. Finds an additional
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s1, s2: numpy arrays of fractional coordinates. len(s1) >= len(s2)
avg_lattice: Lattice on which to calculate distances
mask: numpy array of booleans... | pymatgen/analysis/structure_matcher.py | def _cart_dists(self, s1, s2, avg_lattice, mask, normalization, lll_frac_tol=None):
"""
Finds a matching in cartesian space. Finds an additional
fractional translation vector to minimize RMS distance
Args:
s1, s2: numpy arrays of fractional coordinates. len(s1) >= len(s2)
... | def _cart_dists(self, s1, s2, avg_lattice, mask, normalization, lll_frac_tol=None):
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Finds a matching in cartesian space. Finds an additional
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train | StructureMatcher._get_mask | Returns mask for matching struct2 to struct1. If struct1 has sites
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aabbcc (rather than abcabc)
Returns:
mask, struct1 translation indices, struct2 translation index | pymatgen/analysis/structure_matcher.py | def _get_mask(self, struct1, struct2, fu, s1_supercell):
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train | StructureMatcher.fit | Fit two structures.
Args:
struct1 (Structure): 1st structure
struct2 (Structure): 2nd structure
Returns:
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Fit two structures.
Args:
struct1 (Structure): 1st structure
struct2 (Structure): 2nd structure
Returns:
True or False.
"""
struct1, struct2 = self._process_species([struct1, struct2])
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Fit two structures.
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struct1 (Structure): 1st structure
struct2 (Structure): 2nd structure
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train | StructureMatcher.get_rms_dist | Calculate RMS displacement between two structures
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struct1 (Structure): 1st structure
struct2 (Structure): 2nd structure
Returns:
rms displacement normalized by (Vol / nsites) ** (1/3)
and maximum distance between paired sites. If no matching
... | pymatgen/analysis/structure_matcher.py | def get_rms_dist(self, struct1, struct2):
"""
Calculate RMS displacement between two structures
Args:
struct1 (Structure): 1st structure
struct2 (Structure): 2nd structure
Returns:
rms displacement normalized by (Vol / nsites) ** (1/3)
an... | def get_rms_dist(self, struct1, struct2):
"""
Calculate RMS displacement between two structures
Args:
struct1 (Structure): 1st structure
struct2 (Structure): 2nd structure
Returns:
rms displacement normalized by (Vol / nsites) ** (1/3)
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train | StructureMatcher._preprocess | Rescales, finds the reduced structures (primitive and niggli),
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s2 | pymatgen/analysis/structure_matcher.py | def _preprocess(self, struct1, struct2, niggli=True):
"""
Rescales, finds the reduced structures (primitive and niggli),
and finds fu, the supercell size to make struct1 comparable to
s2
"""
struct1 = struct1.copy()
struct2 = struct2.copy()
if niggli:
... | def _preprocess(self, struct1, struct2, niggli=True):
"""
Rescales, finds the reduced structures (primitive and niggli),
and finds fu, the supercell size to make struct1 comparable to
s2
"""
struct1 = struct1.copy()
struct2 = struct2.copy()
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train | StructureMatcher._match | Matches one struct onto the other | pymatgen/analysis/structure_matcher.py | def _match(self, struct1, struct2, fu, s1_supercell=True, use_rms=False,
break_on_match=False):
"""
Matches one struct onto the other
"""
ratio = fu if s1_supercell else 1/fu
if len(struct1) * ratio >= len(struct2):
return self._strict_match(
... | def _match(self, struct1, struct2, fu, s1_supercell=True, use_rms=False,
break_on_match=False):
"""
Matches one struct onto the other
"""
ratio = fu if s1_supercell else 1/fu
if len(struct1) * ratio >= len(struct2):
return self._strict_match(
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train | StructureMatcher._strict_match | Matches struct2 onto struct1 (which should contain all sites in
struct2).
Args:
struct1, struct2 (Structure): structures to be matched
fu (int): size of supercell to create
s1_supercell (bool): whether to create the supercell of
struct1 (vs struct2)
... | pymatgen/analysis/structure_matcher.py | def _strict_match(self, struct1, struct2, fu, s1_supercell=True,
use_rms=False, break_on_match=False):
"""
Matches struct2 onto struct1 (which should contain all sites in
struct2).
Args:
struct1, struct2 (Structure): structures to be matched
... | def _strict_match(self, struct1, struct2, fu, s1_supercell=True,
use_rms=False, break_on_match=False):
"""
Matches struct2 onto struct1 (which should contain all sites in
struct2).
Args:
struct1, struct2 (Structure): structures to be matched
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train | StructureMatcher.group_structures | Given a list of structures, use fit to group
them by structural equality.
Args:
s_list ([Structure]): List of structures to be grouped
anonymous (bool): Wheher to use anonymous mode.
Returns:
A list of lists of matched structures
Assumption: if s... | pymatgen/analysis/structure_matcher.py | def group_structures(self, s_list, anonymous=False):
"""
Given a list of structures, use fit to group
them by structural equality.
Args:
s_list ([Structure]): List of structures to be grouped
anonymous (bool): Wheher to use anonymous mode.
Returns:
... | def group_structures(self, s_list, anonymous=False):
"""
Given a list of structures, use fit to group
them by structural equality.
Args:
s_list ([Structure]): List of structures to be grouped
anonymous (bool): Wheher to use anonymous mode.
Returns:
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train | StructureMatcher._anonymous_match | Tries all permutations of matching struct1 to struct2.
Args:
struct1, struct2 (Structure): Preprocessed input structures
Returns:
List of (mapping, match) | pymatgen/analysis/structure_matcher.py | def _anonymous_match(self, struct1, struct2, fu, s1_supercell=True,
use_rms=False, break_on_match=False, single_match=False):
"""
Tries all permutations of matching struct1 to struct2.
Args:
struct1, struct2 (Structure): Preprocessed input structures
... | def _anonymous_match(self, struct1, struct2, fu, s1_supercell=True,
use_rms=False, break_on_match=False, single_match=False):
"""
Tries all permutations of matching struct1 to struct2.
Args:
struct1, struct2 (Structure): Preprocessed input structures
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... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | StructureMatcher.get_rms_anonymous | Performs an anonymous fitting, which allows distinct species in one
structure to map to another. E.g., to compare if the Li2O and Na2O
structures are similar.
Args:
struct1 (Structure): 1st structure
struct2 (Structure): 2nd structure
Returns:
(min_r... | pymatgen/analysis/structure_matcher.py | def get_rms_anonymous(self, struct1, struct2):
"""
Performs an anonymous fitting, which allows distinct species in one
structure to map to another. E.g., to compare if the Li2O and Na2O
structures are similar.
Args:
struct1 (Structure): 1st structure
stru... | def get_rms_anonymous(self, struct1, struct2):
"""
Performs an anonymous fitting, which allows distinct species in one
structure to map to another. E.g., to compare if the Li2O and Na2O
structures are similar.
Args:
struct1 (Structure): 1st structure
stru... | [
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... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | StructureMatcher.get_best_electronegativity_anonymous_mapping | Performs an anonymous fitting, which allows distinct species in one
structure to map to another. E.g., to compare if the Li2O and Na2O
structures are similar. If multiple substitutions are within tolerance
this will return the one which minimizes the difference in
electronegativity betwe... | pymatgen/analysis/structure_matcher.py | def get_best_electronegativity_anonymous_mapping(self, struct1, struct2):
"""
Performs an anonymous fitting, which allows distinct species in one
structure to map to another. E.g., to compare if the Li2O and Na2O
structures are similar. If multiple substitutions are within tolerance
... | def get_best_electronegativity_anonymous_mapping(self, struct1, struct2):
"""
Performs an anonymous fitting, which allows distinct species in one
structure to map to another. E.g., to compare if the Li2O and Na2O
structures are similar. If multiple substitutions are within tolerance
... | [
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... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | StructureMatcher.get_all_anonymous_mappings | Performs an anonymous fitting, which allows distinct species in one
structure to map to another. Returns a dictionary of species
substitutions that are within tolerance
Args:
struct1 (Structure): 1st structure
struct2 (Structure): 2nd structure
niggli (bool):... | pymatgen/analysis/structure_matcher.py | def get_all_anonymous_mappings(self, struct1, struct2, niggli=True,
include_dist=False):
"""
Performs an anonymous fitting, which allows distinct species in one
structure to map to another. Returns a dictionary of species
substitutions that are within t... | def get_all_anonymous_mappings(self, struct1, struct2, niggli=True,
include_dist=False):
"""
Performs an anonymous fitting, which allows distinct species in one
structure to map to another. Returns a dictionary of species
substitutions that are within t... | [
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train | StructureMatcher.fit_anonymous | Performs an anonymous fitting, which allows distinct species in one
structure to map to another. E.g., to compare if the Li2O and Na2O
structures are similar.
Args:
struct1 (Structure): 1st structure
struct2 (Structure): 2nd structure
Returns:
True/F... | pymatgen/analysis/structure_matcher.py | def fit_anonymous(self, struct1, struct2, niggli=True):
"""
Performs an anonymous fitting, which allows distinct species in one
structure to map to another. E.g., to compare if the Li2O and Na2O
structures are similar.
Args:
struct1 (Structure): 1st structure
... | def fit_anonymous(self, struct1, struct2, niggli=True):
"""
Performs an anonymous fitting, which allows distinct species in one
structure to map to another. E.g., to compare if the Li2O and Na2O
structures are similar.
Args:
struct1 (Structure): 1st structure
... | [
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"... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
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