partition stringclasses 3
values | func_name stringlengths 1 134 | docstring stringlengths 1 46.9k | path stringlengths 4 223 | original_string stringlengths 75 104k | code stringlengths 75 104k | docstring_tokens listlengths 1 1.97k | repo stringlengths 7 55 | language stringclasses 1
value | url stringlengths 87 315 | code_tokens listlengths 19 28.4k | sha stringlengths 40 40 |
|---|---|---|---|---|---|---|---|---|---|---|---|
train | SiteCollection.extract_cluster | Extracts a cluster of atoms based on bond lengths
Args:
target_sites ([Site]): List of initial sites to nucleate cluster.
\\*\\*kwargs: kwargs passed through to CovalentBond.is_bonded.
Returns:
[Site/PeriodicSite] Cluster of atoms. | pymatgen/core/structure.py | def extract_cluster(self, target_sites, **kwargs):
"""
Extracts a cluster of atoms based on bond lengths
Args:
target_sites ([Site]): List of initial sites to nucleate cluster.
\\*\\*kwargs: kwargs passed through to CovalentBond.is_bonded.
Returns:
[... | def extract_cluster(self, target_sites, **kwargs):
"""
Extracts a cluster of atoms based on bond lengths
Args:
target_sites ([Site]): List of initial sites to nucleate cluster.
\\*\\*kwargs: kwargs passed through to CovalentBond.is_bonded.
Returns:
[... | [
"Extracts",
"a",
"cluster",
"of",
"atoms",
"based",
"on",
"bond",
"lengths"
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L495-L520 | [
"def",
"extract_cluster",
"(",
"self",
",",
"target_sites",
",",
"*",
"*",
"kwargs",
")",
":",
"cluster",
"=",
"list",
"(",
"target_sites",
")",
"others",
"=",
"[",
"site",
"for",
"site",
"in",
"self",
"if",
"site",
"not",
"in",
"cluster",
"]",
"size",... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IStructure.from_sites | Convenience constructor to make a Structure from a list of sites.
Args:
sites: Sequence of PeriodicSites. Sites must have the same
lattice.
validate_proximity (bool): Whether to check if there are sites
that are less than 0.01 Ang apart. Defaults to False... | pymatgen/core/structure.py | def from_sites(cls, sites, charge=None, validate_proximity=False,
to_unit_cell=False):
"""
Convenience constructor to make a Structure from a list of sites.
Args:
sites: Sequence of PeriodicSites. Sites must have the same
lattice.
valid... | def from_sites(cls, sites, charge=None, validate_proximity=False,
to_unit_cell=False):
"""
Convenience constructor to make a Structure from a list of sites.
Args:
sites: Sequence of PeriodicSites. Sites must have the same
lattice.
valid... | [
"Convenience",
"constructor",
"to",
"make",
"a",
"Structure",
"from",
"a",
"list",
"of",
"sites",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L603-L644 | [
"def",
"from_sites",
"(",
"cls",
",",
"sites",
",",
"charge",
"=",
"None",
",",
"validate_proximity",
"=",
"False",
",",
"to_unit_cell",
"=",
"False",
")",
":",
"if",
"len",
"(",
"sites",
")",
"<",
"1",
":",
"raise",
"ValueError",
"(",
"\"You need at lea... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IStructure.from_spacegroup | Generate a structure using a spacegroup. Note that only symmetrically
distinct species and coords should be provided. All equivalent sites
are generated from the spacegroup operations.
Args:
sg (str/int): The spacegroup. If a string, it will be interpreted
as one of ... | pymatgen/core/structure.py | def from_spacegroup(cls, sg, lattice, species, coords, site_properties=None,
coords_are_cartesian=False, tol=1e-5):
"""
Generate a structure using a spacegroup. Note that only symmetrically
distinct species and coords should be provided. All equivalent sites
are g... | def from_spacegroup(cls, sg, lattice, species, coords, site_properties=None,
coords_are_cartesian=False, tol=1e-5):
"""
Generate a structure using a spacegroup. Note that only symmetrically
distinct species and coords should be provided. All equivalent sites
are g... | [
"Generate",
"a",
"structure",
"using",
"a",
"spacegroup",
".",
"Note",
"that",
"only",
"symmetrically",
"distinct",
"species",
"and",
"coords",
"should",
"be",
"provided",
".",
"All",
"equivalent",
"sites",
"are",
"generated",
"from",
"the",
"spacegroup",
"opera... | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L647-L730 | [
"def",
"from_spacegroup",
"(",
"cls",
",",
"sg",
",",
"lattice",
",",
"species",
",",
"coords",
",",
"site_properties",
"=",
"None",
",",
"coords_are_cartesian",
"=",
"False",
",",
"tol",
"=",
"1e-5",
")",
":",
"from",
"pymatgen",
".",
"symmetry",
".",
"... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IStructure.from_magnetic_spacegroup | Generate a structure using a magnetic spacegroup. Note that only
symmetrically distinct species, coords and magmoms should be provided.]
All equivalent sites are generated from the spacegroup operations.
Args:
msg (str/list/:class:`pymatgen.symmetry.maggroups.MagneticSpaceGroup`):
... | pymatgen/core/structure.py | def from_magnetic_spacegroup(
cls, msg, lattice, species, coords, site_properties,
transform_setting=None, coords_are_cartesian=False, tol=1e-5):
"""
Generate a structure using a magnetic spacegroup. Note that only
symmetrically distinct species, coords and magmoms should... | def from_magnetic_spacegroup(
cls, msg, lattice, species, coords, site_properties,
transform_setting=None, coords_are_cartesian=False, tol=1e-5):
"""
Generate a structure using a magnetic spacegroup. Note that only
symmetrically distinct species, coords and magmoms should... | [
"Generate",
"a",
"structure",
"using",
"a",
"magnetic",
"spacegroup",
".",
"Note",
"that",
"only",
"symmetrically",
"distinct",
"species",
"coords",
"and",
"magmoms",
"should",
"be",
"provided",
".",
"]",
"All",
"equivalent",
"sites",
"are",
"generated",
"from",... | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L733-L834 | [
"def",
"from_magnetic_spacegroup",
"(",
"cls",
",",
"msg",
",",
"lattice",
",",
"species",
",",
"coords",
",",
"site_properties",
",",
"transform_setting",
"=",
"None",
",",
"coords_are_cartesian",
"=",
"False",
",",
"tol",
"=",
"1e-5",
")",
":",
"from",
"py... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IStructure.density | Returns the density in units of g/cc | pymatgen/core/structure.py | def density(self):
"""
Returns the density in units of g/cc
"""
m = Mass(self.composition.weight, "amu")
return m.to("g") / (self.volume * Length(1, "ang").to("cm") ** 3) | def density(self):
"""
Returns the density in units of g/cc
"""
m = Mass(self.composition.weight, "amu")
return m.to("g") / (self.volume * Length(1, "ang").to("cm") ** 3) | [
"Returns",
"the",
"density",
"in",
"units",
"of",
"g",
"/",
"cc"
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L870-L875 | [
"def",
"density",
"(",
"self",
")",
":",
"m",
"=",
"Mass",
"(",
"self",
".",
"composition",
".",
"weight",
",",
"\"amu\"",
")",
"return",
"m",
".",
"to",
"(",
"\"g\"",
")",
"/",
"(",
"self",
".",
"volume",
"*",
"Length",
"(",
"1",
",",
"\"ang\"",... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IStructure.get_space_group_info | Convenience method to quickly get the spacegroup of a structure.
Args:
symprec (float): Same definition as in SpacegroupAnalyzer.
Defaults to 1e-2.
angle_tolerance (float): Same definition as in SpacegroupAnalyzer.
Defaults to 5 degrees.
Returns:... | pymatgen/core/structure.py | def get_space_group_info(self, symprec=1e-2, angle_tolerance=5.0):
"""
Convenience method to quickly get the spacegroup of a structure.
Args:
symprec (float): Same definition as in SpacegroupAnalyzer.
Defaults to 1e-2.
angle_tolerance (float): Same defini... | def get_space_group_info(self, symprec=1e-2, angle_tolerance=5.0):
"""
Convenience method to quickly get the spacegroup of a structure.
Args:
symprec (float): Same definition as in SpacegroupAnalyzer.
Defaults to 1e-2.
angle_tolerance (float): Same defini... | [
"Convenience",
"method",
"to",
"quickly",
"get",
"the",
"spacegroup",
"of",
"a",
"structure",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L877-L894 | [
"def",
"get_space_group_info",
"(",
"self",
",",
"symprec",
"=",
"1e-2",
",",
"angle_tolerance",
"=",
"5.0",
")",
":",
"# Import within method needed to avoid cyclic dependency.",
"from",
"pymatgen",
".",
"symmetry",
".",
"analyzer",
"import",
"SpacegroupAnalyzer",
"a",... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IStructure.matches | Check whether this structure is similar to another structure.
Basically a convenience method to call structure matching fitting.
Args:
other (IStructure/Structure): Another structure.
**kwargs: Same **kwargs as in
:class:`pymatgen.analysis.structure_matcher.Struc... | pymatgen/core/structure.py | def matches(self, other, **kwargs):
"""
Check whether this structure is similar to another structure.
Basically a convenience method to call structure matching fitting.
Args:
other (IStructure/Structure): Another structure.
**kwargs: Same **kwargs as in
... | def matches(self, other, **kwargs):
"""
Check whether this structure is similar to another structure.
Basically a convenience method to call structure matching fitting.
Args:
other (IStructure/Structure): Another structure.
**kwargs: Same **kwargs as in
... | [
"Check",
"whether",
"this",
"structure",
"is",
"similar",
"to",
"another",
"structure",
".",
"Basically",
"a",
"convenience",
"method",
"to",
"call",
"structure",
"matching",
"fitting",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L896-L912 | [
"def",
"matches",
"(",
"self",
",",
"other",
",",
"*",
"*",
"kwargs",
")",
":",
"from",
"pymatgen",
".",
"analysis",
".",
"structure_matcher",
"import",
"StructureMatcher",
"m",
"=",
"StructureMatcher",
"(",
"*",
"*",
"kwargs",
")",
"return",
"m",
".",
"... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IStructure.get_distance | Get distance between site i and j assuming periodic boundary
conditions. If the index jimage of two sites atom j is not specified it
selects the jimage nearest to the i atom and returns the distance and
jimage indices in terms of lattice vector translations if the index
jimage of atom j ... | pymatgen/core/structure.py | def get_distance(self, i, j, jimage=None):
"""
Get distance between site i and j assuming periodic boundary
conditions. If the index jimage of two sites atom j is not specified it
selects the jimage nearest to the i atom and returns the distance and
jimage indices in terms of lat... | def get_distance(self, i, j, jimage=None):
"""
Get distance between site i and j assuming periodic boundary
conditions. If the index jimage of two sites atom j is not specified it
selects the jimage nearest to the i atom and returns the distance and
jimage indices in terms of lat... | [
"Get",
"distance",
"between",
"site",
"i",
"and",
"j",
"assuming",
"periodic",
"boundary",
"conditions",
".",
"If",
"the",
"index",
"jimage",
"of",
"two",
"sites",
"atom",
"j",
"is",
"not",
"specified",
"it",
"selects",
"the",
"jimage",
"nearest",
"to",
"t... | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L1000-L1018 | [
"def",
"get_distance",
"(",
"self",
",",
"i",
",",
"j",
",",
"jimage",
"=",
"None",
")",
":",
"return",
"self",
"[",
"i",
"]",
".",
"distance",
"(",
"self",
"[",
"j",
"]",
",",
"jimage",
")"
] | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IStructure.get_sites_in_sphere | Find all sites within a sphere from the point. This includes sites
in other periodic images.
Algorithm:
1. place sphere of radius r in crystal and determine minimum supercell
(parallelpiped) which would contain a sphere of radius r. for this
we need the projection of a_1 ... | pymatgen/core/structure.py | def get_sites_in_sphere(self, pt, r, include_index=False, include_image=False):
"""
Find all sites within a sphere from the point. This includes sites
in other periodic images.
Algorithm:
1. place sphere of radius r in crystal and determine minimum supercell
(paralle... | def get_sites_in_sphere(self, pt, r, include_index=False, include_image=False):
"""
Find all sites within a sphere from the point. This includes sites
in other periodic images.
Algorithm:
1. place sphere of radius r in crystal and determine minimum supercell
(paralle... | [
"Find",
"all",
"sites",
"within",
"a",
"sphere",
"from",
"the",
"point",
".",
"This",
"includes",
"sites",
"in",
"other",
"periodic",
"images",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L1020-L1062 | [
"def",
"get_sites_in_sphere",
"(",
"self",
",",
"pt",
",",
"r",
",",
"include_index",
"=",
"False",
",",
"include_image",
"=",
"False",
")",
":",
"site_fcoords",
"=",
"np",
".",
"mod",
"(",
"self",
".",
"frac_coords",
",",
"1",
")",
"neighbors",
"=",
"... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IStructure.get_neighbors | Get all neighbors to a site within a sphere of radius r. Excludes the
site itself.
Args:
site (Site): Which is the center of the sphere.
r (float): Radius of sphere.
include_index (bool): Whether the non-supercell site index
is included in the return... | pymatgen/core/structure.py | def get_neighbors(self, site, r, include_index=False, include_image=False):
"""
Get all neighbors to a site within a sphere of radius r. Excludes the
site itself.
Args:
site (Site): Which is the center of the sphere.
r (float): Radius of sphere.
incl... | def get_neighbors(self, site, r, include_index=False, include_image=False):
"""
Get all neighbors to a site within a sphere of radius r. Excludes the
site itself.
Args:
site (Site): Which is the center of the sphere.
r (float): Radius of sphere.
incl... | [
"Get",
"all",
"neighbors",
"to",
"a",
"site",
"within",
"a",
"sphere",
"of",
"radius",
"r",
".",
"Excludes",
"the",
"site",
"itself",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L1064-L1088 | [
"def",
"get_neighbors",
"(",
"self",
",",
"site",
",",
"r",
",",
"include_index",
"=",
"False",
",",
"include_image",
"=",
"False",
")",
":",
"nn",
"=",
"self",
".",
"get_sites_in_sphere",
"(",
"site",
".",
"coords",
",",
"r",
",",
"include_index",
"=",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IStructure.get_all_neighbors | Get neighbors for each atom in the unit cell, out to a distance r
Returns a list of list of neighbors for each site in structure.
Use this method if you are planning on looping over all sites in the
crystal. If you only want neighbors for a particular site, use the
method get_neighbors a... | pymatgen/core/structure.py | def get_all_neighbors(self, r, include_index=False, include_image=False):
"""
Get neighbors for each atom in the unit cell, out to a distance r
Returns a list of list of neighbors for each site in structure.
Use this method if you are planning on looping over all sites in the
cry... | def get_all_neighbors(self, r, include_index=False, include_image=False):
"""
Get neighbors for each atom in the unit cell, out to a distance r
Returns a list of list of neighbors for each site in structure.
Use this method if you are planning on looping over all sites in the
cry... | [
"Get",
"neighbors",
"for",
"each",
"atom",
"in",
"the",
"unit",
"cell",
"out",
"to",
"a",
"distance",
"r",
"Returns",
"a",
"list",
"of",
"list",
"of",
"neighbors",
"for",
"each",
"site",
"in",
"structure",
".",
"Use",
"this",
"method",
"if",
"you",
"ar... | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L1090-L1157 | [
"def",
"get_all_neighbors",
"(",
"self",
",",
"r",
",",
"include_index",
"=",
"False",
",",
"include_image",
"=",
"False",
")",
":",
"# Use same algorithm as get_sites_in_sphere to determine supercell but",
"# loop over all atoms in crystal",
"recp_len",
"=",
"np",
".",
"... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IStructure.get_neighbors_in_shell | Returns all sites in a shell centered on origin (coords) between radii
r-dr and r+dr.
Args:
origin (3x1 array): Cartesian coordinates of center of sphere.
r (float): Inner radius of shell.
dr (float): Width of shell.
include_index (bool): Whether to inclu... | pymatgen/core/structure.py | def get_neighbors_in_shell(self, origin, r, dr, include_index=False, include_image=False):
"""
Returns all sites in a shell centered on origin (coords) between radii
r-dr and r+dr.
Args:
origin (3x1 array): Cartesian coordinates of center of sphere.
r (float): In... | def get_neighbors_in_shell(self, origin, r, dr, include_index=False, include_image=False):
"""
Returns all sites in a shell centered on origin (coords) between radii
r-dr and r+dr.
Args:
origin (3x1 array): Cartesian coordinates of center of sphere.
r (float): In... | [
"Returns",
"all",
"sites",
"in",
"a",
"shell",
"centered",
"on",
"origin",
"(",
"coords",
")",
"between",
"radii",
"r",
"-",
"dr",
"and",
"r",
"+",
"dr",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L1159-L1186 | [
"def",
"get_neighbors_in_shell",
"(",
"self",
",",
"origin",
",",
"r",
",",
"dr",
",",
"include_index",
"=",
"False",
",",
"include_image",
"=",
"False",
")",
":",
"outer",
"=",
"self",
".",
"get_sites_in_sphere",
"(",
"origin",
",",
"r",
"+",
"dr",
",",... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IStructure.get_sorted_structure | Get a sorted copy of the structure. The parameters have the same
meaning as in list.sort. By default, sites are sorted by the
electronegativity of the species.
Args:
key: Specifies a function of one argument that is used to extract
a comparison key from each list ele... | pymatgen/core/structure.py | def get_sorted_structure(self, key=None, reverse=False):
"""
Get a sorted copy of the structure. The parameters have the same
meaning as in list.sort. By default, sites are sorted by the
electronegativity of the species.
Args:
key: Specifies a function of one argumen... | def get_sorted_structure(self, key=None, reverse=False):
"""
Get a sorted copy of the structure. The parameters have the same
meaning as in list.sort. By default, sites are sorted by the
electronegativity of the species.
Args:
key: Specifies a function of one argumen... | [
"Get",
"a",
"sorted",
"copy",
"of",
"the",
"structure",
".",
"The",
"parameters",
"have",
"the",
"same",
"meaning",
"as",
"in",
"list",
".",
"sort",
".",
"By",
"default",
"sites",
"are",
"sorted",
"by",
"the",
"electronegativity",
"of",
"the",
"species",
... | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L1188-L1202 | [
"def",
"get_sorted_structure",
"(",
"self",
",",
"key",
"=",
"None",
",",
"reverse",
"=",
"False",
")",
":",
"sites",
"=",
"sorted",
"(",
"self",
",",
"key",
"=",
"key",
",",
"reverse",
"=",
"reverse",
")",
"return",
"self",
".",
"__class__",
".",
"f... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IStructure.get_reduced_structure | Get a reduced structure.
Args:
reduction_algo (str): The lattice reduction algorithm to use.
Currently supported options are "niggli" or "LLL". | pymatgen/core/structure.py | def get_reduced_structure(self, reduction_algo="niggli"):
"""
Get a reduced structure.
Args:
reduction_algo (str): The lattice reduction algorithm to use.
Currently supported options are "niggli" or "LLL".
"""
if reduction_algo == "niggli":
... | def get_reduced_structure(self, reduction_algo="niggli"):
"""
Get a reduced structure.
Args:
reduction_algo (str): The lattice reduction algorithm to use.
Currently supported options are "niggli" or "LLL".
"""
if reduction_algo == "niggli":
... | [
"Get",
"a",
"reduced",
"structure",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L1204-L1226 | [
"def",
"get_reduced_structure",
"(",
"self",
",",
"reduction_algo",
"=",
"\"niggli\"",
")",
":",
"if",
"reduction_algo",
"==",
"\"niggli\"",
":",
"reduced_latt",
"=",
"self",
".",
"_lattice",
".",
"get_niggli_reduced_lattice",
"(",
")",
"elif",
"reduction_algo",
"... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IStructure.copy | Convenience method to get a copy of the structure, with options to add
site properties.
Args:
site_properties (dict): Properties to add or override. The
properties are specified in the same way as the constructor,
i.e., as a dict of the form {property: [value... | pymatgen/core/structure.py | def copy(self, site_properties=None, sanitize=False):
"""
Convenience method to get a copy of the structure, with options to add
site properties.
Args:
site_properties (dict): Properties to add or override. The
properties are specified in the same way as the ... | def copy(self, site_properties=None, sanitize=False):
"""
Convenience method to get a copy of the structure, with options to add
site properties.
Args:
site_properties (dict): Properties to add or override. The
properties are specified in the same way as the ... | [
"Convenience",
"method",
"to",
"get",
"a",
"copy",
"of",
"the",
"structure",
"with",
"options",
"to",
"add",
"site",
"properties",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L1228-L1272 | [
"def",
"copy",
"(",
"self",
",",
"site_properties",
"=",
"None",
",",
"sanitize",
"=",
"False",
")",
":",
"props",
"=",
"self",
".",
"site_properties",
"if",
"site_properties",
":",
"props",
".",
"update",
"(",
"site_properties",
")",
"if",
"not",
"sanitiz... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IStructure.interpolate | Interpolate between this structure and end_structure. Useful for
construction of NEB inputs.
Args:
end_structure (Structure): structure to interpolate between this
structure and end.
nimages (int): No. of interpolation images. Defaults to 10 images.
i... | pymatgen/core/structure.py | def interpolate(self, end_structure, nimages=10,
interpolate_lattices=False, pbc=True, autosort_tol=0):
"""
Interpolate between this structure and end_structure. Useful for
construction of NEB inputs.
Args:
end_structure (Structure): structure to interpol... | def interpolate(self, end_structure, nimages=10,
interpolate_lattices=False, pbc=True, autosort_tol=0):
"""
Interpolate between this structure and end_structure. Useful for
construction of NEB inputs.
Args:
end_structure (Structure): structure to interpol... | [
"Interpolate",
"between",
"this",
"structure",
"and",
"end_structure",
".",
"Useful",
"for",
"construction",
"of",
"NEB",
"inputs",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L1274-L1375 | [
"def",
"interpolate",
"(",
"self",
",",
"end_structure",
",",
"nimages",
"=",
"10",
",",
"interpolate_lattices",
"=",
"False",
",",
"pbc",
"=",
"True",
",",
"autosort_tol",
"=",
"0",
")",
":",
"# Check length of structures",
"if",
"len",
"(",
"self",
")",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IStructure.get_miller_index_from_site_indexes | Get the Miller index of a plane from a set of sites indexes.
A minimum of 3 sites are required. If more than 3 sites are given
the best plane that minimises the distance to all points will be
calculated.
Args:
site_ids (list of int): A list of site indexes to consider. A
... | pymatgen/core/structure.py | def get_miller_index_from_site_indexes(self, site_ids, round_dp=4,
verbose=True):
"""
Get the Miller index of a plane from a set of sites indexes.
A minimum of 3 sites are required. If more than 3 sites are given
the best plane that minimises t... | def get_miller_index_from_site_indexes(self, site_ids, round_dp=4,
verbose=True):
"""
Get the Miller index of a plane from a set of sites indexes.
A minimum of 3 sites are required. If more than 3 sites are given
the best plane that minimises t... | [
"Get",
"the",
"Miller",
"index",
"of",
"a",
"plane",
"from",
"a",
"set",
"of",
"sites",
"indexes",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L1377-L1400 | [
"def",
"get_miller_index_from_site_indexes",
"(",
"self",
",",
"site_ids",
",",
"round_dp",
"=",
"4",
",",
"verbose",
"=",
"True",
")",
":",
"return",
"self",
".",
"lattice",
".",
"get_miller_index_from_coords",
"(",
"self",
".",
"frac_coords",
"[",
"site_ids",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IStructure.get_primitive_structure | This finds a smaller unit cell than the input. Sometimes it doesn"t
find the smallest possible one, so this method is recursively called
until it is unable to find a smaller cell.
NOTE: if the tolerance is greater than 1/2 the minimum inter-site
distance in the primitive cell, the algor... | pymatgen/core/structure.py | def get_primitive_structure(self, tolerance=0.25, use_site_props=False,
constrain_latt=None):
"""
This finds a smaller unit cell than the input. Sometimes it doesn"t
find the smallest possible one, so this method is recursively called
until it is unable to... | def get_primitive_structure(self, tolerance=0.25, use_site_props=False,
constrain_latt=None):
"""
This finds a smaller unit cell than the input. Sometimes it doesn"t
find the smallest possible one, so this method is recursively called
until it is unable to... | [
"This",
"finds",
"a",
"smaller",
"unit",
"cell",
"than",
"the",
"input",
".",
"Sometimes",
"it",
"doesn",
"t",
"find",
"the",
"smallest",
"possible",
"one",
"so",
"this",
"method",
"is",
"recursively",
"called",
"until",
"it",
"is",
"unable",
"to",
"find",... | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L1402-L1602 | [
"def",
"get_primitive_structure",
"(",
"self",
",",
"tolerance",
"=",
"0.25",
",",
"use_site_props",
"=",
"False",
",",
"constrain_latt",
"=",
"None",
")",
":",
"if",
"constrain_latt",
"is",
"None",
":",
"constrain_latt",
"=",
"[",
"]",
"def",
"site_label",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IStructure.as_dict | Dict representation of Structure.
Args:
verbosity (int): Verbosity level. Default of 1 includes both
direct and cartesian coordinates for all sites, lattice
parameters, etc. Useful for reading and for insertion into a
database. Set to 0 for an extreme... | pymatgen/core/structure.py | def as_dict(self, verbosity=1, fmt=None, **kwargs):
"""
Dict representation of Structure.
Args:
verbosity (int): Verbosity level. Default of 1 includes both
direct and cartesian coordinates for all sites, lattice
parameters, etc. Useful for reading an... | def as_dict(self, verbosity=1, fmt=None, **kwargs):
"""
Dict representation of Structure.
Args:
verbosity (int): Verbosity level. Default of 1 includes both
direct and cartesian coordinates for all sites, lattice
parameters, etc. Useful for reading an... | [
"Dict",
"representation",
"of",
"Structure",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L1644-L1683 | [
"def",
"as_dict",
"(",
"self",
",",
"verbosity",
"=",
"1",
",",
"fmt",
"=",
"None",
",",
"*",
"*",
"kwargs",
")",
":",
"if",
"fmt",
"==",
"\"abivars\"",
":",
"\"\"\"Returns a dictionary with the ABINIT variables.\"\"\"",
"from",
"pymatgen",
".",
"io",
".",
"... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IStructure.from_dict | Reconstitute a Structure object from a dict representation of Structure
created using as_dict().
Args:
d (dict): Dict representation of structure.
Returns:
Structure object | pymatgen/core/structure.py | def from_dict(cls, d, fmt=None):
"""
Reconstitute a Structure object from a dict representation of Structure
created using as_dict().
Args:
d (dict): Dict representation of structure.
Returns:
Structure object
"""
if fmt == "abivars":
... | def from_dict(cls, d, fmt=None):
"""
Reconstitute a Structure object from a dict representation of Structure
created using as_dict().
Args:
d (dict): Dict representation of structure.
Returns:
Structure object
"""
if fmt == "abivars":
... | [
"Reconstitute",
"a",
"Structure",
"object",
"from",
"a",
"dict",
"representation",
"of",
"Structure",
"created",
"using",
"as_dict",
"()",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L1686-L1704 | [
"def",
"from_dict",
"(",
"cls",
",",
"d",
",",
"fmt",
"=",
"None",
")",
":",
"if",
"fmt",
"==",
"\"abivars\"",
":",
"from",
"pymatgen",
".",
"io",
".",
"abinit",
".",
"abiobjects",
"import",
"structure_from_abivars",
"return",
"structure_from_abivars",
"(",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IStructure.to | Outputs the structure to a file or string.
Args:
fmt (str): Format to output to. Defaults to JSON unless filename
is provided. If fmt is specifies, it overrides whatever the
filename is. Options include "cif", "poscar", "cssr", "json".
Non-case sensit... | pymatgen/core/structure.py | def to(self, fmt=None, filename=None, **kwargs):
"""
Outputs the structure to a file or string.
Args:
fmt (str): Format to output to. Defaults to JSON unless filename
is provided. If fmt is specifies, it overrides whatever the
filename is. Options inc... | def to(self, fmt=None, filename=None, **kwargs):
"""
Outputs the structure to a file or string.
Args:
fmt (str): Format to output to. Defaults to JSON unless filename
is provided. If fmt is specifies, it overrides whatever the
filename is. Options inc... | [
"Outputs",
"the",
"structure",
"to",
"a",
"file",
"or",
"string",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L1706-L1775 | [
"def",
"to",
"(",
"self",
",",
"fmt",
"=",
"None",
",",
"filename",
"=",
"None",
",",
"*",
"*",
"kwargs",
")",
":",
"filename",
"=",
"filename",
"or",
"\"\"",
"fmt",
"=",
"\"\"",
"if",
"fmt",
"is",
"None",
"else",
"fmt",
".",
"lower",
"(",
")",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IStructure.from_str | Reads a structure from a string.
Args:
input_string (str): String to parse.
fmt (str): A format specification.
primitive (bool): Whether to find a primitive cell. Defaults to
False.
sort (bool): Whether to sort the sites in accordance to the defau... | pymatgen/core/structure.py | def from_str(cls, input_string, fmt, primitive=False, sort=False,
merge_tol=0.0):
"""
Reads a structure from a string.
Args:
input_string (str): String to parse.
fmt (str): A format specification.
primitive (bool): Whether to find a primitive... | def from_str(cls, input_string, fmt, primitive=False, sort=False,
merge_tol=0.0):
"""
Reads a structure from a string.
Args:
input_string (str): String to parse.
fmt (str): A format specification.
primitive (bool): Whether to find a primitive... | [
"Reads",
"a",
"structure",
"from",
"a",
"string",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L1778-L1830 | [
"def",
"from_str",
"(",
"cls",
",",
"input_string",
",",
"fmt",
",",
"primitive",
"=",
"False",
",",
"sort",
"=",
"False",
",",
"merge_tol",
"=",
"0.0",
")",
":",
"from",
"pymatgen",
".",
"io",
".",
"cif",
"import",
"CifParser",
"from",
"pymatgen",
"."... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IStructure.from_file | Reads a structure from a file. For example, anything ending in
a "cif" is assumed to be a Crystallographic Information Format file.
Supported formats include CIF, POSCAR/CONTCAR, CHGCAR, LOCPOT,
vasprun.xml, CSSR, Netcdf and pymatgen's JSON serialized structures.
Args:
filen... | pymatgen/core/structure.py | def from_file(cls, filename, primitive=False, sort=False, merge_tol=0.0):
"""
Reads a structure from a file. For example, anything ending in
a "cif" is assumed to be a Crystallographic Information Format file.
Supported formats include CIF, POSCAR/CONTCAR, CHGCAR, LOCPOT,
vasprun... | def from_file(cls, filename, primitive=False, sort=False, merge_tol=0.0):
"""
Reads a structure from a file. For example, anything ending in
a "cif" is assumed to be a Crystallographic Information Format file.
Supported formats include CIF, POSCAR/CONTCAR, CHGCAR, LOCPOT,
vasprun... | [
"Reads",
"a",
"structure",
"from",
"a",
"file",
".",
"For",
"example",
"anything",
"ending",
"in",
"a",
"cif",
"is",
"assumed",
"to",
"be",
"a",
"Crystallographic",
"Information",
"Format",
"file",
".",
"Supported",
"formats",
"include",
"CIF",
"POSCAR",
"/"... | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L1833-L1915 | [
"def",
"from_file",
"(",
"cls",
",",
"filename",
",",
"primitive",
"=",
"False",
",",
"sort",
"=",
"False",
",",
"merge_tol",
"=",
"0.0",
")",
":",
"filename",
"=",
"str",
"(",
"filename",
")",
"if",
"filename",
".",
"endswith",
"(",
"\".nc\"",
")",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IMolecule.center_of_mass | Center of mass of molecule. | pymatgen/core/structure.py | def center_of_mass(self):
"""
Center of mass of molecule.
"""
center = np.zeros(3)
total_weight = 0
for site in self:
wt = site.species.weight
center += site.coords * wt
total_weight += wt
return center / total_weight | def center_of_mass(self):
"""
Center of mass of molecule.
"""
center = np.zeros(3)
total_weight = 0
for site in self:
wt = site.species.weight
center += site.coords * wt
total_weight += wt
return center / total_weight | [
"Center",
"of",
"mass",
"of",
"molecule",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2012-L2022 | [
"def",
"center_of_mass",
"(",
"self",
")",
":",
"center",
"=",
"np",
".",
"zeros",
"(",
"3",
")",
"total_weight",
"=",
"0",
"for",
"site",
"in",
"self",
":",
"wt",
"=",
"site",
".",
"species",
".",
"weight",
"center",
"+=",
"site",
".",
"coords",
"... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IMolecule.from_sites | Convenience constructor to make a Molecule from a list of sites.
Args:
sites ([Site]): Sequence of Sites.
charge (int): Charge of molecule. Defaults to 0.
spin_multiplicity (int): Spin multicipity. Defaults to None,
in which it is determined automatically.
... | pymatgen/core/structure.py | def from_sites(cls, sites, charge=0, spin_multiplicity=None,
validate_proximity=False):
"""
Convenience constructor to make a Molecule from a list of sites.
Args:
sites ([Site]): Sequence of Sites.
charge (int): Charge of molecule. Defaults to 0.
... | def from_sites(cls, sites, charge=0, spin_multiplicity=None,
validate_proximity=False):
"""
Convenience constructor to make a Molecule from a list of sites.
Args:
sites ([Site]): Sequence of Sites.
charge (int): Charge of molecule. Defaults to 0.
... | [
"Convenience",
"constructor",
"to",
"make",
"a",
"Molecule",
"from",
"a",
"list",
"of",
"sites",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2032-L2053 | [
"def",
"from_sites",
"(",
"cls",
",",
"sites",
",",
"charge",
"=",
"0",
",",
"spin_multiplicity",
"=",
"None",
",",
"validate_proximity",
"=",
"False",
")",
":",
"props",
"=",
"collections",
".",
"defaultdict",
"(",
"list",
")",
"for",
"site",
"in",
"sit... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IMolecule.break_bond | Returns two molecules based on breaking the bond between atoms at index
ind1 and ind2.
Args:
ind1 (int): Index of first site.
ind2 (int): Index of second site.
tol (float): Relative tolerance to test. Basically, the code
checks if the distance between... | pymatgen/core/structure.py | def break_bond(self, ind1, ind2, tol=0.2):
"""
Returns two molecules based on breaking the bond between atoms at index
ind1 and ind2.
Args:
ind1 (int): Index of first site.
ind2 (int): Index of second site.
tol (float): Relative tolerance to test. Bas... | def break_bond(self, ind1, ind2, tol=0.2):
"""
Returns two molecules based on breaking the bond between atoms at index
ind1 and ind2.
Args:
ind1 (int): Index of first site.
ind2 (int): Index of second site.
tol (float): Relative tolerance to test. Bas... | [
"Returns",
"two",
"molecules",
"based",
"on",
"breaking",
"the",
"bond",
"between",
"atoms",
"at",
"index",
"ind1",
"and",
"ind2",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2055-L2098 | [
"def",
"break_bond",
"(",
"self",
",",
"ind1",
",",
"ind2",
",",
"tol",
"=",
"0.2",
")",
":",
"sites",
"=",
"self",
".",
"_sites",
"clusters",
"=",
"[",
"[",
"sites",
"[",
"ind1",
"]",
"]",
",",
"[",
"sites",
"[",
"ind2",
"]",
"]",
"]",
"sites"... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IMolecule.get_covalent_bonds | Determines the covalent bonds in a molecule.
Args:
tol (float): The tol to determine bonds in a structure. See
CovalentBond.is_bonded.
Returns:
List of bonds | pymatgen/core/structure.py | def get_covalent_bonds(self, tol=0.2):
"""
Determines the covalent bonds in a molecule.
Args:
tol (float): The tol to determine bonds in a structure. See
CovalentBond.is_bonded.
Returns:
List of bonds
"""
bonds = []
for si... | def get_covalent_bonds(self, tol=0.2):
"""
Determines the covalent bonds in a molecule.
Args:
tol (float): The tol to determine bonds in a structure. See
CovalentBond.is_bonded.
Returns:
List of bonds
"""
bonds = []
for si... | [
"Determines",
"the",
"covalent",
"bonds",
"in",
"a",
"molecule",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2100-L2115 | [
"def",
"get_covalent_bonds",
"(",
"self",
",",
"tol",
"=",
"0.2",
")",
":",
"bonds",
"=",
"[",
"]",
"for",
"site1",
",",
"site2",
"in",
"itertools",
".",
"combinations",
"(",
"self",
".",
"_sites",
",",
"2",
")",
":",
"if",
"CovalentBond",
".",
"is_b... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IMolecule.as_dict | Json-serializable dict representation of Molecule | pymatgen/core/structure.py | def as_dict(self):
"""
Json-serializable dict representation of Molecule
"""
d = {"@module": self.__class__.__module__,
"@class": self.__class__.__name__,
"charge": self._charge,
"spin_multiplicity": self._spin_multiplicity,
"sites": []... | def as_dict(self):
"""
Json-serializable dict representation of Molecule
"""
d = {"@module": self.__class__.__module__,
"@class": self.__class__.__name__,
"charge": self._charge,
"spin_multiplicity": self._spin_multiplicity,
"sites": []... | [
"Json",
"-",
"serializable",
"dict",
"representation",
"of",
"Molecule"
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2156-L2170 | [
"def",
"as_dict",
"(",
"self",
")",
":",
"d",
"=",
"{",
"\"@module\"",
":",
"self",
".",
"__class__",
".",
"__module__",
",",
"\"@class\"",
":",
"self",
".",
"__class__",
".",
"__name__",
",",
"\"charge\"",
":",
"self",
".",
"_charge",
",",
"\"spin_multi... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IMolecule.from_dict | Reconstitute a Molecule object from a dict representation created using
as_dict().
Args:
d (dict): dict representation of Molecule.
Returns:
Molecule object | pymatgen/core/structure.py | def from_dict(cls, d):
"""
Reconstitute a Molecule object from a dict representation created using
as_dict().
Args:
d (dict): dict representation of Molecule.
Returns:
Molecule object
"""
sites = [Site.from_dict(sd) for sd in d["sites"]]
... | def from_dict(cls, d):
"""
Reconstitute a Molecule object from a dict representation created using
as_dict().
Args:
d (dict): dict representation of Molecule.
Returns:
Molecule object
"""
sites = [Site.from_dict(sd) for sd in d["sites"]]
... | [
"Reconstitute",
"a",
"Molecule",
"object",
"from",
"a",
"dict",
"representation",
"created",
"using",
"as_dict",
"()",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2173-L2187 | [
"def",
"from_dict",
"(",
"cls",
",",
"d",
")",
":",
"sites",
"=",
"[",
"Site",
".",
"from_dict",
"(",
"sd",
")",
"for",
"sd",
"in",
"d",
"[",
"\"sites\"",
"]",
"]",
"charge",
"=",
"d",
".",
"get",
"(",
"\"charge\"",
",",
"0",
")",
"spin_multiplic... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IMolecule.get_sites_in_sphere | Find all sites within a sphere from a point.
Args:
pt (3x1 array): Cartesian coordinates of center of sphere.
r (float): Radius of sphere.
Returns:
[(site, dist) ...] since most of the time, subsequent processing
requires the distance. | pymatgen/core/structure.py | def get_sites_in_sphere(self, pt, r):
"""
Find all sites within a sphere from a point.
Args:
pt (3x1 array): Cartesian coordinates of center of sphere.
r (float): Radius of sphere.
Returns:
[(site, dist) ...] since most of the time, subsequent proces... | def get_sites_in_sphere(self, pt, r):
"""
Find all sites within a sphere from a point.
Args:
pt (3x1 array): Cartesian coordinates of center of sphere.
r (float): Radius of sphere.
Returns:
[(site, dist) ...] since most of the time, subsequent proces... | [
"Find",
"all",
"sites",
"within",
"a",
"sphere",
"from",
"a",
"point",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2202-L2219 | [
"def",
"get_sites_in_sphere",
"(",
"self",
",",
"pt",
",",
"r",
")",
":",
"neighbors",
"=",
"[",
"]",
"for",
"site",
"in",
"self",
".",
"_sites",
":",
"dist",
"=",
"site",
".",
"distance_from_point",
"(",
"pt",
")",
"if",
"dist",
"<=",
"r",
":",
"n... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IMolecule.get_neighbors | Get all neighbors to a site within a sphere of radius r. Excludes the
site itself.
Args:
site (Site): Site at the center of the sphere.
r (float): Radius of sphere.
Returns:
[(site, dist) ...] since most of the time, subsequent processing
requir... | pymatgen/core/structure.py | def get_neighbors(self, site, r):
"""
Get all neighbors to a site within a sphere of radius r. Excludes the
site itself.
Args:
site (Site): Site at the center of the sphere.
r (float): Radius of sphere.
Returns:
[(site, dist) ...] since most... | def get_neighbors(self, site, r):
"""
Get all neighbors to a site within a sphere of radius r. Excludes the
site itself.
Args:
site (Site): Site at the center of the sphere.
r (float): Radius of sphere.
Returns:
[(site, dist) ...] since most... | [
"Get",
"all",
"neighbors",
"to",
"a",
"site",
"within",
"a",
"sphere",
"of",
"radius",
"r",
".",
"Excludes",
"the",
"site",
"itself",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2221-L2235 | [
"def",
"get_neighbors",
"(",
"self",
",",
"site",
",",
"r",
")",
":",
"nn",
"=",
"self",
".",
"get_sites_in_sphere",
"(",
"site",
".",
"coords",
",",
"r",
")",
"return",
"[",
"(",
"s",
",",
"dist",
")",
"for",
"(",
"s",
",",
"dist",
")",
"in",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IMolecule.get_neighbors_in_shell | Returns all sites in a shell centered on origin (coords) between radii
r-dr and r+dr.
Args:
origin (3x1 array): Cartesian coordinates of center of sphere.
r (float): Inner radius of shell.
dr (float): Width of shell.
Returns:
[(site, dist) ...] s... | pymatgen/core/structure.py | def get_neighbors_in_shell(self, origin, r, dr):
"""
Returns all sites in a shell centered on origin (coords) between radii
r-dr and r+dr.
Args:
origin (3x1 array): Cartesian coordinates of center of sphere.
r (float): Inner radius of shell.
dr (float... | def get_neighbors_in_shell(self, origin, r, dr):
"""
Returns all sites in a shell centered on origin (coords) between radii
r-dr and r+dr.
Args:
origin (3x1 array): Cartesian coordinates of center of sphere.
r (float): Inner radius of shell.
dr (float... | [
"Returns",
"all",
"sites",
"in",
"a",
"shell",
"centered",
"on",
"origin",
"(",
"coords",
")",
"between",
"radii",
"r",
"-",
"dr",
"and",
"r",
"+",
"dr",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2237-L2253 | [
"def",
"get_neighbors_in_shell",
"(",
"self",
",",
"origin",
",",
"r",
",",
"dr",
")",
":",
"outer",
"=",
"self",
".",
"get_sites_in_sphere",
"(",
"origin",
",",
"r",
"+",
"dr",
")",
"inner",
"=",
"r",
"-",
"dr",
"return",
"[",
"(",
"site",
",",
"d... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IMolecule.get_boxed_structure | Creates a Structure from a Molecule by putting the Molecule in the
center of a orthorhombic box. Useful for creating Structure for
calculating molecules using periodic codes.
Args:
a (float): a-lattice parameter.
b (float): b-lattice parameter.
c (float): c-l... | pymatgen/core/structure.py | def get_boxed_structure(self, a, b, c, images=(1, 1, 1),
random_rotation=False, min_dist=1, cls=None,
offset=None, no_cross=False):
"""
Creates a Structure from a Molecule by putting the Molecule in the
center of a orthorhombic box. Useful ... | def get_boxed_structure(self, a, b, c, images=(1, 1, 1),
random_rotation=False, min_dist=1, cls=None,
offset=None, no_cross=False):
"""
Creates a Structure from a Molecule by putting the Molecule in the
center of a orthorhombic box. Useful ... | [
"Creates",
"a",
"Structure",
"from",
"a",
"Molecule",
"by",
"putting",
"the",
"Molecule",
"in",
"the",
"center",
"of",
"a",
"orthorhombic",
"box",
".",
"Useful",
"for",
"creating",
"Structure",
"for",
"calculating",
"molecules",
"using",
"periodic",
"codes",
"... | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2255-L2344 | [
"def",
"get_boxed_structure",
"(",
"self",
",",
"a",
",",
"b",
",",
"c",
",",
"images",
"=",
"(",
"1",
",",
"1",
",",
"1",
")",
",",
"random_rotation",
"=",
"False",
",",
"min_dist",
"=",
"1",
",",
"cls",
"=",
"None",
",",
"offset",
"=",
"None",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IMolecule.get_centered_molecule | Returns a Molecule centered at the center of mass.
Returns:
Molecule centered with center of mass at origin. | pymatgen/core/structure.py | def get_centered_molecule(self):
"""
Returns a Molecule centered at the center of mass.
Returns:
Molecule centered with center of mass at origin.
"""
center = self.center_of_mass
new_coords = np.array(self.cart_coords) - center
return self.__class__(s... | def get_centered_molecule(self):
"""
Returns a Molecule centered at the center of mass.
Returns:
Molecule centered with center of mass at origin.
"""
center = self.center_of_mass
new_coords = np.array(self.cart_coords) - center
return self.__class__(s... | [
"Returns",
"a",
"Molecule",
"centered",
"at",
"the",
"center",
"of",
"mass",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2346-L2358 | [
"def",
"get_centered_molecule",
"(",
"self",
")",
":",
"center",
"=",
"self",
".",
"center_of_mass",
"new_coords",
"=",
"np",
".",
"array",
"(",
"self",
".",
"cart_coords",
")",
"-",
"center",
"return",
"self",
".",
"__class__",
"(",
"self",
".",
"species_... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IMolecule.to | Outputs the molecule to a file or string.
Args:
fmt (str): Format to output to. Defaults to JSON unless filename
is provided. If fmt is specifies, it overrides whatever the
filename is. Options include "xyz", "gjf", "g03", "json". If
you have OpenBabe... | pymatgen/core/structure.py | def to(self, fmt=None, filename=None):
"""
Outputs the molecule to a file or string.
Args:
fmt (str): Format to output to. Defaults to JSON unless filename
is provided. If fmt is specifies, it overrides whatever the
filename is. Options include "xyz",... | def to(self, fmt=None, filename=None):
"""
Outputs the molecule to a file or string.
Args:
fmt (str): Format to output to. Defaults to JSON unless filename
is provided. If fmt is specifies, it overrides whatever the
filename is. Options include "xyz",... | [
"Outputs",
"the",
"molecule",
"to",
"a",
"file",
"or",
"string",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2360-L2415 | [
"def",
"to",
"(",
"self",
",",
"fmt",
"=",
"None",
",",
"filename",
"=",
"None",
")",
":",
"from",
"pymatgen",
".",
"io",
".",
"xyz",
"import",
"XYZ",
"from",
"pymatgen",
".",
"io",
".",
"gaussian",
"import",
"GaussianInput",
"from",
"pymatgen",
".",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IMolecule.from_str | Reads the molecule from a string.
Args:
input_string (str): String to parse.
fmt (str): Format to output to. Defaults to JSON unless filename
is provided. If fmt is specifies, it overrides whatever the
filename is. Options include "xyz", "gjf", "g03", "js... | pymatgen/core/structure.py | def from_str(cls, input_string, fmt):
"""
Reads the molecule from a string.
Args:
input_string (str): String to parse.
fmt (str): Format to output to. Defaults to JSON unless filename
is provided. If fmt is specifies, it overrides whatever the
... | def from_str(cls, input_string, fmt):
"""
Reads the molecule from a string.
Args:
input_string (str): String to parse.
fmt (str): Format to output to. Defaults to JSON unless filename
is provided. If fmt is specifies, it overrides whatever the
... | [
"Reads",
"the",
"molecule",
"from",
"a",
"string",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2418-L2450 | [
"def",
"from_str",
"(",
"cls",
",",
"input_string",
",",
"fmt",
")",
":",
"from",
"pymatgen",
".",
"io",
".",
"xyz",
"import",
"XYZ",
"from",
"pymatgen",
".",
"io",
".",
"gaussian",
"import",
"GaussianInput",
"if",
"fmt",
".",
"lower",
"(",
")",
"==",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | IMolecule.from_file | Reads a molecule from a file. Supported formats include xyz,
gaussian input (gjf|g03|g09|com|inp), Gaussian output (.out|and
pymatgen's JSON serialized molecules. Using openbabel,
many more extensions are supported but requires openbabel to be
installed.
Args:
filena... | pymatgen/core/structure.py | def from_file(cls, filename):
"""
Reads a molecule from a file. Supported formats include xyz,
gaussian input (gjf|g03|g09|com|inp), Gaussian output (.out|and
pymatgen's JSON serialized molecules. Using openbabel,
many more extensions are supported but requires openbabel to be
... | def from_file(cls, filename):
"""
Reads a molecule from a file. Supported formats include xyz,
gaussian input (gjf|g03|g09|com|inp), Gaussian output (.out|and
pymatgen's JSON serialized molecules. Using openbabel,
many more extensions are supported but requires openbabel to be
... | [
"Reads",
"a",
"molecule",
"from",
"a",
"file",
".",
"Supported",
"formats",
"include",
"xyz",
"gaussian",
"input",
"(",
"gjf|g03|g09|com|inp",
")",
"Gaussian",
"output",
"(",
".",
"out|and",
"pymatgen",
"s",
"JSON",
"serialized",
"molecules",
".",
"Using",
"op... | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2453-L2494 | [
"def",
"from_file",
"(",
"cls",
",",
"filename",
")",
":",
"filename",
"=",
"str",
"(",
"filename",
")",
"from",
"pymatgen",
".",
"io",
".",
"gaussian",
"import",
"GaussianOutput",
"with",
"zopen",
"(",
"filename",
")",
"as",
"f",
":",
"contents",
"=",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Structure.append | Append a site to the structure.
Args:
species: Species of inserted site
coords (3x1 array): Coordinates of inserted site
coords_are_cartesian (bool): Whether coordinates are cartesian.
Defaults to False.
validate_proximity (bool): Whether to check... | pymatgen/core/structure.py | def append(self, species, coords, coords_are_cartesian=False,
validate_proximity=False, properties=None):
"""
Append a site to the structure.
Args:
species: Species of inserted site
coords (3x1 array): Coordinates of inserted site
coords_are_ca... | def append(self, species, coords, coords_are_cartesian=False,
validate_proximity=False, properties=None):
"""
Append a site to the structure.
Args:
species: Species of inserted site
coords (3x1 array): Coordinates of inserted site
coords_are_ca... | [
"Append",
"a",
"site",
"to",
"the",
"structure",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2636-L2656 | [
"def",
"append",
"(",
"self",
",",
"species",
",",
"coords",
",",
"coords_are_cartesian",
"=",
"False",
",",
"validate_proximity",
"=",
"False",
",",
"properties",
"=",
"None",
")",
":",
"return",
"self",
".",
"insert",
"(",
"len",
"(",
"self",
")",
",",... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Structure.insert | Insert a site to the structure.
Args:
i (int): Index to insert site
species (species-like): Species of inserted site
coords (3x1 array): Coordinates of inserted site
coords_are_cartesian (bool): Whether coordinates are cartesian.
Defaults to False... | pymatgen/core/structure.py | def insert(self, i, species, coords, coords_are_cartesian=False,
validate_proximity=False, properties=None):
"""
Insert a site to the structure.
Args:
i (int): Index to insert site
species (species-like): Species of inserted site
coords (3x1 ar... | def insert(self, i, species, coords, coords_are_cartesian=False,
validate_proximity=False, properties=None):
"""
Insert a site to the structure.
Args:
i (int): Index to insert site
species (species-like): Species of inserted site
coords (3x1 ar... | [
"Insert",
"a",
"site",
"to",
"the",
"structure",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2658-L2690 | [
"def",
"insert",
"(",
"self",
",",
"i",
",",
"species",
",",
"coords",
",",
"coords_are_cartesian",
"=",
"False",
",",
"validate_proximity",
"=",
"False",
",",
"properties",
"=",
"None",
")",
":",
"if",
"not",
"coords_are_cartesian",
":",
"new_site",
"=",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Structure.replace | Replace a single site. Takes either a species or a dict of species and
occupations.
Args:
i (int): Index of the site in the _sites list.
species (species-like): Species of replacement site
coords (3x1 array): Coordinates of replacement site. If None,
... | pymatgen/core/structure.py | def replace(self, i, species, coords=None, coords_are_cartesian=False,
properties=None):
"""
Replace a single site. Takes either a species or a dict of species and
occupations.
Args:
i (int): Index of the site in the _sites list.
species (species-... | def replace(self, i, species, coords=None, coords_are_cartesian=False,
properties=None):
"""
Replace a single site. Takes either a species or a dict of species and
occupations.
Args:
i (int): Index of the site in the _sites list.
species (species-... | [
"Replace",
"a",
"single",
"site",
".",
"Takes",
"either",
"a",
"species",
"or",
"a",
"dict",
"of",
"species",
"and",
"occupations",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2692-L2716 | [
"def",
"replace",
"(",
"self",
",",
"i",
",",
"species",
",",
"coords",
"=",
"None",
",",
"coords_are_cartesian",
"=",
"False",
",",
"properties",
"=",
"None",
")",
":",
"if",
"coords",
"is",
"None",
":",
"frac_coords",
"=",
"self",
"[",
"i",
"]",
".... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Structure.substitute | Substitute atom at index with a functional group.
Args:
index (int): Index of atom to substitute.
func_grp: Substituent molecule. There are two options:
1. Providing an actual Molecule as the input. The first atom
must be a DummySpecie X, indicating t... | pymatgen/core/structure.py | def substitute(self, index, func_grp, bond_order=1):
"""
Substitute atom at index with a functional group.
Args:
index (int): Index of atom to substitute.
func_grp: Substituent molecule. There are two options:
1. Providing an actual Molecule as the input... | def substitute(self, index, func_grp, bond_order=1):
"""
Substitute atom at index with a functional group.
Args:
index (int): Index of atom to substitute.
func_grp: Substituent molecule. There are two options:
1. Providing an actual Molecule as the input... | [
"Substitute",
"atom",
"at",
"index",
"with",
"a",
"functional",
"group",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2718-L2819 | [
"def",
"substitute",
"(",
"self",
",",
"index",
",",
"func_grp",
",",
"bond_order",
"=",
"1",
")",
":",
"# Find the nearest neighbor that is not a terminal atom.",
"all_non_terminal_nn",
"=",
"[",
"]",
"for",
"nn",
",",
"dist",
"in",
"self",
".",
"get_neighbors",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Structure.remove_species | Remove all occurrences of several species from a structure.
Args:
species: Sequence of species to remove, e.g., ["Li", "Na"]. | pymatgen/core/structure.py | def remove_species(self, species):
"""
Remove all occurrences of several species from a structure.
Args:
species: Sequence of species to remove, e.g., ["Li", "Na"].
"""
new_sites = []
species = [get_el_sp(s) for s in species]
for site in self._sites:... | def remove_species(self, species):
"""
Remove all occurrences of several species from a structure.
Args:
species: Sequence of species to remove, e.g., ["Li", "Na"].
"""
new_sites = []
species = [get_el_sp(s) for s in species]
for site in self._sites:... | [
"Remove",
"all",
"occurrences",
"of",
"several",
"species",
"from",
"a",
"structure",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2821-L2838 | [
"def",
"remove_species",
"(",
"self",
",",
"species",
")",
":",
"new_sites",
"=",
"[",
"]",
"species",
"=",
"[",
"get_el_sp",
"(",
"s",
")",
"for",
"s",
"in",
"species",
"]",
"for",
"site",
"in",
"self",
".",
"_sites",
":",
"new_sp_occu",
"=",
"{",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Structure.remove_sites | Delete sites with at indices.
Args:
indices: Sequence of indices of sites to delete. | pymatgen/core/structure.py | def remove_sites(self, indices):
"""
Delete sites with at indices.
Args:
indices: Sequence of indices of sites to delete.
"""
self._sites = [s for i, s in enumerate(self._sites)
if i not in indices] | def remove_sites(self, indices):
"""
Delete sites with at indices.
Args:
indices: Sequence of indices of sites to delete.
"""
self._sites = [s for i, s in enumerate(self._sites)
if i not in indices] | [
"Delete",
"sites",
"with",
"at",
"indices",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2840-L2848 | [
"def",
"remove_sites",
"(",
"self",
",",
"indices",
")",
":",
"self",
".",
"_sites",
"=",
"[",
"s",
"for",
"i",
",",
"s",
"in",
"enumerate",
"(",
"self",
".",
"_sites",
")",
"if",
"i",
"not",
"in",
"indices",
"]"
] | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Structure.apply_operation | Apply a symmetry operation to the structure and return the new
structure. The lattice is operated by the rotation matrix only.
Coords are operated in full and then transformed to the new lattice.
Args:
symmop (SymmOp): Symmetry operation to apply.
fractional (bool): Whet... | pymatgen/core/structure.py | def apply_operation(self, symmop, fractional=False):
"""
Apply a symmetry operation to the structure and return the new
structure. The lattice is operated by the rotation matrix only.
Coords are operated in full and then transformed to the new lattice.
Args:
symmop (... | def apply_operation(self, symmop, fractional=False):
"""
Apply a symmetry operation to the structure and return the new
structure. The lattice is operated by the rotation matrix only.
Coords are operated in full and then transformed to the new lattice.
Args:
symmop (... | [
"Apply",
"a",
"symmetry",
"operation",
"to",
"the",
"structure",
"and",
"return",
"the",
"new",
"structure",
".",
"The",
"lattice",
"is",
"operated",
"by",
"the",
"rotation",
"matrix",
"only",
".",
"Coords",
"are",
"operated",
"in",
"full",
"and",
"then",
... | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2850-L2883 | [
"def",
"apply_operation",
"(",
"self",
",",
"symmop",
",",
"fractional",
"=",
"False",
")",
":",
"if",
"not",
"fractional",
":",
"self",
".",
"_lattice",
"=",
"Lattice",
"(",
"[",
"symmop",
".",
"apply_rotation_only",
"(",
"row",
")",
"for",
"row",
"in",... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Structure.modify_lattice | Modify the lattice of the structure. Mainly used for changing the
basis.
Args:
new_lattice (Lattice): New lattice | pymatgen/core/structure.py | def modify_lattice(self, new_lattice):
"""
Modify the lattice of the structure. Mainly used for changing the
basis.
Args:
new_lattice (Lattice): New lattice
"""
self._lattice = new_lattice
for site in self._sites:
site.lattice = new_latti... | def modify_lattice(self, new_lattice):
"""
Modify the lattice of the structure. Mainly used for changing the
basis.
Args:
new_lattice (Lattice): New lattice
"""
self._lattice = new_lattice
for site in self._sites:
site.lattice = new_latti... | [
"Modify",
"the",
"lattice",
"of",
"the",
"structure",
".",
"Mainly",
"used",
"for",
"changing",
"the",
"basis",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2886-L2896 | [
"def",
"modify_lattice",
"(",
"self",
",",
"new_lattice",
")",
":",
"self",
".",
"_lattice",
"=",
"new_lattice",
"for",
"site",
"in",
"self",
".",
"_sites",
":",
"site",
".",
"lattice",
"=",
"new_lattice"
] | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Structure.apply_strain | Apply a strain to the lattice.
Args:
strain (float or list): Amount of strain to apply. Can be a float,
or a sequence of 3 numbers. E.g., 0.01 means all lattice
vectors are increased by 1%. This is equivalent to calling
modify_lattice with a lattice w... | pymatgen/core/structure.py | def apply_strain(self, strain):
"""
Apply a strain to the lattice.
Args:
strain (float or list): Amount of strain to apply. Can be a float,
or a sequence of 3 numbers. E.g., 0.01 means all lattice
vectors are increased by 1%. This is equivalent to cal... | def apply_strain(self, strain):
"""
Apply a strain to the lattice.
Args:
strain (float or list): Amount of strain to apply. Can be a float,
or a sequence of 3 numbers. E.g., 0.01 means all lattice
vectors are increased by 1%. This is equivalent to cal... | [
"Apply",
"a",
"strain",
"to",
"the",
"lattice",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2898-L2910 | [
"def",
"apply_strain",
"(",
"self",
",",
"strain",
")",
":",
"s",
"=",
"(",
"1",
"+",
"np",
".",
"array",
"(",
"strain",
")",
")",
"*",
"np",
".",
"eye",
"(",
"3",
")",
"self",
".",
"lattice",
"=",
"Lattice",
"(",
"np",
".",
"dot",
"(",
"self... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Structure.sort | Sort a structure in place. The parameters have the same meaning as in
list.sort. By default, sites are sorted by the electronegativity of
the species. The difference between this method and
get_sorted_structure (which also works in IStructure) is that the
latter returns a new Structure, ... | pymatgen/core/structure.py | def sort(self, key=None, reverse=False):
"""
Sort a structure in place. The parameters have the same meaning as in
list.sort. By default, sites are sorted by the electronegativity of
the species. The difference between this method and
get_sorted_structure (which also works in ISt... | def sort(self, key=None, reverse=False):
"""
Sort a structure in place. The parameters have the same meaning as in
list.sort. By default, sites are sorted by the electronegativity of
the species. The difference between this method and
get_sorted_structure (which also works in ISt... | [
"Sort",
"a",
"structure",
"in",
"place",
".",
"The",
"parameters",
"have",
"the",
"same",
"meaning",
"as",
"in",
"list",
".",
"sort",
".",
"By",
"default",
"sites",
"are",
"sorted",
"by",
"the",
"electronegativity",
"of",
"the",
"species",
".",
"The",
"d... | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2912-L2928 | [
"def",
"sort",
"(",
"self",
",",
"key",
"=",
"None",
",",
"reverse",
"=",
"False",
")",
":",
"self",
".",
"_sites",
".",
"sort",
"(",
"key",
"=",
"key",
",",
"reverse",
"=",
"reverse",
")"
] | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Structure.translate_sites | Translate specific sites by some vector, keeping the sites within the
unit cell.
Args:
indices: Integer or List of site indices on which to perform the
translation.
vector: Translation vector for sites.
frac_coords (bool): Whether the vector correspon... | pymatgen/core/structure.py | def translate_sites(self, indices, vector, frac_coords=True,
to_unit_cell=True):
"""
Translate specific sites by some vector, keeping the sites within the
unit cell.
Args:
indices: Integer or List of site indices on which to perform the
... | def translate_sites(self, indices, vector, frac_coords=True,
to_unit_cell=True):
"""
Translate specific sites by some vector, keeping the sites within the
unit cell.
Args:
indices: Integer or List of site indices on which to perform the
... | [
"Translate",
"specific",
"sites",
"by",
"some",
"vector",
"keeping",
"the",
"sites",
"within",
"the",
"unit",
"cell",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2930-L2957 | [
"def",
"translate_sites",
"(",
"self",
",",
"indices",
",",
"vector",
",",
"frac_coords",
"=",
"True",
",",
"to_unit_cell",
"=",
"True",
")",
":",
"if",
"not",
"isinstance",
"(",
"indices",
",",
"collections",
".",
"abc",
".",
"Iterable",
")",
":",
"indi... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Structure.rotate_sites | Rotate specific sites by some angle around vector at anchor.
Args:
indices (list): List of site indices on which to perform the
translation.
theta (float): Angle in radians
axis (3x1 array): Rotation axis vector.
anchor (3x1 array): Point of rotat... | pymatgen/core/structure.py | def rotate_sites(self, indices=None, theta=0, axis=None, anchor=None,
to_unit_cell=True):
"""
Rotate specific sites by some angle around vector at anchor.
Args:
indices (list): List of site indices on which to perform the
translation.
... | def rotate_sites(self, indices=None, theta=0, axis=None, anchor=None,
to_unit_cell=True):
"""
Rotate specific sites by some angle around vector at anchor.
Args:
indices (list): List of site indices on which to perform the
translation.
... | [
"Rotate",
"specific",
"sites",
"by",
"some",
"angle",
"around",
"vector",
"at",
"anchor",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L2959-L3000 | [
"def",
"rotate_sites",
"(",
"self",
",",
"indices",
"=",
"None",
",",
"theta",
"=",
"0",
",",
"axis",
"=",
"None",
",",
"anchor",
"=",
"None",
",",
"to_unit_cell",
"=",
"True",
")",
":",
"from",
"numpy",
".",
"linalg",
"import",
"norm",
"from",
"nump... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Structure.perturb | Performs a random perturbation of the sites in a structure to break
symmetries.
Args:
distance (float): Distance in angstroms by which to perturb each
site. | pymatgen/core/structure.py | def perturb(self, distance):
"""
Performs a random perturbation of the sites in a structure to break
symmetries.
Args:
distance (float): Distance in angstroms by which to perturb each
site.
"""
def get_rand_vec():
# deals with zer... | def perturb(self, distance):
"""
Performs a random perturbation of the sites in a structure to break
symmetries.
Args:
distance (float): Distance in angstroms by which to perturb each
site.
"""
def get_rand_vec():
# deals with zer... | [
"Performs",
"a",
"random",
"perturbation",
"of",
"the",
"sites",
"in",
"a",
"structure",
"to",
"break",
"symmetries",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L3002-L3019 | [
"def",
"perturb",
"(",
"self",
",",
"distance",
")",
":",
"def",
"get_rand_vec",
"(",
")",
":",
"# deals with zero vectors.",
"vector",
"=",
"np",
".",
"random",
".",
"randn",
"(",
"3",
")",
"vnorm",
"=",
"np",
".",
"linalg",
".",
"norm",
"(",
"vector"... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Structure.make_supercell | Create a supercell.
Args:
scaling_matrix: A scaling matrix for transforming the lattice
vectors. Has to be all integers. Several options are possible:
a. A full 3x3 scaling matrix defining the linear combination
the old lattice vectors. E.g., [[2,... | pymatgen/core/structure.py | def make_supercell(self, scaling_matrix, to_unit_cell=True):
"""
Create a supercell.
Args:
scaling_matrix: A scaling matrix for transforming the lattice
vectors. Has to be all integers. Several options are possible:
a. A full 3x3 scaling matrix defin... | def make_supercell(self, scaling_matrix, to_unit_cell=True):
"""
Create a supercell.
Args:
scaling_matrix: A scaling matrix for transforming the lattice
vectors. Has to be all integers. Several options are possible:
a. A full 3x3 scaling matrix defin... | [
"Create",
"a",
"supercell",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L3021-L3046 | [
"def",
"make_supercell",
"(",
"self",
",",
"scaling_matrix",
",",
"to_unit_cell",
"=",
"True",
")",
":",
"s",
"=",
"self",
"*",
"scaling_matrix",
"if",
"to_unit_cell",
":",
"for",
"site",
"in",
"s",
":",
"site",
".",
"to_unit_cell",
"(",
"in_place",
"=",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Structure.merge_sites | Merges sites (adding occupancies) within tol of each other.
Removes site properties.
Args:
tol (float): Tolerance for distance to merge sites.
mode (str): Three modes supported. "delete" means duplicate sites are
deleted. "sum" means the occupancies are summed fo... | pymatgen/core/structure.py | def merge_sites(self, tol=0.01, mode="sum"):
"""
Merges sites (adding occupancies) within tol of each other.
Removes site properties.
Args:
tol (float): Tolerance for distance to merge sites.
mode (str): Three modes supported. "delete" means duplicate sites are
... | def merge_sites(self, tol=0.01, mode="sum"):
"""
Merges sites (adding occupancies) within tol of each other.
Removes site properties.
Args:
tol (float): Tolerance for distance to merge sites.
mode (str): Three modes supported. "delete" means duplicate sites are
... | [
"Merges",
"sites",
"(",
"adding",
"occupancies",
")",
"within",
"tol",
"of",
"each",
"other",
".",
"Removes",
"site",
"properties",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L3058-L3103 | [
"def",
"merge_sites",
"(",
"self",
",",
"tol",
"=",
"0.01",
",",
"mode",
"=",
"\"sum\"",
")",
":",
"mode",
"=",
"mode",
".",
"lower",
"(",
")",
"[",
"0",
"]",
"from",
"scipy",
".",
"spatial",
".",
"distance",
"import",
"squareform",
"from",
"scipy",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Molecule.append | Appends a site to the molecule.
Args:
species: Species of inserted site
coords: Coordinates of inserted site
validate_proximity (bool): Whether to check if inserted site is
too close to an existing site. Defaults to True.
properties (dict): A dict... | pymatgen/core/structure.py | def append(self, species, coords, validate_proximity=True, properties=None):
"""
Appends a site to the molecule.
Args:
species: Species of inserted site
coords: Coordinates of inserted site
validate_proximity (bool): Whether to check if inserted site is
... | def append(self, species, coords, validate_proximity=True, properties=None):
"""
Appends a site to the molecule.
Args:
species: Species of inserted site
coords: Coordinates of inserted site
validate_proximity (bool): Whether to check if inserted site is
... | [
"Appends",
"a",
"site",
"to",
"the",
"molecule",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L3199-L3215 | [
"def",
"append",
"(",
"self",
",",
"species",
",",
"coords",
",",
"validate_proximity",
"=",
"True",
",",
"properties",
"=",
"None",
")",
":",
"return",
"self",
".",
"insert",
"(",
"len",
"(",
"self",
")",
",",
"species",
",",
"coords",
",",
"validate_... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Molecule.set_charge_and_spin | Set the charge and spin multiplicity.
Args:
charge (int): Charge for the molecule. Defaults to 0.
spin_multiplicity (int): Spin multiplicity for molecule.
Defaults to None, which means that the spin multiplicity is
set to 1 if the molecule has no unpaired... | pymatgen/core/structure.py | def set_charge_and_spin(self, charge, spin_multiplicity=None):
"""
Set the charge and spin multiplicity.
Args:
charge (int): Charge for the molecule. Defaults to 0.
spin_multiplicity (int): Spin multiplicity for molecule.
Defaults to None, which means tha... | def set_charge_and_spin(self, charge, spin_multiplicity=None):
"""
Set the charge and spin multiplicity.
Args:
charge (int): Charge for the molecule. Defaults to 0.
spin_multiplicity (int): Spin multiplicity for molecule.
Defaults to None, which means tha... | [
"Set",
"the",
"charge",
"and",
"spin",
"multiplicity",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L3217-L3244 | [
"def",
"set_charge_and_spin",
"(",
"self",
",",
"charge",
",",
"spin_multiplicity",
"=",
"None",
")",
":",
"self",
".",
"_charge",
"=",
"charge",
"nelectrons",
"=",
"0",
"for",
"site",
"in",
"self",
".",
"_sites",
":",
"for",
"sp",
",",
"amt",
"in",
"s... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Molecule.insert | Insert a site to the molecule.
Args:
i (int): Index to insert site
species: species of inserted site
coords (3x1 array): coordinates of inserted site
validate_proximity (bool): Whether to check if inserted site is
too close to an existing site. De... | pymatgen/core/structure.py | def insert(self, i, species, coords, validate_proximity=False,
properties=None):
"""
Insert a site to the molecule.
Args:
i (int): Index to insert site
species: species of inserted site
coords (3x1 array): coordinates of inserted site
... | def insert(self, i, species, coords, validate_proximity=False,
properties=None):
"""
Insert a site to the molecule.
Args:
i (int): Index to insert site
species: species of inserted site
coords (3x1 array): coordinates of inserted site
... | [
"Insert",
"a",
"site",
"to",
"the",
"molecule",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L3246-L3268 | [
"def",
"insert",
"(",
"self",
",",
"i",
",",
"species",
",",
"coords",
",",
"validate_proximity",
"=",
"False",
",",
"properties",
"=",
"None",
")",
":",
"new_site",
"=",
"Site",
"(",
"species",
",",
"coords",
",",
"properties",
"=",
"properties",
")",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Molecule.remove_species | Remove all occurrences of a species from a molecule.
Args:
species: Species to remove. | pymatgen/core/structure.py | def remove_species(self, species):
"""
Remove all occurrences of a species from a molecule.
Args:
species: Species to remove.
"""
new_sites = []
species = [get_el_sp(sp) for sp in species]
for site in self._sites:
new_sp_occu = {sp: amt fo... | def remove_species(self, species):
"""
Remove all occurrences of a species from a molecule.
Args:
species: Species to remove.
"""
new_sites = []
species = [get_el_sp(sp) for sp in species]
for site in self._sites:
new_sp_occu = {sp: amt fo... | [
"Remove",
"all",
"occurrences",
"of",
"a",
"species",
"from",
"a",
"molecule",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L3270-L3285 | [
"def",
"remove_species",
"(",
"self",
",",
"species",
")",
":",
"new_sites",
"=",
"[",
"]",
"species",
"=",
"[",
"get_el_sp",
"(",
"sp",
")",
"for",
"sp",
"in",
"species",
"]",
"for",
"site",
"in",
"self",
".",
"_sites",
":",
"new_sp_occu",
"=",
"{",... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Molecule.remove_sites | Delete sites with at indices.
Args:
indices: Sequence of indices of sites to delete. | pymatgen/core/structure.py | def remove_sites(self, indices):
"""
Delete sites with at indices.
Args:
indices: Sequence of indices of sites to delete.
"""
self._sites = [self._sites[i] for i in range(len(self._sites))
if i not in indices] | def remove_sites(self, indices):
"""
Delete sites with at indices.
Args:
indices: Sequence of indices of sites to delete.
"""
self._sites = [self._sites[i] for i in range(len(self._sites))
if i not in indices] | [
"Delete",
"sites",
"with",
"at",
"indices",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L3287-L3295 | [
"def",
"remove_sites",
"(",
"self",
",",
"indices",
")",
":",
"self",
".",
"_sites",
"=",
"[",
"self",
".",
"_sites",
"[",
"i",
"]",
"for",
"i",
"in",
"range",
"(",
"len",
"(",
"self",
".",
"_sites",
")",
")",
"if",
"i",
"not",
"in",
"indices",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Molecule.translate_sites | Translate specific sites by some vector, keeping the sites within the
unit cell.
Args:
indices (list): List of site indices on which to perform the
translation.
vector (3x1 array): Translation vector for sites. | pymatgen/core/structure.py | def translate_sites(self, indices=None, vector=None):
"""
Translate specific sites by some vector, keeping the sites within the
unit cell.
Args:
indices (list): List of site indices on which to perform the
translation.
vector (3x1 array): Translat... | def translate_sites(self, indices=None, vector=None):
"""
Translate specific sites by some vector, keeping the sites within the
unit cell.
Args:
indices (list): List of site indices on which to perform the
translation.
vector (3x1 array): Translat... | [
"Translate",
"specific",
"sites",
"by",
"some",
"vector",
"keeping",
"the",
"sites",
"within",
"the",
"unit",
"cell",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L3297-L3315 | [
"def",
"translate_sites",
"(",
"self",
",",
"indices",
"=",
"None",
",",
"vector",
"=",
"None",
")",
":",
"if",
"indices",
"is",
"None",
":",
"indices",
"=",
"range",
"(",
"len",
"(",
"self",
")",
")",
"if",
"vector",
"is",
"None",
":",
"vector",
"... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Molecule.apply_operation | Apply a symmetry operation to the molecule.
Args:
symmop (SymmOp): Symmetry operation to apply. | pymatgen/core/structure.py | def apply_operation(self, symmop):
"""
Apply a symmetry operation to the molecule.
Args:
symmop (SymmOp): Symmetry operation to apply.
"""
def operate_site(site):
new_cart = symmop.operate(site.coords)
return Site(site.species, new_cart,
... | def apply_operation(self, symmop):
"""
Apply a symmetry operation to the molecule.
Args:
symmop (SymmOp): Symmetry operation to apply.
"""
def operate_site(site):
new_cart = symmop.operate(site.coords)
return Site(site.species, new_cart,
... | [
"Apply",
"a",
"symmetry",
"operation",
"to",
"the",
"molecule",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L3375-L3388 | [
"def",
"apply_operation",
"(",
"self",
",",
"symmop",
")",
":",
"def",
"operate_site",
"(",
"site",
")",
":",
"new_cart",
"=",
"symmop",
".",
"operate",
"(",
"site",
".",
"coords",
")",
"return",
"Site",
"(",
"site",
".",
"species",
",",
"new_cart",
",... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | DefectTransformation.apply_transformation | :param structure (bulk structure to be scaled up - typically conventional unit cell)
:return:
defect_structure, with charge applied | pymatgen/transformations/defect_transformations.py | def apply_transformation(self, structure):
"""
:param structure (bulk structure to be scaled up - typically conventional unit cell)
:return:
defect_structure, with charge applied
"""
if structure != self.defect.bulk_structure:
raise ValueError("Defect bulk... | def apply_transformation(self, structure):
"""
:param structure (bulk structure to be scaled up - typically conventional unit cell)
:return:
defect_structure, with charge applied
"""
if structure != self.defect.bulk_structure:
raise ValueError("Defect bulk... | [
":",
"param",
"structure",
"(",
"bulk",
"structure",
"to",
"be",
"scaled",
"up",
"-",
"typically",
"conventional",
"unit",
"cell",
")",
":",
"return",
":",
"defect_structure",
"with",
"charge",
"applied"
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/transformations/defect_transformations.py#L33-L44 | [
"def",
"apply_transformation",
"(",
"self",
",",
"structure",
")",
":",
"if",
"structure",
"!=",
"self",
".",
"defect",
".",
"bulk_structure",
":",
"raise",
"ValueError",
"(",
"\"Defect bulk_structure is not the same as input structure.\"",
")",
"def_structure",
"=",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Polymer._create | create the polymer from the monomer
Args:
monomer (Molecule)
mon_vector (numpy.array): molecule vector that starts from the
start atom index to the end atom index | pymatgen/io/lammps/utils.py | def _create(self, monomer, mon_vector):
"""
create the polymer from the monomer
Args:
monomer (Molecule)
mon_vector (numpy.array): molecule vector that starts from the
start atom index to the end atom index
"""
while self.length != (self.n... | def _create(self, monomer, mon_vector):
"""
create the polymer from the monomer
Args:
monomer (Molecule)
mon_vector (numpy.array): molecule vector that starts from the
start atom index to the end atom index
"""
while self.length != (self.n... | [
"create",
"the",
"polymer",
"from",
"the",
"monomer"
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/io/lammps/utils.py#L93-L107 | [
"def",
"_create",
"(",
"self",
",",
"monomer",
",",
"mon_vector",
")",
":",
"while",
"self",
".",
"length",
"!=",
"(",
"self",
".",
"n_units",
"-",
"1",
")",
":",
"if",
"self",
".",
"linear_chain",
":",
"move_direction",
"=",
"np",
".",
"array",
"(",... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Polymer._next_move_direction | pick a move at random from the list of moves | pymatgen/io/lammps/utils.py | def _next_move_direction(self):
"""
pick a move at random from the list of moves
"""
nmoves = len(self.moves)
move = np.random.randint(1, nmoves+1)
while self.prev_move == (move + 3) % nmoves:
move = np.random.randint(1, nmoves+1)
self.prev_move = move... | def _next_move_direction(self):
"""
pick a move at random from the list of moves
"""
nmoves = len(self.moves)
move = np.random.randint(1, nmoves+1)
while self.prev_move == (move + 3) % nmoves:
move = np.random.randint(1, nmoves+1)
self.prev_move = move... | [
"pick",
"a",
"move",
"at",
"random",
"from",
"the",
"list",
"of",
"moves"
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/io/lammps/utils.py#L109-L118 | [
"def",
"_next_move_direction",
"(",
"self",
")",
":",
"nmoves",
"=",
"len",
"(",
"self",
".",
"moves",
")",
"move",
"=",
"np",
".",
"random",
".",
"randint",
"(",
"1",
",",
"nmoves",
"+",
"1",
")",
"while",
"self",
".",
"prev_move",
"==",
"(",
"mov... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Polymer._align_monomer | rotate the monomer so that it is aligned along the move direction
Args:
monomer (Molecule)
mon_vector (numpy.array): molecule vector that starts from the
start atom index to the end atom index
move_direction (numpy.array): the direction of the polymer chain
... | pymatgen/io/lammps/utils.py | def _align_monomer(self, monomer, mon_vector, move_direction):
"""
rotate the monomer so that it is aligned along the move direction
Args:
monomer (Molecule)
mon_vector (numpy.array): molecule vector that starts from the
start atom index to the end atom i... | def _align_monomer(self, monomer, mon_vector, move_direction):
"""
rotate the monomer so that it is aligned along the move direction
Args:
monomer (Molecule)
mon_vector (numpy.array): molecule vector that starts from the
start atom index to the end atom i... | [
"rotate",
"the",
"monomer",
"so",
"that",
"it",
"is",
"aligned",
"along",
"the",
"move",
"direction"
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/io/lammps/utils.py#L120-L135 | [
"def",
"_align_monomer",
"(",
"self",
",",
"monomer",
",",
"mon_vector",
",",
"move_direction",
")",
":",
"axis",
"=",
"np",
".",
"cross",
"(",
"mon_vector",
",",
"move_direction",
")",
"origin",
"=",
"monomer",
"[",
"self",
".",
"start",
"]",
".",
"coor... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Polymer._add_monomer | extend the polymer molecule by adding a monomer along mon_vector direction
Args:
monomer (Molecule): monomer molecule
mon_vector (numpy.array): monomer vector that points from head to tail.
move_direction (numpy.array): direction along which the monomer
will ... | pymatgen/io/lammps/utils.py | def _add_monomer(self, monomer, mon_vector, move_direction):
"""
extend the polymer molecule by adding a monomer along mon_vector direction
Args:
monomer (Molecule): monomer molecule
mon_vector (numpy.array): monomer vector that points from head to tail.
move... | def _add_monomer(self, monomer, mon_vector, move_direction):
"""
extend the polymer molecule by adding a monomer along mon_vector direction
Args:
monomer (Molecule): monomer molecule
mon_vector (numpy.array): monomer vector that points from head to tail.
move... | [
"extend",
"the",
"polymer",
"molecule",
"by",
"adding",
"a",
"monomer",
"along",
"mon_vector",
"direction"
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/io/lammps/utils.py#L137-L166 | [
"def",
"_add_monomer",
"(",
"self",
",",
"monomer",
",",
"mon_vector",
",",
"move_direction",
")",
":",
"translate_by",
"=",
"self",
".",
"molecule",
".",
"cart_coords",
"[",
"self",
".",
"end",
"]",
"+",
"self",
".",
"link_distance",
"*",
"move_direction",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | PackmolRunner._format_param_val | Internal method to format values in the packmol parameter dictionaries
Args:
param_val:
Some object to turn into String
Returns:
string representation of the object | pymatgen/io/lammps/utils.py | def _format_param_val(self, param_val):
"""
Internal method to format values in the packmol parameter dictionaries
Args:
param_val:
Some object to turn into String
Returns:
string representation of the object
"""
if isinst... | def _format_param_val(self, param_val):
"""
Internal method to format values in the packmol parameter dictionaries
Args:
param_val:
Some object to turn into String
Returns:
string representation of the object
"""
if isinst... | [
"Internal",
"method",
"to",
"format",
"values",
"in",
"the",
"packmol",
"parameter",
"dictionaries"
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/io/lammps/utils.py#L224-L238 | [
"def",
"_format_param_val",
"(",
"self",
",",
"param_val",
")",
":",
"if",
"isinstance",
"(",
"param_val",
",",
"list",
")",
":",
"return",
"' '",
".",
"join",
"(",
"str",
"(",
"x",
")",
"for",
"x",
"in",
"param_val",
")",
"else",
":",
"return",
"str... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | PackmolRunner._set_box | Set the box size for the molecular assembly | pymatgen/io/lammps/utils.py | def _set_box(self):
"""
Set the box size for the molecular assembly
"""
net_volume = 0.0
for idx, mol in enumerate(self.mols):
length = max([np.max(mol.cart_coords[:, i])-np.min(mol.cart_coords[:, i])
for i in range(3)]) + 2.0
ne... | def _set_box(self):
"""
Set the box size for the molecular assembly
"""
net_volume = 0.0
for idx, mol in enumerate(self.mols):
length = max([np.max(mol.cart_coords[:, i])-np.min(mol.cart_coords[:, i])
for i in range(3)]) + 2.0
ne... | [
"Set",
"the",
"box",
"size",
"for",
"the",
"molecular",
"assembly"
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/io/lammps/utils.py#L240-L252 | [
"def",
"_set_box",
"(",
"self",
")",
":",
"net_volume",
"=",
"0.0",
"for",
"idx",
",",
"mol",
"in",
"enumerate",
"(",
"self",
".",
"mols",
")",
":",
"length",
"=",
"max",
"(",
"[",
"np",
".",
"max",
"(",
"mol",
".",
"cart_coords",
"[",
":",
",",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | PackmolRunner._write_input | Write the packmol input file to the input directory.
Args:
input_dir (string): path to the input directory | pymatgen/io/lammps/utils.py | def _write_input(self, input_dir="."):
"""
Write the packmol input file to the input directory.
Args:
input_dir (string): path to the input directory
"""
with open(os.path.join(input_dir, self.input_file), 'wt', encoding="utf-8") as inp:
for k, v in self.... | def _write_input(self, input_dir="."):
"""
Write the packmol input file to the input directory.
Args:
input_dir (string): path to the input directory
"""
with open(os.path.join(input_dir, self.input_file), 'wt', encoding="utf-8") as inp:
for k, v in self.... | [
"Write",
"the",
"packmol",
"input",
"file",
"to",
"the",
"input",
"directory",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/io/lammps/utils.py#L254-L288 | [
"def",
"_write_input",
"(",
"self",
",",
"input_dir",
"=",
"\".\"",
")",
":",
"with",
"open",
"(",
"os",
".",
"path",
".",
"join",
"(",
"input_dir",
",",
"self",
".",
"input_file",
")",
",",
"'wt'",
",",
"encoding",
"=",
"\"utf-8\"",
")",
"as",
"inp"... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | PackmolRunner.run | Write the input file to the scratch directory, run packmol and return
the packed molecule.
Args:
copy_to_current_on_exit (bool): Whether or not to copy the packmol
input/output files from the scratch directory to the current
directory.
site_proper... | pymatgen/io/lammps/utils.py | def run(self, copy_to_current_on_exit=False, site_property=None):
"""
Write the input file to the scratch directory, run packmol and return
the packed molecule.
Args:
copy_to_current_on_exit (bool): Whether or not to copy the packmol
input/output files from t... | def run(self, copy_to_current_on_exit=False, site_property=None):
"""
Write the input file to the scratch directory, run packmol and return
the packed molecule.
Args:
copy_to_current_on_exit (bool): Whether or not to copy the packmol
input/output files from t... | [
"Write",
"the",
"input",
"file",
"to",
"the",
"scratch",
"directory",
"run",
"packmol",
"and",
"return",
"the",
"packed",
"molecule",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/io/lammps/utils.py#L290-L324 | [
"def",
"run",
"(",
"self",
",",
"copy_to_current_on_exit",
"=",
"False",
",",
"site_property",
"=",
"None",
")",
":",
"scratch",
"=",
"tempfile",
".",
"gettempdir",
"(",
")",
"with",
"ScratchDir",
"(",
"scratch",
",",
"copy_to_current_on_exit",
"=",
"copy_to_c... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | PackmolRunner.write_pdb | dump the molecule into pdb file with custom residue name and number. | pymatgen/io/lammps/utils.py | def write_pdb(self, mol, filename, name=None, num=None):
"""
dump the molecule into pdb file with custom residue name and number.
"""
# ugly hack to get around the openbabel issues with inconsistent
# residue labelling.
scratch = tempfile.gettempdir()
with Scratc... | def write_pdb(self, mol, filename, name=None, num=None):
"""
dump the molecule into pdb file with custom residue name and number.
"""
# ugly hack to get around the openbabel issues with inconsistent
# residue labelling.
scratch = tempfile.gettempdir()
with Scratc... | [
"dump",
"the",
"molecule",
"into",
"pdb",
"file",
"with",
"custom",
"residue",
"name",
"and",
"number",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/io/lammps/utils.py#L326-L347 | [
"def",
"write_pdb",
"(",
"self",
",",
"mol",
",",
"filename",
",",
"name",
"=",
"None",
",",
"num",
"=",
"None",
")",
":",
"# ugly hack to get around the openbabel issues with inconsistent",
"# residue labelling.",
"scratch",
"=",
"tempfile",
".",
"gettempdir",
"(",... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | PackmolRunner._set_residue_map | map each residue to the corresponding molecule. | pymatgen/io/lammps/utils.py | def _set_residue_map(self):
"""
map each residue to the corresponding molecule.
"""
self.map_residue_to_mol = {}
lookup = {}
for idx, mol in enumerate(self.mols):
if not mol.formula in lookup:
mol.translate_sites(indices=range(len(mol)),
... | def _set_residue_map(self):
"""
map each residue to the corresponding molecule.
"""
self.map_residue_to_mol = {}
lookup = {}
for idx, mol in enumerate(self.mols):
if not mol.formula in lookup:
mol.translate_sites(indices=range(len(mol)),
... | [
"map",
"each",
"residue",
"to",
"the",
"corresponding",
"molecule",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/io/lammps/utils.py#L349-L360 | [
"def",
"_set_residue_map",
"(",
"self",
")",
":",
"self",
".",
"map_residue_to_mol",
"=",
"{",
"}",
"lookup",
"=",
"{",
"}",
"for",
"idx",
",",
"mol",
"in",
"enumerate",
"(",
"self",
".",
"mols",
")",
":",
"if",
"not",
"mol",
".",
"formula",
"in",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | PackmolRunner.convert_obatoms_to_molecule | Convert list of openbabel atoms to MOlecule.
Args:
atoms ([OBAtom]): list of OBAtom objects
residue_name (str): the key in self.map_residue_to_mol. Usec to
restore the site properties in the final packed molecule.
site_property (str): the site property to be ... | pymatgen/io/lammps/utils.py | def convert_obatoms_to_molecule(self, atoms, residue_name=None, site_property="ff_map"):
"""
Convert list of openbabel atoms to MOlecule.
Args:
atoms ([OBAtom]): list of OBAtom objects
residue_name (str): the key in self.map_residue_to_mol. Usec to
restor... | def convert_obatoms_to_molecule(self, atoms, residue_name=None, site_property="ff_map"):
"""
Convert list of openbabel atoms to MOlecule.
Args:
atoms ([OBAtom]): list of OBAtom objects
residue_name (str): the key in self.map_residue_to_mol. Usec to
restor... | [
"Convert",
"list",
"of",
"openbabel",
"atoms",
"to",
"MOlecule",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/io/lammps/utils.py#L362-L406 | [
"def",
"convert_obatoms_to_molecule",
"(",
"self",
",",
"atoms",
",",
"residue_name",
"=",
"None",
",",
"site_property",
"=",
"\"ff_map\"",
")",
":",
"restore_site_props",
"=",
"True",
"if",
"residue_name",
"is",
"not",
"None",
"else",
"False",
"if",
"restore_si... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | PackmolRunner.restore_site_properties | Restore the site properties for the final packed molecule.
Args:
site_property (str):
filename (str): path to the final packed molecule.
Returns:
Molecule | pymatgen/io/lammps/utils.py | def restore_site_properties(self, site_property="ff_map", filename=None):
"""
Restore the site properties for the final packed molecule.
Args:
site_property (str):
filename (str): path to the final packed molecule.
Returns:
Molecule
"""
... | def restore_site_properties(self, site_property="ff_map", filename=None):
"""
Restore the site properties for the final packed molecule.
Args:
site_property (str):
filename (str): path to the final packed molecule.
Returns:
Molecule
"""
... | [
"Restore",
"the",
"site",
"properties",
"for",
"the",
"final",
"packed",
"molecule",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/io/lammps/utils.py#L408-L443 | [
"def",
"restore_site_properties",
"(",
"self",
",",
"site_property",
"=",
"\"ff_map\"",
",",
"filename",
"=",
"None",
")",
":",
"# only for pdb",
"if",
"not",
"self",
".",
"control_params",
"[",
"\"filetype\"",
"]",
"==",
"\"pdb\"",
":",
"raise",
"ValueError",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | LammpsRunner.run | Write the input/data files and run LAMMPS. | pymatgen/io/lammps/utils.py | def run(self):
"""
Write the input/data files and run LAMMPS.
"""
lammps_cmd = self.lammps_bin + ['-in', self.input_filename]
print("Running: {}".format(" ".join(lammps_cmd)))
p = Popen(lammps_cmd, stdout=PIPE, stderr=PIPE)
(stdout, stderr) = p.communicate()
... | def run(self):
"""
Write the input/data files and run LAMMPS.
"""
lammps_cmd = self.lammps_bin + ['-in', self.input_filename]
print("Running: {}".format(" ".join(lammps_cmd)))
p = Popen(lammps_cmd, stdout=PIPE, stderr=PIPE)
(stdout, stderr) = p.communicate()
... | [
"Write",
"the",
"input",
"/",
"data",
"files",
"and",
"run",
"LAMMPS",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/io/lammps/utils.py#L464-L472 | [
"def",
"run",
"(",
"self",
")",
":",
"lammps_cmd",
"=",
"self",
".",
"lammps_bin",
"+",
"[",
"'-in'",
",",
"self",
".",
"input_filename",
"]",
"print",
"(",
"\"Running: {}\"",
".",
"format",
"(",
"\" \"",
".",
"join",
"(",
"lammps_cmd",
")",
")",
")",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | get_el_sp | Utility method to get an Element or Specie from an input obj.
If obj is in itself an element or a specie, it is returned automatically.
If obj is an int or a string representing an integer, the Element
with the atomic number obj is returned.
If obj is a string, Specie parsing will be attempted (e.g., Mn... | pymatgen/core/periodic_table.py | def get_el_sp(obj):
"""
Utility method to get an Element or Specie from an input obj.
If obj is in itself an element or a specie, it is returned automatically.
If obj is an int or a string representing an integer, the Element
with the atomic number obj is returned.
If obj is a string, Specie par... | def get_el_sp(obj):
"""
Utility method to get an Element or Specie from an input obj.
If obj is in itself an element or a specie, it is returned automatically.
If obj is an int or a string representing an integer, the Element
with the atomic number obj is returned.
If obj is a string, Specie par... | [
"Utility",
"method",
"to",
"get",
"an",
"Element",
"or",
"Specie",
"from",
"an",
"input",
"obj",
".",
"If",
"obj",
"is",
"in",
"itself",
"an",
"element",
"or",
"a",
"specie",
"it",
"is",
"returned",
"automatically",
".",
"If",
"obj",
"is",
"an",
"int",... | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L1554-L1602 | [
"def",
"get_el_sp",
"(",
"obj",
")",
":",
"if",
"isinstance",
"(",
"obj",
",",
"(",
"Element",
",",
"Specie",
",",
"DummySpecie",
")",
")",
":",
"return",
"obj",
"if",
"isinstance",
"(",
"obj",
",",
"(",
"list",
",",
"tuple",
")",
")",
":",
"return... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Element.average_ionic_radius | Average ionic radius for element (with units). The average is taken
over all oxidation states of the element for which data is present. | pymatgen/core/periodic_table.py | def average_ionic_radius(self):
"""
Average ionic radius for element (with units). The average is taken
over all oxidation states of the element for which data is present.
"""
if "Ionic radii" in self._data:
radii = self._data["Ionic radii"]
return sum(rad... | def average_ionic_radius(self):
"""
Average ionic radius for element (with units). The average is taken
over all oxidation states of the element for which data is present.
"""
if "Ionic radii" in self._data:
radii = self._data["Ionic radii"]
return sum(rad... | [
"Average",
"ionic",
"radius",
"for",
"element",
"(",
"with",
"units",
")",
".",
"The",
"average",
"is",
"taken",
"over",
"all",
"oxidation",
"states",
"of",
"the",
"element",
"for",
"which",
"data",
"is",
"present",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L494-L503 | [
"def",
"average_ionic_radius",
"(",
"self",
")",
":",
"if",
"\"Ionic radii\"",
"in",
"self",
".",
"_data",
":",
"radii",
"=",
"self",
".",
"_data",
"[",
"\"Ionic radii\"",
"]",
"return",
"sum",
"(",
"radii",
".",
"values",
"(",
")",
")",
"/",
"len",
"(... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Element.average_cationic_radius | Average cationic radius for element (with units). The average is
taken over all positive oxidation states of the element for which
data is present. | pymatgen/core/periodic_table.py | def average_cationic_radius(self):
"""
Average cationic radius for element (with units). The average is
taken over all positive oxidation states of the element for which
data is present.
"""
if "Ionic radii" in self._data:
radii = [v for k, v in self._data["Io... | def average_cationic_radius(self):
"""
Average cationic radius for element (with units). The average is
taken over all positive oxidation states of the element for which
data is present.
"""
if "Ionic radii" in self._data:
radii = [v for k, v in self._data["Io... | [
"Average",
"cationic",
"radius",
"for",
"element",
"(",
"with",
"units",
")",
".",
"The",
"average",
"is",
"taken",
"over",
"all",
"positive",
"oxidation",
"states",
"of",
"the",
"element",
"for",
"which",
"data",
"is",
"present",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L507-L518 | [
"def",
"average_cationic_radius",
"(",
"self",
")",
":",
"if",
"\"Ionic radii\"",
"in",
"self",
".",
"_data",
":",
"radii",
"=",
"[",
"v",
"for",
"k",
",",
"v",
"in",
"self",
".",
"_data",
"[",
"\"Ionic radii\"",
"]",
".",
"items",
"(",
")",
"if",
"i... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Element.ionic_radii | All ionic radii of the element as a dict of
{oxidation state: ionic radii}. Radii are given in ang. | pymatgen/core/periodic_table.py | def ionic_radii(self):
"""
All ionic radii of the element as a dict of
{oxidation state: ionic radii}. Radii are given in ang.
"""
if "Ionic radii" in self._data:
return {int(k): v for k, v in self._data["Ionic radii"].items()}
else:
return {} | def ionic_radii(self):
"""
All ionic radii of the element as a dict of
{oxidation state: ionic radii}. Radii are given in ang.
"""
if "Ionic radii" in self._data:
return {int(k): v for k, v in self._data["Ionic radii"].items()}
else:
return {} | [
"All",
"ionic",
"radii",
"of",
"the",
"element",
"as",
"a",
"dict",
"of",
"{",
"oxidation",
"state",
":",
"ionic",
"radii",
"}",
".",
"Radii",
"are",
"given",
"in",
"ang",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L537-L545 | [
"def",
"ionic_radii",
"(",
"self",
")",
":",
"if",
"\"Ionic radii\"",
"in",
"self",
".",
"_data",
":",
"return",
"{",
"int",
"(",
"k",
")",
":",
"v",
"for",
"k",
",",
"v",
"in",
"self",
".",
"_data",
"[",
"\"Ionic radii\"",
"]",
".",
"items",
"(",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Element.full_electronic_structure | Full electronic structure as tuple.
E.g., The electronic structure for Fe is represented as:
[(1, "s", 2), (2, "s", 2), (2, "p", 6), (3, "s", 2), (3, "p", 6),
(3, "d", 6), (4, "s", 2)] | pymatgen/core/periodic_table.py | def full_electronic_structure(self):
"""
Full electronic structure as tuple.
E.g., The electronic structure for Fe is represented as:
[(1, "s", 2), (2, "s", 2), (2, "p", 6), (3, "s", 2), (3, "p", 6),
(3, "d", 6), (4, "s", 2)]
"""
estr = self._data["Electronic stru... | def full_electronic_structure(self):
"""
Full electronic structure as tuple.
E.g., The electronic structure for Fe is represented as:
[(1, "s", 2), (2, "s", 2), (2, "p", 6), (3, "s", 2), (3, "p", 6),
(3, "d", 6), (4, "s", 2)]
"""
estr = self._data["Electronic stru... | [
"Full",
"electronic",
"structure",
"as",
"tuple",
".",
"E",
".",
"g",
".",
"The",
"electronic",
"structure",
"for",
"Fe",
"is",
"represented",
"as",
":",
"[",
"(",
"1",
"s",
"2",
")",
"(",
"2",
"s",
"2",
")",
"(",
"2",
"p",
"6",
")",
"(",
"3",
... | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L591-L610 | [
"def",
"full_electronic_structure",
"(",
"self",
")",
":",
"estr",
"=",
"self",
".",
"_data",
"[",
"\"Electronic structure\"",
"]",
"def",
"parse_orbital",
"(",
"orbstr",
")",
":",
"m",
"=",
"re",
".",
"match",
"(",
"r\"(\\d+)([spdfg]+)<sup>(\\d+)</sup>\"",
",",... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Element.valence | # From full electron config obtain valence subshell
# angular moment (L) and number of valence e- (v_e) | pymatgen/core/periodic_table.py | def valence(self):
"""
# From full electron config obtain valence subshell
# angular moment (L) and number of valence e- (v_e)
"""
# the number of valence of noble gas is 0
if self.group == 18:
return (np.nan, 0)
L_symbols = 'SPDFGHIKLMNOQRTUVWXYZ'
... | def valence(self):
"""
# From full electron config obtain valence subshell
# angular moment (L) and number of valence e- (v_e)
"""
# the number of valence of noble gas is 0
if self.group == 18:
return (np.nan, 0)
L_symbols = 'SPDFGHIKLMNOQRTUVWXYZ'
... | [
"#",
"From",
"full",
"electron",
"config",
"obtain",
"valence",
"subshell",
"#",
"angular",
"moment",
"(",
"L",
")",
"and",
"number",
"of",
"valence",
"e",
"-",
"(",
"v_e",
")"
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L613-L633 | [
"def",
"valence",
"(",
"self",
")",
":",
"# the number of valence of noble gas is 0",
"if",
"self",
".",
"group",
"==",
"18",
":",
"return",
"(",
"np",
".",
"nan",
",",
"0",
")",
"L_symbols",
"=",
"'SPDFGHIKLMNOQRTUVWXYZ'",
"valence",
"=",
"[",
"]",
"full_el... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Element.term_symbols | All possible Russell-Saunders term symbol of the Element
eg. L = 1, n_e = 2 (s2)
returns
[['1D2'], ['3P0', '3P1', '3P2'], ['1S0']] | pymatgen/core/periodic_table.py | def term_symbols(self):
"""
All possible Russell-Saunders term symbol of the Element
eg. L = 1, n_e = 2 (s2)
returns
[['1D2'], ['3P0', '3P1', '3P2'], ['1S0']]
"""
L_symbols = 'SPDFGHIKLMNOQRTUVWXYZ'
L, v_e = self.valence
# for one electron i... | def term_symbols(self):
"""
All possible Russell-Saunders term symbol of the Element
eg. L = 1, n_e = 2 (s2)
returns
[['1D2'], ['3P0', '3P1', '3P2'], ['1S0']]
"""
L_symbols = 'SPDFGHIKLMNOQRTUVWXYZ'
L, v_e = self.valence
# for one electron i... | [
"All",
"possible",
"Russell",
"-",
"Saunders",
"term",
"symbol",
"of",
"the",
"Element",
"eg",
".",
"L",
"=",
"1",
"n_e",
"=",
"2",
"(",
"s2",
")",
"returns",
"[[",
"1D2",
"]",
"[",
"3P0",
"3P1",
"3P2",
"]",
"[",
"1S0",
"]]"
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L636-L689 | [
"def",
"term_symbols",
"(",
"self",
")",
":",
"L_symbols",
"=",
"'SPDFGHIKLMNOQRTUVWXYZ'",
"L",
",",
"v_e",
"=",
"self",
".",
"valence",
"# for one electron in subshell L",
"ml",
"=",
"list",
"(",
"range",
"(",
"-",
"L",
",",
"L",
"+",
"1",
")",
")",
"ms... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Element.ground_state_term_symbol | Ground state term symbol
Selected based on Hund's Rule | pymatgen/core/periodic_table.py | def ground_state_term_symbol(self):
"""
Ground state term symbol
Selected based on Hund's Rule
"""
L_symbols = 'SPDFGHIKLMNOQRTUVWXYZ'
term_symbols = self.term_symbols
term_symbol_flat = {term: {"multiplicity": int(term[0]),
"L... | def ground_state_term_symbol(self):
"""
Ground state term symbol
Selected based on Hund's Rule
"""
L_symbols = 'SPDFGHIKLMNOQRTUVWXYZ'
term_symbols = self.term_symbols
term_symbol_flat = {term: {"multiplicity": int(term[0]),
"L... | [
"Ground",
"state",
"term",
"symbol",
"Selected",
"based",
"on",
"Hund",
"s",
"Rule"
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L692-L723 | [
"def",
"ground_state_term_symbol",
"(",
"self",
")",
":",
"L_symbols",
"=",
"'SPDFGHIKLMNOQRTUVWXYZ'",
"term_symbols",
"=",
"self",
".",
"term_symbols",
"term_symbol_flat",
"=",
"{",
"term",
":",
"{",
"\"multiplicity\"",
":",
"int",
"(",
"term",
"[",
"0",
"]",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Element.from_Z | Get an element from an atomic number.
Args:
z (int): Atomic number
Returns:
Element with atomic number z. | pymatgen/core/periodic_table.py | def from_Z(z: int):
"""
Get an element from an atomic number.
Args:
z (int): Atomic number
Returns:
Element with atomic number z.
"""
for sym, data in _pt_data.items():
if data["Atomic no"] == z:
return Element(sym)
... | def from_Z(z: int):
"""
Get an element from an atomic number.
Args:
z (int): Atomic number
Returns:
Element with atomic number z.
"""
for sym, data in _pt_data.items():
if data["Atomic no"] == z:
return Element(sym)
... | [
"Get",
"an",
"element",
"from",
"an",
"atomic",
"number",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L756-L769 | [
"def",
"from_Z",
"(",
"z",
":",
"int",
")",
":",
"for",
"sym",
",",
"data",
"in",
"_pt_data",
".",
"items",
"(",
")",
":",
"if",
"data",
"[",
"\"Atomic no\"",
"]",
"==",
"z",
":",
"return",
"Element",
"(",
"sym",
")",
"raise",
"ValueError",
"(",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Element.from_row_and_group | Returns an element from a row and group number.
Args:
row (int): Row number
group (int): Group number
.. note::
The 18 group number system is used, i.e., Noble gases are group 18. | pymatgen/core/periodic_table.py | def from_row_and_group(row: int, group: int):
"""
Returns an element from a row and group number.
Args:
row (int): Row number
group (int): Group number
.. note::
The 18 group number system is used, i.e., Noble gases are group 18.
"""
... | def from_row_and_group(row: int, group: int):
"""
Returns an element from a row and group number.
Args:
row (int): Row number
group (int): Group number
.. note::
The 18 group number system is used, i.e., Noble gases are group 18.
"""
... | [
"Returns",
"an",
"element",
"from",
"a",
"row",
"and",
"group",
"number",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L772-L787 | [
"def",
"from_row_and_group",
"(",
"row",
":",
"int",
",",
"group",
":",
"int",
")",
":",
"for",
"sym",
"in",
"_pt_data",
".",
"keys",
"(",
")",
":",
"el",
"=",
"Element",
"(",
"sym",
")",
"if",
"el",
".",
"row",
"==",
"row",
"and",
"el",
".",
"... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Element.row | Returns the periodic table row of the element. | pymatgen/core/periodic_table.py | def row(self):
"""
Returns the periodic table row of the element.
"""
z = self.Z
total = 0
if 57 <= z <= 71:
return 8
elif 89 <= z <= 103:
return 9
for i in range(len(_pt_row_sizes)):
total += _pt_row_sizes[i]
... | def row(self):
"""
Returns the periodic table row of the element.
"""
z = self.Z
total = 0
if 57 <= z <= 71:
return 8
elif 89 <= z <= 103:
return 9
for i in range(len(_pt_row_sizes)):
total += _pt_row_sizes[i]
... | [
"Returns",
"the",
"periodic",
"table",
"row",
"of",
"the",
"element",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L808-L823 | [
"def",
"row",
"(",
"self",
")",
":",
"z",
"=",
"self",
".",
"Z",
"total",
"=",
"0",
"if",
"57",
"<=",
"z",
"<=",
"71",
":",
"return",
"8",
"elif",
"89",
"<=",
"z",
"<=",
"103",
":",
"return",
"9",
"for",
"i",
"in",
"range",
"(",
"len",
"(",... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Element.group | Returns the periodic table group of the element. | pymatgen/core/periodic_table.py | def group(self):
"""
Returns the periodic table group of the element.
"""
z = self.Z
if z == 1:
return 1
if z == 2:
return 18
if 3 <= z <= 18:
if (z - 2) % 8 == 0:
return 18
elif (z - 2) % 8 <= 2:
... | def group(self):
"""
Returns the periodic table group of the element.
"""
z = self.Z
if z == 1:
return 1
if z == 2:
return 18
if 3 <= z <= 18:
if (z - 2) % 8 == 0:
return 18
elif (z - 2) % 8 <= 2:
... | [
"Returns",
"the",
"periodic",
"table",
"group",
"of",
"the",
"element",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L826-L854 | [
"def",
"group",
"(",
"self",
")",
":",
"z",
"=",
"self",
".",
"Z",
"if",
"z",
"==",
"1",
":",
"return",
"1",
"if",
"z",
"==",
"2",
":",
"return",
"18",
"if",
"3",
"<=",
"z",
"<=",
"18",
":",
"if",
"(",
"z",
"-",
"2",
")",
"%",
"8",
"=="... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Element.block | Return the block character "s,p,d,f" | pymatgen/core/periodic_table.py | def block(self):
"""
Return the block character "s,p,d,f"
"""
if (self.is_actinoid or self.is_lanthanoid) and self.Z not in [71, 103]:
return "f"
elif self.is_actinoid or self.is_lanthanoid:
return "d"
elif self.group in [1, 2]:
return ... | def block(self):
"""
Return the block character "s,p,d,f"
"""
if (self.is_actinoid or self.is_lanthanoid) and self.Z not in [71, 103]:
return "f"
elif self.is_actinoid or self.is_lanthanoid:
return "d"
elif self.group in [1, 2]:
return ... | [
"Return",
"the",
"block",
"character",
"s",
"p",
"d",
"f"
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L857-L871 | [
"def",
"block",
"(",
"self",
")",
":",
"if",
"(",
"self",
".",
"is_actinoid",
"or",
"self",
".",
"is_lanthanoid",
")",
"and",
"self",
".",
"Z",
"not",
"in",
"[",
"71",
",",
"103",
"]",
":",
"return",
"\"f\"",
"elif",
"self",
".",
"is_actinoid",
"or... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Element.is_transition_metal | True if element is a transition metal. | pymatgen/core/periodic_table.py | def is_transition_metal(self):
"""
True if element is a transition metal.
"""
ns = list(range(21, 31))
ns.extend(list(range(39, 49)))
ns.append(57)
ns.extend(list(range(72, 81)))
ns.append(89)
ns.extend(list(range(104, 113)))
return self.Z ... | def is_transition_metal(self):
"""
True if element is a transition metal.
"""
ns = list(range(21, 31))
ns.extend(list(range(39, 49)))
ns.append(57)
ns.extend(list(range(72, 81)))
ns.append(89)
ns.extend(list(range(104, 113)))
return self.Z ... | [
"True",
"if",
"element",
"is",
"a",
"transition",
"metal",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L881-L891 | [
"def",
"is_transition_metal",
"(",
"self",
")",
":",
"ns",
"=",
"list",
"(",
"range",
"(",
"21",
",",
"31",
")",
")",
"ns",
".",
"extend",
"(",
"list",
"(",
"range",
"(",
"39",
",",
"49",
")",
")",
")",
"ns",
".",
"append",
"(",
"57",
")",
"n... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Element.nmr_quadrupole_moment | Get a dictionary the nuclear electric quadrupole moment in units of
e*millibarns for various isotopes | pymatgen/core/periodic_table.py | def nmr_quadrupole_moment(self):
"""
Get a dictionary the nuclear electric quadrupole moment in units of
e*millibarns for various isotopes
"""
return {k: FloatWithUnit(v, "mbarn")
for k, v in self.data.get("NMR Quadrupole Moment", {}).items()} | def nmr_quadrupole_moment(self):
"""
Get a dictionary the nuclear electric quadrupole moment in units of
e*millibarns for various isotopes
"""
return {k: FloatWithUnit(v, "mbarn")
for k, v in self.data.get("NMR Quadrupole Moment", {}).items()} | [
"Get",
"a",
"dictionary",
"the",
"nuclear",
"electric",
"quadrupole",
"moment",
"in",
"units",
"of",
"e",
"*",
"millibarns",
"for",
"various",
"isotopes"
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L970-L976 | [
"def",
"nmr_quadrupole_moment",
"(",
"self",
")",
":",
"return",
"{",
"k",
":",
"FloatWithUnit",
"(",
"v",
",",
"\"mbarn\"",
")",
"for",
"k",
",",
"v",
"in",
"self",
".",
"data",
".",
"get",
"(",
"\"NMR Quadrupole Moment\"",
",",
"{",
"}",
")",
".",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Element.as_dict | Makes Element obey the general json interface used in pymatgen for
easier serialization. | pymatgen/core/periodic_table.py | def as_dict(self):
"""
Makes Element obey the general json interface used in pymatgen for
easier serialization.
"""
return {"@module": self.__class__.__module__,
"@class": self.__class__.__name__,
"element": self.symbol} | def as_dict(self):
"""
Makes Element obey the general json interface used in pymatgen for
easier serialization.
"""
return {"@module": self.__class__.__module__,
"@class": self.__class__.__name__,
"element": self.symbol} | [
"Makes",
"Element",
"obey",
"the",
"general",
"json",
"interface",
"used",
"in",
"pymatgen",
"for",
"easier",
"serialization",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L999-L1006 | [
"def",
"as_dict",
"(",
"self",
")",
":",
"return",
"{",
"\"@module\"",
":",
"self",
".",
"__class__",
".",
"__module__",
",",
"\"@class\"",
":",
"self",
".",
"__class__",
".",
"__name__",
",",
"\"element\"",
":",
"self",
".",
"symbol",
"}"
] | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Element.print_periodic_table | A pretty ASCII printer for the periodic table, based on some
filter_function.
Args:
filter_function: A filtering function taking an Element as input
and returning a boolean. For example, setting
filter_function = lambda el: el.X > 2 will print a periodic
... | pymatgen/core/periodic_table.py | def print_periodic_table(filter_function: callable = None):
"""
A pretty ASCII printer for the periodic table, based on some
filter_function.
Args:
filter_function: A filtering function taking an Element as input
and returning a boolean. For example, setting
... | def print_periodic_table(filter_function: callable = None):
"""
A pretty ASCII printer for the periodic table, based on some
filter_function.
Args:
filter_function: A filtering function taking an Element as input
and returning a boolean. For example, setting
... | [
"A",
"pretty",
"ASCII",
"printer",
"for",
"the",
"periodic",
"table",
"based",
"on",
"some",
"filter_function",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L1009-L1031 | [
"def",
"print_periodic_table",
"(",
"filter_function",
":",
"callable",
"=",
"None",
")",
":",
"for",
"row",
"in",
"range",
"(",
"1",
",",
"10",
")",
":",
"rowstr",
"=",
"[",
"]",
"for",
"group",
"in",
"range",
"(",
"1",
",",
"19",
")",
":",
"try",... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Specie.ionic_radius | Ionic radius of specie. Returns None if data is not present. | pymatgen/core/periodic_table.py | def ionic_radius(self):
"""
Ionic radius of specie. Returns None if data is not present.
"""
if self._oxi_state in self.ionic_radii:
return self.ionic_radii[self._oxi_state]
d = self._el.data
oxstr = str(int(self._oxi_state))
if oxstr in d.get("Ionic ... | def ionic_radius(self):
"""
Ionic radius of specie. Returns None if data is not present.
"""
if self._oxi_state in self.ionic_radii:
return self.ionic_radii[self._oxi_state]
d = self._el.data
oxstr = str(int(self._oxi_state))
if oxstr in d.get("Ionic ... | [
"Ionic",
"radius",
"of",
"specie",
".",
"Returns",
"None",
"if",
"data",
"is",
"not",
"present",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L1137-L1155 | [
"def",
"ionic_radius",
"(",
"self",
")",
":",
"if",
"self",
".",
"_oxi_state",
"in",
"self",
".",
"ionic_radii",
":",
"return",
"self",
".",
"ionic_radii",
"[",
"self",
".",
"_oxi_state",
"]",
"d",
"=",
"self",
".",
"_el",
".",
"data",
"oxstr",
"=",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Specie.from_string | Returns a Specie from a string representation.
Args:
species_string (str): A typical string representation of a
species, e.g., "Mn2+", "Fe3+", "O2-".
Returns:
A Specie object.
Raises:
ValueError if species_string cannot be intepreted. | pymatgen/core/periodic_table.py | def from_string(species_string: str):
"""
Returns a Specie from a string representation.
Args:
species_string (str): A typical string representation of a
species, e.g., "Mn2+", "Fe3+", "O2-".
Returns:
A Specie object.
Raises:
... | def from_string(species_string: str):
"""
Returns a Specie from a string representation.
Args:
species_string (str): A typical string representation of a
species, e.g., "Mn2+", "Fe3+", "O2-".
Returns:
A Specie object.
Raises:
... | [
"Returns",
"a",
"Specie",
"from",
"a",
"string",
"representation",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L1165-L1190 | [
"def",
"from_string",
"(",
"species_string",
":",
"str",
")",
":",
"m",
"=",
"re",
".",
"search",
"(",
"r\"([A-Z][a-z]*)([0-9.]*)([+\\-])(.*)\"",
",",
"species_string",
")",
"if",
"m",
":",
"sym",
"=",
"m",
".",
"group",
"(",
"1",
")",
"oxi",
"=",
"1",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Specie.get_nmr_quadrupole_moment | Gets the nuclear electric quadrupole moment in units of
e*millibarns
Args:
isotope (str): the isotope to get the quadrupole moment for
default is None, which gets the lowest mass isotope | pymatgen/core/periodic_table.py | def get_nmr_quadrupole_moment(self, isotope=None):
"""
Gets the nuclear electric quadrupole moment in units of
e*millibarns
Args:
isotope (str): the isotope to get the quadrupole moment for
default is None, which gets the lowest mass isotope
"""
... | def get_nmr_quadrupole_moment(self, isotope=None):
"""
Gets the nuclear electric quadrupole moment in units of
e*millibarns
Args:
isotope (str): the isotope to get the quadrupole moment for
default is None, which gets the lowest mass isotope
"""
... | [
"Gets",
"the",
"nuclear",
"electric",
"quadrupole",
"moment",
"in",
"units",
"of",
"e",
"*",
"millibarns"
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L1206-L1229 | [
"def",
"get_nmr_quadrupole_moment",
"(",
"self",
",",
"isotope",
"=",
"None",
")",
":",
"quad_mom",
"=",
"self",
".",
"_el",
".",
"nmr_quadrupole_moment",
"if",
"len",
"(",
"quad_mom",
")",
"==",
"0",
":",
"return",
"0.0",
"if",
"isotope",
"is",
"None",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Specie.get_shannon_radius | Get the local environment specific ionic radius for species.
Args:
cn (str): Coordination using roman letters. Supported values are
I-IX, as well as IIIPY, IVPY and IVSQ.
spin (str): Some species have different radii for different
spins. You can get speci... | pymatgen/core/periodic_table.py | def get_shannon_radius(self, cn: str, spin: str = "",
radius_type: str = "ionic"):
"""
Get the local environment specific ionic radius for species.
Args:
cn (str): Coordination using roman letters. Supported values are
I-IX, as well as IIIP... | def get_shannon_radius(self, cn: str, spin: str = "",
radius_type: str = "ionic"):
"""
Get the local environment specific ionic radius for species.
Args:
cn (str): Coordination using roman letters. Supported values are
I-IX, as well as IIIP... | [
"Get",
"the",
"local",
"environment",
"specific",
"ionic",
"radius",
"for",
"species",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L1231-L1281 | [
"def",
"get_shannon_radius",
"(",
"self",
",",
"cn",
":",
"str",
",",
"spin",
":",
"str",
"=",
"\"\"",
",",
"radius_type",
":",
"str",
"=",
"\"ionic\"",
")",
":",
"radii",
"=",
"self",
".",
"_el",
".",
"data",
"[",
"\"Shannon radii\"",
"]",
"# if cn ==... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | Specie.get_crystal_field_spin | Calculate the crystal field spin based on coordination and spin
configuration. Only works for transition metal species.
Args:
coordination (str): Only oct and tet are supported at the moment.
spin_config (str): Supported keywords are "high" or "low".
Returns:
... | pymatgen/core/periodic_table.py | def get_crystal_field_spin(self, coordination: str = "oct",
spin_config: str = "high"):
"""
Calculate the crystal field spin based on coordination and spin
configuration. Only works for transition metal species.
Args:
coordination (str): Only o... | def get_crystal_field_spin(self, coordination: str = "oct",
spin_config: str = "high"):
"""
Calculate the crystal field spin based on coordination and spin
configuration. Only works for transition metal species.
Args:
coordination (str): Only o... | [
"Calculate",
"the",
"crystal",
"field",
"spin",
"based",
"on",
"coordination",
"and",
"spin",
"configuration",
".",
"Only",
"works",
"for",
"transition",
"metal",
"species",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L1283-L1334 | [
"def",
"get_crystal_field_spin",
"(",
"self",
",",
"coordination",
":",
"str",
"=",
"\"oct\"",
",",
"spin_config",
":",
"str",
"=",
"\"high\"",
")",
":",
"if",
"coordination",
"not",
"in",
"(",
"\"oct\"",
",",
"\"tet\"",
")",
"or",
"spin_config",
"not",
"i... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | DummySpecie.from_string | Returns a Dummy from a string representation.
Args:
species_string (str): A string representation of a dummy
species, e.g., "X2+", "X3+".
Returns:
A DummySpecie object.
Raises:
ValueError if species_string cannot be intepreted. | pymatgen/core/periodic_table.py | def from_string(species_string: str):
"""
Returns a Dummy from a string representation.
Args:
species_string (str): A string representation of a dummy
species, e.g., "X2+", "X3+".
Returns:
A DummySpecie object.
Raises:
ValueE... | def from_string(species_string: str):
"""
Returns a Dummy from a string representation.
Args:
species_string (str): A string representation of a dummy
species, e.g., "X2+", "X3+".
Returns:
A DummySpecie object.
Raises:
ValueE... | [
"Returns",
"a",
"Dummy",
"from",
"a",
"string",
"representation",
"."
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L1479-L1506 | [
"def",
"from_string",
"(",
"species_string",
":",
"str",
")",
":",
"m",
"=",
"re",
".",
"search",
"(",
"r\"([A-Z][a-z]*)([0-9.]*)([+\\-]*)(.*)\"",
",",
"species_string",
")",
"if",
"m",
":",
"sym",
"=",
"m",
".",
"group",
"(",
"1",
")",
"if",
"m",
".",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | DummySpecie.safe_from_composition | Returns a DummySpecie object that can be safely used
with (i.e. not present in) a given composition | pymatgen/core/periodic_table.py | def safe_from_composition(cls, comp: "Composition",
oxidation_state: float = 0):
"""
Returns a DummySpecie object that can be safely used
with (i.e. not present in) a given composition
"""
# We don't want to add a DummySpecie with the same
# ... | def safe_from_composition(cls, comp: "Composition",
oxidation_state: float = 0):
"""
Returns a DummySpecie object that can be safely used
with (i.e. not present in) a given composition
"""
# We don't want to add a DummySpecie with the same
# ... | [
"Returns",
"a",
"DummySpecie",
"object",
"that",
"can",
"be",
"safely",
"used",
"with",
"(",
"i",
".",
"e",
".",
"not",
"present",
"in",
")",
"a",
"given",
"composition"
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/periodic_table.py#L1509-L1523 | [
"def",
"safe_from_composition",
"(",
"cls",
",",
"comp",
":",
"\"Composition\"",
",",
"oxidation_state",
":",
"float",
"=",
"0",
")",
":",
"# We don't want to add a DummySpecie with the same",
"# symbol as anything in the composition, even if the",
"# oxidation state is different... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | DefectCompatibility.process_entry | Process a given Defect entry with qualifiers given from initialization of class.
Order of processing is:
1) perform all possible defect corrections with information given
2) consider delocalization analyses based on qualifier metrics
given initialization of class. If delocali... | pymatgen/analysis/defects/defect_compatibility.py | def process_entry(self, defect_entry):
"""
Process a given Defect entry with qualifiers given from initialization of class.
Order of processing is:
1) perform all possible defect corrections with information given
2) consider delocalization analyses based on qualifier met... | def process_entry(self, defect_entry):
"""
Process a given Defect entry with qualifiers given from initialization of class.
Order of processing is:
1) perform all possible defect corrections with information given
2) consider delocalization analyses based on qualifier met... | [
"Process",
"a",
"given",
"Defect",
"entry",
"with",
"qualifiers",
"given",
"from",
"initialization",
"of",
"class",
".",
"Order",
"of",
"processing",
"is",
":",
"1",
")",
"perform",
"all",
"possible",
"defect",
"corrections",
"with",
"information",
"given",
"2... | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/analysis/defects/defect_compatibility.py#L74-L166 | [
"def",
"process_entry",
"(",
"self",
",",
"defect_entry",
")",
":",
"self",
".",
"perform_all_corrections",
"(",
"defect_entry",
")",
"self",
".",
"delocalization_analysis",
"(",
"defect_entry",
")",
"# apply corrections based on delocalization analysis",
"corrections",
"... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | DefectCompatibility.delocalization_analysis | Do delocalization analysis. To do this, one considers:
i) sampling region of planar averaged electrostatic potential (freysoldt approach)
ii) sampling region of atomic site averaged potentials (kumagai approach)
iii) structural relaxation amount outside of radius considered in kumaga... | pymatgen/analysis/defects/defect_compatibility.py | def delocalization_analysis(self, defect_entry):
"""
Do delocalization analysis. To do this, one considers:
i) sampling region of planar averaged electrostatic potential (freysoldt approach)
ii) sampling region of atomic site averaged potentials (kumagai approach)
iii... | def delocalization_analysis(self, defect_entry):
"""
Do delocalization analysis. To do this, one considers:
i) sampling region of planar averaged electrostatic potential (freysoldt approach)
ii) sampling region of atomic site averaged potentials (kumagai approach)
iii... | [
"Do",
"delocalization",
"analysis",
".",
"To",
"do",
"this",
"one",
"considers",
":",
"i",
")",
"sampling",
"region",
"of",
"planar",
"averaged",
"electrostatic",
"potential",
"(",
"freysoldt",
"approach",
")",
"ii",
")",
"sampling",
"region",
"of",
"atomic",
... | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/analysis/defects/defect_compatibility.py#L275-L318 | [
"def",
"delocalization_analysis",
"(",
"self",
",",
"defect_entry",
")",
":",
"defect_entry",
".",
"parameters",
".",
"update",
"(",
"{",
"'is_compatible'",
":",
"True",
"}",
")",
"#this will be switched to False if delocalization is detected",
"if",
"'freysoldt_meta'",
... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | get_d | Determine the distance of space between
each layer of atoms along c | pymatgen/core/surface.py | def get_d(slab):
"""
Determine the distance of space between
each layer of atoms along c
"""
sorted_sites = sorted(slab, key=lambda site: site.frac_coords[2])
for i, site in enumerate(sorted_sites):
if "%.6f" % (site.frac_coords[2]) == \
"%.6f" % (sorted_sites[i +... | def get_d(slab):
"""
Determine the distance of space between
each layer of atoms along c
"""
sorted_sites = sorted(slab, key=lambda site: site.frac_coords[2])
for i, site in enumerate(sorted_sites):
if "%.6f" % (site.frac_coords[2]) == \
"%.6f" % (sorted_sites[i +... | [
"Determine",
"the",
"distance",
"of",
"space",
"between",
"each",
"layer",
"of",
"atoms",
"along",
"c"
] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/surface.py#L1520-L1534 | [
"def",
"get_d",
"(",
"slab",
")",
":",
"sorted_sites",
"=",
"sorted",
"(",
"slab",
",",
"key",
"=",
"lambda",
"site",
":",
"site",
".",
"frac_coords",
"[",
"2",
"]",
")",
"for",
"i",
",",
"site",
"in",
"enumerate",
"(",
"sorted_sites",
")",
":",
"i... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.