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train | Plane.is_in_list | Checks whether the plane is identical to one of the Planes in the plane_list list of Planes
:param plane_list: List of Planes to be compared to
:return: True if the plane is in the list, False otherwise | pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py | def is_in_list(self, plane_list):
"""
Checks whether the plane is identical to one of the Planes in the plane_list list of Planes
:param plane_list: List of Planes to be compared to
:return: True if the plane is in the list, False otherwise
"""
for plane in plane_list:
... | def is_in_list(self, plane_list):
"""
Checks whether the plane is identical to one of the Planes in the plane_list list of Planes
:param plane_list: List of Planes to be compared to
:return: True if the plane is in the list, False otherwise
"""
for plane in plane_list:
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train | Plane.indices_separate | Returns three lists containing the indices of the points lying on one side of the plane, on the plane
and on the other side of the plane. The dist_tolerance parameter controls the tolerance to which a point
is considered to lie on the plane or not (distance to the plane)
:param points: list of p... | pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py | def indices_separate(self, points, dist_tolerance):
"""
Returns three lists containing the indices of the points lying on one side of the plane, on the plane
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Returns three lists containing the indices of the points lying on one side of the plane, on the plane
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train | Plane.distance_to_point | Computes the absolute distance from the plane to the point
:param point: Point for which distance is computed
:return: Distance between the plane and the point | pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py | def distance_to_point(self, point):
"""
Computes the absolute distance from the plane to the point
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"""
return np.abs(np.dot(self.normal_vector, point) + self.d) | def distance_to_point(self, point):
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Computes the absolute distance from the plane to the point
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"""
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train | Plane.distances | Computes the distances from the plane to each of the points. Positive distances are on the side of the
normal of the plane while negative distances are on the other side
:param points: Points for which distances are computed
:return: Distances from the plane to the points (positive values on the... | pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py | def distances(self, points):
"""
Computes the distances from the plane to each of the points. Positive distances are on the side of the
normal of the plane while negative distances are on the other side
:param points: Points for which distances are computed
:return: Distances fro... | def distances(self, points):
"""
Computes the distances from the plane to each of the points. Positive distances are on the side of the
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train | Plane.distances_indices_sorted | Computes the distances from the plane to each of the points. Positive distances are on the side of the
normal of the plane while negative distances are on the other side. Indices sorting the points from closest
to furthest is also computed.
:param points: Points for which distances are computed
... | pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py | def distances_indices_sorted(self, points, sign=False):
"""
Computes the distances from the plane to each of the points. Positive distances are on the side of the
normal of the plane while negative distances are on the other side. Indices sorting the points from closest
to furthest is al... | def distances_indices_sorted(self, points, sign=False):
"""
Computes the distances from the plane to each of the points. Positive distances are on the side of the
normal of the plane while negative distances are on the other side. Indices sorting the points from closest
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train | Plane.distances_indices_groups | Computes the distances from the plane to each of the points. Positive distances are on the side of the
normal of the plane while negative distances are on the other side. Indices sorting the points from closest
to furthest is also computed. Grouped indices are also given, for which indices of the distan... | pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py | def distances_indices_groups(self, points, delta=None, delta_factor=0.05, sign=False):
"""
Computes the distances from the plane to each of the points. Positive distances are on the side of the
normal of the plane while negative distances are on the other side. Indices sorting the points from cl... | def distances_indices_groups(self, points, delta=None, delta_factor=0.05, sign=False):
"""
Computes the distances from the plane to each of the points. Positive distances are on the side of the
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train | Plane.projectionpoints | Projects each points in the point list pps on plane and returns the list of projected points
:param pps: List of points to project on plane
:return: List of projected point on plane | pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py | def projectionpoints(self, pps):
"""
Projects each points in the point list pps on plane and returns the list of projected points
:param pps: List of points to project on plane
:return: List of projected point on plane
"""
return [pp - np.dot(pp - self.p1, self.normal_vec... | def projectionpoints(self, pps):
"""
Projects each points in the point list pps on plane and returns the list of projected points
:param pps: List of points to project on plane
:return: List of projected point on plane
"""
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train | Plane.orthonormal_vectors | Returns a list of three orthogonal vectors, the two first being parallel to the plane and the
third one is the normal vector of the plane
:return: List of orthogonal vectors
:raise: ValueError if all the coefficients are zero or if there is some other strange error | pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py | def orthonormal_vectors(self):
"""
Returns a list of three orthogonal vectors, the two first being parallel to the plane and the
third one is the normal vector of the plane
:return: List of orthogonal vectors
:raise: ValueError if all the coefficients are zero or if there is some... | def orthonormal_vectors(self):
"""
Returns a list of three orthogonal vectors, the two first being parallel to the plane and the
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train | Plane.orthonormal_vectors_old | Returns a list of three orthogonal vectors, the two first being parallel to the plane and the
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:return: List of orthogonal vectors
:raise: ValueError if all the coefficients are zero or if there is some other strange error | pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py | def orthonormal_vectors_old(self):
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Returns a list of three orthogonal vectors, the two first being parallel to the plane and the
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Returns a list of three orthogonal vectors, the two first being parallel to the plane and the
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train | Plane.project_and_to2dim_ordered_indices | Projects each points in the point list pps on plane and returns the indices that would sort the
list of projected points in anticlockwise order
:param pps: List of points to project on plane
:return: List of indices that would sort the list of projected points | pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py | def project_and_to2dim_ordered_indices(self, pps, plane_center='mean'):
"""
Projects each points in the point list pps on plane and returns the indices that would sort the
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:param pps: List of points to project on plane
:return: List... | def project_and_to2dim_ordered_indices(self, pps, plane_center='mean'):
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Projects each points in the point list pps on plane and returns the indices that would sort the
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train | Plane.project_and_to2dim | Projects the list of points pps to the plane and changes the basis from 3D to the 2D basis of the plane
:param pps: List of points to be projected
:return: :raise: | pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py | def project_and_to2dim(self, pps, plane_center):
"""
Projects the list of points pps to the plane and changes the basis from 3D to the 2D basis of the plane
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proj = self.projectionpoints(pps)
[u1, u2, ... | def project_and_to2dim(self, pps, plane_center):
"""
Projects the list of points pps to the plane and changes the basis from 3D to the 2D basis of the plane
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proj = self.projectionpoints(pps)
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train | open_ring | Function to actually open a ring using OpenBabel's local opt. Given a molecule
graph and a bond, convert the molecule graph into an OpenBabel molecule, remove
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self.steps, and then convert the resulting structure back into a molecul... | pymatgen/analysis/fragmenter.py | def open_ring(mol_graph, bond, opt_steps):
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Function to actually open a ring using OpenBabel's local opt. Given a molecule
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Function to actually open a ring using OpenBabel's local opt. Given a molecule
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train | Fragmenter._fragment_one_level | Perform one step of iterative fragmentation on a list of molecule graphs. Loop through the graphs,
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"""
Perform one step of iterative fragmentation on a list of molecule graphs. Loop through the graphs,
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train | Cohp.as_dict | Json-serializable dict representation of COHP. | pymatgen/electronic_structure/cohp.py | def as_dict(self):
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Json-serializable dict representation of COHP.
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spin: Spin. Can be parsed as spin object, integer (-1/1)
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spin: Spin. Can be parsed as spin object, integer (-1/1)
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energy: Energy to return the COHP value for.
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train | Cohp.has_antibnd_states_below_efermi | Returns dict indicating if there are antibonding states below the Fermi level depending on the spin
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train | Cohp.from_dict | Returns a COHP object from a dict representation of the COHP. | pymatgen/electronic_structure/cohp.py | def from_dict(cls, d):
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train | CompleteCohp.as_dict | Json-serializable dict representation of CompleteCohp. | pymatgen/electronic_structure/cohp.py | def as_dict(self):
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train | CompleteCohp.get_summed_cohp_by_label_and_orbital_list | Returns a COHP object that includes a summed COHP divided by divisor
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label_list: list of labels for the COHP that should be included in the summed cohp
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train | CompleteCohp.from_dict | Returns CompleteCohp object from dict representation. | pymatgen/electronic_structure/cohp.py | def from_dict(cls, d):
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Creates a CompleteCohp object from an output file of a COHP
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Creates a CompleteCohp object from an output file of a COHP
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train | IcohpValue.icohpvalue | Args:
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icohpvalue (float) corresponding to chosen spin | pymatgen/electronic_structure/cohp.py | def icohpvalue(self, spin=Spin.up):
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spin: Spin.up or Spin.down
Returns:
icohpvalue (float) corresponding to chosen spin
"""
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spin: Spin.up or Spin.down
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icohpvalue (float) corresponding to chosen spin
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train | IcohpValue.summed_icohp | Adds ICOHPs of both spin channels for spin polarized compounds
Returns:
icohp value in eV | pymatgen/electronic_structure/cohp.py | def summed_icohp(self):
"""
Adds ICOHPs of both spin channels for spin polarized compounds
Returns:
icohp value in eV
"""
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Adds ICOHPs of both spin channels for spin polarized compounds
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icohp value in eV
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train | IcohpCollection.get_icohp_by_label | get an icohp value for a certain bond as indicated by the label (bond labels starting by "1" as in ICOHPLIST/ICOOPLIST)
Args:
label: label in str format (usually the bond number in Icohplist.lobster/Icooplist.lobster
summed_spin_channels: Boolean to indicate whether the ICOHPs/ICOOPs of ... | pymatgen/electronic_structure/cohp.py | def get_icohp_by_label(self, label, summed_spin_channels=True, spin=Spin.up):
"""
get an icohp value for a certain bond as indicated by the label (bond labels starting by "1" as in ICOHPLIST/ICOOPLIST)
Args:
label: label in str format (usually the bond number in Icohplist.lobster/Ico... | def get_icohp_by_label(self, label, summed_spin_channels=True, spin=Spin.up):
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get an icohp value for a certain bond as indicated by the label (bond labels starting by "1" as in ICOHPLIST/ICOOPLIST)
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train | IcohpCollection.get_summed_icohp_by_label_list | get the sum of several ICOHP values that are indicated by a list of labels (labels of the bonds are the same as in ICOHPLIST/ICOOPLIST)
Args:
label_list: list of labels of the ICOHPs/ICOOPs that should be summed
divisor: is used to divide the sum
summed_spin_channels: Boolean... | pymatgen/electronic_structure/cohp.py | def get_summed_icohp_by_label_list(self, label_list, divisor=1.0, summed_spin_channels=True, spin=Spin.up):
"""
get the sum of several ICOHP values that are indicated by a list of labels (labels of the bonds are the same as in ICOHPLIST/ICOOPLIST)
Args:
label_list: list of labels of ... | def get_summed_icohp_by_label_list(self, label_list, divisor=1.0, summed_spin_channels=True, spin=Spin.up):
"""
get the sum of several ICOHP values that are indicated by a list of labels (labels of the bonds are the same as in ICOHPLIST/ICOOPLIST)
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label_list: list of labels of ... | [
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train | IcohpCollection.get_icohp_dict_by_bondlengths | get a dict of IcohpValues corresponding to certaind bond lengths
Args:
minbondlength: defines the minimum of the bond lengths of the bonds
maxbondlength: defines the maximum of the bond lengths of the bonds
Returns:
dict of IcohpValues, the keys correspond to the val... | pymatgen/electronic_structure/cohp.py | def get_icohp_dict_by_bondlengths(self, minbondlength=0.0, maxbondlength=8.0):
"""
get a dict of IcohpValues corresponding to certaind bond lengths
Args:
minbondlength: defines the minimum of the bond lengths of the bonds
maxbondlength: defines the maximum of the bond len... | def get_icohp_dict_by_bondlengths(self, minbondlength=0.0, maxbondlength=8.0):
"""
get a dict of IcohpValues corresponding to certaind bond lengths
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minbondlength: defines the minimum of the bond lengths of the bonds
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train | IcohpCollection.get_icohp_dict_of_site | get a dict of IcohpValue for a certain site (indicated by integer)
Args:
site: integer describing the site of interest, order as in Icohplist.lobster/Icooplist.lobster, starts at 0
minsummedicohp: float, minimal icohp/icoop of the bonds that are considered. It is the summed ICOHP value f... | pymatgen/electronic_structure/cohp.py | def get_icohp_dict_of_site(self, site, minsummedicohp=None, maxsummedicohp=None, minbondlength=0.0,
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"""
get a dict of IcohpValue for a certain site (indicated by integer)
Args:
site: integer describing the site of... | def get_icohp_dict_of_site(self, site, minsummedicohp=None, maxsummedicohp=None, minbondlength=0.0,
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"""
get a dict of IcohpValue for a certain site (indicated by integer)
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train | IcohpCollection.extremum_icohpvalue | get ICOHP/ICOOP of strongest bond
Args:
summed_spin_channels: Boolean to indicate whether the ICOHPs/ICOOPs of both spin channels should be summed
spin: if summed_spin_channels is equal to False, this spin indicates which spin channel should be returned
Returns:
lowe... | pymatgen/electronic_structure/cohp.py | def extremum_icohpvalue(self, summed_spin_channels=True, spin=Spin.up):
"""
get ICOHP/ICOOP of strongest bond
Args:
summed_spin_channels: Boolean to indicate whether the ICOHPs/ICOOPs of both spin channels should be summed
spin: if summed_spin_channels is equal to False,... | def extremum_icohpvalue(self, summed_spin_channels=True, spin=Spin.up):
"""
get ICOHP/ICOOP of strongest bond
Args:
summed_spin_channels: Boolean to indicate whether the ICOHPs/ICOOPs of both spin channels should be summed
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train | Site.distance | Get distance between two sites.
Args:
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Returns:
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"""
Get distance between two sites.
Args:
other: Other site.
Returns:
Distance (float)
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return np.linalg.norm(other.coords - self.coords) | def distance(self, other):
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train | Site.distance_from_point | Returns distance between the site and a point in space.
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pt: Cartesian coordinates of point.
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Distance (float) | pymatgen/core/sites.py | def distance_from_point(self, pt):
"""
Returns distance between the site and a point in space.
Args:
pt: Cartesian coordinates of point.
Returns:
Distance (float)
"""
return np.linalg.norm(np.array(pt) - self.coords) | def distance_from_point(self, pt):
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train | Site.species_string | String representation of species on the site. | pymatgen/core/sites.py | def species_string(self):
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String representation of species on the site.
"""
if self.is_ordered:
return list(self.species.keys())[0].__str__()
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sorted_species = sorted(self.species.keys())
return ", ".join(["{}:{:.3f}".format(sp, self.s... | def species_string(self):
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String representation of species on the site.
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train | Site.is_ordered | True if site is an ordered site, i.e., with a single species with
occupancy 1. | pymatgen/core/sites.py | def is_ordered(self):
"""
True if site is an ordered site, i.e., with a single species with
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"""
totaloccu = self.species.num_atoms
return totaloccu == 1 and len(self.species) == 1 | def is_ordered(self):
"""
True if site is an ordered site, i.e., with a single species with
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totaloccu = self.species.num_atoms
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train | Site.as_dict | Json-serializable dict representation for Site. | pymatgen/core/sites.py | def as_dict(self):
"""
Json-serializable dict representation for Site.
"""
species_list = []
for spec, occu in self.species.items():
d = spec.as_dict()
del d["@module"]
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d["occu"] = occu
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species_list = []
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train | Site.from_dict | Create Site from dict representation | pymatgen/core/sites.py | def from_dict(cls, d):
"""
Create Site from dict representation
"""
atoms_n_occu = {}
for sp_occu in d["species"]:
if "oxidation_state" in sp_occu and Element.is_valid_symbol(
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... | def from_dict(cls, d):
"""
Create Site from dict representation
"""
atoms_n_occu = {}
for sp_occu in d["species"]:
if "oxidation_state" in sp_occu and Element.is_valid_symbol(
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Sets Lattice associated with PeriodicSite
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train | PeriodicSite.coords | Fractional a coordinate | pymatgen/core/sites.py | def coords(self, coords):
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Fractional a coordinate
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self._coords = np.array(coords)
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Fractional a coordinate
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train | PeriodicSite.frac_coords | Fractional a coordinate | pymatgen/core/sites.py | def frac_coords(self, frac_coords):
"""
Fractional a coordinate
"""
self._frac_coords = np.array(frac_coords)
self._coords = self._lattice.get_cartesian_coords(self._frac_coords) | def frac_coords(self, frac_coords):
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train | PeriodicSite.to_unit_cell | Move frac coords to within the unit cell cell. | pymatgen/core/sites.py | def to_unit_cell(self, in_place=False):
"""
Move frac coords to within the unit cell cell.
"""
frac_coords = np.mod(self.frac_coords, 1)
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train | PeriodicSite.is_periodic_image | Returns True if sites are periodic images of each other.
Args:
other (PeriodicSite): Other site
tolerance (float): Tolerance to compare fractional coordinates
check_lattice (bool): Whether to check if the two sites have the
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Returns:
... | pymatgen/core/sites.py | def is_periodic_image(self, other, tolerance=1e-8, check_lattice=True):
"""
Returns True if sites are periodic images of each other.
Args:
other (PeriodicSite): Other site
tolerance (float): Tolerance to compare fractional coordinates
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Returns True if sites are periodic images of each other.
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train | PeriodicSite.distance_and_image_from_frac_coords | Gets distance between site and a fractional coordinate assuming
periodic boundary conditions. If the index jimage of two sites atom j
is not specified it selects the j image nearest to the i atom and
returns the distance and jimage indices in terms of lattice vector
translations. If the ... | pymatgen/core/sites.py | def distance_and_image_from_frac_coords(self, fcoords, jimage=None):
"""
Gets distance between site and a fractional coordinate assuming
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is not specified it selects the j image nearest to the i atom and
returns... | def distance_and_image_from_frac_coords(self, fcoords, jimage=None):
"""
Gets distance between site and a fractional coordinate assuming
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Json-serializable dict representation of PeriodicSite.
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verbosity (int): Verbosity level. Default of 0 only includes the
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Json-serializable dict representation of PeriodicSite.
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train | get_energies | Doc string. | pymatgen/cli/pmg_analyze.py | def get_energies(rootdir, reanalyze, verbose, detailed, sort, fmt):
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Doc string.
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train | NDCalculator.get_pattern | Calculates the powder neutron diffraction pattern for a structure.
Args:
structure (Structure): Input structure
scaled (bool): Whether to return scaled intensities. The maximum
peak is set to a value of 100. Defaults to True. Use False if
you need the abs... | pymatgen/analysis/diffraction/neutron.py | def get_pattern(self, structure, scaled=True, two_theta_range=(0, 90)):
"""
Calculates the powder neutron diffraction pattern for a structure.
Args:
structure (Structure): Input structure
scaled (bool): Whether to return scaled intensities. The maximum
pe... | def get_pattern(self, structure, scaled=True, two_theta_range=(0, 90)):
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Calculates the powder neutron diffraction pattern for a structure.
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structure (Structure): Input structure
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train | SymmetrizedStructure.find_equivalent_sites | Finds all symmetrically equivalent sites for a particular site
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site (PeriodicSite): A site in the structure
Returns:
([PeriodicSite]): List of all symmetrically equivalent sites. | pymatgen/symmetry/structure.py | def find_equivalent_sites(self, site):
"""
Finds all symmetrically equivalent sites for a particular site
Args:
site (PeriodicSite): A site in the structure
Returns:
([PeriodicSite]): List of all symmetrically equivalent sites.
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Finds all symmetrically equivalent sites for a particular site
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site (PeriodicSite): A site in the structure
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([PeriodicSite]): List of all symmetrically equivalent sites.
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train | Nwchem2Fiesta.run | Performs actual NWCHEM2FIESTA run | pymatgen/io/fiesta.py | def run(self):
"""
Performs actual NWCHEM2FIESTA run
"""
init_folder = os.getcwd()
os.chdir(self.folder)
with zopen(self.log_file, 'w') as fout:
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"""
Performs actual NWCHEM2FIESTA run
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os.chdir(self.folder)
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train | Fiesta_run.gw_run | Performs FIESTA (gw) run | pymatgen/io/fiesta.py | def gw_run(self):
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Performs FIESTA (gw) run
"""
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Performs FIESTA (gw) run
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train | Basis_set_reader.set_n_nlmo | :return: the number of nlm orbitals for the basis set | pymatgen/io/fiesta.py | def set_n_nlmo(self):
"""
:return: the number of nlm orbitals for the basis set
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data_tmp.pop('lmax')
data_tmp.pop('n_nlo')
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nnlmo = 0
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train | Basis_set_reader.infos_on_basis_set | infos on the basis set as in Fiesta log | pymatgen/io/fiesta.py | def infos_on_basis_set(self):
"""
infos on the basis set as in Fiesta log
"""
o = []
o.append("=========================================")
o.append("Reading basis set:")
o.append("")
o.append(" Basis set for {} atom ".format(str(self.filename)))
o.... | def infos_on_basis_set(self):
"""
infos on the basis set as in Fiesta log
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train | FiestaInput.set_auxiliary_basis_set | copy in the desired folder the needed auxiliary basis set "X2.ion" where X is a specie.
:param auxiliary_folder: folder where the auxiliary basis sets are stored
:param auxiliary_basis_set_type: type of basis set (string to be found in the extension of the file name; must be in lower case)
... | pymatgen/io/fiesta.py | def set_auxiliary_basis_set(self, folder, auxiliary_folder,
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"""
copy in the desired folder the needed auxiliary basis set "X2.ion" where X is a specie.
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copy in the desired folder the needed auxiliary basis set "X2.ion" where X is a specie.
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train | FiestaInput.set_GW_options | Set parameters in cell.in for a GW computation
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:param nc_band: number of conduction bands to correct with GW
:param n_iteration: number of iteration
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Set parameters in cell.in for a GW computation
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Set parameters in cell.in for a GW computation
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train | FiestaInput.make_FULL_BSE_Densities_folder | mkdir "FULL_BSE_Densities" folder (needed for bse run) in the desired folder | pymatgen/io/fiesta.py | def make_FULL_BSE_Densities_folder(self, folder):
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train | FiestaInput.set_BSE_options | Set parameters in cell.in for a BSE computation
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Set parameters in cell.in for a BSE computation
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train | FiestaInput.dump_BSE_data_in_GW_run | :param BSE_dump: boolean
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train | FiestaInput.infos_on_system | Returns infos on initial parameters as in the log file of Fiesta | pymatgen/io/fiesta.py | def infos_on_system(self):
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Returns infos on initial parameters as in the log file of Fiesta
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train | FiestaInput.from_string | Read an FiestaInput from a string. Currently tested to work with
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train | TransformedStructure.undo_last_change | Undo the last change in the TransformedStructure.
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Undo the last change in the TransformedStructure.
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Undo the last change in the TransformedStructure.
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train | TransformedStructure.redo_next_change | Redo the last undone change in the TransformedStructure.
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train | TransformedStructure.get_vasp_input | Returns VASP input as a dict of vasp objects.
Args:
vasp_input_set (pymatgen.io.vaspio_set.VaspInputSet): input set
to create vasp input files from structures | pymatgen/alchemy/materials.py | def get_vasp_input(self, vasp_input_set=MPRelaxSet, **kwargs):
"""
Returns VASP input as a dict of vasp objects.
Args:
vasp_input_set (pymatgen.io.vaspio_set.VaspInputSet): input set
to create vasp input files from structures
"""
d = vasp_input_set(se... | def get_vasp_input(self, vasp_input_set=MPRelaxSet, **kwargs):
"""
Returns VASP input as a dict of vasp objects.
Args:
vasp_input_set (pymatgen.io.vaspio_set.VaspInputSet): input set
to create vasp input files from structures
"""
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train | TransformedStructure.write_vasp_input | Writes VASP input to an output_dir.
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output_dir: Directory to output files
create_directory: Create the directory if not present... | pymatgen/alchemy/materials.py | def write_vasp_input(self, vasp_input_set=MPRelaxSet, output_dir=".",
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"""
Writes VASP input to an output_dir.
Args:
vasp_input_set:
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"""
Writes VASP input to an output_dir.
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train | TransformedStructure.structures | Copy of all structures in the TransformedStructure. A
structure is stored after every single transformation. | pymatgen/alchemy/materials.py | def structures(self):
"""
Copy of all structures in the TransformedStructure. A
structure is stored after every single transformation.
"""
hstructs = [Structure.from_dict(s['input_structure'])
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return hst... | def structures(self):
"""
Copy of all structures in the TransformedStructure. A
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"""
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train | TransformedStructure.from_cif_string | Generates TransformedStructure from a cif string.
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cif_string (str): Input cif string. Should contain only one
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Generates TransformedStructure from a cif string.
Args:
cif_string (str): Input cif string. Should contain only one
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train | TransformedStructure.from_poscar_string | Generates TransformedStructure from a poscar string.
Args:
poscar_string (str): Input POSCAR string.
transformations ([Transformations]): Sequence of transformations
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"""
Generates TransformedStructure from a poscar string.
Args:
poscar_string (str): Input POSCAR string.
transformations ([Transformations]): Sequence of transformations
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Generates TransformedStructure from a poscar string.
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poscar_string (str): Input POSCAR string.
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train | TransformedStructure.as_dict | Dict representation of the TransformedStructure. | pymatgen/alchemy/materials.py | def as_dict(self):
"""
Dict representation of the TransformedStructure.
"""
d = self.final_structure.as_dict()
d["@module"] = self.__class__.__module__
d["@class"] = self.__class__.__name__
d["history"] = jsanitize(self.history)
d["version"] = __version__
... | def as_dict(self):
"""
Dict representation of the TransformedStructure.
"""
d = self.final_structure.as_dict()
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d["@class"] = self.__class__.__name__
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train | TransformedStructure.from_dict | Creates a TransformedStructure from a dict. | pymatgen/alchemy/materials.py | def from_dict(cls, d):
"""
Creates a TransformedStructure from a dict.
"""
s = Structure.from_dict(d)
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train | TransformedStructure.from_snl | Create TransformedStructure from SNL.
Args:
snl (StructureNL): Starting snl
Returns:
TransformedStructure | pymatgen/alchemy/materials.py | def from_snl(cls, snl):
"""
Create TransformedStructure from SNL.
Args:
snl (StructureNL): Starting snl
Returns:
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"""
hist = []
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Create TransformedStructure from SNL.
Args:
snl (StructureNL): Starting snl
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TransformedStructure
"""
hist = []
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train | LDos.from_file | Creates LDos object from raw Feff ldos files by
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ldos02.dat...
Args:
feff_inp_file (str): input file of run to obtain structure
ldos_file (str): output ldos file of run to obtain dos info, etc. | pymatgen/io/feff/outputs.py | def from_file(feff_inp_file='feff.inp', ldos_file='ldos'):
""""
Creates LDos object from raw Feff ldos files by
by assuming they are numbered consecutively, i.e. ldos01.dat
ldos02.dat...
Args:
feff_inp_file (str): input file of run to obtain structure
ldo... | def from_file(feff_inp_file='feff.inp', ldos_file='ldos'):
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Creates LDos object from raw Feff ldos files by
by assuming they are numbered consecutively, i.e. ldos01.dat
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feff_inp_file (str): input file of run to obtain structure
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train | LDos.charge_transfer_from_file | Get charge transfer from file.
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feff_inp_file (str): name of feff.inp file for run
ldos_file (str): ldos filename for run, assume consequetive order,
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dictionary of dictionaries in order of potential site... | pymatgen/io/feff/outputs.py | def charge_transfer_from_file(feff_inp_file, ldos_file):
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Get charge transfer from file.
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feff_inp_file (str): name of feff.inp file for run
ldos_file (str): ldos filename for run, assume consequetive order,
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... | def charge_transfer_from_file(feff_inp_file, ldos_file):
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Get charge transfer from file.
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feff_inp_file (str): name of feff.inp file for run
ldos_file (str): ldos filename for run, assume consequetive order,
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train | LDos.charge_transfer_to_string | returns shrage transfer as string | pymatgen/io/feff/outputs.py | def charge_transfer_to_string(self):
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ch = self.charge_transfer
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train | Xmu.from_file | Get Xmu from file.
Args:
xmu_dat_file (str): filename and path for xmu.dat
feff_inp_file (str): filename and path of feff.inp input file
Returns:
Xmu object | pymatgen/io/feff/outputs.py | def from_file(xmu_dat_file="xmu.dat", feff_inp_file="feff.inp"):
"""
Get Xmu from file.
Args:
xmu_dat_file (str): filename and path for xmu.dat
feff_inp_file (str): filename and path of feff.inp input file
Returns:
Xmu object
"""
dat... | def from_file(xmu_dat_file="xmu.dat", feff_inp_file="feff.inp"):
"""
Get Xmu from file.
Args:
xmu_dat_file (str): filename and path for xmu.dat
feff_inp_file (str): filename and path of feff.inp input file
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Xmu object
"""
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train | Xmu.material_formula | Returns chemical formula of material from feff.inp file | pymatgen/io/feff/outputs.py | def material_formula(self):
"""
Returns chemical formula of material from feff.inp file
"""
try:
form = self.header.formula
except IndexError:
form = 'No formula provided'
return "".join(map(str, form)) | def material_formula(self):
"""
Returns chemical formula of material from feff.inp file
"""
try:
form = self.header.formula
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form = 'No formula provided'
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train | Xmu.as_dict | Returns dict representations of Xmu object | pymatgen/io/feff/outputs.py | def as_dict(self):
"""
Returns dict representations of Xmu object
"""
d = MSONable.as_dict(self)
d["data"] = self.data.tolist()
return d | def as_dict(self):
"""
Returns dict representations of Xmu object
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d = MSONable.as_dict(self)
d["data"] = self.data.tolist()
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train | iterlines | A generator form of s.split('\n') for reducing memory overhead.
Parameters
----------
s : str
A multi-line string.
Yields
------
line : str
A string. | pymatgen/io/adf.py | def iterlines(s):
"""
A generator form of s.split('\n') for reducing memory overhead.
Parameters
----------
s : str
A multi-line string.
Yields
------
line : str
A string.
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if next... | def iterlines(s):
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A generator form of s.split('\n') for reducing memory overhead.
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A multi-line string.
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line : str
A string.
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"""
Parse the ADF outputs. There are two files: one is 'logfile', the other
is the ADF output file. The final energy and structures are parsed from
the 'logfile'. Frequencies and normal modes are parsed from the ADF
output file.
"""
workdir = os.... | def _parse(self):
"""
Parse the ADF outputs. There are two files: one is 'logfile', the other
is the ADF output file. The final energy and structures are parsed from
the 'logfile'. Frequencies and normal modes are parsed from the ADF
output file.
"""
workdir = os.... | [
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... | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/io/adf.py#L718-L744 | [
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train | AdfOutput._parse_logfile | Parse the formatted logfile. | pymatgen/io/adf.py | def _parse_logfile(self, logfile):
"""
Parse the formatted logfile.
"""
cycle_patt = re.compile(r"Coordinates\sin\sGeometry\sCycle\s(\d+)")
coord_patt = re.compile(r"\s+([0-9]+)\.([A-Za-z]+)"+3*r"\s+([-\.0-9]+)")
energy_patt = re.compile(r"<.*>\s<.*>\s+current\senergy\s+... | def _parse_logfile(self, logfile):
"""
Parse the formatted logfile.
"""
cycle_patt = re.compile(r"Coordinates\sin\sGeometry\sCycle\s(\d+)")
coord_patt = re.compile(r"\s+([0-9]+)\.([A-Za-z]+)"+3*r"\s+([-\.0-9]+)")
energy_patt = re.compile(r"<.*>\s<.*>\s+current\senergy\s+... | [
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] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/io/adf.py#L765-L876 | [
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train | AdfOutput._parse_adf_output | Parse the standard ADF output file. | pymatgen/io/adf.py | def _parse_adf_output(self):
"""
Parse the standard ADF output file.
"""
numerical_freq_patt = re.compile(
r"\s+\*\s+F\sR\sE\sQ\sU\sE\sN\sC\sI\sE\sS\s+\*")
analytic_freq_patt = re.compile(
r"\s+\*\s+F\sR\sE\sQ\sU\sE\sN\sC\sY\s+A\sN\sA\sL\sY\sS\sI\sS\s+\*")... | def _parse_adf_output(self):
"""
Parse the standard ADF output file.
"""
numerical_freq_patt = re.compile(
r"\s+\*\s+F\sR\sE\sQ\sU\sE\sN\sC\sI\sE\sS\s+\*")
analytic_freq_patt = re.compile(
r"\s+\*\s+F\sR\sE\sQ\sU\sE\sN\sC\sY\s+A\sN\sA\sL\sY\sS\sI\sS\s+\*")... | [
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] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/io/adf.py#L878-L967 | [
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"r\"\\s+\\*\\s+F\\sR\\sE\\sQ\\sU\\sE\\sN\\s... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | get_reconstructed_band_structure | This method takes a list of band structures and reconstructs
one band structure object from all of them.
This is typically very useful when you split non self consistent
band structure runs in several independent jobs and want to merge back
the results
Args:
list_bs: A list of BandStructur... | pymatgen/electronic_structure/bandstructure.py | def get_reconstructed_band_structure(list_bs, efermi=None):
"""
This method takes a list of band structures and reconstructs
one band structure object from all of them.
This is typically very useful when you split non self consistent
band structure runs in several independent jobs and want to merge... | def get_reconstructed_band_structure(list_bs, efermi=None):
"""
This method takes a list of band structures and reconstructs
one band structure object from all of them.
This is typically very useful when you split non self consistent
band structure runs in several independent jobs and want to merge... | [
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] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/electronic_structure/bandstructure.py#L962-L1019 | [
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... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
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