INSTRUCTION stringlengths 1 46.3k | RESPONSE stringlengths 75 80.2k |
|---|---|
An internal method to get a "default" covalent/element radius
Args:
site: (Site)
Returns:
Covalent radius of element on site, or Atomic radius if unavailable | def _get_default_radius(site):
"""
An internal method to get a "default" covalent/element radius
Args:
site: (Site)
Returns:
Covalent radius of element on site, or Atomic radius if unavailable
"""
try:
return CovalentRadius.radius[sit... |
An internal method to get the expected radius for a site with
oxidation state.
Args:
site: (Site)
Returns:
Oxidation-state dependent radius: ionic, covalent, or atomic.
Returns 0 if no oxidation state or appropriate radius is found. | def _get_radius(site):
"""
An internal method to get the expected radius for a site with
oxidation state.
Args:
site: (Site)
Returns:
Oxidation-state dependent radius: ionic, covalent, or atomic.
Returns 0 if no oxidation state or appropriate ... |
Given NNData, transforms data to the specified fingerprint length
Args:
nndata: (NNData)
length: (int) desired length of NNData | def transform_to_length(nndata, length):
"""
Given NNData, transforms data to the specified fingerprint length
Args:
nndata: (NNData)
length: (int) desired length of NNData
"""
if length is None:
return nndata
if length:
f... |
Initialise a CutOffDictNN according to a preset set of cut-offs.
Args:
preset (str): A preset name. The list of supported presets are:
- "vesta_2019": The distance cut-offs used by the VESTA
visualisation program.
Returns:
A CutOffDictNN using... | def from_preset(preset):
"""
Initialise a CutOffDictNN according to a preset set of cut-offs.
Args:
preset (str): A preset name. The list of supported presets are:
- "vesta_2019": The distance cut-offs used by the VESTA
visualisation program.
... |
Returns a structure in mcsqs rndstr.in format.
:return (str): | def to_string(self):
"""
Returns a structure in mcsqs rndstr.in format.
:return (str):
"""
# define coord system, use Cartesian
output = ["1.0 0.0 0.0",
"0.0 1.0 0.0",
"0.0 0.0 1.0"]
# add lattice vectors
m = self.struct... |
Parses a rndstr.in or lat.in file into pymatgen's
Structure format.
:param data: contents of a rndstr.in or lat.in file
:return: Structure object | def structure_from_string(data):
"""
Parses a rndstr.in or lat.in file into pymatgen's
Structure format.
:param data: contents of a rndstr.in or lat.in file
:return: Structure object
"""
data = data.splitlines()
data = [x.split() for x in data if x] # r... |
Analyze the void space in the input structure using voronoi decomposition
Calls Zeo++ for Voronoi decomposition.
Args:
structure: pymatgen.core.structure.Structure
rad_dict (optional): Dictionary of radii of elements in structure.
If not given, Zeo++ default values are used.
... | def get_voronoi_nodes(structure, rad_dict=None, probe_rad=0.1):
"""
Analyze the void space in the input structure using voronoi decomposition
Calls Zeo++ for Voronoi decomposition.
Args:
structure: pymatgen.core.structure.Structure
rad_dict (optional): Dictionary of radii of elements in... |
Analyze the void space in the input structure using high accuracy
voronoi decomposition.
Calls Zeo++ for Voronoi decomposition.
Args:
structure: pymatgen.core.structure.Structure
rad_dict (optional): Dictionary of radii of elements in structure.
If not given, Zeo++ default value... | def get_high_accuracy_voronoi_nodes(structure, rad_dict, probe_rad=0.1):
"""
Analyze the void space in the input structure using high accuracy
voronoi decomposition.
Calls Zeo++ for Voronoi decomposition.
Args:
structure: pymatgen.core.structure.Structure
rad_dict (optional): Dictio... |
Analyze the void space in the input structure using voronoi decomposition
Calls Zeo++ for Voronoi decomposition.
Args:
structure: pymatgen.core.structure.Structure
rad_dict (optional): Dictionary of radii of elements in structure.
If not given, Zeo++ default values are used.
... | def get_free_sphere_params(structure, rad_dict=None, probe_rad=0.1):
"""
Analyze the void space in the input structure using voronoi decomposition
Calls Zeo++ for Voronoi decomposition.
Args:
structure: pymatgen.core.structure.Structure
rad_dict (optional): Dictionary of radii of elemen... |
Computes the volume and surface area of isolated void using Zeo++.
Useful to compute the volume and surface area of vacant site.
Args:
structure: pymatgen Structure containing vacancy
rad_dict(optional): Dictionary with short name of elements and their
radii.
chan_rad(option... | def get_void_volume_surfarea(structure, rad_dict=None, chan_rad=0.3,
probe_rad=0.1):
"""
Computes the volume and surface area of isolated void using Zeo++.
Useful to compute the volume and surface area of vacant site.
Args:
structure: pymatgen Structure containing v... |
Reads a string representation to a ZeoCssr object.
Args:
string: A string representation of a ZeoCSSR.
Returns:
ZeoCssr object. | def from_string(string):
"""
Reads a string representation to a ZeoCssr object.
Args:
string: A string representation of a ZeoCSSR.
Returns:
ZeoCssr object.
"""
lines = string.split("\n")
toks = lines[0].split()
lengths = [float(i... |
Creates Zeo++ Voronoi XYZ object from a string.
from_string method of XYZ class is being redefined.
Args:
contents: String representing Zeo++ Voronoi XYZ file.
Returns:
ZeoVoronoiXYZ object | def from_string(contents):
"""
Creates Zeo++ Voronoi XYZ object from a string.
from_string method of XYZ class is being redefined.
Args:
contents: String representing Zeo++ Voronoi XYZ file.
Returns:
ZeoVoronoiXYZ object
"""
lines = conte... |
:param velocities (au): list of list of atom velocities
:return: | def set_velocities(self, velocities):
"""
:param velocities (au): list of list of atom velocities
:return:
"""
assert len(velocities) == len(self.mol)
self.params["velocity"] = velocities |
Set the maxium allowed memory.
Args:
total: The total memory. Integer. Unit: MBytes. If set to None,
this parameter will be neglected.
static: The static memory. Integer. Unit MBytes. If set to None,
this parameterwill be neglected. | def set_memory(self, total=None, static=None):
"""
Set the maxium allowed memory.
Args:
total: The total memory. Integer. Unit: MBytes. If set to None,
this parameter will be neglected.
static: The static memory. Integer. Unit MBytes. If set to None,
... |
Set algorithm used for converging SCF and max number of SCF iterations.
Args:
algorithm: The algorithm used for converging SCF. (str)
iterations: The max number of SCF iterations. (Integer) | def set_scf_algorithm_and_iterations(self, algorithm="diis",
iterations=50):
"""
Set algorithm used for converging SCF and max number of SCF iterations.
Args:
algorithm: The algorithm used for converging SCF. (str)
iterations: The... |
Set the grid for DFT numerical integrations.
Args:
radical_points: Radical points. (Integer)
angular_points: Angular points. (Integer)
grid_type: The type of of the grid. There are two standard grids:
SG-1 and SG-0. The other two supported grids are "Lebedev"... | def set_dft_grid(self, radical_points=128, angular_points=302,
grid_type="Lebedev"):
"""
Set the grid for DFT numerical integrations.
Args:
radical_points: Radical points. (Integer)
angular_points: Angular points. (Integer)
grid_type: The... |
Set initial guess method to be used for SCF
Args:
guess: The initial guess method. (str) | def set_scf_initial_guess(self, guess="SAD"):
"""
Set initial guess method to be used for SCF
Args:
guess: The initial guess method. (str)
"""
availabel_guesses = {"core", "sad", "gwh", "read", "fragmo"}
if guess.lower() not in availabel_guesses:
... |
Set the coordinates system used in geometry optimization.
"cartesian" --- always cartesian coordinates.
"internal" --- always internal coordinates.
"internal-switch" --- try internal coordinates first, if fails, switch
to cartesian coordinates.
"z-matrix" --- ... | def set_geom_opt_coords_type(self, coords_type="internal_switch"):
"""
Set the coordinates system used in geometry optimization.
"cartesian" --- always cartesian coordinates.
"internal" --- always internal coordinates.
"internal-switch" --- try internal coordinates f... |
Adjust the convergence criteria of geometry optimization.
Args:
gradient: the scale factor for gradient criteria. If less than
1.0, you are tightening the threshold. The base value is
300 × 10E−6
displacement: the scale factor for atomic displacement. If ... | def scale_geom_opt_threshold(self, gradient=0.1, displacement=0.1,
energy=0.1):
"""
Adjust the convergence criteria of geometry optimization.
Args:
gradient: the scale factor for gradient criteria. If less than
1.0, you are tightening... |
Set the solvent model to PCM. Default parameters are trying to comply to
gaussian default value
Args:
pcm_params (dict): The parameters of "$pcm" section.
solvent_key (str): for versions < 4.2 the section name is "pcm_solvent"
solvent_params (dict): The parameters of... | def use_pcm(self, pcm_params=None, solvent_key="solvent", solvent_params=None,
radii_force_field=None):
"""
Set the solvent model to PCM. Default parameters are trying to comply to
gaussian default value
Args:
pcm_params (dict): The parameters of "$pcm" secti... |
Creates QcInput from a string.
Args:
contents: String representing a QChem input file.
Returns:
QcInput object | def from_string(cls, contents):
"""
Creates QcInput from a string.
Args:
contents: String representing a QChem input file.
Returns:
QcInput object
"""
mol = None
charge = None
spin_multiplicity = None
params = dict()
... |
Calculates 'magnetic deformation proxy',
a measure of deformation (norm of finite strain)
between 'non-magnetic' (non-spin-polarized) and
ferromagnetic structures.
Adapted from Bocarsly et al. 2017,
doi: 10.1021/acs.chemmater.6b04729
:param structure_A: Structure
:param structure_B: Struct... | def magnetic_deformation(structure_A, structure_B):
"""
Calculates 'magnetic deformation proxy',
a measure of deformation (norm of finite strain)
between 'non-magnetic' (non-spin-polarized) and
ferromagnetic structures.
Adapted from Bocarsly et al. 2017,
doi: 10.1021/acs.chemmater.6b04729
... |
If round_magmoms_mode is an integer, simply round to that number
of decimal places, else if set to a float will try and round
intelligently by grouping magmoms. | def _round_magmoms(magmoms, round_magmoms_mode: Union[int, float]):
"""
If round_magmoms_mode is an integer, simply round to that number
of decimal places, else if set to a float will try and round
intelligently by grouping magmoms.
"""
if isinstance(round_magmoms_mode, ... |
Returns a Structure with species decorated with spin values instead
of using magmom site properties.
:return: Structure | def get_structure_with_spin(self):
"""
Returns a Structure with species decorated with spin values instead
of using magmom site properties.
:return: Structure
"""
structure = self.structure.copy()
structure.add_spin_by_site(structure.site_properties["magmom"])
... |
Returns a Structure with only magnetic atoms present.
:return: Structure | def get_structure_with_only_magnetic_atoms(self, make_primitive=True):
"""
Returns a Structure with only magnetic atoms present.
:return: Structure
"""
sites = [site for site in self.structure if abs(site.properties["magmom"]) > 0]
structure = Structure.from_sites(sites... |
Returns a Structure without magnetic moments defined.
:param make_primitive (bool): Return a primitive
structure, defaults to True.
:return: Structure | def get_nonmagnetic_structure(self, make_primitive=True):
"""
Returns a Structure without magnetic moments defined.
:param make_primitive (bool): Return a primitive
structure, defaults to True.
:return: Structure
"""
structure = self.structure.copy()
stru... |
Returns a Structure with all magnetic moments positive
or zero.
:param make_primitive (bool): Return a primitive
structure, defaults to True.
:return: Structure | def get_ferromagnetic_structure(self, make_primitive=True):
"""
Returns a Structure with all magnetic moments positive
or zero.
:param make_primitive (bool): Return a primitive
structure, defaults to True.
:return: Structure
"""
structure = self.structure... |
Returns a dict of magnetic species and the magnitude of
their associated magmoms. Will return a set if there are
multiple magmoms per species.
:return: dict of magnetic species and magmoms | def magnetic_species_and_magmoms(self):
"""
Returns a dict of magnetic species and the magnitude of
their associated magmoms. Will return a set if there are
multiple magmoms per species.
:return: dict of magnetic species and magmoms
"""
structure = self.get_ferr... |
:param symprec (float): same as in SpacegroupAnalyzer
:param angle_tolerance (float): same as in SpacegroupAnalyzer
:return (int): Number of symmetrically-distinct magnetic sites present
in structure. | def number_of_unique_magnetic_sites(self, symprec=1e-3, angle_tolerance=5):
"""
:param symprec (float): same as in SpacegroupAnalyzer
:param angle_tolerance (float): same as in SpacegroupAnalyzer
:return (int): Number of symmetrically-distinct magnetic sites present
in structure.... |
Applies heuristics to return a magnetic ordering for a collinear
magnetic structure. Result is not guaranteed for correctness.
:return: Ordering Enum ('FiM' is used as the abbreviation for
ferrimagnetic) | def ordering(self):
"""
Applies heuristics to return a magnetic ordering for a collinear
magnetic structure. Result is not guaranteed for correctness.
:return: Ordering Enum ('FiM' is used as the abbreviation for
ferrimagnetic)
"""
if not self.is_collinear:
... |
Returns the information on the symmetry of the Hamiltonian
describing the exchange energy of the system, taking into
account relative direction of magnetic moments but not their
absolute direction.
This is not strictly accurate (e.g. some/many atoms will
have zero magnetic momen... | def get_exchange_group_info(self, symprec=1e-2, angle_tolerance=5.0):
"""
Returns the information on the symmetry of the Hamiltonian
describing the exchange energy of the system, taking into
account relative direction of magnetic moments but not their
absolute direction.
... |
Compares the magnetic orderings of one structure with another.
:param other: Structure
:return (bool): | def matches_ordering(self, other):
"""
Compares the magnetic orderings of one structure with another.
:param other: Structure
:return (bool):
"""
a = CollinearMagneticStructureAnalyzer(
self.structure, overwrite_magmom_mode="normalize"
).get_structure... |
Sanitize our input structure by removing magnetic information
and making primitive.
Args:
input_structure: Structure
Returns: Structure | def _sanitize_input_structure(input_structure):
"""
Sanitize our input structure by removing magnetic information
and making primitive.
Args:
input_structure: Structure
Returns: Structure
"""
input_structure = input_structure.copy()
# remov... |
The central problem with trying to enumerate magnetic orderings is
that we have to enumerate orderings that might plausibly be magnetic
ground states, while not enumerating orderings that are physically
implausible. The problem is that it is not always obvious by e.g.
symmetry arguments ... | def _generate_transformations(self, structure):
"""
The central problem with trying to enumerate magnetic orderings is
that we have to enumerate orderings that might plausibly be magnetic
ground states, while not enumerating orderings that are physically
implausible. The problem ... |
Apply our input structure to our list of transformations and output a list
of ordered structures that have been pruned for duplicates and for those
with low symmetry (optional).
Args:
sanitized_input_structure: A sanitized input structure
(_sanitize_input_structure)
... | def _generate_ordered_structures(self, sanitized_input_structure, transformations):
"""
Apply our input structure to our list of transformations and output a list
of ordered structures that have been pruned for duplicates and for those
with low symmetry (optional).
Args:
... |
Remove uncertainty brackets from strings and return the float. | def str2float(text):
"""
Remove uncertainty brackets from strings and return the float.
"""
try:
# Note that the ending ) is sometimes missing. That is why the code has
# been modified to treat it as optional. Same logic applies to lists.
return float(re.sub(r"\(.+\)*", "", text... |
Some CIF files do not conform to spec. This function corrects
known issues, particular in regards to Springer materials/
Pauling files.
This function is here so that CifParser can assume its
input conforms to spec, simplifying its implementation.
:param data: CifBlock
:r... | def _sanitize_data(self, data):
"""
Some CIF files do not conform to spec. This function corrects
known issues, particular in regards to Springer materials/
Pauling files.
This function is here so that CifParser can assume its
input conforms to spec, simplifying its impl... |
Generate unique coordinates using coord and symmetry positions
and also their corresponding magnetic moments, if supplied. | def _unique_coords(self, coords_in, magmoms_in=None, lattice=None):
"""
Generate unique coordinates using coord and symmetry positions
and also their corresponding magnetic moments, if supplied.
"""
coords = []
if magmoms_in:
magmoms = []
if len(ma... |
Generate the lattice from the provided lattice parameters. In
the absence of all six lattice parameters, the crystal system
and necessary parameters are parsed | def get_lattice(self, data, length_strings=("a", "b", "c"),
angle_strings=("alpha", "beta", "gamma"),
lattice_type=None):
"""
Generate the lattice from the provided lattice parameters. In
the absence of all six lattice parameters, the crystal system
... |
In order to generate symmetry equivalent positions, the symmetry
operations are parsed. If the symops are not present, the space
group symbol is parsed, and symops are generated. | def get_symops(self, data):
"""
In order to generate symmetry equivalent positions, the symmetry
operations are parsed. If the symops are not present, the space
group symbol is parsed, and symops are generated.
"""
symops = []
for symmetry_label in ["_symmetry_equ... |
Equivalent to get_symops except for magnetic symmetry groups.
Separate function since additional operation for time reversal symmetry
(which changes magnetic moments on sites) needs to be returned. | def get_magsymops(self, data):
"""
Equivalent to get_symops except for magnetic symmetry groups.
Separate function since additional operation for time reversal symmetry
(which changes magnetic moments on sites) needs to be returned.
"""
magsymmops = []
# check to... |
Parse oxidation states from data dictionary | def parse_oxi_states(self, data):
"""
Parse oxidation states from data dictionary
"""
try:
oxi_states = {
data["_atom_type_symbol"][i]:
str2float(data["_atom_type_oxidation_number"][i])
for i in range(len(data["_atom_type_sy... |
Parse atomic magnetic moments from data dictionary | def parse_magmoms(self, data, lattice=None):
"""
Parse atomic magnetic moments from data dictionary
"""
if lattice is None:
raise Exception(
'Magmoms given in terms of crystal axes in magCIF spec.')
try:
magmoms = {
data["_a... |
Parse a string with a symbol to extract a string representing an element.
Args:
sym (str): A symbol to be parsed.
Returns:
A string with the parsed symbol. None if no parsing was possible. | def _parse_symbol(self, sym):
"""
Parse a string with a symbol to extract a string representing an element.
Args:
sym (str): A symbol to be parsed.
Returns:
A string with the parsed symbol. None if no parsing was possible.
"""
# Common representa... |
Generate structure from part of the cif. | def _get_structure(self, data, primitive):
"""
Generate structure from part of the cif.
"""
def get_num_implicit_hydrogens(sym):
num_h = {"Wat": 2, "wat": 2, "O-H": 1}
return num_h.get(sym[:3], 0)
lattice = self.get_lattice(data)
# if magCIF, ge... |
Return list of structures in CIF file. primitive boolean sets whether a
conventional cell structure or primitive cell structure is returned.
Args:
primitive (bool): Set to False to return conventional unit cells.
Defaults to True. With magnetic CIF files, will return primiti... | def get_structures(self, primitive=True):
"""
Return list of structures in CIF file. primitive boolean sets whether a
conventional cell structure or primitive cell structure is returned.
Args:
primitive (bool): Set to False to return conventional unit cells.
... |
Get BibTeX reference from CIF file.
:param data:
:return: BibTeX string | def get_bibtex_string(self):
"""
Get BibTeX reference from CIF file.
:param data:
:return: BibTeX string
"""
bibtex_keys = {'author': ('_publ_author_name', '_citation_author_name'),
'title': ('_publ_section_title', '_citation_title'),
... |
Converts a list of SlabEntry to an appropriate dictionary. It is
assumed that if there is no adsorbate, then it is a clean SlabEntry
and that adsorbed SlabEntry has the clean_entry parameter set.
Args:
all_slab_entries (list): List of SlabEntry objects
Returns:
(dict): Dictionary of Sl... | def entry_dict_from_list(all_slab_entries):
"""
Converts a list of SlabEntry to an appropriate dictionary. It is
assumed that if there is no adsorbate, then it is a clean SlabEntry
and that adsorbed SlabEntry has the clean_entry parameter set.
Args:
all_slab_entries (list): List of SlabEntr... |
Uses dot product of numpy array to sub chemical potentials
into the surface grand potential. This is much faster
than using the subs function in sympy.
Args:
gamma_dict (dict): Surface grand potential equation
as a coefficient dictionary
chempots (dict): Dictionary assign... | def sub_chempots(gamma_dict, chempots):
"""
Uses dot product of numpy array to sub chemical potentials
into the surface grand potential. This is much faster
than using the subs function in sympy.
Args:
gamma_dict (dict): Surface grand potential equation
as a coefficient d... |
Returns dict which contains Slab Entry data. | def as_dict(self):
"""
Returns dict which contains Slab Entry data.
"""
d = {"@module": self.__class__.__module__,
"@class": self.__class__.__name__}
d["structure"] = self.structure
d["energy"] = self.energy
d["miller_index"] = self.miller_index
... |
Returns the adsorption energy or Gibb's binding energy
of an adsorbate on a surface
Args:
eads (bool): Whether to calculate the adsorption energy
(True) or the binding energy (False) which is just
adsorption energy normalized by number of adsorbates. | def gibbs_binding_energy(self, eads=False):
"""
Returns the adsorption energy or Gibb's binding energy
of an adsorbate on a surface
Args:
eads (bool): Whether to calculate the adsorption energy
(True) or the binding energy (False) which is just
... |
Calculates the surface energy of this SlabEntry.
Args:
ucell_entry (entry): An entry object for the bulk
ref_entries (list: [entry]): A list of entries for each type
of element to be used as a reservoir for nonstoichiometric
systems. The length of this lis... | def surface_energy(self, ucell_entry, ref_entries=None):
"""
Calculates the surface energy of this SlabEntry.
Args:
ucell_entry (entry): An entry object for the bulk
ref_entries (list: [entry]): A list of entries for each type
of element to be used as a re... |
Returns the surface area of the adsorbed system per
unit area of the primitive slab system. | def get_unit_primitive_area(self):
"""
Returns the surface area of the adsorbed system per
unit area of the primitive slab system.
"""
A_ads = self.surface_area
A_clean = self.clean_entry.surface_area
n = (A_ads / A_clean)
return n |
Returns the primitive unit surface area density of the
adsorbate. | def get_monolayer(self):
"""
Returns the primitive unit surface area density of the
adsorbate.
"""
unit_a = self.get_unit_primitive_area
Nsurfs = self.Nsurfs_ads_in_slab
Nads = self.Nads_in_slab
return Nads / (unit_a * Nsurfs) |
Returns the TOTAL number of adsorbates in the slab on BOTH sides | def Nads_in_slab(self):
"""
Returns the TOTAL number of adsorbates in the slab on BOTH sides
"""
return sum([self.composition.as_dict()[a] for a \
in self.ads_entries_dict.keys()]) |
Returns the TOTAL number of adsorbed surfaces in the slab | def Nsurfs_ads_in_slab(self):
"""
Returns the TOTAL number of adsorbed surfaces in the slab
"""
struct = self.structure
weights = [s.species.weight for s in struct]
center_of_mass = np.average(struct.frac_coords,
weights=weights, axis=... |
Returns a SlabEntry by reading in an dictionary | def from_dict(cls, d):
"""
Returns a SlabEntry by reading in an dictionary
"""
structure = SlabEntry.from_dict(d["structure"])
energy = SlabEntry.from_dict(d["energy"])
miller_index = d["miller_index"]
label = d["label"]
coverage = d["coverage"]
a... |
Returns a slab with the adsorbates removed | def cleaned_up_slab(self):
"""
Returns a slab with the adsorbates removed
"""
ads_strs = list(self.ads_entries_dict.keys())
cleaned = self.structure.copy()
cleaned.remove_species(ads_strs)
return cleaned |
Returns a label (str) for this particular slab based
on composition, coverage and Miller index. | def create_slab_label(self):
"""
Returns a label (str) for this particular slab based
on composition, coverage and Miller index.
"""
if "label" in self.data.keys():
return self.data["label"]
label = str(self.miller_index)
ads_strs = list(self.ads... |
Returns SlabEntry from a ComputedStructureEntry | def from_computed_structure_entry(entry, miller_index, label=None,
adsorbates=None, clean_entry=None, **kwargs):
"""
Returns SlabEntry from a ComputedStructureEntry
"""
return SlabEntry(entry.structure, entry.energy, miller_index, label=label,
... |
Returns the entry corresponding to the most stable slab for a particular
facet at a specific chempot. We assume that surface energy is constant
so all free variables must be set with delu_dict, otherwise they are
assumed to be equal to delu_default.
Args:
miller_... | def get_stable_entry_at_u(self, miller_index, delu_dict=None, delu_default=0,
no_doped=False, no_clean=False):
"""
Returns the entry corresponding to the most stable slab for a particular
facet at a specific chempot. We assume that surface energy is constant
... |
Method to get the Wulff shape at a specific chemical potential.
Args:
delu_dict (Dict): Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol("delu_el") where el is the name of the element.
... | def wulff_from_chempot(self, delu_dict=None, delu_default=0, symprec=1e-5,
no_clean=False, no_doped=False):
"""
Method to get the Wulff shape at a specific chemical potential.
Args:
delu_dict (Dict): Dictionary of the chemical potentials to be set as
... |
Takes in a list of SlabEntries and calculates the chemical potentials
at which all slabs in the list coexists simultaneously. Useful for
building surface phase diagrams. Note that to solve for x equations
(x slab_entries), there must be x free variables (chemical potentials).
... | def get_surface_equilibrium(self, slab_entries, delu_dict=None):
"""
Takes in a list of SlabEntries and calculates the chemical potentials
at which all slabs in the list coexists simultaneously. Useful for
building surface phase diagrams. Note that to solve for x equations
... |
Creates a dictionary where each entry is a key pointing to a
chemical potential range where the surface of that entry is stable.
Does so by enumerating through all possible solutions (intersect)
for surface energies of a specific facet.
Args:
chempot_range ([max_chempot, min... | def stable_u_range_dict(self, chempot_range, ref_delu, no_doped=True,
no_clean=False, delu_dict={}, miller_index=(),
dmu_at_0=False, return_se_dict=False):
"""
Creates a dictionary where each entry is a key pointing to a
chemical potential ... |
Helper function to assign each facet a unique color using a dictionary.
Args:
alpha (float): Degree of transparency
return (dict): Dictionary of colors (r,g,b,a) when plotting surface
energy stability. The keys are individual surface entries where
clean surfaces hav... | def color_palette_dict(self, alpha=0.35):
"""
Helper function to assign each facet a unique color using a dictionary.
Args:
alpha (float): Degree of transparency
return (dict): Dictionary of colors (r,g,b,a) when plotting surface
energy stability. The keys are i... |
Helper function to help plot the surface energy of a
single SlabEntry as a function of chemical potential.
Args:
plt (Plot): A plot.
entry (SlabEntry): Entry of the slab whose surface energy we want
to plot
ref_delu (sympy Symbol): The range stabilit... | def chempot_vs_gamma_plot_one(self, plt, entry, ref_delu, chempot_range,
delu_dict={}, delu_default=0, label='', JPERM2=False):
"""
Helper function to help plot the surface energy of a
single SlabEntry as a function of chemical potential.
Args:
... |
Plots the surface energy as a function of chemical potential.
Each facet will be associated with its own distinct colors.
Dashed lines will represent stoichiometries different from that
of the mpid's compound. Transparent lines indicates adsorption.
Args:
ref_del... | def chempot_vs_gamma(self, ref_delu, chempot_range, miller_index=(),
delu_dict={}, delu_default=0, JPERM2=False,
show_unstable=False, ylim=[], plt=None,
no_clean=False, no_doped=False,
use_entry_labels=False, no_label=Fa... |
Plots the binding energy energy as a function of monolayers (ML), i.e.
the fractional area adsorbate density for all facets. For each
facet at a specific monlayer, only plot the lowest binding energy.
Args:
plot_eads (bool): Option to plot the adsorption energy (binding
... | def monolayer_vs_BE(self, plot_eads=False):
"""
Plots the binding energy energy as a function of monolayers (ML), i.e.
the fractional area adsorbate density for all facets. For each
facet at a specific monlayer, only plot the lowest binding energy.
Args:
plot... |
Helper function to a chempot plot look nicer.
Args:
plt (Plot) Plot to add things to.
xrange (list): xlim parameter
ref_el (str): Element of the referenced chempot.
axes(axes) Axes object from matplotlib
pad (float) For tight layout
rect (... | def chempot_plot_addons(self, plt, xrange, ref_el, axes, pad=2.4,
rect=[-0.047, 0, 0.84, 1], ylim=[]):
"""
Helper function to a chempot plot look nicer.
Args:
plt (Plot) Plot to add things to.
xrange (list): xlim parameter
ref_el ... |
For each facet, plot the clean surface energy against the most
stable binding energy.
Args:
delu_dict (Dict): Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol("delu_el") where e... | def BE_vs_clean_SE(self, delu_dict, delu_default=0, plot_eads=False,
annotate_monolayer=True, JPERM2=False):
"""
For each facet, plot the clean surface energy against the most
stable binding energy.
Args:
delu_dict (Dict): Dictionary of the chemical... |
Adapted from the get_chempot_range_map() method in the PhaseDiagram
class. Plot the chemical potential range map based on surface
energy stability. Currently works only for 2-component PDs. At
the moment uses a brute force method by enumerating through the
range of the fi... | def surface_chempot_range_map(self, elements, miller_index, ranges,
incr=50, no_doped=False, no_clean=False,
delu_dict=None, plt=None, annotate=True,
show_unphyiscal_only=False, fontsize=10):
"""
Adapte... |
Sets all chemical potential values and returns a dictionary where
the key is a sympy Symbol and the value is a float (chempot).
Args:
entry (SlabEntry): Computed structure entry of the slab
delu_dict (Dict): Dictionary of the chemical potentials to be set as
... | def set_all_variables(self, delu_dict, delu_default):
"""
Sets all chemical potential values and returns a dictionary where
the key is a sympy Symbol and the value is a float (chempot).
Args:
entry (SlabEntry): Computed structure entry of the slab
delu_dict (... |
Returns a plot of the local potential (eV) vs the
position along the c axis of the slab model (Ang)
Args:
label_energies (bool): Whether to label relevant energy
quantities such as the work function, Fermi energy,
vacuum locpot, bulk-like locpot
... | def get_locpot_along_slab_plot(self, label_energies=True,
plt=None, label_fontsize=10):
"""
Returns a plot of the local potential (eV) vs the
position along the c axis of the slab model (Ang)
Args:
label_energies (bool): Whether to labe... |
Handles the optional labelling of the plot with relevant quantities
Args:
plt (plt): Plot of the locpot vs c axis
label_fontsize (float): Fontsize of labels
Returns Labelled plt | def get_labels(self, plt, label_fontsize=10):
"""
Handles the optional labelling of the plot with relevant quantities
Args:
plt (plt): Plot of the locpot vs c axis
label_fontsize (float): Fontsize of labels
Returns Labelled plt
"""
# center of vac... |
A well converged work function should have a flat electrostatic
potential within some distance (min_point) about where the peak
electrostatic potential is found along the c direction of the
slab. This is dependent on the size of the slab.
Args:
min_point (fraction... | def is_converged(self, min_points_frac=0.015, tol=0.0025):
"""
A well converged work function should have a flat electrostatic
potential within some distance (min_point) about where the peak
electrostatic potential is found along the c direction of the
slab. This is d... |
Gives the radial size of two particles where equilibrium is reached
between both particles. NOTE: the solution here is not the same
as the solution visualized in the plot because solving for r
requires that both the total surface area and volume of the
particles are funct... | def solve_equilibrium_point(self, analyzer1, analyzer2,
delu_dict={}, delu_default=0, units="nanometers"):
"""
Gives the radial size of two particles where equilibrium is reached
between both particles. NOTE: the solution here is not the same
as th... |
Calculates the formation energy of the particle with arbitrary radius r.
Args:
wulffshape (WulffShape): Initial, unscaled WulffShape
bulk_entry (ComputedStructureEntry): Entry of the corresponding bulk.
r (float (Ang)): Arbitrary effective radius of the WulffShape
... | def wulff_gform_and_r(self, wulffshape, bulk_entry, r, from_sphere_area=False,
r_units="nanometers", e_units="keV", normalize=False,
scale_per_atom=False):
"""
Calculates the formation energy of the particle with arbitrary radius r.
Args:
... |
Scales the Wulff shape with an effective radius r. Note that the resulting
Wulff does not neccesarily have the same effective radius as the one
provided. The Wulff shape is scaled by its surface energies where first
the surface energies are scale by the minimum surface energy and the... | def scaled_wulff(self, wulffshape, r):
"""
Scales the Wulff shape with an effective radius r. Note that the resulting
Wulff does not neccesarily have the same effective radius as the one
provided. The Wulff shape is scaled by its surface energies where first
the surfa... |
Returns the plot of the formation energy of a particle against its
effect radius
Args:
analyzer (SurfaceEnergyPlotter): Analyzer associated with the
first polymorph
max_r (float): The maximum radius of the particle to plot up to.
delu_dict (Dict):... | def plot_one_stability_map(self, analyzer, max_r, delu_dict=None, label="",
increments=50, delu_default=0, plt=None,
from_sphere_area=False, e_units="keV",
r_units="nanometers", normalize=False,
s... |
Returns the plot of the formation energy of a particles
of different polymorphs against its effect radius
Args:
max_r (float): The maximum radius of the particle to plot up to.
increments (int): Number of plot points
delu_dict (Dict): Dictionary of the chemical p... | def plot_all_stability_map(self, max_r, increments=50, delu_dict=None,
delu_default=0, plt=None, labels=None,
from_sphere_area=False, e_units="keV",
r_units="nanometers", normalize=False,
scale_pe... |
Maximum volume change along insertion | def max_delta_volume(self):
"""
Maximum volume change along insertion
"""
vols = [v.vol_charge for v in self.voltage_pairs]
vols.extend([v.vol_discharge for v in self.voltage_pairs])
return max(vols) / min(vols) - 1 |
Maximum absolute difference in adjacent voltage steps | def max_voltage_step(self):
"""
Maximum absolute difference in adjacent voltage steps
"""
steps = [self.voltage_pairs[i].voltage
- self.voltage_pairs[i + 1].voltage
for i in range(len(self.voltage_pairs) - 1)]
return max(steps) if len(steps) > 0 ... |
Average voltage for path satisfying between a min and max voltage.
Args:
min_voltage (float): The minimum allowable voltage for a given
step.
max_voltage (float): The maximum allowable voltage allowable for a
given step.
Returns:
Aver... | def get_average_voltage(self, min_voltage=None, max_voltage=None):
"""
Average voltage for path satisfying between a min and max voltage.
Args:
min_voltage (float): The minimum allowable voltage for a given
step.
max_voltage (float): The maximum allowable... |
Get the gravimetric capacity of the electrode.
Args:
min_voltage (float): The minimum allowable voltage for a given
step.
max_voltage (float): The maximum allowable voltage allowable for a
given step.
use_overall_normalization (booL): If False... | def get_capacity_grav(self, min_voltage=None, max_voltage=None,
use_overall_normalization=True):
"""
Get the gravimetric capacity of the electrode.
Args:
min_voltage (float): The minimum allowable voltage for a given
step.
max_vo... |
Get the volumetric capacity of the electrode.
Args:
min_voltage (float): The minimum allowable voltage for a given
step.
max_voltage (float): The maximum allowable voltage allowable for a
given step.
use_overall_normalization (booL): If False,... | def get_capacity_vol(self, min_voltage=None, max_voltage=None,
use_overall_normalization=True):
"""
Get the volumetric capacity of the electrode.
Args:
min_voltage (float): The minimum allowable voltage for a given
step.
max_volta... |
Returns the specific energy of the battery in mAh/g.
Args:
min_voltage (float): The minimum allowable voltage for a given
step.
max_voltage (float): The maximum allowable voltage allowable for a
given step.
use_overall_normalization (booL): If... | def get_specific_energy(self, min_voltage=None, max_voltage=None,
use_overall_normalization=True):
"""
Returns the specific energy of the battery in mAh/g.
Args:
min_voltage (float): The minimum allowable voltage for a given
step.
... |
Args:
min_voltage (float): The minimum allowable voltage for a given
step.
max_voltage (float): The maximum allowable voltage allowable for a
given step.
use_overall_normalization (booL): If False, normalize by the
discharged state of o... | def get_energy_density(self, min_voltage=None, max_voltage=None,
use_overall_normalization=True):
"""
Args:
min_voltage (float): The minimum allowable voltage for a given
step.
max_voltage (float): The maximum allowable voltage allowable... |
Selects VoltagePairs within a certain voltage range.
Args:
min_voltage (float): The minimum allowable voltage for a given
step.
max_voltage (float): The maximum allowable voltage allowable for a
given step.
Returns:
A list of VoltageP... | def _select_in_voltage_range(self, min_voltage=None, max_voltage=None):
"""
Selects VoltagePairs within a certain voltage range.
Args:
min_voltage (float): The minimum allowable voltage for a given
step.
max_voltage (float): The maximum allowable voltage ... |
Returns pymatgen Molecule object. | def pymatgen_mol(self):
"""
Returns pymatgen Molecule object.
"""
sp = []
coords = []
for atom in ob.OBMolAtomIter(self._obmol):
sp.append(atom.GetAtomicNum())
coords.append([atom.GetX(), atom.GetY(), atom.GetZ()])
return Molecule(sp, coord... |
A wrapper to pybel's localopt method to optimize a Molecule.
Args:
forcefield: Default is mmff94. Options are 'gaff', 'ghemical',
'mmff94', 'mmff94s', and 'uff'.
steps: Default is 500. | def localopt(self, forcefield='mmff94', steps=500):
"""
A wrapper to pybel's localopt method to optimize a Molecule.
Args:
forcefield: Default is mmff94. Options are 'gaff', 'ghemical',
'mmff94', 'mmff94s', and 'uff'.
steps: Default is 500.
"""
... |
A wrapper to pybel's make3D method generate a 3D structure from a
2D or 0D structure.
The 3D structure is made very quickly using a combination of rules
(e.g. sp3 atoms should have four bonds arranged in a tetrahedron) and
ring templates (e.g. cyclohexane is shaped like a chair). Once 3D... | def make3d(self, forcefield="mmff94", steps=50):
"""
A wrapper to pybel's make3D method generate a 3D structure from a
2D or 0D structure.
The 3D structure is made very quickly using a combination of rules
(e.g. sp3 atoms should have four bonds arranged in a tetrahedron) and
... |
Remove a bond from an openbabel molecule
Args:
idx1: The atom index of one of the atoms participating the in bond
idx2: The atom index of the other atom participating in the bond | def remove_bond(self, idx1, idx2):
"""
Remove a bond from an openbabel molecule
Args:
idx1: The atom index of one of the atoms participating the in bond
idx2: The atom index of the other atom participating in the bond
"""
for obbond in ob.OBMolBondIter(s... |
Conformer search based on several Rotor Search algorithms of openbabel.
If the input molecule is not 3D, make3d will be called (generate 3D
structure, add hydrogen, a quick localopt). All hydrogen atoms need
to be made explicit.
Args:
rotor_args: pass args to Rotor Search in... | def rotor_conformer(self, *rotor_args, algo="WeightedRotorSearch",
forcefield="mmff94"):
"""
Conformer search based on several Rotor Search algorithms of openbabel.
If the input molecule is not 3D, make3d will be called (generate 3D
structure, add hydrogen, a quic... |
A combined method to first generate 3D structures from 0D or 2D
structures and then find the minimum energy conformer:
1. Use OBBuilder to create a 3D structure using rules and ring templates
2. Do 250 steps of a steepest descent geometry optimization with the
MMFF94 forcefield
... | def gen3d_conformer(self):
"""
A combined method to first generate 3D structures from 0D or 2D
structures and then find the minimum energy conformer:
1. Use OBBuilder to create a 3D structure using rules and ring templates
2. Do 250 steps of a steepest descent geometry optimizati... |
Conformer generation based on Confab to generate all diverse low-energy
conformers for molecules. This is different from rotor_conformer or
gen3d_conformer as it aims to not simply to find a low energy
conformation but to generate several different conformations.
Args:
force... | def confab_conformers(self, forcefield="mmff94", freeze_atoms=None,
rmsd_cutoff=0.5, energy_cutoff=50.0,
conf_cutoff=100000, verbose=False):
"""
Conformer generation based on Confab to generate all diverse low-energy
conformers for molecules. T... |
Uses OpenBabel to output all supported formats.
Args:
filename: Filename of file to output
file_format: String specifying any OpenBabel supported formats. | def write_file(self, filename, file_format="xyz"):
"""
Uses OpenBabel to output all supported formats.
Args:
filename: Filename of file to output
file_format: String specifying any OpenBabel supported formats.
"""
mol = pb.Molecule(self._obmol)
re... |
Uses OpenBabel to read a molecule from a file in all supported formats.
Args:
filename: Filename of input file
file_format: String specifying any OpenBabel supported formats.
Returns:
BabelMolAdaptor object | def from_file(filename, file_format="xyz"):
"""
Uses OpenBabel to read a molecule from a file in all supported formats.
Args:
filename: Filename of input file
file_format: String specifying any OpenBabel supported formats.
Returns:
BabelMolAdaptor ob... |
Uses OpenBabel to read a molecule from a string in all supported
formats.
Args:
string_data: String containing molecule data.
file_format: String specifying any OpenBabel supported formats.
Returns:
BabelMolAdaptor object | def from_string(string_data, file_format="xyz"):
"""
Uses OpenBabel to read a molecule from a string in all supported
formats.
Args:
string_data: String containing molecule data.
file_format: String specifying any OpenBabel supported formats.
Returns:
... |
Finds the list of bonded atoms.
Args:
struct (Structure): Input structure
tolerance: length in angstroms used in finding bonded atoms. Two atoms are considered bonded if (radius of atom 1) + (radius of atom 2) + (tolerance) < (distance between atoms 1 and 2). Default value = 0.45, the value used by... | def find_connected_atoms(struct, tolerance=0.45, ldict=JmolNN().el_radius):
"""
Finds the list of bonded atoms.
Args:
struct (Structure): Input structure
tolerance: length in angstroms used in finding bonded atoms. Two atoms are considered bonded if (radius of atom 1) + (radius of atom 2) +... |
Finds bonded clusters of atoms in the structure with periodic boundary conditions.
If there are atoms that are not bonded to anything, returns [0,1,0].(For faster computation time in FindDimension())
Args:
struct (Structure): Input structure
connected_list: Must be made from the same structure ... | def find_clusters(struct, connected_list):
"""
Finds bonded clusters of atoms in the structure with periodic boundary conditions.
If there are atoms that are not bonded to anything, returns [0,1,0].(For faster computation time in FindDimension())
Args:
struct (Structure): Input structure
... |
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