vasppy.rdf module¶
- class RadialDistributionFunction(structures: list[pymatgen.core.structure.Structure], indices_i: list[int], indices_j: list[int] | None = None, nbins: int = 500, r_min: float = 0.0, r_max: float = 10.0, weights: list[float] | None = None)[source]¶
Bases:
object
Class for computing radial distribution functions.
- nbins¶
Number of bins.
- Type:
int
- range¶
Minimum and maximum values of r.
- Type:
(float, float)
- intervals¶
r values of the bin edges.
- Type:
np.array(float)
- dr¶
bin width.
- Type:
float
- r¶
mid-points of each bin.
- Type:
float
- rdf¶
RDF values.
- Type:
np.array(float)
- coordination_number¶
Volume integral of the RDF.
- Type:
np.array(float)
Initialise a RadialDistributionFunction instance.
- Parameters:
structures (list(pymatgen.Structure)) – List of pymatgen Structure objects.
indices_i (list(int)) – List of indices for species i.
indices_j (
list(int)
, optional) – List of indices for species j. Optional, default is None.nbins (
int
, optional) – Number of bins used for the RDF. Optional, default is 500.rmin (
float
, optional) – Minimum r value. Optional, default is 0.0.rmax (
float
, optional) – Maximum r value. Optional, default is 10.0.weights (
list(float)
, optional) – List of weights for each structure. Optional, default is None.
- Returns:
None
- classmethod from_species_strings(structures: list[pymatgen.core.structure.Structure], species_i: str, species_j: str | None = None, **kwargs) RadialDistributionFunction [source]¶
Initialise a RadialDistributionFunction instance by specifying species strings.
- Parameters:
structures (list(pymatgen.Structure)) – List of pymatgen Structure objects.
species_i (str) – String for species i, e.g.
"Na"
.species_j (
str
, optional) – String for species j, e.g."Cl"
. Optional default is None.**kwargs – Variable length keyword argument list. See
vasppy.rdf.RadialDistributionFunction()
for the full list of accepted arguments.
- Returns:
(RadialDistributionFunction)
- class VanHoveAnalysis(structures: list[pymatgen.core.structure.Structure], indices: list[int], d_steps: int, nbins: int = 500, r_min: float = 0.0, r_max: float = 10.0)[source]¶
Bases:
object
Class for computing Van Hove correlation functions.
- nbins¶
Number of bins.
- Type:
int
- range¶
Minimum and maximum values of r.
- Type:
(float, float)
- intervals¶
r values of the bin edges.
- Type:
np.array(float)
- dr¶
bin width.
- Type:
float
- r¶
mid-points of each bin.
- Type:
float
- gsrt¶
Self part of the Van Hove correlation function.
- Type:
np.array(float)
- gdrt¶
Distinct part of the Van Hove correlation function.
- Type:
np.array(float)
Initialise a VanHoveCorrelationFunction instance.
- Parameters:
structures (list(pymatgen.Structure)) – List of pymatgen Structure objects.
indices (list(int)) – List of indices for species to consider.
d_steps (int) – number of steps between structures at dt=0 and dt=t.
nbins (
int
, optional) – Number of bins used for the RDF. Optional, default is 500.rmin (
float
, optional) – Minimum r value. Optional, default is 0.0.rmax (
float
, optional) – Maximum r value. Optional, default is 10.0.
- Returns:
None
- distinct(sigma: float | None = None) ndarray [source]¶
Returns the distinct part of the Van Hove correlation function.
- Parameters:
sigma (
float
, optional) – Optional smearing width.- Returns:
(np.ndarray)
- self(sigma: float | None = None) ndarray [source]¶
Returns the self part of the Van Hove correlation function.
- Parameters:
sigma (
float
, optional) – Optional smearing width.- Returns:
(np.ndarray)