@@ -223,7 +224,7 @@ Quick search
-
+
diff --git a/docs/pymatgen.analysis.diffusion.aimd.clustering.html b/docs/pymatgen.analysis.diffusion.aimd.clustering.html
index 17f1deb1..eef8c292 100644
--- a/docs/pymatgen.analysis.diffusion.aimd.clustering.html
+++ b/docs/pymatgen.analysis.diffusion.aimd.clustering.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.aimd.clustering module — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.aimd.clustering module — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.aimd.clustering module
@@ -47,185 +48,8 @@ Navigation
-
-pymatgen.analysis.diffusion.aimd.clustering module
-This module implements clustering algorithms to determine centroids, with
-adaption for periodic boundary conditions. This can be used, for example, to
-determine likely atomic positions from MD trajectories.
-
-
-class Kmeans ( max_iterations : int = 1000 ) [source]
-Bases: object
-Simple kmeans clustering.
-
-Parameters
-max_iterations (int ) – Maximum number of iterations to run KMeans algo.
-
-
-
-
-cluster ( points , k , initial_centroids = None ) [source]
-
-Parameters
-
-points (ndarray ) – Data points as a mxn ndarray, where m is the
-number of features and n is the number of data points.
-k (int ) – Number of means.
-initial_centroids (np.array ) – Initial guess for the centroids. If
-None, a randomized array of points is used.
-
-
-Returns
-centroids are the final centroids, labels
-provide the index for each point, and ss in the final sum squared
-distances.
-
-Return type
-centroids, labels, ss
-
-
-
-
-
-
-static get_centroids ( points , labels , k , centroids ) [source]
-Each centroid is the geometric mean of the points that
-have that centroid’s label. Important: If a centroid is empty (no
-points have that centroid’s label) you should randomly re-initialize it.
-
-Parameters
-
-
-
-
-
-
-
-static get_labels ( points , centroids ) [source]
-For each element in the dataset, chose the closest centroid.
-Make that centroid the element’s label.
-
-Parameters
-
-
-
-
-
-
-
-should_stop ( old_centroids , centroids , iterations ) [source]
-Check for stopping conditions.
-
-Parameters
-
-old_centroids – List of old centroids
-centroids – List of centroids
-iterations – Number of iterations thus far.
-
-
-
-
-
-
-
-
-
-class KmeansPBC ( lattice , max_iterations = 1000 ) [source]
-Bases: pymatgen.analysis.diffusion.aimd.clustering.Kmeans
-A version of KMeans that work with PBC. Distance metrics have to change,
-as well as new centroid determination. The points supplied should be
-fractional coordinates.
-
-Parameters
-
-
-
-
-
-get_centroids ( points , labels , k , centroids ) [source]
-Each centroid is the geometric mean of the points that
-have that centroid’s label. Important: If a centroid is empty (no
-points have that centroid’s label) you should randomly re-initialize it.
-
-Parameters
-
-
-
-
-
-
-
-get_labels ( points , centroids ) [source]
-For each element in the dataset, chose the closest centroid.
-Make that centroid the element’s label.
-
-Parameters
-
-
-
-
-
-
-
-should_stop ( old_centroids , centroids , iterations ) [source]
-Check for stopping conditions.
-
-Parameters
-
-old_centroids – List of old centroids
-centroids – List of centroids
-iterations – Number of iterations thus far.
-
-
-
-
-
-
-
-
-
-get_random_centroid ( points ) [source]
-Generate a random centroid based on points.
-
-Parameters
-points – List of points.
-
-
-
-
-
-
-get_random_centroids ( points , k ) [source]
-Generate k random centroids based on points.
-
-Parameters
-
-points – List of points.
-k – Number of means.
-
-
-
-
-
+
+pymatgen.analysis.diffusion.aimd.clustering module
@@ -255,7 +79,7 @@ Quick search
-
+
diff --git a/docs/pymatgen.analysis.diffusion.aimd.html b/docs/pymatgen.analysis.diffusion.aimd.html
index 5dd84a5d..a4214d9f 100644
--- a/docs/pymatgen.analysis.diffusion.aimd.html
+++ b/docs/pymatgen.analysis.diffusion.aimd.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.aimd package — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.aimd package — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.aimd package
@@ -48,14 +49,14 @@ Navigation
-pymatgen.analysis.diffusion.aimd package
+pymatgen.analysis.diffusion.aimd package
-Subpackages
+Subpackages
-
+
diff --git a/docs/pymatgen.analysis.diffusion.aimd.pathway.html b/docs/pymatgen.analysis.diffusion.aimd.pathway.html
index a93a0dd1..b793fcc8 100644
--- a/docs/pymatgen.analysis.diffusion.aimd.pathway.html
+++ b/docs/pymatgen.analysis.diffusion.aimd.pathway.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.aimd.pathway module — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.aimd.pathway module — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.aimd.pathway module
@@ -48,7 +49,7 @@ Navigation
-pymatgen.analysis.diffusion.aimd.pathway module
+pymatgen.analysis.diffusion.aimd.pathway module
Algorithms for diffusion pathway analysis
@@ -71,7 +72,7 @@ Navigation
(2) in fractional coordinates.
-Parameters
+Parameters:
@@ -48,11 +49,11 @@ Navigation
-pymatgen.analysis.diffusion.aimd.tests.test_rdf module
+pymatgen.analysis.diffusion.aimd.tests.test_rdf module
class RDFTest ( methodName = 'runTest' ) [source]
-Bases: unittest.case.TestCase
+Bases: TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
@@ -97,7 +98,7 @@ Quick search
-
+
diff --git a/docs/pymatgen.analysis.diffusion.aimd.tests.test_van_hove.html b/docs/pymatgen.analysis.diffusion.aimd.tests.test_van_hove.html
index 9fb9a315..a5ded43f 100644
--- a/docs/pymatgen.analysis.diffusion.aimd.tests.test_van_hove.html
+++ b/docs/pymatgen.analysis.diffusion.aimd.tests.test_van_hove.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.aimd.tests.test_van_hove module — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.aimd.tests.test_van_hove module — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.aimd.tests.test_van_hove module
@@ -48,11 +49,11 @@ Navigation
-pymatgen.analysis.diffusion.aimd.tests.test_van_hove module
+pymatgen.analysis.diffusion.aimd.tests.test_van_hove module
class EvolutionAnalyzerTest ( methodName = 'runTest' ) [source]
-Bases: unittest.case.TestCase
+Bases: TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
@@ -66,7 +67,7 @@ Navigation
class RDFTest ( methodName = 'runTest' ) [source]
-Bases: unittest.case.TestCase
+Bases: TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
@@ -116,7 +117,7 @@ Navigation
class VanHoveTest ( methodName = 'runTest' ) [source]
-Bases: unittest.case.TestCase
+Bases: TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
@@ -156,7 +157,7 @@ Quick search
-
+
diff --git a/docs/pymatgen.analysis.diffusion.aimd.van_hove.html b/docs/pymatgen.analysis.diffusion.aimd.van_hove.html
index d97f689c..b9e68063 100644
--- a/docs/pymatgen.analysis.diffusion.aimd.van_hove.html
+++ b/docs/pymatgen.analysis.diffusion.aimd.van_hove.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.aimd.van_hove module — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.aimd.van_hove module — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.aimd.van_hove module
@@ -48,7 +49,7 @@ Navigation
-pymatgen.analysis.diffusion.aimd.van_hove module
+pymatgen.analysis.diffusion.aimd.van_hove module
Van Hove analysis for correlations.
@@ -65,7 +66,7 @@ Navigation
All-Solid-State Sodium-Ion Batteries with First-Principles
Calculations”, Chem. Mater. (2018), 30(1), pp 163-173.
-Parameters
+Parameters:
-static atom_dist ( structure : pymatgen.core.structure.Structure , specie : str , ngrid : int = 101 , window : float = 1 , direction : str = 'c' ) [source]
+static atom_dist ( structure : Structure , specie : str , ngrid : int = 101 , window : float = 1 , direction : str = 'c' ) [source]
Get atomic distribution for a given specie.
-Parameters
+Parameters:
structure (Structure ) – input structure
specie (str ) – species string for an element
@@ -91,10 +92,10 @@ Navigation
direction (str ) – Choose from “a”, “b” and “c”. Default is “c”.
-Returns
+Returns:
atomic concentration along one direction.
-Return type
+Return type:
density (np.array)
@@ -106,7 +107,7 @@ Navigation
Get the data frame for a given pair. This step would be very slow if
there are hundreds or more structures to parse.
-Parameters
+Parameters:
func (FunctionType ) –
structure to spectrum function. choose from
rdf (to get radial distribution function, pair required) or
@@ -130,14 +131,14 @@
Navigation
save_csv (str ) – save pandas DataFrame to csv.
-Returns
+Returns:
index is the radial distance in Angstrom, and column is the time step in ps.
-Return type
+Return type:
pandas.DataFrame object
@@ -145,17 +146,17 @@ Navigation
-static get_min_dist ( df : pandas.core.frame.DataFrame , tol : float = 1e-10 ) [source]
+static get_min_dist ( df : DataFrame , tol : float = 1e-10 ) [source]
Get the shortest pair distance from the given DataFrame.
-Parameters
+Parameters:
df (DataFrame ) – index is the radial distance in Angstrom, and
column is the time step in ps.
tol (float ) – any float number less than tol is considered as zero.
-Returns
+Returns:
The shortest pair distance throughout the table.
@@ -163,13 +164,13 @@ Navigation
-static get_pairs ( structure : pymatgen.core.structure.Structure ) [source]
+static get_pairs ( structure : Structure ) [source]
Get all element pairs in a structure.
-Parameters
+Parameters:
structure (Structure ) – structure
-Returns
+Returns:
list of tuples
@@ -177,10 +178,10 @@ Navigation
-plot_atomic_evolution ( specie: str , direction: str = 'c' , cmap=<matplotlib.colors.LinearSegmentedColormap object> , df: typing.Optional[pandas.core.frame.DataFrame] = None ) [source]
+plot_atomic_evolution ( specie: str , direction: str = 'c' , cmap=<matplotlib.colors.LinearSegmentedColormap object> , df: ~typing.Optional[~pandas.core.frame.DataFrame] = None ) [source]
Plot the atomic distribution evolution with time for a given species.
-Parameters
+Parameters:
specie (str ) – species string for an element.
direction (str ) – Choose from “a”, “b”, “c”. Default to “c”.
@@ -189,7 +190,7 @@ Navigation
Angstrom, and column is the time step in ps.
-Returns
+Returns:
matplotlib.axes._subplots.AxesSubplot object
@@ -197,12 +198,12 @@ Navigation
-static plot_evolution_from_data ( df: pandas.core.frame.DataFrame , x_label: typing.Optional[str] = None , cb_label: typing.Optional[str] = None , cmap=<matplotlib.colors.ListedColormap object> ) [source]
+static plot_evolution_from_data ( df: ~pandas.core.frame.DataFrame , x_label: ~typing.Optional[str] = None , cb_label: ~typing.Optional[str] = None , cmap=<matplotlib.colors.ListedColormap object> ) [source]
Plot the evolution with time for a given DataFrame. It can be RDF,
atomic distribution or other characterization data we might
implement in the future.
-Parameters
+Parameters:
-Returns
+Returns:
matplotlib.axes._subplots.AxesSubplot object
@@ -220,10 +221,10 @@ Navigation
-plot_rdf_evolution ( pair: typing.Tuple , cmap=<matplotlib.colors.ListedColormap object> , df: typing.Optional[pandas.core.frame.DataFrame] = None ) [source]
+plot_rdf_evolution ( pair: ~typing.Tuple , cmap=<matplotlib.colors.ListedColormap object> , df: ~typing.Optional[~pandas.core.frame.DataFrame] = None ) [source]
Plot the RDF evolution with time for a given pair.
-Parameters
+Parameters:
pair (str tuple ) – e.g. (“Na”, “Na”)
cmap (color map ) – the color map used in heat map.
@@ -232,7 +233,7 @@
Navigation
Angstrom, and column is the time step in ps.
-Returns
+Returns:
matplotlib.axes._subplots.AxesSubplot object
@@ -240,10 +241,10 @@ Navigation
-static rdf ( structure : pymatgen.core.structure.Structure , pair : Tuple , ngrid : int = 101 , rmax : float = 10 ) [source]
+static rdf ( structure : Structure , pair : Tuple , ngrid : int = 101 , rmax : float = 10 ) [source]
Process rdf from a given structure and pair.
-Parameters
+Parameters:
structure (Structure ) – input structure.
pair (str tuple ) – e.g. (“Na”, “Na”).
@@ -251,7 +252,7 @@ Navigation
rmax (float ) – Maximum of radial grid (the minimum is always zero).
-Returns
+Returns:
rdf (np.array)
@@ -261,7 +262,7 @@ Navigation
-class VanHoveAnalysis ( diffusion_analyzer : pymatgen.analysis.diffusion.analyzer.DiffusionAnalyzer , avg_nsteps : int = 50 , ngrid : int = 101 , rmax : float = 10.0 , step_skip : int = 50 , sigma : float = 0.1 , cell_range : int = 1 , species : Union [ Tuple , List ] = ('Li', 'Na') , reference_species : Optional [ Union [ Tuple , List ] ] = None , indices : Optional [ List ] = None ) [source]
+class VanHoveAnalysis ( diffusion_analyzer : DiffusionAnalyzer , avg_nsteps : int = 50 , ngrid : int = 101 , rmax : float = 10.0 , step_skip : int = 50 , sigma : float = 0.1 , cell_range : int = 1 , species : Union [ Tuple , List ] = ('Li', 'Na') , reference_species : Optional [ Union [ Tuple , List ] ] = None , indices : Optional [ List ] = None ) [source]
Bases: object
Class for van Hove function analysis. In particular, self-part (Gs) and
distinct-part (Gd) of the van Hove correlation function G(r,t)
@@ -272,7 +273,7 @@
Navigation
Superionic Conductor”. Chem. Mater. (2015), 27, pp 8318–8325
Initiation.
-Parameters
+Parameters:
-
+
diff --git a/docs/pymatgen.analysis.diffusion.analyzer.html b/docs/pymatgen.analysis.diffusion.analyzer.html
index cb39fafd..91098782 100644
--- a/docs/pymatgen.analysis.diffusion.analyzer.html
+++ b/docs/pymatgen.analysis.diffusion.analyzer.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.analyzer module — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.analyzer module — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.analyzer module
@@ -48,7 +49,7 @@ Navigation
-pymatgen.analysis.diffusion.analyzer module
+pymatgen.analysis.diffusion.analyzer module
A module to perform diffusion analyses (e.g. calculating diffusivity from
mean square displacements etc.). If you use this module, please consider
citing the following papers:
@@ -66,7 +67,7 @@ Navigation
class DiffusionAnalyzer ( structure , displacements , specie , temperature , time_step , step_skip , smoothed = 'max' , min_obs = 30 , avg_nsteps = 1000 , lattices = None ) [source]
-Bases: monty.json.MSONable
+Bases: MSONable
Class for performing diffusion analysis.
This constructor is meant to be used with pre-processed data.
Other convenient constructors are provided as class methods (see
@@ -81,7 +82,7 @@
Navigation
time to obtain the slope, which is then related to the diffusivity.
For traditional analysis, use smoothed=False and weighted=False.
-Parameters
+Parameters:
structure (Structure ) – Initial structure.
displacements (array ) – Numpy array of with shape [site,
@@ -137,7 +138,7 @@
Navigation
Writes MSD data to a csv file that can be easily plotted in other
software.
-Parameters
+Parameters:
filename (str ) – Filename. Supported formats are csv and dat. If
the extension is csv, a csv file is written. Otherwise,
a dat format is assumed.
@@ -149,7 +150,7 @@ Navigation
classmethod from_dict ( d ) [source]
-Parameters
+Parameters:
d (dict ) – Dict representation
@@ -162,7 +163,7 @@ Navigation
Convenient constructor that takes in a list of vasprun.xml paths to
perform diffusion analysis.
-Parameters
+Parameters:
filepaths ([ str ] ) – List of paths to vasprun.xml files of runs. (
must be ordered in sequence of MD simulation). For example,
@@ -204,7 +205,7 @@
Navigation
Convenient constructor that takes in a list of Structure objects to
perform diffusion analysis.
-Parameters
+Parameters:
structures ([ Structure ] ) – list of Structure objects (must be
ordered in sequence of run). E.g., you may have performed
@@ -239,7 +240,7 @@
Navigation
Convenient constructor that takes in a list of Vasprun objects to
perform diffusion analysis.
-Parameters
+Parameters:
vaspruns ([ Vasprun ] ) – List of Vaspruns (must be ordered in
sequence of MD simulation). E.g., you may have performed
@@ -270,7 +271,7 @@
Navigation
iterator is to reduce memory usage as # of structures in MD can be
huge. You don’t often need all the structures all at once.
-Parameters
+Parameters:
start (int ) – applies a start/stop/step to the iterator.
Faster than applying it after generation, as it reduces the
@@ -294,7 +295,7 @@
Navigation
or similar mechanism (which would show up in max framework displacement
but doesn’t constitute melting).
-Parameters
+Parameters:
plt (matplotlib.pyplot ) – If plt is supplied, changes will be made
to an existing plot. Otherwise, a new plot will be created.
@@ -315,7 +316,7 @@ Navigation
Get the plot of the smoothed msd vs time graph. Useful for
checking convergence. This can be written to an image file.
-Parameters
+Parameters:
plt – A plot object. Defaults to None, which means one will be
generated.
@@ -332,7 +333,7 @@ Navigation
get_summary_dict ( include_msd_t = False , include_mscd_t = False ) [source]
Provides a summary of diffusion information.
-Parameters
+Parameters:
-Returns
+Returns:
(dict) of diffusion and conductivity data.
@@ -351,7 +352,7 @@ Navigation
plot_msd ( mode = 'default' ) [source]
Plot the smoothed msd vs time graph. Useful for checking convergence.
-Parameters
+Parameters:
mode (str ) – Can be “default” (the default, shows only the MSD for
the diffusing specie, and its components), “ions” (individual
square displacements of all ions), “species” (mean square
@@ -371,7 +372,7 @@
Navigation
-Parameters
+Parameters:
temps ([ float ] ) – A sequence of temperatures. units: K
diffusivities ([ float ] ) – A sequence of diffusivities (e.g.,
@@ -386,7 +387,7 @@
Navigation
get_arrhenius_plot ( temps , diffusivities , diffusivity_errors = None , ** kwargs ) [source]
Returns an Arrhenius plot.
-Parameters
+Parameters:
temps ([ float ] ) – A sequence of temperatures.
diffusivities ([ float ] ) – A sequence of diffusivities (e.g.,
@@ -396,7 +397,7 @@
Navigation
\*\*kwargs – Any keyword args supported by matplotlib.pyplot.plot.
-Returns
+Returns:
A matplotlib.pyplot object. Do plt.show() to show the plot.
@@ -411,14 +412,14 @@ Navigation
species (where available), or else the number of valence electrons
(usually a good guess, esp for main group ions).
-Parameters
+Parameters:
structure (Structure ) – Input structure.
species (Element/Species ) – Diffusing species.
temperature (float ) – Temperature of the diffusion run in Kelvin.
-Returns
+Returns:
Conversion factor.
Conductivity (in mS/cm) = Conversion Factor * Diffusivity (in cm^2/s)
@@ -430,7 +431,7 @@ Navigation
get_extrapolated_conductivity ( temps , diffusivities , new_temp , structure , species ) [source]
Returns extrapolated mS/cm conductivity.
-Parameters
+Parameters:
temps ([ float ] ) – A sequence of temperatures. units: K
diffusivities ([ float ] ) – A sequence of diffusivities (e.g.,
@@ -440,7 +441,7 @@
Navigation
species (string/Species ) – conducting species
-Returns
+Returns:
(float) Conductivity at extrapolated temp in mS/cm.
@@ -451,7 +452,7 @@ Navigation
get_extrapolated_diffusivity ( temps , diffusivities , new_temp ) [source]
Returns (Arrhenius) extrapolated diffusivity at new_temp
-Parameters
+Parameters:
temps ([ float ] ) – A sequence of temperatures. units: K
diffusivities ([ float ] ) – A sequence of diffusivities (e.g.,
@@ -459,7 +460,7 @@
Navigation
new_temp (float ) – desired temperature. units: K
-Returns
+Returns:
(float) Diffusivity at extrapolated temp in cm^2/s.
@@ -494,7 +495,7 @@ Quick search
-
+
diff --git a/docs/pymatgen.analysis.diffusion.html b/docs/pymatgen.analysis.diffusion.html
index c4559ecc..647f611a 100644
--- a/docs/pymatgen.analysis.diffusion.html
+++ b/docs/pymatgen.analysis.diffusion.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion package — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion package — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion package
@@ -48,9 +49,9 @@ Navigation
-pymatgen.analysis.diffusion package
+pymatgen.analysis.diffusion package
-Subpackages
+Subpackages
-
+
diff --git a/docs/pymatgen.analysis.diffusion.neb.full_path_mapper.html b/docs/pymatgen.analysis.diffusion.neb.full_path_mapper.html
index ebb70b48..71a35ae4 100644
--- a/docs/pymatgen.analysis.diffusion.neb.full_path_mapper.html
+++ b/docs/pymatgen.analysis.diffusion.neb.full_path_mapper.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.neb.full_path_mapper module — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.neb.full_path_mapper module — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.neb.full_path_mapper module
@@ -48,12 +49,12 @@ Navigation
-pymatgen.analysis.diffusion.neb.full_path_mapper module
+pymatgen.analysis.diffusion.neb.full_path_mapper module
Migraiton Graph Analysis
-class ChargeBarrierGraph ( structure : pymatgen.core.structure.Structure , m_graph : pymatgen.analysis.graphs.StructureGraph , potential_field : pymatgen.io.vasp.outputs.VolumetricData , potential_data_key : str , ** kwargs ) [source]
-Bases: pymatgen.analysis.diffusion.neb.full_path_mapper.MigrationGraph
+class ChargeBarrierGraph ( structure : Structure , m_graph : StructureGraph , potential_field : VolumetricData , potential_data_key : str , ** kwargs ) [source]
+Bases: MigrationGraph
A Migration graph with additional charge density analysis on the charge density of the host material
Construct the MigrationGraph object using a VolumetricData object.
The graph is constructure using the structure, and cost values are assigned based on charge density analysis.
@@ -62,7 +63,7 @@
Navigation
not have to contains all the metastable sites.
-Parameters
+Parameters:
-Parameters
+Parameters:
-add_data_to_similar_edges ( target_label : Union [ int , str ] , data : dict , m_hop : Optional [ pymatgen.analysis.diffusion.neb.pathfinder.MigrationHop ] = None ) [source]
+add_data_to_similar_edges ( target_label : Union [ int , str ] , data : dict , m_hop : Optional [ MigrationHop ] = None ) [source]
Insert data to all edges with the same label
:param target_label: The edge uniqueness label are adding data
:param data: The data to passed to the different edges
@@ -156,7 +157,7 @@
Navigation
or any other neighboring UC not containing p1.
-Parameters
+Parameters:
max_val – Filter the graph by a cost
flip_hops – If true, hops in paths returned will be flipped so
@@ -165,10 +166,10 @@
Navigation
from the migration graph.
-Returns
+Returns:
Each dict contains the information of a hop
-Return type
+Return type:
Generator for List of Dicts
@@ -176,11 +177,11 @@ Navigation
-static get_structure_from_entries ( entries : List [ pymatgen.entries.computed_entries.ComputedStructureEntry ] , migrating_ion_entry : pymatgen.entries.computed_entries.ComputedEntry , ** kwargs ) → List [ pymatgen.core.structure.Structure ] [source]
+static get_structure_from_entries ( entries : List [ ComputedStructureEntry ] , migrating_ion_entry : ComputedEntry , ** kwargs ) → List [ Structure ] [source]
Read in a list of base entries and inserted entries. Return a list of structures that contains metastable
sites for the migration species decorated with a “insertion_energy” property.
-Parameters
+Parameters:
-Returns
+Returns:
a list of host structures with working ion on all the metastable sites.
The structures are ranked by the number of metastable sites (most is first)
If the given entries are not enough to construct such a structure, return an empty list.
@@ -215,19 +216,19 @@ Navigation
-property host_structure : pymatgen.core.structure.Structure
+property host_structure : Structure
A structure that only contains the non-migrating species
-property only_sites : pymatgen.core.structure.Structure
+property only_sites : Structure
A structure that only contains the migrating species
-property symm_structure : pymatgen.symmetry.structure.SymmetrizedStructure
+property symm_structure : SymmetrizedStructure
The symmetrized structure with the present item’s symprec value
@@ -239,13 +240,13 @@ Navigation
-classmethod with_base_structure ( base_structure : pymatgen.core.structure.Structure , m_graph : pymatgen.analysis.graphs.StructureGraph , ** kwargs ) → pymatgen.analysis.diffusion.neb.full_path_mapper.MigrationGraph [source]
+classmethod with_base_structure ( base_structure : Structure , m_graph : StructureGraph , ** kwargs ) → MigrationGraph [source]
-Parameters
+Parameters:
base_structure – base framework structure that does not contain any
migrating sites.
-Returns
+Returns:
A constructed MigrationGraph object
@@ -253,7 +254,7 @@ Navigation
-classmethod with_distance ( structure : pymatgen.core.structure.Structure , migrating_specie : str , max_distance : float , ** kwargs ) → pymatgen.analysis.diffusion.neb.full_path_mapper.MigrationGraph [source]
+classmethod with_distance ( structure : Structure , migrating_specie : str , max_distance : float , ** kwargs ) → MigrationGraph [source]
Using a specific nn strategy to get the connectivity graph between all the migrating ion sites.
:param max_distance: Maximum length of NEB path in the unit
@@ -261,7 +262,7 @@ Navigation
value to the min cutoff until finding 1D or >1D percolating paths.
-Returns
+Returns:
A constructed MigrationGraph object
@@ -269,13 +270,13 @@ Navigation
-classmethod with_local_env_strategy ( structure : pymatgen.core.structure.Structure , migrating_specie : str , nn : pymatgen.analysis.local_env.NearNeighbors , ** kwargs ) → pymatgen.analysis.diffusion.neb.full_path_mapper.MigrationGraph [source]
+classmethod with_local_env_strategy ( structure : Structure , migrating_specie : str , nn : NearNeighbors , ** kwargs ) → MigrationGraph [source]
Using a specific nn strategy to get the connectivity graph between all the migrating ion sites.
:param structure: Input structure that contains all sites.
:param migrating_specie: The specie that migrates. E.g. “Li”.
:param nn: The specific local environment object used to connect the migrating ion sites.
-Returns
+Returns:
A constructed MigrationGraph object
@@ -297,7 +298,7 @@ Navigation
:param sc_hop: MigrationHop object form pymatgen-diffusion.
:param uc_hop: MigrationHop object form pymatgen-diffusion.
-Returns
+Returns:
image vector of lenght 3
Is the UC hop flip of the SC hop
@@ -306,12 +307,12 @@ Navigation
-generic_groupby ( list_in: list , comp: typing.Callable = <built-in function eq> ) [source]
+generic_groupby ( list_in: list , comp: ~typing.Callable = <built-in function eq> ) [source]
Group a list of unsortable objects
:param list_in: A list of generic objects
:param comp: (Default value = operator.eq) The comparator
-Returns
+Returns:
[int] list of labels for the input list
@@ -326,7 +327,7 @@ Navigation
:param key: property to track in a hop (e.g.: “hop_distance”)
:type key: optional
-Returns
+Returns:
String representation of the hop sequence (and property values if any)
@@ -334,15 +335,15 @@ Navigation
-get_only_sites_from_structure ( structure : pymatgen.core.structure.Structure , migrating_specie : str ) → pymatgen.core.structure.Structure [source]
+get_only_sites_from_structure ( structure : Structure , migrating_specie : str ) → Structure [source]
Get a copy of the structure with only the migrating sites.
:param structure: The full_structure that contains all the sites
:param migrating_specie: The name of migrating species
-Returns
+Returns:
Structure with all possible migrating ion sites
-Return type
+Return type:
Structure
@@ -350,7 +351,7 @@ Navigation
-map_hop_sc2uc ( sc_hop : pymatgen.analysis.diffusion.neb.pathfinder.MigrationHop , mg : pymatgen.analysis.diffusion.neb.full_path_mapper.MigrationGraph ) [source]
+map_hop_sc2uc ( sc_hop : MigrationHop , mg : MigrationGraph ) [source]
Map a given hop in the SC onto the UC.
:param sc_hop: MigrationHop object form pymatgen-diffusion.
:param mg: MigrationGraph object from pymatgen-diffusion.
@@ -376,7 +377,7 @@ Navigation
:param hop_list: a list of the data on a sequence of hops
:param start_u: the site index of the starting sites
-Returns
+Returns:
a list of the data on a sequence of hops with hops in coherent orientation
@@ -411,7 +412,7 @@ Quick search
-
+
diff --git a/docs/pymatgen.analysis.diffusion.neb.html b/docs/pymatgen.analysis.diffusion.neb.html
index ff04a89e..ff5ae7f0 100644
--- a/docs/pymatgen.analysis.diffusion.neb.html
+++ b/docs/pymatgen.analysis.diffusion.neb.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.neb package — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.neb package — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.neb package
@@ -48,14 +49,14 @@ Navigation
-pymatgen.analysis.diffusion.neb package
+pymatgen.analysis.diffusion.neb package
-Subpackages
+Subpackages
-
+
diff --git a/docs/pymatgen.analysis.diffusion.neb.io.html b/docs/pymatgen.analysis.diffusion.neb.io.html
index 5c447561..4015b3e4 100644
--- a/docs/pymatgen.analysis.diffusion.neb.io.html
+++ b/docs/pymatgen.analysis.diffusion.neb.io.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.neb.io module — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.neb.io module — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.neb.io module
@@ -48,15 +49,15 @@ Navigation
-pymatgen.analysis.diffusion.neb.io module
+pymatgen.analysis.diffusion.neb.io module
Generate input fiels for NEB calculations.
class MVLCINEBEndPointSet ( structure , ** kwargs ) [source]
-Bases: pymatgen.io.vasp.sets.MITRelaxSet
+Bases: MITRelaxSet
Class for writing NEB end points relaxation inputs.
-Parameters
+Parameters:
-
+
diff --git a/docs/pymatgen.analysis.diffusion.neb.pathfinder.html b/docs/pymatgen.analysis.diffusion.neb.pathfinder.html
index ae166519..ada61d51 100644
--- a/docs/pymatgen.analysis.diffusion.neb.pathfinder.html
+++ b/docs/pymatgen.analysis.diffusion.neb.pathfinder.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.neb.pathfinder module — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.neb.pathfinder module — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.neb.pathfinder module
@@ -48,7 +49,7 @@ Navigation
-pymatgen.analysis.diffusion.neb.pathfinder module
+pymatgen.analysis.diffusion.neb.pathfinder module
Algorithms for NEB migration path analysis.
@@ -59,7 +60,7 @@ Navigation
diffusion (assuming site positions are known). Note that this works mainly
for atomic mechanism, and does not work for correlated migration.
-Parameters
+Parameters:
structure – Input structure that contains all sites.
migrating_specie (Specie-like ) – The specie that migrates. E.g.,
@@ -78,7 +79,7 @@
Navigation
get_paths ( ) [source]
-Returns
+Returns:
[MigrationHop] All distinct migration paths.
@@ -91,7 +92,7 @@ Navigation
the images. H is chosen as it is the smallest atom. This is extremely
useful for path visualization in a standard software like VESTA.
-Parameters
+Parameters:
-Returns
+Returns:
[Structure] Complete IDPP path (including end-point structures)
@@ -180,11 +181,11 @@ Navigation
-class MigrationHop ( isite : pymatgen.core.sites.Site , esite : pymatgen.core.sites.Site , symm_structure : pymatgen.symmetry.structure.SymmetrizedStructure , host_symm_struct : Optional [ pymatgen.symmetry.structure.SymmetrizedStructure ] = None , symprec : float = 0.001 ) [source]
-Bases: monty.json.MSONable
+class MigrationHop ( isite : Site , esite : Site , symm_structure : SymmetrizedStructure , host_symm_struct : Optional [ SymmetrizedStructure ] = None , symprec : float = 0.001 ) [source]
+Bases: MSONable
A convenience container representing a migration path.
-Parameters
+Parameters:
isite – Initial site
esite – End site
@@ -196,10 +197,10 @@ Navigation
-get_sc_structures ( vac_mode : bool , min_atoms : int = 80 , max_atoms : int = 240 , min_length : float = 10.0 , tol : float = 1e-05 ) → Tuple [ pymatgen.core.structure.Structure , pymatgen.core.structure.Structure , pymatgen.core.structure.Structure ] [source]
+get_sc_structures ( vac_mode : bool , min_atoms : int = 80 , max_atoms : int = 240 , min_length : float = 10.0 , tol : float = 1e-05 ) → Tuple [ Structure , Structure , Structure ] [source]
Construct supercells that represents the start and end positions for migration analysis.
-Parameters
+Parameters:
vac_mode – If true simulate vacancy diffusion.
max_atoms – Maximum number of atoms allowed in the supercell.
@@ -208,7 +209,7 @@ Navigation
tol – toleranace for identifying isite/esite within base_struct
-Returns
+Returns:
Start, End, Base Structures.
If not vacancy mode, the base structure is just the host lattice.
If in vacancy mode, the base structure is the fully intercalated structure
@@ -222,7 +223,7 @@ Navigation
get_structures ( nimages = 5 , vac_mode = True , idpp = False , ** idpp_kwargs ) [source]
Generate structures for NEB calculation.
-Parameters
+Parameters:
-Returns
+Returns:
[Structure] Note that the first site of each structure is always
the migrating ion. This makes it easier to perform subsequent
analysis.
@@ -263,7 +264,7 @@ Navigation
write_path ( fname , ** kwargs ) [source]
Write the path to a file for easy viewing.
-Parameters
+Parameters:
-
+
diff --git a/docs/pymatgen.analysis.diffusion.neb.periodic_dijkstra.html b/docs/pymatgen.analysis.diffusion.neb.periodic_dijkstra.html
index 7c9bf0a4..8addb25a 100644
--- a/docs/pymatgen.analysis.diffusion.neb.periodic_dijkstra.html
+++ b/docs/pymatgen.analysis.diffusion.neb.periodic_dijkstra.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.neb.periodic_dijkstra module — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.neb.periodic_dijkstra module — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.neb.periodic_dijkstra module
@@ -48,7 +49,7 @@ Navigation
-pymatgen.analysis.diffusion.neb.periodic_dijkstra module
+pymatgen.analysis.diffusion.neb.periodic_dijkstra module
Dijkstra’s path search on a graph where the nodes are on a periodic graph
@@ -58,12 +59,12 @@ Navigation
-periodic_dijkstra ( G: networkx.classes.graph.Graph , sources: set , weight: str = 'weight' , max_image: int = 2 , target_reached: typing.Callable = <function <lambda>> ) [source]
+periodic_dijkstra ( G: ~networkx.classes.graph.Graph , sources: set , weight: str = 'weight' , max_image: int = 2 , target_reached: ~typing.Callable = <function <lambda>> ) [source]
Find the lowest cost pathway from a source point in the periodic graph.
Since the search can move many cells away without finding the target
we have to limit how many cells away from (0,0,0) to search.
-Parameters
+Parameters:
-Returns
+Returns:
a dictionary of the best cost found to periodic node keyed by (site_index, jimage)
path_parent: dictionary of optimal path parent for each node given in index-image pairs.
-Return type
+Return type:
best_ans
@@ -87,12 +88,12 @@ Navigation
-periodic_dijkstra_on_sgraph ( sgraph: pymatgen.analysis.graphs.StructureGraph , sources: typing.Set , weight: str = 'weight' , max_image: int = 1 , target_reached: typing.Callable = <function <lambda>> ) [source]
+periodic_dijkstra_on_sgraph ( sgraph: ~pymatgen.analysis.graphs.StructureGraph , sources: ~typing.Set , weight: str = 'weight' , max_image: int = 1 , target_reached: ~typing.Callable = <function <lambda>> ) [source]
Find the lowest cost pathway from a source point in the periodic graph.
Since the search can move many cells away without finding the target
we have to limit how many cells away from (0,0,0) to search.
-Parameters
+Parameters:
-Returns
+Returns:
a dictionary of the best cost found to periodic node keyed by (site_index, jimage)
path_parent: dictionary of optimal path parent for each node given in index-image pairs.
-Return type
+Return type:
best_ans
@@ -142,7 +143,7 @@ Quick search
-
+
diff --git a/docs/pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper.html b/docs/pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper.html
index 70658af1..fd03d2ea 100644
--- a/docs/pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper.html
+++ b/docs/pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper module — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper module — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper module
@@ -48,11 +49,11 @@ Navigation
-pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper module
+pymatgen.analysis.diffusion.neb.tests.test_full_path_mapper module
class ChargeBarrierGraphTest ( methodName = 'runTest' ) [source]
-Bases: unittest.case.TestCase
+Bases: TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
@@ -85,7 +86,7 @@ Navigation
class MigrationGraphComplexTest ( methodName = 'runTest' ) [source]
-Bases: unittest.case.TestCase
+Bases: TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
@@ -147,7 +148,7 @@ Navigation
class MigrationGraphFromEntriesTest ( methodName = 'runTest' ) [source]
-Bases: unittest.case.TestCase
+Bases: TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
@@ -172,7 +173,7 @@ Navigation
class MigrationGraphSimpleTest ( methodName = 'runTest' ) [source]
-Bases: unittest.case.TestCase
+Bases: TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
@@ -224,7 +225,7 @@ Quick search
-
+
diff --git a/docs/pymatgen.analysis.diffusion.neb.tests.test_io.html b/docs/pymatgen.analysis.diffusion.neb.tests.test_io.html
index c3bd2d46..ae674239 100644
--- a/docs/pymatgen.analysis.diffusion.neb.tests.test_io.html
+++ b/docs/pymatgen.analysis.diffusion.neb.tests.test_io.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.neb.tests.test_io module — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.neb.tests.test_io module — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.neb.tests.test_io module
@@ -48,17 +49,17 @@ Navigation
-pymatgen.analysis.diffusion.neb.tests.test_io module
+pymatgen.analysis.diffusion.neb.tests.test_io module
class MVLCINEBEndPointSetTest ( methodName = 'runTest' ) [source]
-Bases: unittest.case.TestCase
+Bases: TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
-endpoint = Structure Summary Lattice abc : 8.815000056846058 8.815000056846058 9.131710473490111 angles : 61.14080369885537 61.14080369885537 59.9999995733517 volume : 510.2218449146199 A : -4.4075 -7.634014 -0.0 B : 4.4075 -7.634014 0.0 C : -0.0 -5.089343 7.582 PeriodicSite: Na (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Zr (0.0000, -10.1787, 0.4774) [0.6457, 0.6457, 0.0630] PeriodicSite: Zr (-0.0000, -5.0893, 4.2684) [0.1457, 0.1457, 0.5630] PeriodicSite: Zr (-0.0000, -10.1787, 7.1046) [0.3543, 0.3543, 0.9370] PeriodicSite: Zr (-0.0000, -15.2680, 3.3136) [0.8543, 0.8543, 0.4370] PeriodicSite: P (-1.8370, -7.6340, 5.6865) [0.4584, 0.0416, 0.7500] PeriodicSite: P (3.1223, -9.8601, 5.6865) [0.0416, 0.7500, 0.7500] PeriodicSite: P (-1.2852, -13.0419, 5.6865) [0.7500, 0.4584, 0.7500] PeriodicSite: P (-3.1223, -10.4973, 1.8955) [0.9584, 0.2500, 0.2500] PeriodicSite: P (1.2852, -7.3154, 1.8955) [0.2500, 0.5416, 0.2500] PeriodicSite: P (1.8370, -12.7234, 1.8955) [0.5416, 0.9584, 0.2500] PeriodicSite: O (1.6956, -15.1421, 6.9239) [0.4950, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.7994, 6.9239) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.8626, 6.9239) [0.7121, 0.4950, 0.9132] PeriodicSite: O (-3.4506, -11.3179, 3.1329) [0.9950, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.6207, 3.1329) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.7119, -12.5974, 3.1329) [0.3797, 0.9950, 0.4132] PeriodicSite: O (-1.6956, -5.2153, 0.6581) [0.5050, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.5580, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.4948, 0.6581) [0.2879, 0.5050, 0.0868] PeriodicSite: O (3.4506, -9.0394, 4.4491) [0.0050, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.7366, 4.4491) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.7119, -7.7600, 4.4491) [0.6203, 0.0050, 0.5868] PeriodicSite: O (0.9463, -11.4574, 1.7985) [0.5640, 0.7787, 0.2372] PeriodicSite: O (-1.5805, -10.3588, 1.7985) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.7198, 1.7985) [0.4201, 0.5640, 0.2372] PeriodicSite: O (3.7733, -11.2645, 5.5895) [0.0640, 0.9201, 0.7372] PeriodicSite: O (-2.8270, -12.9035, 5.5895) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.3680, 5.5895) [0.2787, 0.0640, 0.7372] PeriodicSite: O (-0.9463, -8.9000, 5.7835) [0.4360, 0.2213, 0.7628] PeriodicSite: O (1.5805, -9.9985, 5.7835) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.6375, 5.7835) [0.5799, 0.4360, 0.7628] PeriodicSite: O (-3.7733, -9.0929, 1.9925) [0.9360, 0.0799, 0.2628] PeriodicSite: O (2.8270, -7.4539, 1.9925) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.9893, 1.9925) [0.7213, 0.9360, 0.2628]
+endpoint = Structure Summary Lattice abc : 8.815000056846058 8.815000056846058 9.131710473490111 angles : 61.14080369885537 61.14080369885537 59.9999995733517 volume : 510.2218449146199 A : -4.4075 -7.634014 -0.0 B : 4.4075 -7.634014 0.0 C : -0.0 -5.089343 7.582 pbc : True True True PeriodicSite: Na (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Zr (0.0000, -10.1787, 0.4774) [0.6457, 0.6457, 0.0630] PeriodicSite: Zr (-0.0000, -5.0893, 4.2684) [0.1457, 0.1457, 0.5630] PeriodicSite: Zr (-0.0000, -10.1787, 7.1046) [0.3543, 0.3543, 0.9370] PeriodicSite: Zr (-0.0000, -15.2680, 3.3136) [0.8543, 0.8543, 0.4370] PeriodicSite: P (-1.8370, -7.6340, 5.6865) [0.4584, 0.0416, 0.7500] PeriodicSite: P (3.1223, -9.8601, 5.6865) [0.0416, 0.7500, 0.7500] PeriodicSite: P (-1.2852, -13.0419, 5.6865) [0.7500, 0.4584, 0.7500] PeriodicSite: P (-3.1223, -10.4973, 1.8955) [0.9584, 0.2500, 0.2500] PeriodicSite: P (1.2852, -7.3154, 1.8955) [0.2500, 0.5416, 0.2500] PeriodicSite: P (1.8370, -12.7234, 1.8955) [0.5416, 0.9584, 0.2500] PeriodicSite: O (1.6956, -15.1421, 6.9239) [0.4950, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.7994, 6.9239) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.8626, 6.9239) [0.7121, 0.4950, 0.9132] PeriodicSite: O (-3.4506, -11.3179, 3.1329) [0.9950, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.6207, 3.1329) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.7119, -12.5974, 3.1329) [0.3797, 0.9950, 0.4132] PeriodicSite: O (-1.6956, -5.2153, 0.6581) [0.5050, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.5580, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.4948, 0.6581) [0.2879, 0.5050, 0.0868] PeriodicSite: O (3.4506, -9.0394, 4.4491) [0.0050, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.7366, 4.4491) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.7119, -7.7600, 4.4491) [0.6203, 0.0050, 0.5868] PeriodicSite: O (0.9463, -11.4574, 1.7985) [0.5640, 0.7787, 0.2372] PeriodicSite: O (-1.5805, -10.3588, 1.7985) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.7198, 1.7985) [0.4201, 0.5640, 0.2372] PeriodicSite: O (3.7733, -11.2645, 5.5895) [0.0640, 0.9201, 0.7372] PeriodicSite: O (-2.8270, -12.9035, 5.5895) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.3680, 5.5895) [0.2787, 0.0640, 0.7372] PeriodicSite: O (-0.9463, -8.9000, 5.7835) [0.4360, 0.2213, 0.7628] PeriodicSite: O (1.5805, -9.9985, 5.7835) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.6375, 5.7835) [0.5799, 0.4360, 0.7628] PeriodicSite: O (-3.7733, -9.0929, 1.9925) [0.9360, 0.0799, 0.2628] PeriodicSite: O (2.8270, -7.4539, 1.9925) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.9893, 1.9925) [0.7213, 0.9360, 0.2628]
@@ -76,13 +77,13 @@ Navigation
class MVLCINEBSetTest ( methodName = 'runTest' ) [source]
-Bases: unittest.case.TestCase
+Bases: TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
-structures = [Structure Summary Lattice abc : 8.815000056846058 8.815000056846058 9.131710473490111 angles : 61.14080369885537 61.14080369885537 59.9999995733517 volume : 510.2218449146199 A : -4.4075 -7.634014 -0.0 B : 4.4075 -7.634014 0.0 C : -0.0 -5.089343 7.582 PeriodicSite: Na (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Zr (0.0000, -10.1787, 0.4774) [0.6457, 0.6457, 0.0630] PeriodicSite: Zr (-0.0000, -5.0893, 4.2684) [0.1457, 0.1457, 0.5630] PeriodicSite: Zr (-0.0000, -10.1787, 7.1046) [0.3543, 0.3543, 0.9370] PeriodicSite: Zr (-0.0000, -15.2680, 3.3136) [0.8543, 0.8543, 0.4370] PeriodicSite: P (-1.8370, -7.6340, 5.6865) [0.4584, 0.0416, 0.7500] PeriodicSite: P (3.1223, -9.8601, 5.6865) [0.0416, 0.7500, 0.7500] PeriodicSite: P (-1.2852, -13.0419, 5.6865) [0.7500, 0.4584, 0.7500] PeriodicSite: P (-3.1223, -10.4973, 1.8955) [0.9584, 0.2500, 0.2500] PeriodicSite: P (1.2852, -7.3154, 1.8955) [0.2500, 0.5416, 0.2500] PeriodicSite: P (1.8370, -12.7234, 1.8955) [0.5416, 0.9584, 0.2500] PeriodicSite: O (1.6956, -15.1421, 6.9239) [0.4950, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.7994, 6.9239) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.8626, 6.9239) [0.7121, 0.4950, 0.9132] PeriodicSite: O (-3.4506, -11.3179, 3.1329) [0.9950, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.6207, 3.1329) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.7119, -12.5974, 3.1329) [0.3797, 0.9950, 0.4132] PeriodicSite: O (-1.6956, -5.2153, 0.6581) [0.5050, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.5580, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.4948, 0.6581) [0.2879, 0.5050, 0.0868] PeriodicSite: O (3.4506, -9.0394, 4.4491) [0.0050, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.7366, 4.4491) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.7119, -7.7600, 4.4491) [0.6203, 0.0050, 0.5868] PeriodicSite: O (0.9463, -11.4574, 1.7985) [0.5640, 0.7787, 0.2372] PeriodicSite: O (-1.5805, -10.3588, 1.7985) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.7198, 1.7985) [0.4201, 0.5640, 0.2372] PeriodicSite: O (3.7733, -11.2645, 5.5895) [0.0640, 0.9201, 0.7372] PeriodicSite: O (-2.8270, -12.9035, 5.5895) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.3680, 5.5895) [0.2787, 0.0640, 0.7372] PeriodicSite: O (-0.9463, -8.9000, 5.7835) [0.4360, 0.2213, 0.7628] PeriodicSite: O (1.5805, -9.9985, 5.7835) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.6375, 5.7835) [0.5799, 0.4360, 0.7628] PeriodicSite: O (-3.7733, -9.0929, 1.9925) [0.9360, 0.0799, 0.2628] PeriodicSite: O (2.8270, -7.4539, 1.9925) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.9893, 1.9925) [0.7213, 0.9360, 0.2628], Structure Summary Lattice abc : 8.815000056846058 8.815000056846058 9.131710473490111 angles : 61.14080369885537 61.14080369885537 59.9999995733517 volume : 510.2218449146199 A : -4.4075 -7.634014 -0.0 B : 4.4075 -7.634014 0.0 C : -0.0 -5.089343 7.582 PeriodicSite: Na (0.0000, -5.0893, 1.8955) [0.2500, 0.2500, 0.2500] PeriodicSite: Zr (0.0000, -10.1787, 0.4774) [0.6457, 0.6457, 0.0630] PeriodicSite: Zr (0.0000, -5.0893, 4.2684) [0.1457, 0.1457, 0.5630] PeriodicSite: Zr (0.0000, -10.1787, 7.1046) [0.3543, 0.3543, 0.9370] PeriodicSite: Zr (-0.0000, -15.2680, 3.3136) [0.8543, 0.8543, 0.4370] PeriodicSite: P (-1.8370, -7.6340, 5.6865) [0.4584, 0.0416, 0.7500] PeriodicSite: P (3.1223, -9.8601, 5.6865) [0.0416, 0.7500, 0.7500] PeriodicSite: P (-1.2852, -13.0419, 5.6865) [0.7500, 0.4584, 0.7500] PeriodicSite: P (-3.1223, -10.4973, 1.8955) [0.9584, 0.2500, 0.2500] PeriodicSite: P (1.2852, -7.3154, 1.8955) [0.2500, 0.5416, 0.2500] PeriodicSite: P (1.8370, -12.7234, 1.8955) [0.5416, 0.9584, 0.2500] PeriodicSite: O (1.6956, -15.1421, 6.9239) [0.4950, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.7994, 6.9239) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.8626, 6.9239) [0.7121, 0.4950, 0.9132] PeriodicSite: O (-3.4506, -11.3179, 3.1329) [0.9950, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.6207, 3.1329) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.7119, -12.5974, 3.1329) [0.3797, 0.9950, 0.4132] PeriodicSite: O (-1.6956, -5.2153, 0.6581) [0.5050, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.5580, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.4948, 0.6581) [0.2879, 0.5050, 0.0868] PeriodicSite: O (3.4506, -9.0394, 4.4491) [0.0050, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.7366, 4.4491) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.7119, -7.7600, 4.4491) [0.6203, 0.0050, 0.5868] PeriodicSite: O (0.9463, -11.4574, 1.7985) [0.5640, 0.7787, 0.2372] PeriodicSite: O (-1.5805, -10.3588, 1.7985) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.7198, 1.7985) [0.4201, 0.5640, 0.2372] PeriodicSite: O (3.7733, -11.2645, 5.5895) [0.0640, 0.9201, 0.7372] PeriodicSite: O (-2.8270, -12.9035, 5.5895) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.3680, 5.5895) [0.2787, 0.0640, 0.7372] PeriodicSite: O (-0.9463, -8.9000, 5.7835) [0.4360, 0.2213, 0.7628] PeriodicSite: O (1.5805, -9.9985, 5.7835) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.6375, 5.7835) [0.5799, 0.4360, 0.7628] PeriodicSite: O (-3.7733, -9.0929, 1.9925) [0.9360, 0.0799, 0.2628] PeriodicSite: O (2.8270, -7.4539, 1.9925) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.9893, 1.9925) [0.7213, 0.9360, 0.2628], Structure Summary Lattice abc : 8.815000056846058 8.815000056846058 9.131710473490111 angles : 61.14080369885537 61.14080369885537 59.9999995733517 volume : 510.2218449146199 A : -4.4075 -7.634014 -0.0 B : 4.4075 -7.634014 0.0 C : -0.0 -5.089343 7.582 PeriodicSite: Na (0.0000, -10.1787, 3.7910) [0.5000, 0.5000, 0.5000] PeriodicSite: Zr (0.0000, -10.1787, 0.4774) [0.6457, 0.6457, 0.0630] PeriodicSite: Zr (-0.0000, -5.0893, 4.2684) [0.1457, 0.1457, 0.5630] PeriodicSite: Zr (-0.0000, -10.1787, 7.1046) [0.3543, 0.3543, 0.9370] PeriodicSite: Zr (-0.0000, -15.2680, 3.3136) [0.8543, 0.8543, 0.4370] PeriodicSite: P (-1.8370, -7.6340, 5.6865) [0.4584, 0.0416, 0.7500] PeriodicSite: P (3.1223, -9.8601, 5.6865) [0.0416, 0.7500, 0.7500] PeriodicSite: P (-1.2852, -13.0419, 5.6865) [0.7500, 0.4584, 0.7500] PeriodicSite: P (-3.1223, -10.4973, 1.8955) [0.9584, 0.2500, 0.2500] PeriodicSite: P (1.2852, -7.3154, 1.8955) [0.2500, 0.5416, 0.2500] PeriodicSite: P (1.8370, -12.7234, 1.8955) [0.5416, 0.9584, 0.2500] PeriodicSite: O (1.6956, -15.1421, 6.9239) [0.4950, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.7994, 6.9239) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.8626, 6.9239) [0.7121, 0.4950, 0.9132] PeriodicSite: O (-3.4506, -11.3179, 3.1329) [0.9950, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.6207, 3.1329) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.7119, -12.5974, 3.1329) [0.3797, 0.9950, 0.4132] PeriodicSite: O (-1.6956, -5.2153, 0.6581) [0.5050, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.5580, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.4948, 0.6581) [0.2879, 0.5050, 0.0868] PeriodicSite: O (3.4506, -9.0394, 4.4491) [0.0050, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.7366, 4.4491) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.7119, -7.7600, 4.4491) [0.6203, 0.0050, 0.5868] PeriodicSite: O (0.9463, -11.4574, 1.7985) [0.5640, 0.7787, 0.2372] PeriodicSite: O (-1.5805, -10.3588, 1.7985) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.7198, 1.7985) [0.4201, 0.5640, 0.2372] PeriodicSite: O (3.7733, -11.2645, 5.5895) [0.0640, 0.9201, 0.7372] PeriodicSite: O (-2.8270, -12.9035, 5.5895) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.3680, 5.5895) [0.2787, 0.0640, 0.7372] PeriodicSite: O (-0.9463, -8.9000, 5.7835) [0.4360, 0.2213, 0.7628] PeriodicSite: O (1.5805, -9.9985, 5.7835) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.6375, 5.7835) [0.5799, 0.4360, 0.7628] PeriodicSite: O (-3.7733, -9.0929, 1.9925) [0.9360, 0.0799, 0.2628] PeriodicSite: O (2.8270, -7.4539, 1.9925) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.9893, 1.9925) [0.7213, 0.9360, 0.2628]]
+structures = [Structure Summary Lattice abc : 8.815000056846058 8.815000056846058 9.131710473490111 angles : 61.14080369885537 61.14080369885537 59.9999995733517 volume : 510.2218449146199 A : -4.4075 -7.634014 -0.0 B : 4.4075 -7.634014 0.0 C : -0.0 -5.089343 7.582 pbc : True True True PeriodicSite: Na (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Zr (0.0000, -10.1787, 0.4774) [0.6457, 0.6457, 0.0630] PeriodicSite: Zr (-0.0000, -5.0893, 4.2684) [0.1457, 0.1457, 0.5630] PeriodicSite: Zr (-0.0000, -10.1787, 7.1046) [0.3543, 0.3543, 0.9370] PeriodicSite: Zr (-0.0000, -15.2680, 3.3136) [0.8543, 0.8543, 0.4370] PeriodicSite: P (-1.8370, -7.6340, 5.6865) [0.4584, 0.0416, 0.7500] PeriodicSite: P (3.1223, -9.8601, 5.6865) [0.0416, 0.7500, 0.7500] PeriodicSite: P (-1.2852, -13.0419, 5.6865) [0.7500, 0.4584, 0.7500] PeriodicSite: P (-3.1223, -10.4973, 1.8955) [0.9584, 0.2500, 0.2500] PeriodicSite: P (1.2852, -7.3154, 1.8955) [0.2500, 0.5416, 0.2500] PeriodicSite: P (1.8370, -12.7234, 1.8955) [0.5416, 0.9584, 0.2500] PeriodicSite: O (1.6956, -15.1421, 6.9239) [0.4950, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.7994, 6.9239) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.8626, 6.9239) [0.7121, 0.4950, 0.9132] PeriodicSite: O (-3.4506, -11.3179, 3.1329) [0.9950, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.6207, 3.1329) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.7119, -12.5974, 3.1329) [0.3797, 0.9950, 0.4132] PeriodicSite: O (-1.6956, -5.2153, 0.6581) [0.5050, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.5580, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.4948, 0.6581) [0.2879, 0.5050, 0.0868] PeriodicSite: O (3.4506, -9.0394, 4.4491) [0.0050, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.7366, 4.4491) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.7119, -7.7600, 4.4491) [0.6203, 0.0050, 0.5868] PeriodicSite: O (0.9463, -11.4574, 1.7985) [0.5640, 0.7787, 0.2372] PeriodicSite: O (-1.5805, -10.3588, 1.7985) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.7198, 1.7985) [0.4201, 0.5640, 0.2372] PeriodicSite: O (3.7733, -11.2645, 5.5895) [0.0640, 0.9201, 0.7372] PeriodicSite: O (-2.8270, -12.9035, 5.5895) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.3680, 5.5895) [0.2787, 0.0640, 0.7372] PeriodicSite: O (-0.9463, -8.9000, 5.7835) [0.4360, 0.2213, 0.7628] PeriodicSite: O (1.5805, -9.9985, 5.7835) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.6375, 5.7835) [0.5799, 0.4360, 0.7628] PeriodicSite: O (-3.7733, -9.0929, 1.9925) [0.9360, 0.0799, 0.2628] PeriodicSite: O (2.8270, -7.4539, 1.9925) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.9893, 1.9925) [0.7213, 0.9360, 0.2628], Structure Summary Lattice abc : 8.815000056846058 8.815000056846058 9.131710473490111 angles : 61.14080369885537 61.14080369885537 59.9999995733517 volume : 510.2218449146199 A : -4.4075 -7.634014 -0.0 B : 4.4075 -7.634014 0.0 C : -0.0 -5.089343 7.582 pbc : True True True PeriodicSite: Na (0.0000, -5.0893, 1.8955) [0.2500, 0.2500, 0.2500] PeriodicSite: Zr (0.0000, -10.1787, 0.4774) [0.6457, 0.6457, 0.0630] PeriodicSite: Zr (0.0000, -5.0893, 4.2684) [0.1457, 0.1457, 0.5630] PeriodicSite: Zr (0.0000, -10.1787, 7.1046) [0.3543, 0.3543, 0.9370] PeriodicSite: Zr (-0.0000, -15.2680, 3.3136) [0.8543, 0.8543, 0.4370] PeriodicSite: P (-1.8370, -7.6340, 5.6865) [0.4584, 0.0416, 0.7500] PeriodicSite: P (3.1223, -9.8601, 5.6865) [0.0416, 0.7500, 0.7500] PeriodicSite: P (-1.2852, -13.0419, 5.6865) [0.7500, 0.4584, 0.7500] PeriodicSite: P (-3.1223, -10.4973, 1.8955) [0.9584, 0.2500, 0.2500] PeriodicSite: P (1.2852, -7.3154, 1.8955) [0.2500, 0.5416, 0.2500] PeriodicSite: P (1.8370, -12.7234, 1.8955) [0.5416, 0.9584, 0.2500] PeriodicSite: O (1.6956, -15.1421, 6.9239) [0.4950, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.7994, 6.9239) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.8626, 6.9239) [0.7121, 0.4950, 0.9132] PeriodicSite: O (-3.4506, -11.3179, 3.1329) [0.9950, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.6207, 3.1329) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.7119, -12.5974, 3.1329) [0.3797, 0.9950, 0.4132] PeriodicSite: O (-1.6956, -5.2153, 0.6581) [0.5050, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.5580, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.4948, 0.6581) [0.2879, 0.5050, 0.0868] PeriodicSite: O (3.4506, -9.0394, 4.4491) [0.0050, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.7366, 4.4491) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.7119, -7.7600, 4.4491) [0.6203, 0.0050, 0.5868] PeriodicSite: O (0.9463, -11.4574, 1.7985) [0.5640, 0.7787, 0.2372] PeriodicSite: O (-1.5805, -10.3588, 1.7985) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.7198, 1.7985) [0.4201, 0.5640, 0.2372] PeriodicSite: O (3.7733, -11.2645, 5.5895) [0.0640, 0.9201, 0.7372] PeriodicSite: O (-2.8270, -12.9035, 5.5895) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.3680, 5.5895) [0.2787, 0.0640, 0.7372] PeriodicSite: O (-0.9463, -8.9000, 5.7835) [0.4360, 0.2213, 0.7628] PeriodicSite: O (1.5805, -9.9985, 5.7835) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.6375, 5.7835) [0.5799, 0.4360, 0.7628] PeriodicSite: O (-3.7733, -9.0929, 1.9925) [0.9360, 0.0799, 0.2628] PeriodicSite: O (2.8270, -7.4539, 1.9925) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.9893, 1.9925) [0.7213, 0.9360, 0.2628], Structure Summary Lattice abc : 8.815000056846058 8.815000056846058 9.131710473490111 angles : 61.14080369885537 61.14080369885537 59.9999995733517 volume : 510.2218449146199 A : -4.4075 -7.634014 -0.0 B : 4.4075 -7.634014 0.0 C : -0.0 -5.089343 7.582 pbc : True True True PeriodicSite: Na (0.0000, -10.1787, 3.7910) [0.5000, 0.5000, 0.5000] PeriodicSite: Zr (0.0000, -10.1787, 0.4774) [0.6457, 0.6457, 0.0630] PeriodicSite: Zr (-0.0000, -5.0893, 4.2684) [0.1457, 0.1457, 0.5630] PeriodicSite: Zr (-0.0000, -10.1787, 7.1046) [0.3543, 0.3543, 0.9370] PeriodicSite: Zr (-0.0000, -15.2680, 3.3136) [0.8543, 0.8543, 0.4370] PeriodicSite: P (-1.8370, -7.6340, 5.6865) [0.4584, 0.0416, 0.7500] PeriodicSite: P (3.1223, -9.8601, 5.6865) [0.0416, 0.7500, 0.7500] PeriodicSite: P (-1.2852, -13.0419, 5.6865) [0.7500, 0.4584, 0.7500] PeriodicSite: P (-3.1223, -10.4973, 1.8955) [0.9584, 0.2500, 0.2500] PeriodicSite: P (1.2852, -7.3154, 1.8955) [0.2500, 0.5416, 0.2500] PeriodicSite: P (1.8370, -12.7234, 1.8955) [0.5416, 0.9584, 0.2500] PeriodicSite: O (1.6956, -15.1421, 6.9239) [0.4950, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.7994, 6.9239) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.8626, 6.9239) [0.7121, 0.4950, 0.9132] PeriodicSite: O (-3.4506, -11.3179, 3.1329) [0.9950, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.6207, 3.1329) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.7119, -12.5974, 3.1329) [0.3797, 0.9950, 0.4132] PeriodicSite: O (-1.6956, -5.2153, 0.6581) [0.5050, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.5580, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.4948, 0.6581) [0.2879, 0.5050, 0.0868] PeriodicSite: O (3.4506, -9.0394, 4.4491) [0.0050, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.7366, 4.4491) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.7119, -7.7600, 4.4491) [0.6203, 0.0050, 0.5868] PeriodicSite: O (0.9463, -11.4574, 1.7985) [0.5640, 0.7787, 0.2372] PeriodicSite: O (-1.5805, -10.3588, 1.7985) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.7198, 1.7985) [0.4201, 0.5640, 0.2372] PeriodicSite: O (3.7733, -11.2645, 5.5895) [0.0640, 0.9201, 0.7372] PeriodicSite: O (-2.8270, -12.9035, 5.5895) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.3680, 5.5895) [0.2787, 0.0640, 0.7372] PeriodicSite: O (-0.9463, -8.9000, 5.7835) [0.4360, 0.2213, 0.7628] PeriodicSite: O (1.5805, -9.9985, 5.7835) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.6375, 5.7835) [0.5799, 0.4360, 0.7628] PeriodicSite: O (-3.7733, -9.0929, 1.9925) [0.9360, 0.0799, 0.2628] PeriodicSite: O (2.8270, -7.4539, 1.9925) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.9893, 1.9925) [0.7213, 0.9360, 0.2628]]
@@ -100,14 +101,14 @@ Navigation
class UtilityTest ( methodName = 'runTest' ) [source]
-Bases: unittest.case.TestCase
+Bases: TestCase
Unit test for outside methods in io.py
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
-structure = Structure Summary Lattice abc : 8.815000056846058 8.815000056846058 9.131710473490111 angles : 61.14080369885537 61.14080369885537 59.9999995733517 volume : 510.2218449146199 A : -4.4075 -7.634014 -0.0 B : 4.4075 -7.634014 0.0 C : -0.0 -5.089343 7.582 PeriodicSite: Na (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Na (0.0000, -10.1787, 3.7910) [0.5000, 0.5000, 0.5000] PeriodicSite: Zr (0.0000, -10.1787, 0.4774) [0.6457, 0.6457, 0.0630] PeriodicSite: Zr (-0.0000, -5.0893, 4.2684) [0.1457, 0.1457, 0.5630] PeriodicSite: Zr (-0.0000, -10.1787, 7.1046) [0.3543, 0.3543, 0.9370] PeriodicSite: Zr (-0.0000, -15.2680, 3.3136) [0.8543, 0.8543, 0.4370] PeriodicSite: P (-1.8370, -7.6340, 5.6865) [0.4584, 0.0416, 0.7500] PeriodicSite: P (3.1223, -9.8601, 5.6865) [0.0416, 0.7500, 0.7500] PeriodicSite: P (-1.2852, -13.0419, 5.6865) [0.7500, 0.4584, 0.7500] PeriodicSite: P (-3.1223, -10.4973, 1.8955) [0.9584, 0.2500, 0.2500] PeriodicSite: P (1.2852, -7.3154, 1.8955) [0.2500, 0.5416, 0.2500] PeriodicSite: P (1.8370, -12.7234, 1.8955) [0.5416, 0.9584, 0.2500] PeriodicSite: O (1.6956, -15.1421, 6.9239) [0.4950, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.7994, 6.9239) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.8626, 6.9239) [0.7121, 0.4950, 0.9132] PeriodicSite: O (-3.4506, -11.3179, 3.1329) [0.9950, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.6207, 3.1329) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.7119, -12.5974, 3.1329) [0.3797, 0.9950, 0.4132] PeriodicSite: O (-1.6956, -5.2153, 0.6581) [0.5050, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.5580, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.4948, 0.6581) [0.2879, 0.5050, 0.0868] PeriodicSite: O (3.4506, -9.0394, 4.4491) [0.0050, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.7366, 4.4491) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.7119, -7.7600, 4.4491) [0.6203, 0.0050, 0.5868] PeriodicSite: O (0.9463, -11.4574, 1.7985) [0.5640, 0.7787, 0.2372] PeriodicSite: O (-1.5805, -10.3588, 1.7985) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.7198, 1.7985) [0.4201, 0.5640, 0.2372] PeriodicSite: O (3.7733, -11.2645, 5.5895) [0.0640, 0.9201, 0.7372] PeriodicSite: O (-2.8270, -12.9035, 5.5895) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.3680, 5.5895) [0.2787, 0.0640, 0.7372] PeriodicSite: O (-0.9463, -8.9000, 5.7835) [0.4360, 0.2213, 0.7628] PeriodicSite: O (1.5805, -9.9985, 5.7835) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.6375, 5.7835) [0.5799, 0.4360, 0.7628] PeriodicSite: O (-3.7733, -9.0929, 1.9925) [0.9360, 0.0799, 0.2628] PeriodicSite: O (2.8270, -7.4539, 1.9925) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.9893, 1.9925) [0.7213, 0.9360, 0.2628]
+structure = Structure Summary Lattice abc : 8.815000056846058 8.815000056846058 9.131710473490111 angles : 61.14080369885537 61.14080369885537 59.9999995733517 volume : 510.2218449146199 A : -4.4075 -7.634014 -0.0 B : 4.4075 -7.634014 0.0 C : -0.0 -5.089343 7.582 pbc : True True True PeriodicSite: Na (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] PeriodicSite: Na (0.0000, -10.1787, 3.7910) [0.5000, 0.5000, 0.5000] PeriodicSite: Zr (0.0000, -10.1787, 0.4774) [0.6457, 0.6457, 0.0630] PeriodicSite: Zr (-0.0000, -5.0893, 4.2684) [0.1457, 0.1457, 0.5630] PeriodicSite: Zr (-0.0000, -10.1787, 7.1046) [0.3543, 0.3543, 0.9370] PeriodicSite: Zr (-0.0000, -15.2680, 3.3136) [0.8543, 0.8543, 0.4370] PeriodicSite: P (-1.8370, -7.6340, 5.6865) [0.4584, 0.0416, 0.7500] PeriodicSite: P (3.1223, -9.8601, 5.6865) [0.0416, 0.7500, 0.7500] PeriodicSite: P (-1.2852, -13.0419, 5.6865) [0.7500, 0.4584, 0.7500] PeriodicSite: P (-3.1223, -10.4973, 1.8955) [0.9584, 0.2500, 0.2500] PeriodicSite: P (1.2852, -7.3154, 1.8955) [0.2500, 0.5416, 0.2500] PeriodicSite: P (1.8370, -12.7234, 1.8955) [0.5416, 0.9584, 0.2500] PeriodicSite: O (1.6956, -15.1421, 6.9239) [0.4950, 0.8797, 0.9132] PeriodicSite: O (-0.7387, -16.7994, 6.9239) [0.8797, 0.7121, 0.9132] PeriodicSite: O (-0.9569, -13.8626, 6.9239) [0.7121, 0.4950, 0.9132] PeriodicSite: O (-3.4506, -11.3179, 3.1329) [0.9950, 0.2121, 0.4132] PeriodicSite: O (0.7387, -6.6207, 3.1329) [0.2121, 0.3797, 0.4132] PeriodicSite: O (2.7119, -12.5974, 3.1329) [0.3797, 0.9950, 0.4132] PeriodicSite: O (-1.6956, -5.2153, 0.6581) [0.5050, 0.1203, 0.0868] PeriodicSite: O (0.7387, -3.5580, 0.6581) [0.1203, 0.2879, 0.0868] PeriodicSite: O (0.9569, -6.4948, 0.6581) [0.2879, 0.5050, 0.0868] PeriodicSite: O (3.4506, -9.0394, 4.4491) [0.0050, 0.7879, 0.5868] PeriodicSite: O (-0.7387, -13.7366, 4.4491) [0.7879, 0.6203, 0.5868] PeriodicSite: O (-2.7119, -7.7600, 4.4491) [0.6203, 0.0050, 0.5868] PeriodicSite: O (0.9463, -11.4574, 1.7985) [0.5640, 0.7787, 0.2372] PeriodicSite: O (-1.5805, -10.3588, 1.7985) [0.7787, 0.4201, 0.2372] PeriodicSite: O (0.6342, -8.7198, 1.7985) [0.4201, 0.5640, 0.2372] PeriodicSite: O (3.7733, -11.2645, 5.5895) [0.0640, 0.9201, 0.7372] PeriodicSite: O (-2.8270, -12.9035, 5.5895) [0.9201, 0.2787, 0.7372] PeriodicSite: O (-0.9463, -6.3680, 5.5895) [0.2787, 0.0640, 0.7372] PeriodicSite: O (-0.9463, -8.9000, 5.7835) [0.4360, 0.2213, 0.7628] PeriodicSite: O (1.5805, -9.9985, 5.7835) [0.2213, 0.5799, 0.7628] PeriodicSite: O (-0.6342, -11.6375, 5.7835) [0.5799, 0.4360, 0.7628] PeriodicSite: O (-3.7733, -9.0929, 1.9925) [0.9360, 0.0799, 0.2628] PeriodicSite: O (2.8270, -7.4539, 1.9925) [0.0799, 0.7213, 0.2628] PeriodicSite: O (0.9463, -13.9893, 1.9925) [0.7213, 0.9360, 0.2628]
@@ -156,7 +157,7 @@ Quick search
-
+
diff --git a/docs/pymatgen.analysis.diffusion.neb.tests.test_pathfinder.html b/docs/pymatgen.analysis.diffusion.neb.tests.test_pathfinder.html
index 26521227..546d2696 100644
--- a/docs/pymatgen.analysis.diffusion.neb.tests.test_pathfinder.html
+++ b/docs/pymatgen.analysis.diffusion.neb.tests.test_pathfinder.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.neb.tests.test_pathfinder module — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.neb.tests.test_pathfinder module — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.neb.tests.test_pathfinder module
@@ -48,11 +49,11 @@ Navigation
-pymatgen.analysis.diffusion.neb.tests.test_pathfinder module
+pymatgen.analysis.diffusion.neb.tests.test_pathfinder module
class DistinctPathFinderTest ( methodName = 'runTest' ) [source]
-Bases: pymatgen.util.testing.PymatgenTest
+Bases: PymatgenTest
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
@@ -71,18 +72,18 @@ Navigation
class IDPPSolverTest ( methodName = 'runTest' ) [source]
-Bases: unittest.case.TestCase
+Bases: TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
-final_struct = Structure Summary Lattice abc : 10.411723299877 12.0783517723596 9.47759961582329 angles : 90.0 90.0 90.0 volume : 1191.8693444977544 A : 10.411723299877 0.0 0.0 B : 0.0 12.0783517723596 0.0 C : 0.0 0.0 9.47759961582329 PeriodicSite: Li (5.1847, 6.1822, 2.4175) [0.4980, 0.5118, 0.2551] PeriodicSite: Li (5.2270, 11.9354, 2.3213) [0.5020, 0.9882, 0.2449] PeriodicSite: Li (5.1817, 12.0665, 7.0846) [0.4977, 0.9990, 0.7475] PeriodicSite: Li (5.2300, 6.0511, 7.1318) [0.5023, 0.5010, 0.7525] PeriodicSite: Li (0.0005, 3.0181, 0.0043) [0.0000, 0.2499, 0.0005] PeriodicSite: Li (10.4112, 3.0211, 4.7345) [1.0000, 0.2501, 0.4995] PeriodicSite: Li (10.4061, 9.0584, 0.0031) [0.9995, 0.7500, 0.0003] PeriodicSite: Li (0.0057, 9.0592, 4.7357) [0.0005, 0.7500, 0.4997] PeriodicSite: Li (5.2059, 3.0196, 2.3694) [0.5000, 0.2500, 0.2500] PeriodicSite: Li (5.2059, 3.0196, 7.1082) [0.5000, 0.2500, 0.7500] PeriodicSite: Li (5.2059, 9.0588, 7.1082) [0.5000, 0.7500, 0.7500] PeriodicSite: Li (10.4087, 12.0648, 0.0085) [0.9997, 0.9989, 0.0009] PeriodicSite: Li (0.0032, 12.0741, 4.7383) [0.0003, 0.9996, 0.5000] PeriodicSite: Li (10.4086, 6.0435, 0.0005) [0.9997, 0.5004, 0.0000] PeriodicSite: Li (0.0030, 6.0527, 4.7303) [0.0003, 0.5011, 0.4991] PeriodicSite: Fe (8.1412, 1.5110, 2.4871) [0.7819, 0.1251, 0.2624] PeriodicSite: Fe (8.1407, 1.5063, 7.2279) [0.7819, 0.1247, 0.7626] PeriodicSite: Fe (8.1001, 7.5688, 2.4722) [0.7780, 0.6266, 0.2608] PeriodicSite: Fe (8.1373, 7.5452, 7.2347) [0.7816, 0.6247, 0.7633] PeriodicSite: Fe (2.9469, 1.5019, 4.6127) [0.2830, 0.1243, 0.4867] PeriodicSite: Fe (2.9383, 1.5040, 9.3553) [0.2822, 0.1245, 0.9871] PeriodicSite: Fe (2.9571, 7.5783, 4.6085) [0.2840, 0.6274, 0.4863] PeriodicSite: Fe (2.9595, 7.5654, 9.3806) [0.2842, 0.6264, 0.9898] PeriodicSite: Fe (2.2705, 4.5282, 2.2517) [0.2181, 0.3749, 0.2376] PeriodicSite: Fe (2.2711, 4.5329, 6.9885) [0.2181, 0.3753, 0.7374] PeriodicSite: Fe (2.3116, 10.5488, 2.2666) [0.2220, 0.8734, 0.2392] PeriodicSite: Fe (2.2744, 10.5723, 6.9817) [0.2184, 0.8753, 0.7367] PeriodicSite: Fe (7.4648, 4.5373, 0.1261) [0.7170, 0.3757, 0.0133] PeriodicSite: Fe (7.4734, 4.5352, 4.8611) [0.7178, 0.3755, 0.5129] PeriodicSite: Fe (7.4547, 10.5392, 0.1303) [0.7160, 0.8726, 0.0137] PeriodicSite: Fe (7.4522, 10.5521, 4.8358) [0.7158, 0.8736, 0.5102] PeriodicSite: P (6.1978, 1.5072, 0.3753) [0.5953, 0.1248, 0.0396] PeriodicSite: P (6.2113, 1.5136, 5.1114) [0.5966, 0.1253, 0.5393] PeriodicSite: P (6.1961, 7.5476, 0.3633) [0.5951, 0.6249, 0.0383] PeriodicSite: P (6.2203, 7.5145, 5.1196) [0.5974, 0.6221, 0.5402] PeriodicSite: P (0.9887, 1.5041, 1.9896) [0.0950, 0.1245, 0.2099] PeriodicSite: P (0.9865, 1.5133, 6.7275) [0.0948, 0.1253, 0.7098] PeriodicSite: P (0.9818, 7.5439, 1.9926) [0.0943, 0.6246, 0.2102] PeriodicSite: P (0.9911, 7.5461, 6.7377) [0.0952, 0.6248, 0.7109] PeriodicSite: P (4.2139, 4.5319, 4.3635) [0.4047, 0.3752, 0.4604] PeriodicSite: P (4.2004, 4.5256, 9.1050) [0.4034, 0.3747, 0.9607] PeriodicSite: P (4.2156, 10.5699, 4.3756) [0.4049, 0.8751, 0.4617] PeriodicSite: P (4.1914, 10.6030, 9.0968) [0.4026, 0.8779, 0.9598] PeriodicSite: P (9.4230, 4.5351, 2.7492) [0.9050, 0.3755, 0.2901] PeriodicSite: P (9.4252, 4.5259, 7.4889) [0.9053, 0.3747, 0.7902] PeriodicSite: P (9.4299, 10.5737, 2.7462) [0.9057, 0.8754, 0.2898] PeriodicSite: P (9.4207, 10.5714, 7.4786) [0.9048, 0.8752, 0.7891] PeriodicSite: O (6.2228, 1.5268, 3.5773) [0.5977, 0.1264, 0.3775] PeriodicSite: O (6.2093, 1.5125, 8.3155) [0.5964, 0.1252, 0.8774] PeriodicSite: O (6.2747, 7.4398, 3.6014) [0.6027, 0.6160, 0.3800] PeriodicSite: O (6.2119, 7.5449, 8.2933) [0.5966, 0.6247, 0.8750] PeriodicSite: O (0.9902, 1.5124, 3.5258) [0.0951, 0.1252, 0.3720] PeriodicSite: O (0.9889, 1.5120, 8.2636) [0.0950, 0.1252, 0.8719] PeriodicSite: O (0.9898, 7.5475, 3.5295) [0.0951, 0.6249, 0.3724] PeriodicSite: O (0.9929, 7.5401, 8.2739) [0.0954, 0.6243, 0.8730] PeriodicSite: O (4.1889, 4.5124, 1.1615) [0.4023, 0.3736, 0.1225] PeriodicSite: O (4.2024, 4.5266, 5.9009) [0.4036, 0.3748, 0.6226] PeriodicSite: O (4.1370, 10.6778, 1.1374) [0.3973, 0.8840, 0.1200] PeriodicSite: O (4.1999, 10.5726, 5.9231) [0.4034, 0.8753, 0.6250] PeriodicSite: O (9.4215, 4.5268, 1.2130) [0.9049, 0.3748, 0.1280] PeriodicSite: O (9.4228, 4.5272, 5.9528) [0.9050, 0.3748, 0.6281] PeriodicSite: O (9.4220, 10.5700, 1.2093) [0.9049, 0.8751, 0.1276] PeriodicSite: O (9.4189, 10.5774, 5.9425) [0.9046, 0.8757, 0.6270] PeriodicSite: O (9.9678, 1.5135, 1.3791) [0.9574, 0.1253, 0.1455] PeriodicSite: O (9.9659, 1.5224, 6.1189) [0.9572, 0.1260, 0.6456] PeriodicSite: O (9.9630, 7.5428, 1.3832) [0.9569, 0.6245, 0.1459] PeriodicSite: O (9.9719, 7.5406, 6.1245) [0.9578, 0.6243, 0.6462] PeriodicSite: O (4.7657, 1.5202, 0.9751) [0.4577, 0.1259, 0.1029] PeriodicSite: O (4.7779, 1.5132, 5.7181) [0.4589, 0.1253, 0.6033] PeriodicSite: O (4.7627, 7.5033, 0.9219) [0.4574, 0.6212, 0.0973] PeriodicSite: O (4.7799, 7.5423, 5.7118) [0.4591, 0.6244, 0.6027] PeriodicSite: O (0.4439, 4.5256, 3.3597) [0.0426, 0.3747, 0.3545] PeriodicSite: O (0.4458, 4.5167, 8.0975) [0.0428, 0.3740, 0.8544] PeriodicSite: O (0.4487, 10.5747, 3.3556) [0.0431, 0.8755, 0.3541] PeriodicSite: O (0.4398, 10.5769, 8.0919) [0.0422, 0.8757, 0.8538] PeriodicSite: O (5.6461, 4.5190, 3.7637) [0.5423, 0.3741, 0.3971] PeriodicSite: O (5.6338, 4.5260, 8.4983) [0.5411, 0.3747, 0.8967] PeriodicSite: O (5.6490, 10.6142, 3.8169) [0.5426, 0.8788, 0.4027] PeriodicSite: O (5.6318, 10.5752, 8.5046) [0.5409, 0.8756, 0.8973] PeriodicSite: O (6.9383, 0.2665, 0.9991) [0.6664, 0.0221, 0.1054] PeriodicSite: O (6.9618, 0.2813, 5.7394) [0.6687, 0.0233, 0.6056] PeriodicSite: O (6.9424, 6.2988, 0.9884) [0.6668, 0.5215, 0.1043] PeriodicSite: O (6.9414, 6.2829, 5.8049) [0.6667, 0.5202, 0.6125] PeriodicSite: O (1.7379, 2.7394, 1.3635) [0.1669, 0.2268, 0.1439] PeriodicSite: O (1.7390, 2.7463, 6.1020) [0.1670, 0.2274, 0.6438] PeriodicSite: O (1.7293, 8.7758, 1.3621) [0.1661, 0.7266, 0.1437] PeriodicSite: O (1.7278, 8.7874, 6.1173) [0.1659, 0.7275, 0.6454] PeriodicSite: O (3.4593, 3.2999, 3.7365) [0.3322, 0.2732, 0.3942] PeriodicSite: O (3.4611, 3.2876, 8.4676) [0.3324, 0.2722, 0.8934] PeriodicSite: O (3.3893, 9.3739, 3.7965) [0.3255, 0.7761, 0.4006] PeriodicSite: O (3.4444, 9.3601, 8.4821) [0.3308, 0.7749, 0.8950] PeriodicSite: O (8.6876, 5.7754, 3.3730) [0.8344, 0.4782, 0.3559] PeriodicSite: O (8.6907, 5.7645, 8.1192) [0.8347, 0.4773, 0.8567] PeriodicSite: O (8.6853, 11.8141, 3.3664) [0.8342, 0.9781, 0.3552] PeriodicSite: O (8.6685, 11.8020, 8.1098) [0.8326, 0.9771, 0.8557] PeriodicSite: O (3.4734, 5.7727, 3.7397) [0.3336, 0.4779, 0.3946] PeriodicSite: O (3.4499, 5.7579, 8.4770) [0.3313, 0.4767, 0.8944] PeriodicSite: O (3.4693, 11.8187, 3.7504) [0.3332, 0.9785, 0.3957] PeriodicSite: O (3.4703, 11.8347, 8.4115) [0.3333, 0.9798, 0.8875] PeriodicSite: O (8.6738, 3.2998, 3.3753) [0.8331, 0.2732, 0.3561] PeriodicSite: O (8.6727, 3.2929, 8.1143) [0.8330, 0.2726, 0.8562] PeriodicSite: O (8.6824, 9.3417, 3.3767) [0.8339, 0.7734, 0.3563] PeriodicSite: O (8.6840, 9.3302, 8.0991) [0.8341, 0.7725, 0.8546] PeriodicSite: O (6.9525, 2.7393, 1.0023) [0.6678, 0.2268, 0.1058] PeriodicSite: O (6.9506, 2.7516, 5.7488) [0.6676, 0.2278, 0.6066] PeriodicSite: O (7.0224, 8.7437, 0.9423) [0.6745, 0.7239, 0.0994] PeriodicSite: O (6.9673, 8.7574, 5.7343) [0.6692, 0.7251, 0.6050] PeriodicSite: O (1.7242, 0.2638, 1.3658) [0.1656, 0.0218, 0.1441] PeriodicSite: O (1.7210, 0.2747, 6.0972) [0.1653, 0.0227, 0.6433] PeriodicSite: O (1.7264, 6.3034, 1.3724) [0.1658, 0.5219, 0.1448] PeriodicSite: O (1.7432, 6.3156, 6.1066) [0.1674, 0.5229, 0.6443]
+final_struct = Structure Summary Lattice abc : 10.411723299877 12.0783517723596 9.47759961582329 angles : 90.0 90.0 90.0 volume : 1191.8693444977544 A : 10.411723299877 0.0 0.0 B : 0.0 12.0783517723596 0.0 C : 0.0 0.0 9.47759961582329 pbc : True True True PeriodicSite: Li (5.1847, 6.1822, 2.4175) [0.4980, 0.5118, 0.2551] PeriodicSite: Li (5.2270, 11.9354, 2.3213) [0.5020, 0.9882, 0.2449] PeriodicSite: Li (5.1817, 12.0665, 7.0846) [0.4977, 0.9990, 0.7475] PeriodicSite: Li (5.2300, 6.0511, 7.1318) [0.5023, 0.5010, 0.7525] PeriodicSite: Li (0.0005, 3.0181, 0.0043) [0.0000, 0.2499, 0.0005] PeriodicSite: Li (10.4112, 3.0211, 4.7345) [1.0000, 0.2501, 0.4995] PeriodicSite: Li (10.4061, 9.0584, 0.0031) [0.9995, 0.7500, 0.0003] PeriodicSite: Li (0.0057, 9.0592, 4.7357) [0.0005, 0.7500, 0.4997] PeriodicSite: Li (5.2059, 3.0196, 2.3694) [0.5000, 0.2500, 0.2500] PeriodicSite: Li (5.2059, 3.0196, 7.1082) [0.5000, 0.2500, 0.7500] PeriodicSite: Li (5.2059, 9.0588, 7.1082) [0.5000, 0.7500, 0.7500] PeriodicSite: Li (10.4087, 12.0648, 0.0085) [0.9997, 0.9989, 0.0009] PeriodicSite: Li (0.0032, 12.0741, 4.7383) [0.0003, 0.9996, 0.5000] PeriodicSite: Li (10.4086, 6.0435, 0.0005) [0.9997, 0.5004, 0.0000] PeriodicSite: Li (0.0030, 6.0527, 4.7303) [0.0003, 0.5011, 0.4991] PeriodicSite: Fe (8.1412, 1.5110, 2.4871) [0.7819, 0.1251, 0.2624] PeriodicSite: Fe (8.1407, 1.5063, 7.2279) [0.7819, 0.1247, 0.7626] PeriodicSite: Fe (8.1001, 7.5688, 2.4722) [0.7780, 0.6266, 0.2608] PeriodicSite: Fe (8.1373, 7.5452, 7.2347) [0.7816, 0.6247, 0.7633] PeriodicSite: Fe (2.9469, 1.5019, 4.6127) [0.2830, 0.1243, 0.4867] PeriodicSite: Fe (2.9383, 1.5040, 9.3553) [0.2822, 0.1245, 0.9871] PeriodicSite: Fe (2.9571, 7.5783, 4.6085) [0.2840, 0.6274, 0.4863] PeriodicSite: Fe (2.9595, 7.5654, 9.3806) [0.2842, 0.6264, 0.9898] PeriodicSite: Fe (2.2705, 4.5282, 2.2517) [0.2181, 0.3749, 0.2376] PeriodicSite: Fe (2.2711, 4.5329, 6.9885) [0.2181, 0.3753, 0.7374] PeriodicSite: Fe (2.3116, 10.5488, 2.2666) [0.2220, 0.8734, 0.2392] PeriodicSite: Fe (2.2744, 10.5723, 6.9817) [0.2184, 0.8753, 0.7367] PeriodicSite: Fe (7.4648, 4.5373, 0.1261) [0.7170, 0.3757, 0.0133] PeriodicSite: Fe (7.4734, 4.5352, 4.8611) [0.7178, 0.3755, 0.5129] PeriodicSite: Fe (7.4547, 10.5392, 0.1303) [0.7160, 0.8726, 0.0137] PeriodicSite: Fe (7.4522, 10.5521, 4.8358) [0.7158, 0.8736, 0.5102] PeriodicSite: P (6.1978, 1.5072, 0.3753) [0.5953, 0.1248, 0.0396] PeriodicSite: P (6.2113, 1.5136, 5.1114) [0.5966, 0.1253, 0.5393] PeriodicSite: P (6.1961, 7.5476, 0.3633) [0.5951, 0.6249, 0.0383] PeriodicSite: P (6.2203, 7.5145, 5.1196) [0.5974, 0.6221, 0.5402] PeriodicSite: P (0.9887, 1.5041, 1.9896) [0.0950, 0.1245, 0.2099] PeriodicSite: P (0.9865, 1.5133, 6.7275) [0.0948, 0.1253, 0.7098] PeriodicSite: P (0.9818, 7.5439, 1.9926) [0.0943, 0.6246, 0.2102] PeriodicSite: P (0.9911, 7.5461, 6.7377) [0.0952, 0.6248, 0.7109] PeriodicSite: P (4.2139, 4.5319, 4.3635) [0.4047, 0.3752, 0.4604] PeriodicSite: P (4.2004, 4.5256, 9.1050) [0.4034, 0.3747, 0.9607] PeriodicSite: P (4.2156, 10.5699, 4.3756) [0.4049, 0.8751, 0.4617] PeriodicSite: P (4.1914, 10.6030, 9.0968) [0.4026, 0.8779, 0.9598] PeriodicSite: P (9.4230, 4.5351, 2.7492) [0.9050, 0.3755, 0.2901] PeriodicSite: P (9.4252, 4.5259, 7.4889) [0.9053, 0.3747, 0.7902] PeriodicSite: P (9.4299, 10.5737, 2.7462) [0.9057, 0.8754, 0.2898] PeriodicSite: P (9.4207, 10.5714, 7.4786) [0.9048, 0.8752, 0.7891] PeriodicSite: O (6.2228, 1.5268, 3.5773) [0.5977, 0.1264, 0.3775] PeriodicSite: O (6.2093, 1.5125, 8.3155) [0.5964, 0.1252, 0.8774] PeriodicSite: O (6.2747, 7.4398, 3.6014) [0.6027, 0.6160, 0.3800] PeriodicSite: O (6.2119, 7.5449, 8.2933) [0.5966, 0.6247, 0.8750] PeriodicSite: O (0.9902, 1.5124, 3.5258) [0.0951, 0.1252, 0.3720] PeriodicSite: O (0.9889, 1.5120, 8.2636) [0.0950, 0.1252, 0.8719] PeriodicSite: O (0.9898, 7.5475, 3.5295) [0.0951, 0.6249, 0.3724] PeriodicSite: O (0.9929, 7.5401, 8.2739) [0.0954, 0.6243, 0.8730] PeriodicSite: O (4.1889, 4.5124, 1.1615) [0.4023, 0.3736, 0.1225] PeriodicSite: O (4.2024, 4.5266, 5.9009) [0.4036, 0.3748, 0.6226] PeriodicSite: O (4.1370, 10.6778, 1.1374) [0.3973, 0.8840, 0.1200] PeriodicSite: O (4.1999, 10.5726, 5.9231) [0.4034, 0.8753, 0.6250] PeriodicSite: O (9.4215, 4.5268, 1.2130) [0.9049, 0.3748, 0.1280] PeriodicSite: O (9.4228, 4.5272, 5.9528) [0.9050, 0.3748, 0.6281] PeriodicSite: O (9.4220, 10.5700, 1.2093) [0.9049, 0.8751, 0.1276] PeriodicSite: O (9.4189, 10.5774, 5.9425) [0.9046, 0.8757, 0.6270] PeriodicSite: O (9.9678, 1.5135, 1.3791) [0.9574, 0.1253, 0.1455] PeriodicSite: O (9.9659, 1.5224, 6.1189) [0.9572, 0.1260, 0.6456] PeriodicSite: O (9.9630, 7.5428, 1.3832) [0.9569, 0.6245, 0.1459] PeriodicSite: O (9.9719, 7.5406, 6.1245) [0.9578, 0.6243, 0.6462] PeriodicSite: O (4.7657, 1.5202, 0.9751) [0.4577, 0.1259, 0.1029] PeriodicSite: O (4.7779, 1.5132, 5.7181) [0.4589, 0.1253, 0.6033] PeriodicSite: O (4.7627, 7.5033, 0.9219) [0.4574, 0.6212, 0.0973] PeriodicSite: O (4.7799, 7.5423, 5.7118) [0.4591, 0.6244, 0.6027] PeriodicSite: O (0.4439, 4.5256, 3.3597) [0.0426, 0.3747, 0.3545] PeriodicSite: O (0.4458, 4.5167, 8.0975) [0.0428, 0.3740, 0.8544] PeriodicSite: O (0.4487, 10.5747, 3.3556) [0.0431, 0.8755, 0.3541] PeriodicSite: O (0.4398, 10.5769, 8.0919) [0.0422, 0.8757, 0.8538] PeriodicSite: O (5.6461, 4.5190, 3.7637) [0.5423, 0.3741, 0.3971] PeriodicSite: O (5.6338, 4.5260, 8.4983) [0.5411, 0.3747, 0.8967] PeriodicSite: O (5.6490, 10.6142, 3.8169) [0.5426, 0.8788, 0.4027] PeriodicSite: O (5.6318, 10.5752, 8.5046) [0.5409, 0.8756, 0.8973] PeriodicSite: O (6.9383, 0.2665, 0.9991) [0.6664, 0.0221, 0.1054] PeriodicSite: O (6.9618, 0.2813, 5.7394) [0.6687, 0.0233, 0.6056] PeriodicSite: O (6.9424, 6.2988, 0.9884) [0.6668, 0.5215, 0.1043] PeriodicSite: O (6.9414, 6.2829, 5.8049) [0.6667, 0.5202, 0.6125] PeriodicSite: O (1.7379, 2.7394, 1.3635) [0.1669, 0.2268, 0.1439] PeriodicSite: O (1.7390, 2.7463, 6.1020) [0.1670, 0.2274, 0.6438] PeriodicSite: O (1.7293, 8.7758, 1.3621) [0.1661, 0.7266, 0.1437] PeriodicSite: O (1.7278, 8.7874, 6.1173) [0.1659, 0.7275, 0.6454] PeriodicSite: O (3.4593, 3.2999, 3.7365) [0.3322, 0.2732, 0.3942] PeriodicSite: O (3.4611, 3.2876, 8.4676) [0.3324, 0.2722, 0.8934] PeriodicSite: O (3.3893, 9.3739, 3.7965) [0.3255, 0.7761, 0.4006] PeriodicSite: O (3.4444, 9.3601, 8.4821) [0.3308, 0.7749, 0.8950] PeriodicSite: O (8.6876, 5.7754, 3.3730) [0.8344, 0.4782, 0.3559] PeriodicSite: O (8.6907, 5.7645, 8.1192) [0.8347, 0.4773, 0.8567] PeriodicSite: O (8.6853, 11.8141, 3.3664) [0.8342, 0.9781, 0.3552] PeriodicSite: O (8.6685, 11.8020, 8.1098) [0.8326, 0.9771, 0.8557] PeriodicSite: O (3.4734, 5.7727, 3.7397) [0.3336, 0.4779, 0.3946] PeriodicSite: O (3.4499, 5.7579, 8.4770) [0.3313, 0.4767, 0.8944] PeriodicSite: O (3.4693, 11.8187, 3.7504) [0.3332, 0.9785, 0.3957] PeriodicSite: O (3.4703, 11.8347, 8.4115) [0.3333, 0.9798, 0.8875] PeriodicSite: O (8.6738, 3.2998, 3.3753) [0.8331, 0.2732, 0.3561] PeriodicSite: O (8.6727, 3.2929, 8.1143) [0.8330, 0.2726, 0.8562] PeriodicSite: O (8.6824, 9.3417, 3.3767) [0.8339, 0.7734, 0.3563] PeriodicSite: O (8.6840, 9.3302, 8.0991) [0.8341, 0.7725, 0.8546] PeriodicSite: O (6.9525, 2.7393, 1.0023) [0.6678, 0.2268, 0.1058] PeriodicSite: O (6.9506, 2.7516, 5.7488) [0.6676, 0.2278, 0.6066] PeriodicSite: O (7.0224, 8.7437, 0.9423) [0.6745, 0.7239, 0.0994] PeriodicSite: O (6.9673, 8.7574, 5.7343) [0.6692, 0.7251, 0.6050] PeriodicSite: O (1.7242, 0.2638, 1.3658) [0.1656, 0.0218, 0.1441] PeriodicSite: O (1.7210, 0.2747, 6.0972) [0.1653, 0.0227, 0.6433] PeriodicSite: O (1.7264, 6.3034, 1.3724) [0.1658, 0.5219, 0.1448] PeriodicSite: O (1.7432, 6.3156, 6.1066) [0.1674, 0.5229, 0.6443]
-init_struct = Structure Summary Lattice abc : 10.411723299877 12.0783517723596 9.47759961582329 angles : 90.0 90.0 90.0 volume : 1191.8693444977544 A : 10.411723299877 0.0 0.0 B : 0.0 12.0783517723596 0.0 C : 0.0 0.0 9.47759961582329 PeriodicSite: Li (5.1874, 8.9205, 2.4168) [0.4982, 0.7386, 0.2550] PeriodicSite: Li (5.2059, 12.0784, 2.3694) [0.5000, 1.0000, 0.2500] PeriodicSite: Li (5.2059, 12.0784, 7.1082) [0.5000, 1.0000, 0.7500] PeriodicSite: Li (5.2059, 6.0392, 7.1082) [0.5000, 0.5000, 0.7500] PeriodicSite: Li (10.4090, 3.0319, 0.0078) [0.9997, 0.2510, 0.0008] PeriodicSite: Li (0.0030, 3.0234, 4.7387) [0.0003, 0.2503, 0.5000] PeriodicSite: Li (10.4088, 9.0550, 0.0000) [0.9997, 0.7497, 0.0000] PeriodicSite: Li (0.0028, 9.0464, 4.7310) [0.0003, 0.7490, 0.4992] PeriodicSite: Li (5.2243, 3.1578, 2.3220) [0.5018, 0.2614, 0.2450] PeriodicSite: Li (5.1821, 3.0310, 7.0844) [0.4977, 0.2509, 0.7475] PeriodicSite: Li (5.2296, 9.0473, 7.1320) [0.5023, 0.7491, 0.7525] PeriodicSite: Li (0.0004, 0.0009, 0.0057) [0.0000, 0.0001, 0.0006] PeriodicSite: Li (10.4114, 12.0774, 4.7330) [1.0000, 0.9999, 0.4994] PeriodicSite: Li (10.4062, 6.0393, 0.0036) [0.9995, 0.5000, 0.0004] PeriodicSite: Li (0.0055, 6.0390, 4.7352) [0.0005, 0.5000, 0.4996] PeriodicSite: Fe (8.1421, 1.5086, 2.4873) [0.7820, 0.1249, 0.2624] PeriodicSite: Fe (8.1410, 1.5134, 7.2283) [0.7819, 0.1253, 0.7627] PeriodicSite: Fe (8.1009, 7.5290, 2.4716) [0.7781, 0.6233, 0.2608] PeriodicSite: Fe (8.1373, 7.5521, 7.2339) [0.7816, 0.6253, 0.7633] PeriodicSite: Fe (2.9469, 1.5185, 4.6137) [0.2830, 0.1257, 0.4868] PeriodicSite: Fe (2.9385, 1.5169, 9.3552) [0.2822, 0.1256, 0.9871] PeriodicSite: Fe (2.9564, 7.5201, 4.6074) [0.2839, 0.6226, 0.4861] PeriodicSite: Fe (2.9587, 7.5328, 9.3801) [0.2842, 0.6237, 0.9897] PeriodicSite: Fe (2.3108, 4.5494, 2.2672) [0.2219, 0.3767, 0.2392] PeriodicSite: Fe (2.2744, 4.5263, 6.9825) [0.2184, 0.3747, 0.7367] PeriodicSite: Fe (2.2697, 10.5698, 2.2515) [0.2180, 0.8751, 0.2376] PeriodicSite: Fe (2.2707, 10.5649, 6.9880) [0.2181, 0.8747, 0.7373] PeriodicSite: Fe (7.4553, 4.5583, 0.1314) [0.7161, 0.3774, 0.0139] PeriodicSite: Fe (7.4530, 4.5455, 4.8363) [0.7158, 0.3763, 0.5103] PeriodicSite: Fe (7.4648, 10.5599, 0.1251) [0.7170, 0.8743, 0.0132] PeriodicSite: Fe (7.4732, 10.5614, 4.8612) [0.7178, 0.8744, 0.5129] PeriodicSite: P (6.1981, 1.5112, 0.3753) [0.5953, 0.1251, 0.0396] PeriodicSite: P (6.2113, 1.5050, 5.1115) [0.5966, 0.1246, 0.5393] PeriodicSite: P (6.1957, 7.5503, 0.3633) [0.5951, 0.6251, 0.0383] PeriodicSite: P (6.2199, 7.5836, 5.1189) [0.5974, 0.6279, 0.5401] PeriodicSite: P (0.9888, 1.5155, 1.9897) [0.0950, 0.1255, 0.2099] PeriodicSite: P (0.9865, 1.5064, 6.7280) [0.0947, 0.1247, 0.7099] PeriodicSite: P (0.9815, 7.5544, 1.9920) [0.0943, 0.6254, 0.2102] PeriodicSite: P (0.9909, 7.5520, 6.7372) [0.0952, 0.6252, 0.7109] PeriodicSite: P (4.2160, 4.5281, 4.3755) [0.4049, 0.3749, 0.4617] PeriodicSite: P (4.1918, 4.4947, 9.0976) [0.4026, 0.3721, 0.9599] PeriodicSite: P (4.2137, 10.5672, 4.3635) [0.4047, 0.8749, 0.4604] PeriodicSite: P (4.2004, 10.5734, 9.1049) [0.4034, 0.8754, 0.9607] PeriodicSite: P (9.4302, 4.5240, 2.7468) [0.9057, 0.3746, 0.2898] PeriodicSite: P (9.4208, 4.5264, 7.4792) [0.9048, 0.3747, 0.7891] PeriodicSite: P (9.4229, 10.5629, 2.7491) [0.9050, 0.8745, 0.2901] PeriodicSite: P (9.4253, 10.5720, 7.4884) [0.9053, 0.8753, 0.7901] PeriodicSite: O (6.2224, 1.4923, 3.5773) [0.5976, 0.1236, 0.3775] PeriodicSite: O (6.2101, 1.5049, 8.3154) [0.5965, 0.1246, 0.8774] PeriodicSite: O (6.2743, 7.6582, 3.6007) [0.6026, 0.6340, 0.3799] PeriodicSite: O (6.2108, 7.5517, 8.2934) [0.5965, 0.6252, 0.8751] PeriodicSite: O (0.9903, 1.5073, 3.5259) [0.0951, 0.1248, 0.3720] PeriodicSite: O (0.9896, 1.5080, 8.2642) [0.0950, 0.1248, 0.8720] PeriodicSite: O (0.9900, 7.5502, 3.5288) [0.0951, 0.6251, 0.3723] PeriodicSite: O (0.9927, 7.5581, 8.2733) [0.0953, 0.6258, 0.8729] PeriodicSite: O (4.1374, 4.4202, 1.1381) [0.3974, 0.3660, 0.1201] PeriodicSite: O (4.2009, 4.5266, 5.9230) [0.4035, 0.3748, 0.6249] PeriodicSite: O (4.1893, 10.5860, 1.1615) [0.4024, 0.8764, 0.1225] PeriodicSite: O (4.2016, 10.5735, 5.9010) [0.4035, 0.8754, 0.6226] PeriodicSite: O (9.4217, 4.5281, 1.2100) [0.9049, 0.3749, 0.1277] PeriodicSite: O (9.4190, 4.5202, 5.9431) [0.9047, 0.3742, 0.6271] PeriodicSite: O (9.4215, 10.5710, 1.2129) [0.9049, 0.8752, 0.1280] PeriodicSite: O (9.4221, 10.5704, 5.9522) [0.9050, 0.8752, 0.6280] PeriodicSite: O (9.9681, 1.5052, 1.3785) [0.9574, 0.1246, 0.1454] PeriodicSite: O (9.9658, 1.4966, 6.1196) [0.9572, 0.1239, 0.6457] PeriodicSite: O (9.9624, 7.5551, 1.3829) [0.9568, 0.6255, 0.1459] PeriodicSite: O (9.9718, 7.5569, 6.1240) [0.9577, 0.6257, 0.6462] PeriodicSite: O (4.7659, 1.5002, 0.9756) [0.4577, 0.1242, 0.1029] PeriodicSite: O (4.7782, 1.5064, 5.7191) [0.4589, 0.1247, 0.6034] PeriodicSite: O (4.7625, 7.5958, 0.9216) [0.4574, 0.6289, 0.0972] PeriodicSite: O (4.7791, 7.5563, 5.7097) [0.4590, 0.6256, 0.6024] PeriodicSite: O (0.4493, 4.5232, 3.3559) [0.0432, 0.3745, 0.3541] PeriodicSite: O (0.4400, 4.5214, 8.0924) [0.0423, 0.3743, 0.8538] PeriodicSite: O (0.4436, 10.5732, 3.3603) [0.0426, 0.8754, 0.3546] PeriodicSite: O (0.4459, 10.5818, 8.0968) [0.0428, 0.8761, 0.8543] PeriodicSite: O (5.6492, 4.4825, 3.8172) [0.5426, 0.3711, 0.4028] PeriodicSite: O (5.6326, 4.5220, 8.5067) [0.5410, 0.3744, 0.8976] PeriodicSite: O (5.6458, 10.5782, 3.7632) [0.5423, 0.8758, 0.3971] PeriodicSite: O (5.6335, 10.5719, 8.4973) [0.5411, 0.8753, 0.8966] PeriodicSite: O (6.9512, 0.2785, 1.0032) [0.6676, 0.0231, 0.1058] PeriodicSite: O (6.9495, 0.2660, 5.7483) [0.6675, 0.0220, 0.6065] PeriodicSite: O (7.0219, 6.3538, 0.9424) [0.6744, 0.5261, 0.0994] PeriodicSite: O (6.9656, 6.3395, 5.7329) [0.6690, 0.5249, 0.6049] PeriodicSite: O (1.7248, 2.7555, 1.3661) [0.1657, 0.2281, 0.1441] PeriodicSite: O (1.7211, 2.7446, 6.0973) [0.1653, 0.2272, 0.6433] PeriodicSite: O (1.7255, 8.7949, 1.3716) [0.1657, 0.7282, 0.1447] PeriodicSite: O (1.7426, 8.7823, 6.1058) [0.1674, 0.7271, 0.6442] PeriodicSite: O (3.4692, 3.2784, 3.7520) [0.3332, 0.2714, 0.3959] PeriodicSite: O (3.4699, 3.2636, 8.4112) [0.3333, 0.2702, 0.8875] PeriodicSite: O (3.4720, 9.3269, 3.7396) [0.3335, 0.7722, 0.3946] PeriodicSite: O (3.4483, 9.3419, 8.4769) [0.3312, 0.7734, 0.8944] PeriodicSite: O (8.6826, 5.7559, 3.3769) [0.8339, 0.4765, 0.3563] PeriodicSite: O (8.6832, 5.7673, 8.0990) [0.8340, 0.4775, 0.8545] PeriodicSite: O (8.6740, 11.7982, 3.3753) [0.8331, 0.9768, 0.3561] PeriodicSite: O (8.6732, 11.8051, 8.1140) [0.8330, 0.9774, 0.8561] PeriodicSite: O (3.3898, 5.7246, 3.7964) [0.3256, 0.4740, 0.4006] PeriodicSite: O (3.4461, 5.7388, 8.4835) [0.3310, 0.4751, 0.8951] PeriodicSite: O (3.4605, 11.7998, 3.7356) [0.3324, 0.9769, 0.3942] PeriodicSite: O (3.4622, 11.8123, 8.4681) [0.3325, 0.9780, 0.8935] PeriodicSite: O (8.6862, 3.2835, 3.3672) [0.8343, 0.2718, 0.3553] PeriodicSite: O (8.6691, 3.2960, 8.1106) [0.8326, 0.2729, 0.8558] PeriodicSite: O (8.6869, 9.3228, 3.3727) [0.8343, 0.7719, 0.3559] PeriodicSite: O (8.6906, 9.3337, 8.1191) [0.8347, 0.7728, 0.8567] PeriodicSite: O (6.9397, 2.7514, 0.9992) [0.6665, 0.2278, 0.1054] PeriodicSite: O (6.9635, 2.7364, 5.7395) [0.6688, 0.2266, 0.6056] PeriodicSite: O (6.9425, 8.8000, 0.9868) [0.6668, 0.7286, 0.1041] PeriodicSite: O (6.9418, 8.8148, 5.8052) [0.6667, 0.7298, 0.6125] PeriodicSite: O (1.7378, 0.2801, 1.3635) [0.1669, 0.0232, 0.1439] PeriodicSite: O (1.7385, 0.2732, 6.1024) [0.1670, 0.0226, 0.6439] PeriodicSite: O (1.7291, 6.3224, 1.3619) [0.1661, 0.5235, 0.1437] PeriodicSite: O (1.7285, 6.3110, 6.1174) [0.1660, 0.5225, 0.6455]
+init_struct = Structure Summary Lattice abc : 10.411723299877 12.0783517723596 9.47759961582329 angles : 90.0 90.0 90.0 volume : 1191.8693444977544 A : 10.411723299877 0.0 0.0 B : 0.0 12.0783517723596 0.0 C : 0.0 0.0 9.47759961582329 pbc : True True True PeriodicSite: Li (5.1874, 8.9205, 2.4168) [0.4982, 0.7386, 0.2550] PeriodicSite: Li (5.2059, 12.0784, 2.3694) [0.5000, 1.0000, 0.2500] PeriodicSite: Li (5.2059, 12.0784, 7.1082) [0.5000, 1.0000, 0.7500] PeriodicSite: Li (5.2059, 6.0392, 7.1082) [0.5000, 0.5000, 0.7500] PeriodicSite: Li (10.4090, 3.0319, 0.0078) [0.9997, 0.2510, 0.0008] PeriodicSite: Li (0.0030, 3.0234, 4.7387) [0.0003, 0.2503, 0.5000] PeriodicSite: Li (10.4088, 9.0550, 0.0000) [0.9997, 0.7497, 0.0000] PeriodicSite: Li (0.0028, 9.0464, 4.7310) [0.0003, 0.7490, 0.4992] PeriodicSite: Li (5.2243, 3.1578, 2.3220) [0.5018, 0.2614, 0.2450] PeriodicSite: Li (5.1821, 3.0310, 7.0844) [0.4977, 0.2509, 0.7475] PeriodicSite: Li (5.2296, 9.0473, 7.1320) [0.5023, 0.7491, 0.7525] PeriodicSite: Li (0.0004, 0.0009, 0.0057) [0.0000, 0.0001, 0.0006] PeriodicSite: Li (10.4114, 12.0774, 4.7330) [1.0000, 0.9999, 0.4994] PeriodicSite: Li (10.4062, 6.0393, 0.0036) [0.9995, 0.5000, 0.0004] PeriodicSite: Li (0.0055, 6.0390, 4.7352) [0.0005, 0.5000, 0.4996] PeriodicSite: Fe (8.1421, 1.5086, 2.4873) [0.7820, 0.1249, 0.2624] PeriodicSite: Fe (8.1410, 1.5134, 7.2283) [0.7819, 0.1253, 0.7627] PeriodicSite: Fe (8.1009, 7.5290, 2.4716) [0.7781, 0.6233, 0.2608] PeriodicSite: Fe (8.1373, 7.5521, 7.2339) [0.7816, 0.6253, 0.7633] PeriodicSite: Fe (2.9469, 1.5185, 4.6137) [0.2830, 0.1257, 0.4868] PeriodicSite: Fe (2.9385, 1.5169, 9.3552) [0.2822, 0.1256, 0.9871] PeriodicSite: Fe (2.9564, 7.5201, 4.6074) [0.2839, 0.6226, 0.4861] PeriodicSite: Fe (2.9587, 7.5328, 9.3801) [0.2842, 0.6237, 0.9897] PeriodicSite: Fe (2.3108, 4.5494, 2.2672) [0.2219, 0.3767, 0.2392] PeriodicSite: Fe (2.2744, 4.5263, 6.9825) [0.2184, 0.3747, 0.7367] PeriodicSite: Fe (2.2697, 10.5698, 2.2515) [0.2180, 0.8751, 0.2376] PeriodicSite: Fe (2.2707, 10.5649, 6.9880) [0.2181, 0.8747, 0.7373] PeriodicSite: Fe (7.4553, 4.5583, 0.1314) [0.7161, 0.3774, 0.0139] PeriodicSite: Fe (7.4530, 4.5455, 4.8363) [0.7158, 0.3763, 0.5103] PeriodicSite: Fe (7.4648, 10.5599, 0.1251) [0.7170, 0.8743, 0.0132] PeriodicSite: Fe (7.4732, 10.5614, 4.8612) [0.7178, 0.8744, 0.5129] PeriodicSite: P (6.1981, 1.5112, 0.3753) [0.5953, 0.1251, 0.0396] PeriodicSite: P (6.2113, 1.5050, 5.1115) [0.5966, 0.1246, 0.5393] PeriodicSite: P (6.1957, 7.5503, 0.3633) [0.5951, 0.6251, 0.0383] PeriodicSite: P (6.2199, 7.5836, 5.1189) [0.5974, 0.6279, 0.5401] PeriodicSite: P (0.9888, 1.5155, 1.9897) [0.0950, 0.1255, 0.2099] PeriodicSite: P (0.9865, 1.5064, 6.7280) [0.0947, 0.1247, 0.7099] PeriodicSite: P (0.9815, 7.5544, 1.9920) [0.0943, 0.6254, 0.2102] PeriodicSite: P (0.9909, 7.5520, 6.7372) [0.0952, 0.6252, 0.7109] PeriodicSite: P (4.2160, 4.5281, 4.3755) [0.4049, 0.3749, 0.4617] PeriodicSite: P (4.1918, 4.4947, 9.0976) [0.4026, 0.3721, 0.9599] PeriodicSite: P (4.2137, 10.5672, 4.3635) [0.4047, 0.8749, 0.4604] PeriodicSite: P (4.2004, 10.5734, 9.1049) [0.4034, 0.8754, 0.9607] PeriodicSite: P (9.4302, 4.5240, 2.7468) [0.9057, 0.3746, 0.2898] PeriodicSite: P (9.4208, 4.5264, 7.4792) [0.9048, 0.3747, 0.7891] PeriodicSite: P (9.4229, 10.5629, 2.7491) [0.9050, 0.8745, 0.2901] PeriodicSite: P (9.4253, 10.5720, 7.4884) [0.9053, 0.8753, 0.7901] PeriodicSite: O (6.2224, 1.4923, 3.5773) [0.5976, 0.1236, 0.3775] PeriodicSite: O (6.2101, 1.5049, 8.3154) [0.5965, 0.1246, 0.8774] PeriodicSite: O (6.2743, 7.6582, 3.6007) [0.6026, 0.6340, 0.3799] PeriodicSite: O (6.2108, 7.5517, 8.2934) [0.5965, 0.6252, 0.8751] PeriodicSite: O (0.9903, 1.5073, 3.5259) [0.0951, 0.1248, 0.3720] PeriodicSite: O (0.9896, 1.5080, 8.2642) [0.0950, 0.1248, 0.8720] PeriodicSite: O (0.9900, 7.5502, 3.5288) [0.0951, 0.6251, 0.3723] PeriodicSite: O (0.9927, 7.5581, 8.2733) [0.0953, 0.6258, 0.8729] PeriodicSite: O (4.1374, 4.4202, 1.1381) [0.3974, 0.3660, 0.1201] PeriodicSite: O (4.2009, 4.5266, 5.9230) [0.4035, 0.3748, 0.6249] PeriodicSite: O (4.1893, 10.5860, 1.1615) [0.4024, 0.8764, 0.1225] PeriodicSite: O (4.2016, 10.5735, 5.9010) [0.4035, 0.8754, 0.6226] PeriodicSite: O (9.4217, 4.5281, 1.2100) [0.9049, 0.3749, 0.1277] PeriodicSite: O (9.4190, 4.5202, 5.9431) [0.9047, 0.3742, 0.6271] PeriodicSite: O (9.4215, 10.5710, 1.2129) [0.9049, 0.8752, 0.1280] PeriodicSite: O (9.4221, 10.5704, 5.9522) [0.9050, 0.8752, 0.6280] PeriodicSite: O (9.9681, 1.5052, 1.3785) [0.9574, 0.1246, 0.1454] PeriodicSite: O (9.9658, 1.4966, 6.1196) [0.9572, 0.1239, 0.6457] PeriodicSite: O (9.9624, 7.5551, 1.3829) [0.9568, 0.6255, 0.1459] PeriodicSite: O (9.9718, 7.5569, 6.1240) [0.9577, 0.6257, 0.6462] PeriodicSite: O (4.7659, 1.5002, 0.9756) [0.4577, 0.1242, 0.1029] PeriodicSite: O (4.7782, 1.5064, 5.7191) [0.4589, 0.1247, 0.6034] PeriodicSite: O (4.7625, 7.5958, 0.9216) [0.4574, 0.6289, 0.0972] PeriodicSite: O (4.7791, 7.5563, 5.7097) [0.4590, 0.6256, 0.6024] PeriodicSite: O (0.4493, 4.5232, 3.3559) [0.0432, 0.3745, 0.3541] PeriodicSite: O (0.4400, 4.5214, 8.0924) [0.0423, 0.3743, 0.8538] PeriodicSite: O (0.4436, 10.5732, 3.3603) [0.0426, 0.8754, 0.3546] PeriodicSite: O (0.4459, 10.5818, 8.0968) [0.0428, 0.8761, 0.8543] PeriodicSite: O (5.6492, 4.4825, 3.8172) [0.5426, 0.3711, 0.4028] PeriodicSite: O (5.6326, 4.5220, 8.5067) [0.5410, 0.3744, 0.8976] PeriodicSite: O (5.6458, 10.5782, 3.7632) [0.5423, 0.8758, 0.3971] PeriodicSite: O (5.6335, 10.5719, 8.4973) [0.5411, 0.8753, 0.8966] PeriodicSite: O (6.9512, 0.2785, 1.0032) [0.6676, 0.0231, 0.1058] PeriodicSite: O (6.9495, 0.2660, 5.7483) [0.6675, 0.0220, 0.6065] PeriodicSite: O (7.0219, 6.3538, 0.9424) [0.6744, 0.5261, 0.0994] PeriodicSite: O (6.9656, 6.3395, 5.7329) [0.6690, 0.5249, 0.6049] PeriodicSite: O (1.7248, 2.7555, 1.3661) [0.1657, 0.2281, 0.1441] PeriodicSite: O (1.7211, 2.7446, 6.0973) [0.1653, 0.2272, 0.6433] PeriodicSite: O (1.7255, 8.7949, 1.3716) [0.1657, 0.7282, 0.1447] PeriodicSite: O (1.7426, 8.7823, 6.1058) [0.1674, 0.7271, 0.6442] PeriodicSite: O (3.4692, 3.2784, 3.7520) [0.3332, 0.2714, 0.3959] PeriodicSite: O (3.4699, 3.2636, 8.4112) [0.3333, 0.2702, 0.8875] PeriodicSite: O (3.4720, 9.3269, 3.7396) [0.3335, 0.7722, 0.3946] PeriodicSite: O (3.4483, 9.3419, 8.4769) [0.3312, 0.7734, 0.8944] PeriodicSite: O (8.6826, 5.7559, 3.3769) [0.8339, 0.4765, 0.3563] PeriodicSite: O (8.6832, 5.7673, 8.0990) [0.8340, 0.4775, 0.8545] PeriodicSite: O (8.6740, 11.7982, 3.3753) [0.8331, 0.9768, 0.3561] PeriodicSite: O (8.6732, 11.8051, 8.1140) [0.8330, 0.9774, 0.8561] PeriodicSite: O (3.3898, 5.7246, 3.7964) [0.3256, 0.4740, 0.4006] PeriodicSite: O (3.4461, 5.7388, 8.4835) [0.3310, 0.4751, 0.8951] PeriodicSite: O (3.4605, 11.7998, 3.7356) [0.3324, 0.9769, 0.3942] PeriodicSite: O (3.4622, 11.8123, 8.4681) [0.3325, 0.9780, 0.8935] PeriodicSite: O (8.6862, 3.2835, 3.3672) [0.8343, 0.2718, 0.3553] PeriodicSite: O (8.6691, 3.2960, 8.1106) [0.8326, 0.2729, 0.8558] PeriodicSite: O (8.6869, 9.3228, 3.3727) [0.8343, 0.7719, 0.3559] PeriodicSite: O (8.6906, 9.3337, 8.1191) [0.8347, 0.7728, 0.8567] PeriodicSite: O (6.9397, 2.7514, 0.9992) [0.6665, 0.2278, 0.1054] PeriodicSite: O (6.9635, 2.7364, 5.7395) [0.6688, 0.2266, 0.6056] PeriodicSite: O (6.9425, 8.8000, 0.9868) [0.6668, 0.7286, 0.1041] PeriodicSite: O (6.9418, 8.8148, 5.8052) [0.6667, 0.7298, 0.6125] PeriodicSite: O (1.7378, 0.2801, 1.3635) [0.1669, 0.0232, 0.1439] PeriodicSite: O (1.7385, 0.2732, 6.1024) [0.1670, 0.0226, 0.6439] PeriodicSite: O (1.7291, 6.3224, 1.3619) [0.1661, 0.5235, 0.1437] PeriodicSite: O (1.7285, 6.3110, 6.1174) [0.1660, 0.5225, 0.6455]
@@ -105,7 +106,7 @@ Navigation
class MigrationHopTest ( methodName = 'runTest' ) [source]
-Bases: pymatgen.util.testing.PymatgenTest
+Bases: PymatgenTest
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
@@ -135,6 +136,11 @@ Navigation
test_get_start_end_structs_from_hop_vac ( ) [source]
+
+
+test_msonable ( ) [source]
+
+
@@ -171,7 +177,7 @@ Quick search
-
+
diff --git a/docs/pymatgen.analysis.diffusion.tests.test_analyzer.html b/docs/pymatgen.analysis.diffusion.tests.test_analyzer.html
index 68c03686..69cd3789 100644
--- a/docs/pymatgen.analysis.diffusion.tests.test_analyzer.html
+++ b/docs/pymatgen.analysis.diffusion.tests.test_analyzer.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.tests.test_analyzer module — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.tests.test_analyzer module — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.tests.test_analyzer module
@@ -48,11 +49,11 @@ Navigation
-pymatgen.analysis.diffusion.tests.test_analyzer module
+pymatgen.analysis.diffusion.tests.test_analyzer module
class DiffusionAnalyzerTest ( methodName = 'runTest' ) [source]
-Bases: pymatgen.util.testing.PymatgenTest
+Bases: PymatgenTest
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
@@ -76,7 +77,7 @@ Navigation
class FuncTest ( methodName = 'runTest' ) [source]
-Bases: pymatgen.util.testing.PymatgenTest
+Bases: PymatgenTest
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
@@ -121,7 +122,7 @@ Quick search
-
+
diff --git a/docs/pymatgen.analysis.diffusion.tests.test_pathfinder.html b/docs/pymatgen.analysis.diffusion.tests.test_pathfinder.html
new file mode 100644
index 00000000..a32310b6
--- /dev/null
+++ b/docs/pymatgen.analysis.diffusion.tests.test_pathfinder.html
@@ -0,0 +1,120 @@
+
+
+
+
+
+
+
+
+ pymatgen.analysis.diffusion.tests.test_pathfinder module — pymatgen-diffusion 2022.7.21 documentation
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+pymatgen.analysis.diffusion.tests.test_pathfinder module
+
+
+class PathfinderTest ( methodName = 'runTest' ) [source]
+Bases: PymatgenTest
+Create an instance of the class that will use the named test
+method when executed. Raises a ValueError if the instance does
+not have a method with the specified name.
+
+
+test_mhop_msonable ( ) [source]
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/docs/pymatgen.analysis.diffusion.utils.edge_data_from_sc.html b/docs/pymatgen.analysis.diffusion.utils.edge_data_from_sc.html
index bb7e08fe..d89008b6 100644
--- a/docs/pymatgen.analysis.diffusion.utils.edge_data_from_sc.html
+++ b/docs/pymatgen.analysis.diffusion.utils.edge_data_from_sc.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.utils.edge_data_from_sc module — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.utils.edge_data_from_sc module — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.utils.edge_data_from_sc module
@@ -48,15 +49,15 @@ Navigation
-pymatgen.analysis.diffusion.utils.edge_data_from_sc module
+pymatgen.analysis.diffusion.utils.edge_data_from_sc module
Function to add edge data to MigrationGraph through 2 SC structures
-add_edge_data_from_sc ( mg : pymatgen.analysis.diffusion.neb.full_path_mapper.MigrationGraph , i_sc : pymatgen.core.structure.Structure , e_sc : pymatgen.core.structure.Structure , data_array : list , key : str = 'custom_key' , use_host_sg : bool = True ) → None [source]
+add_edge_data_from_sc ( mg : MigrationGraph , i_sc : Structure , e_sc : Structure , data_array : list , key : str = 'custom_key' , use_host_sg : bool = True ) → None [source]
Add a data entry and key to edges within FullPathMapper object with the same hop_label.
These hops are equivalent by symmetry to the 2 positions given in the supercell structures.
-Parameters
+Parameters:
i_sc – Supercell structure containing working ion at initial position
e_sc – Supercell structure containing working ion at ending position
@@ -65,7 +66,7 @@ Navigation
use_host_sg – Flag t whether or not to use the host structure’s spacegroup to initiate MigrationHop
-Returns
+Returns:
None
@@ -73,10 +74,10 @@ Navigation
-get_uc_pos ( isite : pymatgen.core.sites.PeriodicSite , esite : pymatgen.core.sites.PeriodicSite , uc : pymatgen.core.structure.Structure , sc : pymatgen.core.structure.Structure , sm : pymatgen.analysis.structure_matcher.StructureMatcher ) → Tuple [ pymatgen.core.sites.PeriodicSite , pymatgen.core.sites.PeriodicSite , pymatgen.core.sites.PeriodicSite ] [source]
+get_uc_pos ( isite : PeriodicSite , esite : PeriodicSite , uc : Structure , sc : Structure , sm : StructureMatcher ) → Tuple [ PeriodicSite , PeriodicSite , PeriodicSite ] [source]
Take positions in the supercel and transform into the unitcell positions
-Parameters
+Parameters:
isite – initial site in the SC
esite – ending site in the SC
@@ -85,7 +86,7 @@ Navigation
sm – StructureMatcher object with the working ion ignored
-Returns
+Returns:
The positions in the unit cell
@@ -93,10 +94,10 @@ Navigation
-get_unique_hop ( mg : pymatgen.analysis.diffusion.neb.full_path_mapper.MigrationGraph , sc : pymatgen.core.structure.Structure , isite : pymatgen.core.sites.PeriodicSite , esite : pymatgen.core.sites.PeriodicSite , use_host_sg : bool = True ) → Tuple [ int , pymatgen.analysis.diffusion.neb.pathfinder.MigrationHop ] [source]
+get_unique_hop ( mg : MigrationGraph , sc : Structure , isite : PeriodicSite , esite : PeriodicSite , use_host_sg : bool = True ) → Tuple [ int , MigrationHop ] [source]
Get the unique hop label that correspond to two end positions in the SC
-Parameters
+Parameters:
mg – Object containing the migration analysis
sc – Structure of the supercell used for the NEB calculation
@@ -105,7 +106,7 @@ Navigation
use_host_sg – Flag t whether or not to use the host structure’s spacegroup to initiate MigrationHop
-Returns
+Returns:
The index of the unique hop, the MigrationHop object trasformed from the SC
@@ -116,13 +117,13 @@ Navigation
mh_eq ( mh1 , mh2 ) [source]
Allow for symmetric matching of MigrationPath objects with variable precession
-Parameters
+Parameters:
-Returns
+Returns:
Boolean True if they’re equal, False if they are not
@@ -157,7 +158,7 @@ Quick search
-
+
diff --git a/docs/pymatgen.analysis.diffusion.utils.html b/docs/pymatgen.analysis.diffusion.utils.html
index fd207126..e6d476e8 100644
--- a/docs/pymatgen.analysis.diffusion.utils.html
+++ b/docs/pymatgen.analysis.diffusion.utils.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.utils package — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.utils package — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.utils package
@@ -48,14 +49,14 @@ Navigation
-pymatgen.analysis.diffusion.utils package
+pymatgen.analysis.diffusion.utils package
-Subpackages
+Subpackages
-
+
diff --git a/docs/pymatgen.analysis.diffusion.utils.maggma.html b/docs/pymatgen.analysis.diffusion.utils.maggma.html
index 0876e7fb..c88f49d5 100644
--- a/docs/pymatgen.analysis.diffusion.utils.maggma.html
+++ b/docs/pymatgen.analysis.diffusion.utils.maggma.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.utils.maggma module — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.utils.maggma module — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.utils.maggma module
@@ -48,7 +49,7 @@ Navigation
-pymatgen.analysis.diffusion.utils.maggma module
+pymatgen.analysis.diffusion.utils.maggma module
@@ -78,7 +79,7 @@
Quick search
-
+
diff --git a/docs/pymatgen.analysis.diffusion.utils.parse_entries.html b/docs/pymatgen.analysis.diffusion.utils.parse_entries.html
index d7793e2b..9ec79c81 100644
--- a/docs/pymatgen.analysis.diffusion.utils.parse_entries.html
+++ b/docs/pymatgen.analysis.diffusion.utils.parse_entries.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.utils.parse_entries module — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.utils.parse_entries module — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.utils.parse_entries module
@@ -48,17 +49,17 @@ Navigation
-pymatgen.analysis.diffusion.utils.parse_entries module
+pymatgen.analysis.diffusion.utils.parse_entries module
Functions for combining many ComputedEntry objects into MigrationGraph objects.
-get_inserted_on_base ( base_ent : pymatgen.entries.computed_entries.ComputedStructureEntry , inserted_ent : pymatgen.entries.computed_entries.ComputedStructureEntry , migrating_ion_entry : pymatgen.entries.computed_entries.ComputedEntry , sm : pymatgen.analysis.structure_matcher.StructureMatcher ) → Optional [ pymatgen.core.structure.Structure ] [source]
+get_inserted_on_base ( base_ent : ComputedStructureEntry , inserted_ent : ComputedStructureEntry , migrating_ion_entry : ComputedEntry , sm : StructureMatcher ) → Optional [ Structure ] [source]
For a structured-matched pair of base and inserted entries, map all of the Li positions in the inserted entry to
positions in the base entry and return a new structure where all the sites are decorated with the insertion
energy. Since the calculation of the insertion energy needs the energy of the metallic working ion,
a migrating_ion_entry must also be provided.
-Parameters
+Parameters:
base_ent – The entry for the host structure
inserted_ent – The entry for the inserted structure
@@ -66,7 +67,7 @@ Navigation
sm – StructureMatcher object used to obtain the mapping
-Returns
+Returns:
List of entries for each working ion in the list of
@@ -74,13 +75,13 @@ Navigation
-get_insertion_energy ( base_entry : pymatgen.entries.computed_entries.ComputedStructureEntry , inserted_entry : pymatgen.entries.computed_entries.ComputedStructureEntry , migrating_ion_entry : pymatgen.entries.computed_entries.ComputedEntry ) → float [source]
+get_insertion_energy ( base_entry : ComputedStructureEntry , inserted_entry : ComputedStructureEntry , migrating_ion_entry : ComputedEntry ) → float [source]
Calculate the insertion energy for a given inserted entry
:param base_entry: The entry for the host structure
:param inserted_entry: The entry for the inserted structure
:param migrating_ion_entry: The entry for the metallic phase of the working ion
-Returns
+Returns:
The insertion energy defined as (E[inserted] - (E[Base] + n * E[working_ion]))/(n)
Where n is the number of working ions and E[inserted].
Additionally, and E[base] and E[inserted] are for structures of the same size (sans working ion)
@@ -90,23 +91,23 @@ Navigation
-get_matched_structure_mapping ( base : pymatgen.core.structure.Structure , inserted : pymatgen.core.structure.Structure , sm : pymatgen.analysis.structure_matcher.StructureMatcher ) [source]
+get_matched_structure_mapping ( base : Structure , inserted : Structure , sm : StructureMatcher ) [source]
Get the mapping from the inserted structure onto the base structure,
assuming that the inserted structure sans the working ion is some kind
of SC of the base.
-Parameters
+Parameters:
-Returns
+Returns:
supercell matrix to apply to s1 to get s2
total-t : translation to apply on s1 * sc_m to get s2
-Return type
+Return type:
sc_m
@@ -114,11 +115,11 @@ Navigation
-get_sym_migration_ion_sites ( base_struct : pymatgen.core.structure.Structure , inserted_struct : pymatgen.core.structure.Structure , migrating_ion : str , symprec : float = 0.01 , angle_tol : float = 5.0 ) → pymatgen.core.structure.Structure [source]
+get_sym_migration_ion_sites ( base_struct : Structure , inserted_struct : Structure , migrating_ion : str , symprec : float = 0.01 , angle_tol : float = 5.0 ) → Structure [source]
Take one inserted entry then map out all symmetry equivalent copies of the cation sites in base entry.
Each site is decorated with the insertion energy calculated from the base and inserted entries.
-Parameters
+Parameters:
inserted_entry – entry that contains cation
base_struct_entry – the entry containing the base structure
@@ -127,7 +128,7 @@ Navigation
angle_tol – the angle tolerance for the space group analysis
-Returns
+Returns:
Structure with only the migrating ion sites decorated with insertion energies.
@@ -135,12 +136,12 @@ Navigation
-process_entries ( base_entries : List [ pymatgen.entries.computed_entries.ComputedStructureEntry ] , inserted_entries : List [ pymatgen.entries.computed_entries.ComputedStructureEntry ] , migrating_ion_entry : pymatgen.entries.computed_entries.ComputedEntry , symprec : float = 0.01 , ltol : float = 0.2 , stol : float = 0.3 , angle_tol : float = 5.0 ) → List [ Dict ] [source]
+process_entries ( base_entries : List [ ComputedStructureEntry ] , inserted_entries : List [ ComputedStructureEntry ] , migrating_ion_entry : ComputedEntry , symprec : float = 0.01 , ltol : float = 0.2 , stol : float = 0.3 , angle_tol : float = 5.0 ) → List [ Dict ] [source]
Process a list of base entries and inserted entries to create input for migration path analysis Each inserted
entries can be mapped to more than one base entry. Return groups of structures decorated with the working ions
to indicate the metastable sites, ranked by the number of working ion sites (highest number is the first).
-Parameters
+Parameters:
-Returns
+Returns:
List of dictionaries that each contain
{‘base’ : Structure Object of host, ‘inserted’ : Structure object of all inserted sites}
-Return type
+Return type:
list
@@ -193,7 +194,7 @@ Quick search
-
+
diff --git a/docs/pymatgen.analysis.diffusion.utils.supercells.html b/docs/pymatgen.analysis.diffusion.utils.supercells.html
index 4b8fbf20..44df8250 100644
--- a/docs/pymatgen.analysis.diffusion.utils.supercells.html
+++ b/docs/pymatgen.analysis.diffusion.utils.supercells.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.utils.supercells module — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.utils.supercells module — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.utils.supercells module
@@ -48,18 +49,18 @@ Navigation
-pymatgen.analysis.diffusion.utils.supercells module
+pymatgen.analysis.diffusion.utils.supercells module
Functions for creating supercells for NEB calculations
-get_sc_fromstruct ( base_struct : pymatgen.core.structure.Structure , min_atoms : int = 80 , max_atoms : int = 240 , min_length : float = 10.0 ) → List [ List [ int ] ] [source]
+get_sc_fromstruct ( base_struct : Structure , min_atoms : int = 80 , max_atoms : int = 240 , min_length : float = 10.0 ) → List [ List [ int ] ] [source]
Generate the best supercell from a unitcell.
The CubicSupercellTransformation from PMG is much faster but don’t iterate over as many
supercell configurations so it’s less able to find the best configuration in a give cell size.
We try the PMG’s cubic supercell transformation with a cap on the number of atoms (max_atoms).
The min_length is decreased by 10% (geometrically) until a supercell can be constructed.
-Parameters
+Parameters:
base_struct – structure of the unit cell
max_atoms – Maximum number of atoms allowed in the supercell.
@@ -67,10 +68,10 @@ Navigation
min_length – Minimum length of the smallest supercell lattice vector.
-Returns
+Returns:
Supercell that is as close to cubic as possible
-Return type
+Return type:
struc_sc
@@ -78,10 +79,10 @@ Navigation
-get_start_end_structures ( isite : pymatgen.core.sites.PeriodicSite , esite : pymatgen.core.sites.PeriodicSite , base_struct : pymatgen.core.structure.Structure , sc_mat : List [ List [ Union [ int , float ] ] ] , vac_mode : bool , debug : bool = False , tol : float = 1e-05 ) → Tuple [ pymatgen.core.structure.Structure , pymatgen.core.structure.Structure , pymatgen.core.structure.Structure ] [source]
+get_start_end_structures ( isite : PeriodicSite , esite : PeriodicSite , base_struct : Structure , sc_mat : List [ List [ Union [ int , float ] ] ] , vac_mode : bool , debug : bool = False , tol : float = 1e-05 ) → Tuple [ Structure , Structure , Structure ] [source]
Obtain the starting and terminating structures in a supercell for NEB calculations.
-Parameters
+Parameters:
hop – object presenting the migration event
base_struct – unit cell representation of the structure
@@ -89,7 +90,7 @@ Navigation
tol – toleranace for identifying isite/esite within base_struct
-Returns
+Returns:
initial structure, final structure, empty structure all in the supercell
@@ -124,7 +125,7 @@ Quick search
-
+
diff --git a/docs/pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc.html b/docs/pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc.html
index 0ad307b9..066cc2da 100644
--- a/docs/pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc.html
+++ b/docs/pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc module — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc module — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc module
@@ -48,7 +49,7 @@ Navigation
-pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc module
+pymatgen.analysis.diffusion.utils.tests.test_edge_data_from_sc module
test_add_edge_data_from_sc ( ) [source]
@@ -98,7 +99,7 @@ Quick search
-
+
diff --git a/docs/pymatgen.analysis.diffusion.utils.tests.test_maggma.html b/docs/pymatgen.analysis.diffusion.utils.tests.test_maggma.html
index cf814e8c..fd3fadac 100644
--- a/docs/pymatgen.analysis.diffusion.utils.tests.test_maggma.html
+++ b/docs/pymatgen.analysis.diffusion.utils.tests.test_maggma.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.utils.tests.test_maggma module — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.utils.tests.test_maggma module — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.utils.tests.test_maggma module
@@ -48,7 +49,7 @@ Navigation
-pymatgen.analysis.diffusion.utils.tests.test_maggma module
+pymatgen.analysis.diffusion.utils.tests.test_maggma module
@@ -78,7 +79,7 @@
Quick search
-
+
diff --git a/docs/pymatgen.analysis.diffusion.utils.tests.test_parse_entries.html b/docs/pymatgen.analysis.diffusion.utils.tests.test_parse_entries.html
index 729c5ddd..daa153c8 100644
--- a/docs/pymatgen.analysis.diffusion.utils.tests.test_parse_entries.html
+++ b/docs/pymatgen.analysis.diffusion.utils.tests.test_parse_entries.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis.diffusion.utils.tests.test_parse_entries module — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis.diffusion.utils.tests.test_parse_entries module — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis.diffusion.utils.tests.test_parse_entries module
@@ -48,11 +49,11 @@ Navigation
-pymatgen.analysis.diffusion.utils.tests.test_parse_entries module
+pymatgen.analysis.diffusion.utils.tests.test_parse_entries module
class ParseEntriesTest ( methodName = 'runTest' ) [source]
-Bases: unittest.case.TestCase
+Bases: TestCase
Create an instance of the class that will use the named test
method when executed. Raises a ValueError if the instance does
not have a method with the specified name.
@@ -118,7 +119,7 @@ Quick search
-
+
diff --git a/docs/pymatgen.analysis.html b/docs/pymatgen.analysis.html
index 55fab845..e0ad7cf1 100644
--- a/docs/pymatgen.analysis.html
+++ b/docs/pymatgen.analysis.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen.analysis namespace — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen.analysis namespace — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen.analysis namespace
@@ -48,9 +49,9 @@ Navigation
-pymatgen.analysis namespace
+pymatgen.analysis namespace
-Subpackages
+Subpackages
-
+
diff --git a/docs/pymatgen.html b/docs/pymatgen.html
index 9f7ccb83..11c1a5db 100644
--- a/docs/pymatgen.html
+++ b/docs/pymatgen.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen namespace — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen namespace — pymatgen-diffusion 2022.7.21 documentation
+
@@ -41,7 +42,7 @@ Navigation
previous |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen »
pymatgen namespace
@@ -53,7 +54,7 @@ Navigation
-pymatgen namespace
+pymatgen namespace
@@ -86,7 +87,7 @@
Quick search
-
+
diff --git a/docs/pymatgen_diffusion.aimd.html b/docs/pymatgen_diffusion.aimd.html
index ec2a7b88..2a0c7587 100644
--- a/docs/pymatgen_diffusion.aimd.html
+++ b/docs/pymatgen_diffusion.aimd.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen_diffusion.aimd package — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen_diffusion.aimd package — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen_diffusion.aimd package
@@ -48,29 +49,29 @@ Navigation
-pymatgen_diffusion.aimd package
+pymatgen_diffusion.aimd package
-Subpackages
+Subpackages
-pymatgen_diffusion.aimd.clustering module
+pymatgen_diffusion.aimd.clustering module
-pymatgen_diffusion.aimd.pathway module
+pymatgen_diffusion.aimd.pathway module
-pymatgen_diffusion.aimd.rdf module
+pymatgen_diffusion.aimd.rdf module
-pymatgen_diffusion.aimd.van_hove module
+pymatgen_diffusion.aimd.van_hove module
-Module contents
+Module contents
@@ -117,7 +118,7 @@
Quick search
-
+
diff --git a/docs/pymatgen_diffusion.html b/docs/pymatgen_diffusion.html
index bf4cc6e5..97926848 100644
--- a/docs/pymatgen_diffusion.html
+++ b/docs/pymatgen_diffusion.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen_diffusion package — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen_diffusion package — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen_diffusion package
@@ -48,9 +49,9 @@ Navigation
-pymatgen_diffusion package
+pymatgen_diffusion package
-Subpackages
+Subpackages
-
+
diff --git a/docs/pymatgen_diffusion.neb.html b/docs/pymatgen_diffusion.neb.html
index 4cb82427..b6108a70 100644
--- a/docs/pymatgen_diffusion.neb.html
+++ b/docs/pymatgen_diffusion.neb.html
@@ -1,17 +1,18 @@
-
+
-
+
- pymatgen_diffusion.neb package — pymatgen-diffusion 2022.1.15 documentation
+ pymatgen_diffusion.neb package — pymatgen-diffusion 2022.7.21 documentation
+
@@ -37,7 +38,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
pymatgen_diffusion.neb package
@@ -48,29 +49,29 @@ Navigation
-pymatgen_diffusion.neb package
+pymatgen_diffusion.neb package
-Subpackages
+Subpackages
-pymatgen_diffusion.neb.full_path_mapper module
+pymatgen_diffusion.neb.full_path_mapper module
-pymatgen_diffusion.neb.io module
+pymatgen_diffusion.neb.io module
-pymatgen_diffusion.neb.pathfinder module
+pymatgen_diffusion.neb.pathfinder module
-pymatgen_diffusion.neb.periodic_dijkstra module
+pymatgen_diffusion.neb.periodic_dijkstra module
-Module contents
+Module contents
@@ -117,7 +118,7 @@
Quick search
-
+
diff --git a/docs/search.html b/docs/search.html
index 0e38582f..fe148776 100644
--- a/docs/search.html
+++ b/docs/search.html
@@ -1,17 +1,18 @@
-
+
- Search — pymatgen-diffusion 2022.1.15 documentation
+ Search — pymatgen-diffusion 2022.7.21 documentation
+
@@ -42,7 +43,7 @@ Navigation
modules |
- pymatgen-diffusion 2022.1.15 documentation »
+ pymatgen-diffusion 2022.7.21 documentation »
Search
diff --git a/docs/searchindex.js b/docs/searchindex.js
index e77b6596..acb4cb4b 100644
--- a/docs/searchindex.js
+++ b/docs/searchindex.js
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"edge_data_from_sc": 28, "maggma": 29, "parse_entri": 30, "supercel": 31, "test_edge_data_from_sc": 32, "test_maggma": 33, "test_parse_entri": 34, "pymatgen_diffus": [35, 36, 37]}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 6, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1, "sphinx": 56}})
\ No newline at end of file
diff --git a/docs_rst/change_log.rst b/docs_rst/change_log.rst
index c31e6a4c..f26f081d 100644
--- a/docs_rst/change_log.rst
+++ b/docs_rst/change_log.rst
@@ -1,6 +1,10 @@
Change Log
==========
+v2022.4.22
+----------
+* Make MigrationHop MSONAble. (@acrutt)
+
v2021.4.29
----------
* Fixed msite calc order (@hmlli)
diff --git a/pymatgen/analysis/diffusion/__init__.py b/pymatgen/analysis/diffusion/__init__.py
index 27286134..3c349ec4 100644
--- a/pymatgen/analysis/diffusion/__init__.py
+++ b/pymatgen/analysis/diffusion/__init__.py
@@ -4,4 +4,4 @@
__author__ = "Materials Virtual Lab"
__email__ = "ongsp@eng.ucsd.edu"
-__version__ = "2022.1.15"
+__version__ = "2022.7.21"
diff --git a/setup.py b/setup.py
index d2edac25..b0542afa 100644
--- a/setup.py
+++ b/setup.py
@@ -14,7 +14,7 @@
setup(
name="pymatgen-analysis-diffusion",
packages=find_namespace_packages(include=["pymatgen.analysis.*"]),
- version="2022.1.15",
+ version="2022.7.21",
install_requires=["pymatgen>=2022.0.3", "joblib"],
extras_require={},
package_data={},