diff --git a/docs/modules.html b/docs/modules.html index b7a19f6c2e0..892cede7c05 100644 --- a/docs/modules.html +++ b/docs/modules.html @@ -6,7 +6,7 @@ -
Composition.get_wt_fraction()
Composition.hill_formula
Composition.is_element
Composition.items()
Composition.iupac_formula
Composition.num_atoms
Composition.oxi_prob
Trajectory
Trajectory.as_dict()
Trajectory.extend()
Trajectory.from_ase()
Trajectory.from_file()
Trajectory.from_molecules()
Trajectory.from_structures()
Trajectory.get_molecule()
Trajectory.get_structure()
Trajectory.to_ase()
Trajectory.to_displacements()
Trajectory.to_positions()
Trajectory.write_Xdatcar()
MaterialsProjectDFTMixingScheme.get_adjustments()
MaterialsProjectDFTMixingScheme.get_mixing_state_data()
MaterialsProjectDFTMixingScheme.process_entries()
MaterialsProjectDFTMixingScheme.run_type_2
Bases: MSONable
, ABC
Structures that return True when passed to the test() method are retained during transmutation. Those that return False are removed.
Structures that return true are kept in the Transmuter object during filtering.
Bases: AbstractStructureFilter
This filter removes structures that are not charge balanced from the transmuter. This only works if the structure is oxidation state @@ -204,7 +204,7 @@
True if structure is neutral.
Bases: AbstractStructureFilter
Filter for structures containing certain elements or species. By default compares by atomic number.
@@ -230,13 +230,13 @@Get MSONable dict.
dct (dict) – Dict representation.
@@ -249,7 +249,7 @@True if structure does not contain specified species.
Bases: AbstractStructureFilter
This filter removes exact duplicate structures from the transmuter.
Remove duplicate structures based on the structure matcher @@ -275,7 +275,7 @@
structure (Structure) – Input structure to test.
@@ -293,7 +293,7 @@Bases: AbstractStructureFilter
This filter removes structures existing in a given list from the transmuter.
Remove existing structures based on the structure matcher @@ -312,13 +312,13 @@
Get MSONable dict.
True if structure is not in existing list.
Bases: AbstractStructureFilter
This filter removes structures that have certain species that are too close together.
Get MSONable dict.
dct (dict) – Dict representation.
@@ -360,7 +360,7 @@True if structure does not contain species within specified distances.
Bases: AbstractStructureFilter
This filter removes structures that do have two particular species that are not nearest neighbors by a predefined max_dist. For instance, if you are @@ -388,7 +388,7 @@
True if structure contains the two species but their distance is greater than max_dist.
Bases: MSONable
Container for new structures that include history of transformations.
Each transformed structure is made up of a sequence of structures with @@ -420,7 +420,7 @@
Add a filter.
Append a transformation to the TransformedStructure.
Dict representation of the TransformedStructure.
Extend a sequence of transformations to the TransformedStructure.
Generate TransformedStructure from a CIF string.
Create a TransformedStructure from a dict.
Generate TransformedStructure from a poscar string.
Create TransformedStructure from SNL.
Get VASP input as a dict of VASP objects.
Redo the last undone change in the TransformedStructure.
Set a parameter.
Copy of all structures in the TransformedStructure. A structure is stored after every single transformation.
Generate a StructureNL from TransformedStructure.
Undo the last change in the TransformedStructure.
Boolean describing whether the last transformation on the structure made any alterations to it one example of when this would return false is in the case of performing a substitution transformation on the @@ -630,7 +630,7 @@
Write VASP input to an output_dir.
Bases: StandardTransmuter
Generate a Transmuter from a CIF string, possibly containing multiple structures.
Generate a Transmuter from a CIF string, possibly @@ -680,7 +680,7 @@
Generate a TransformedStructureCollection from a cif, possibly containing multiple structures.
Bases: StandardTransmuter
Generate a transmuter from a sequence of POSCARs.
Convenient constructor to generates a POSCAR transmuter from a list of POSCAR filenames.
Bases: object
An example of a Transmuter object, which performs a sequence of transformations on many structures to generate TransformedStructures.
All transformed structures.
Add tags for the structures generated by the transmuter.
Append a transformation to all TransformedStructures.
Overloaded to accept either a list of transformed structures or transmuter, it which case it appends the second transmuter’s structures.
Apply a structure_filter to the list of TransformedStructures in the transmuter.
Extend a sequence of transformations to the TransformedStructure.
Alternative constructor from structures rather than TransformedStructures.
Redo the last undone transformation in the TransformedStructure.
Add parameters to the transmuter. Additional parameters are stored in the as_dict() output.
Undo the last transformation in the TransformedStructure.
Batch write vasp input for a sequence of transformed structures to output_dir, following the format output_dir/{formula}_{number}.
Batch write vasp input for a sequence of transformed structures to output_dir, following the format output_dir/{group}/{formula}_{number}.
Bases: MSONable
Describe the connected components in a structure in terms of coordination environments.
Constructor for the ConnectedComponent object.
@@ -187,7 +187,7 @@Bson-serializable dict representation of the ConnectedComponent object.
algorithm (str) – Algorithm to use to compute the periodicity vectors. Can be @@ -212,19 +212,19 @@
Get the periodicity vectors of the connected component.
Compute periodicity vectors of the connected component.
Get the coordination sequence for a given node.
full (bool) – Whether to return a short or full description.
@@ -290,7 +290,7 @@start_node (Node, optional) – Node to start the elastic centering from. @@ -307,7 +307,7 @@
Reconstructs the ConnectedComponent object from a dict representation of the ConnectedComponent object created using the as_dict method.
Constructor for the ConnectedComponent object from a graph of the connected component.
The Networkx MultiGraph object of this connected component with environment as nodes and links between these nodes as edges with information about the image cell difference if any.
Whether this connected component is 0-dimensional.
Whether this connected component is 1-dimensional.
Whether this connected component is 2-dimensional.
Whether this connected component is 3-dimensional.
Whether this connected component is periodic.
multiplicity (int) – Multiplicity of the super graph.
@@ -395,19 +395,19 @@Periodicity of this connected component.
Periodicity vectors of this connected component.
Displays the graph using the specified drawing type.
Draw network of environments in a matplotlib figure axes.
Make super graph from a graph of environments.
Bases: object
Main class used to find the structure connectivity of a structure.
Constructor for the ConnectivityFinder.
@@ -482,7 +482,7 @@Get the structure connectivity from the coordination environments provided as an input.
Setup of the parameters for the connectivity finder.
Bases: MSONable
Abstract class used to define an environment as a node in a graph.
Constructor for the AbstractEnvironmentNode object.
@@ -528,104 +528,104 @@Symbol of the atom on the central site.
Coordination environment of this node.
Coordination environment of this node.
Coordination environment of this node.
Check equality with respect to another AbstractEnvironmentNode using the index of the central site as well as the central site itself.
Index of the central site.
Coordination environment of this node.
Bases: AbstractEnvironmentNode
Define an environment as a node in a graph.
Constructor for the EnvironmentNode object.
@@ -649,13 +649,13 @@Coordination environment of this node.
Compare with another environment node.
Get the EnvironmentNode class or subclass for the given site and symbol.
Bases: MSONable
Main class containing the connectivity of a structure.
Constructor for the StructureConnectivity object.
@@ -714,7 +714,7 @@Add the bonds for a given site index to the structure connectivity graph.
Add the sites in the structure connectivity graph.
Convert to MSONable dict.
dct (dict)
@@ -772,33 +772,33 @@Print all links in the graph.
Set up the graph for predefined environments and optionally atoms.
Helper method to get the delta image between one environment and another from the ligand’s delta images.
Bases: MSONable
, ABC
Base class to define a Chemenv strategy for the neighbors and coordination environment to be applied to a StructureEnvironments object.
@@ -565,32 +565,32 @@Bson-serializable dict representation of the SimplestChemenvStrategy object.
Get the equivalent site and corresponding symmetry+translation transformations.
Reconstructs the SimpleAbundanceChemenvStrategy object from a dict representation of the SimpleAbundanceChemenvStrategy object created using the as_dict method.
Applies the strategy to the structure_environments object in order to get coordination environments, their fraction, csm, geometry_info, and neighbors.
Applies the strategy to the structure_environments object in order to define the coordination environment of a given site.
Applies the strategy to the structure_environments object in order to define the coordination environment of a given site.
Applies the strategy to the structure_environments object in order to define the coordination environment of a given site.
Applies the strategy to the structure_environments object in order to get the neighbors of a given site.
Prepare the symmetries for the structure contained in the structure environments.
Set up a given option for this strategy.
Set the structure environments to this strategy.
Set up options for this strategy based on a dict.
Type of symmetry measure.
True if the strategy leads to a unique coordination environment.
Bases: int
, StrategyOption
Integer representing an additional condition in a strategy.
Special int representing additional conditions.
MSONable dict.
Initialize additional condition from dict.
Bases: float
, StrategyOption
Angle cutoff in a strategy.
Special float that should be between 0 and 1.
@@ -820,18 +820,18 @@MSONable dict.
Initialize angle cutoff from dict.
Bases: NbSetWeight
Weight of neighbors set based on the angle.
Initialize AngleNbSetWeight estimator.
@@ -855,12 +855,12 @@Sum of all angles in a neighbors set.
Sum of all angles to a given power in a neighbors set.
MSONable dict.
Construct AngleNbSetWeight from dict representation.
Get the weight of a given neighbors set.
Bases: NbSetWeight
Weight of neighbors set based on the angle.
Initialize AnglePlateauNbSetWeight.
@@ -938,18 +938,18 @@MSONable dict.
Initialize from dict.
Get the weight of a given neighbors set.
Bases: NbSetWeight
Weight of neighbors set based on specific biases towards specific coordination numbers.
Initialize CNBiasNbSetWeight.
@@ -1001,18 +1001,18 @@MSONable dict.
Initialize weights explicitly for each coordination.
Initialize weights from description.
Initialize from dict.
Initialize geometrically equidistant weights for each coordination.
weight_cn1: Weight of coordination 1. @@ -1070,7 +1070,7 @@
Initialize linearly equidistant weights for each coordination.
Get the weight of a given neighbors set.
Bases: float
, StrategyOption
Real number representing a Continuous Symmetry Measure.
Special float that should be between 0 and 100.
@@ -1122,18 +1122,18 @@MSONable dict.
Initialize CSM from dict.
Bases: NbSetWeight
Weight of neighbors set based on the differences of CSM.
Initialize DeltaCSMNbSetWeight.
@@ -1162,33 +1162,33 @@MSONable dict.
Initialize DeltaCSMNbSetWeight from specific coordination number differences.
Initialize from dict.
Get the weight of a given neighbors set.
Bases: NbSetWeight
Weight of neighbors set based on the difference of distances.
Initialize DeltaDistanceNbSetWeight.
@@ -1260,18 +1260,18 @@MSONable dict.
Initialize from dict.
Get the weight of a given neighbors set.
Bases: NbSetWeight
Weight of neighbors set based on the area in the distance-angle space.
Initialize CNBiasNbSetWeight.
@@ -1328,28 +1328,28 @@MSONable dict.
Initialize from dict.
Whether a given rectangle crosses the area defined by the upper and lower curves.
Get intersection of the neighbors set area with the surface.
Get intersection of the neighbors set area with the surface.
Get the weight of a given neighbors set.
Bases: float
, StrategyOption
Distance cutoff in a strategy.
Special float that should be between 1 and infinity.
@@ -1452,18 +1452,18 @@MSONable dict.
Initialize distance cutoff from dict.
Bases: NbSetWeight
Weight of neighbors set based on the distance.
Initialize DistanceNbSetWeight.
@@ -1490,18 +1490,18 @@MSOnable dict.
Initialize from dict.
Get the weight of a given neighbors set.
Bases: NbSetWeight
Weight of neighbors set based on the distance.
Initialize DistancePlateauNbSetWeight.
@@ -1553,18 +1553,18 @@MSONable dict.
Initialize from dict.
Get the weight of a given neighbors set.
Bases: WeightedNbSetChemenvStrategy
MultiWeightsChemenvStrategy.
Constructor for the MultiWeightsChemenvStrategy.
@@ -1614,17 +1614,17 @@