public class CoordinationPolyhedronToolkit extends BaseAnalysisToolkit
Options: <atom|cell> [-radical] [-radii <name1> <radius1> <...>]
atom|cell: Whether to print the coordination polyhedron of each atom,
or statistics regarding the entire cell.
-radical: Whether to use a radical-plane Voronoi tessellation
nameN: Symbol of element, use "*" to set a default value
radiusN: Radius of corresponding element. Should be in same units as the cell
Example Usage: atom -radical -radii Cu 1.26 Zr 1.54 * 1.4
Will compute the radical Voronoi tessellation, with radii of 1.26 and 1.54 for Cu
and Zr, respecitively. Any other atoms with have a radius of 1.4. Statistics of
each atom will be printed.
Modifier and Type | Field and Description |
---|---|
protected boolean |
ComputeRadical
Whether to compute a radical plane tessellation
|
protected boolean |
PrintCellStatistics
Report coordination of each atom or cell statistics
|
protected java.util.Map<java.lang.String,java.lang.Double> |
Radii
Radii of each element
|
Constructor and Description |
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CoordinationPolyhedronToolkit() |
Modifier and Type | Method and Description |
---|---|
void |
addRadius(java.lang.String element,
double radius)
Set the radius for a certain element.
|
java.lang.String |
analyzeStructure(Cell cell)
Analyze structure and prepare report of results.
|
void |
clearRadii()
Clear current list of radii
|
java.lang.String |
printUsage()
Print out required format for options.
|
void |
setComputeRadicalTessellation(boolean x)
Set whether to compute a radical plane Voronoi tessellation
|
void |
setOptions(java.util.List<java.lang.String> Options)
Set any options for this object.
|
void |
setPrintCellStatistics(boolean x)
Set whether to print cell statistics or shape of cell around each atom.
|
protected boolean PrintCellStatistics
protected final java.util.Map<java.lang.String,java.lang.Double> Radii
protected boolean ComputeRadical
public void setOptions(java.util.List<java.lang.String> Options) throws java.lang.Exception
Options
Options
- Array of options as Objects - can be null
java.lang.Exception
- if problem with inputspublic java.lang.String printUsage()
Options
public void setPrintCellStatistics(boolean x)
x
- Desired settingpublic void setComputeRadicalTessellation(boolean x)
x
- Desired settingpublic void clearRadii()
public void addRadius(java.lang.String element, double radius)
element
- Symbol of element. Use "*" to set a default valueradius
- Radius of element. Should be in same units as
Cell object passed to analyzeStructure(vassal.data.Cell)public java.lang.String analyzeStructure(Cell cell) throws java.lang.Exception
BaseAnalysisToolkit
analyzeStructure
in class BaseAnalysisToolkit
cell
- Structure to be analyzedjava.lang.Exception