public class PairDistanceAnalysis extends BaseAnalysis
Current operations
Structure
Constructor and Description |
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PairDistanceAnalysis() |
Modifier and Type | Method and Description |
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double[][][] |
computePRDF(int nBin)
Compute the pair radial distribution function.
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java.util.List<org.apache.commons.lang3.tuple.Pair<AtomImage,java.lang.Double>> |
findAllImages(int centerAtom,
int neighborAtom)
Find all images of one atom that are within the cutoff distance of another atom.
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java.util.List<org.apache.commons.lang3.tuple.Pair<AtomImage,java.lang.Double>> |
getAllNeighborsOfAtom(int index)
Compute all neighbors of a certain atom
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double |
getCutoffDistance()
Get the cutoff distance
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protected void |
precompute()
Perform any kind of computations that should only be performed once.
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void |
setCutoffDistance(double CutoffDistance)
Define the cutoff distance.
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analyzeStructure, recompute
protected void precompute()
BaseAnalysis
precompute
in class BaseAnalysis
public double getCutoffDistance()
public void setCutoffDistance(double CutoffDistance)
CutoffDistance
- Desired distanceCutoffDistance
public java.util.List<org.apache.commons.lang3.tuple.Pair<AtomImage,java.lang.Double>> getAllNeighborsOfAtom(int index)
index
- Index of atom being consideredpublic double[][][] computePRDF(int nBin)
nBin
- Number of bins in which to discretize PRDF (must be > 0)public java.util.List<org.apache.commons.lang3.tuple.Pair<AtomImage,java.lang.Double>> findAllImages(int centerAtom, int neighborAtom)
centerAtom
- Atom at the centerneighborAtom
- Neighboring atom