public class CastepReader extends AtomSetCollectionReader
Modifier and Type | Field and Description |
---|---|
private float |
a |
private javax.vecmath.Vector3f[] |
abc |
private float |
alpha |
private float |
b |
private float |
beta |
private float |
c |
private float |
gamma |
private boolean |
iHaveFractionalCoordinates |
private static float[] |
lengthUnitFactors |
private static java.lang.String[] |
lengthUnitIds |
private static int |
lengthUnits |
private java.lang.String[] |
tokens |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCheckUnitCell, doProcessLines, filter, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, symmetry, templateAtomCount, vibrationNumber, viewer
Constructor and Description |
---|
CastepReader() |
Modifier and Type | Method and Description |
---|---|
protected void |
finalizeReader() |
void |
initializeReader() |
private void |
readAtomData(float factor) |
private void |
readLatticeAbc() |
private void |
readLatticeCart() |
private float |
readLengthUnit() |
private void |
readPositionsAbs() |
private void |
readPositionsFrac() |
private int |
tokenizeCastepCell() |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLine, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readLine, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
private java.lang.String[] tokens
private float a
private float b
private float c
private float alpha
private float beta
private float gamma
private javax.vecmath.Vector3f[] abc
private boolean iHaveFractionalCoordinates
private static final java.lang.String[] lengthUnitIds
private static final float[] lengthUnitFactors
private static final int lengthUnits
public void initializeReader() throws java.lang.Exception
initializeReader
in class AtomSetCollectionReader
java.lang.Exception
protected void finalizeReader() throws java.lang.Exception
finalizeReader
in class AtomSetCollectionReader
java.lang.Exception
private void readLatticeAbc() throws java.lang.Exception
java.lang.Exception
private void readLatticeCart() throws java.lang.Exception
java.lang.Exception
private void readPositionsFrac() throws java.lang.Exception
java.lang.Exception
private void readPositionsAbs() throws java.lang.Exception
java.lang.Exception
private float readLengthUnit() throws java.lang.Exception
java.lang.Exception
private void readAtomData(float factor) throws java.lang.Exception
java.lang.Exception
private int tokenizeCastepCell() throws java.lang.Exception
java.lang.Exception