org.jmol.adapter.readers.xtal
Class CastepReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.xtal.CastepReader

public class CastepReader
extends AtomSetCollectionReader

CASTEP (http://www.castep.org) .cell file format relevant section of .cell file are included as comments below

Version:
1.2
Author:
Joerg Meyer, FHI Berlin 2009 (meyer@fhi-berlin.mpg.de)

Field Summary
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
           
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
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 Summary
CastepReader()
           
 
Method Summary
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()
           
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLine, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, createSpaceGroup, 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
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

tokens

private java.lang.String[] tokens

a

private float a

b

private float b

c

private float c

alpha

private float alpha

beta

private float beta

gamma

private float gamma

abc

private javax.vecmath.Vector3f[] abc

iHaveFractionalCoordinates

private boolean iHaveFractionalCoordinates

lengthUnitIds

private static final java.lang.String[] lengthUnitIds

lengthUnitFactors

private static final float[] lengthUnitFactors

lengthUnits

private static final int lengthUnits
Constructor Detail

CastepReader

public CastepReader()
Method Detail

initializeReader

public void initializeReader()
                      throws java.lang.Exception
Overrides:
initializeReader in class AtomSetCollectionReader
Throws:
java.lang.Exception

finalizeReader

protected void finalizeReader()
                       throws java.lang.Exception
Overrides:
finalizeReader in class AtomSetCollectionReader
Throws:
java.lang.Exception

readLatticeAbc

private void readLatticeAbc()
                     throws java.lang.Exception
Throws:
java.lang.Exception

readLatticeCart

private void readLatticeCart()
                      throws java.lang.Exception
Throws:
java.lang.Exception

readPositionsFrac

private void readPositionsFrac()
                        throws java.lang.Exception
Throws:
java.lang.Exception

readPositionsAbs

private void readPositionsAbs()
                       throws java.lang.Exception
Throws:
java.lang.Exception

readLengthUnit

private float readLengthUnit()
                      throws java.lang.Exception
Throws:
java.lang.Exception

readAtomData

private void readAtomData(float factor)
                   throws java.lang.Exception
Throws:
java.lang.Exception

tokenizeCastepCell

private int tokenizeCastepCell()
                        throws java.lang.Exception
Throws:
java.lang.Exception