org.jmol.adapter.readers.xtal

Class CastepReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

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

Fields

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

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

Constructors

Constructor and Description
CastepReader()

Method Summary

Methods

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()

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

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

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