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 preliminary .castep, .phonon frequency reader -- hansonr@stolaf.edu 9/2011 -- Many thanks to Keith Refson for his assistance with this implementation -- atom's mass is encoded as bfactor -- FILTER options include "q=n" where n is an integer or "q={1/4 1/4 0}" -- for non-simple fractions, you must use the exact form of the wavevector description: -- load "xxx.phonon" FILTER "q=(-0.083333 0.083333 0.500000) -- for simple fractions, you can also just specify SUPERCELL {a b c} where -- the number of cells matches a given wavevector -- SUPERCELL {4 4 1}, for example -- following this with ".1" ".2" etc. gives first, second, third, etc. occurance: -- load "xxx.phonon" FILTER "q=1.3" .... -- load "xxx.phonon" FILTER "{0 0 0}.3" ....

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 int	atomCount
private javax.vecmath.Point3f[]	atomPts
private float	b
private float	beta
private float	c
private java.lang.String	desiredQ
private javax.vecmath.Vector3f	desiredQpt
private float	gamma
private boolean	havePhonons
private boolean	isCell
private boolean	isOutput
private boolean	isPhonon
private java.lang.String	lastQPt
private static float[]	lengthUnitFactors
private static java.lang.String[]	lengthUnitIds
private int	qpt2
private java.lang.String[]	tokens
private static double	TWOPI

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

addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer

Constructor Summary

Constructors

Constructor and Description
CastepReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected boolean	checkLine()
protected void	finalizeReader()
private java.lang.String	getFractionalCoord(javax.vecmath.Vector3f qvec)
void	initializeReader()
private static boolean	isInt(float f)
private void	readAtomData(float factor)
private boolean	readFileData()
private void	readLatticeAbc()
private void	readLatticeCart()
private float	readLengthUnit(java.lang.String units)
private void	readOutputAtoms()
private void	readOutputCharges()
private void	readOutputUnitCell()
private void	readPhononFractionalCoord()
private void	readPhononFrequencies()
private void	readPhononTrajectories()
private void	readPhononUnitCell()
private void	readPositionsAbs()
private void	readPositionsFrac()
private void	setDesiredQpt(java.lang.String s)
private void	setLatticeVectors()
private void	setPhononVector(float[] data, Atom atom, javax.vecmath.Vector3f rTrans, javax.vecmath.Vector3f qvec, javax.vecmath.Vector3f v) transform complex vibration vector to a real vector by applying the appropriate translation, storing the results in v
private int	tokenizeCastepCell()

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

addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, 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, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, 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

isPhonon

private boolean isPhonon

isOutput

private boolean isOutput

isCell

private boolean isCell

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

atomCount

private int atomCount

atomPts

private javax.vecmath.Point3f[] atomPts

havePhonons

private boolean havePhonons

lastQPt

private java.lang.String lastQPt

qpt2

private int qpt2

desiredQpt

private javax.vecmath.Vector3f desiredQpt

desiredQ

private java.lang.String desiredQ

lengthUnitIds

private static final java.lang.String[] lengthUnitIds

lengthUnitFactors

private static final float[] lengthUnitFactors

TWOPI

private static final double TWOPI

See Also:

Constant Field Values

Constructor Detail

CastepReader

public CastepReader()

Method Detail

initializeReader

public void initializeReader()
                      throws java.lang.Exception

Overrides:

initializeReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

setDesiredQpt

private void setDesiredQpt(java.lang.String s)

readFileData

private boolean readFileData()
                      throws java.lang.Exception

Throws:

java.lang.Exception

checkLine

protected boolean checkLine()
                     throws java.lang.Exception

Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

java.lang.Exception

readOutputUnitCell

private void readOutputUnitCell()
                         throws java.lang.Exception

Throws:

java.lang.Exception

readOutputAtoms

private void readOutputAtoms()
                      throws java.lang.Exception

Throws:

java.lang.Exception

readOutputCharges

private void readOutputCharges()
                        throws java.lang.Exception

Throws:

java.lang.Exception

readPhononTrajectories

private void readPhononTrajectories()
                             throws java.lang.Exception

Throws:

java.lang.Exception

finalizeReader

protected void finalizeReader()
                       throws java.lang.Exception

Overrides:

finalizeReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

setLatticeVectors

private void setLatticeVectors()

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(java.lang.String units)
                      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

readPhononUnitCell

private void readPhononUnitCell()
                         throws java.lang.Exception

Throws:

java.lang.Exception

readPhononFractionalCoord

private void readPhononFractionalCoord()
                                throws java.lang.Exception

Throws:

java.lang.Exception

readPhononFrequencies

private void readPhononFrequencies()
                            throws java.lang.Exception

Throws:

java.lang.Exception

getFractionalCoord

private java.lang.String getFractionalCoord(javax.vecmath.Vector3f qvec)

isInt

private static boolean isInt(float f)

setPhononVector

private void setPhononVector(float[] data,
                   Atom atom,
                   javax.vecmath.Vector3f rTrans,
                   javax.vecmath.Vector3f qvec,
                   javax.vecmath.Vector3f v)

transform complex vibration vector to a real vector by applying the appropriate translation, storing the results in v

Parameters:

data - from .phonon line parsed for floats

atom -

rTrans - translation vector in unit fractional coord

qvec - q point vector

v - return vector