org.jmol.adapter.readers.xtal

Class CrystalReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.xtal.CrystalReader

public class CrystalReader
extends AtomSetCollectionReader

A reader of OUT and OUTP files for CRYSTAL http://www.crystal.unito.it/

Version:

1.4 for a specific model in the set, use load "xxx.out" n as for all readers, where n is an integer > 0 for final optimized geometry use load "xxx.out" 0 (that is, "read the last model") as for all readers for conventional unit cell -- input coordinates only, use load "xxx.out" filter "conventional" to NOT load vibrations, use load "xxx.out" FILTER "novibrations" to load just the input deck exactly as indicated, use load "xxx.out" FILTER "input" now allows reading of frequencies and atomic values with conventional as long as this is not an optimization.

Author:

Pieremanuele Canepa, Room 104, FM Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom, pc229@kent.ac.uk

Field Summary

Fields

Modifier and Type	Field and Description
private int	atomCount
private int[]	atomFrag
private int	atomIndexLast
private V3[]	directLatticeVectors
private java.lang.Double	energy
private boolean	getLastConventional
private boolean	haveCharges
private boolean	havePrimitiveMapping
private boolean	inputOnly
private boolean	isFreqCalc
private boolean	isLongMode
private boolean	isMolecular
private boolean	isPolymer
private boolean	isPrimitive
private boolean	isProperties
private boolean	isSlab
private boolean	isVersion3
private float[]	nuclearCharges
private Matrix3f	primitiveToCryst
private int[]	primitiveToIndex
private P3	ptOriginShift
private java.lang.String	spaceGroupName
private JmolList<java.lang.String>	vInputCoords

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

addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterAtomTypeStr, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, mustFinalizeModelSet, next, notionalUnitCell, os, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer

Constructor Summary

Constructors

Constructor and Description
CrystalReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected boolean	checkLine()
protected void	finalizeReader() optional reader-specific method run first.
private float	fraction(java.lang.String f)
private int	getAtomicNumber(java.lang.String token)
private int	getAtomIndexFromPrimitiveIndex(int iPrim)
private java.lang.String	getAtomName(java.lang.String s)
private boolean	getPropertyTensors()
protected void	initializeReader()
private void	newAtomSet()
private void	processInputCoords()
private boolean	readAtoms()
private void	readCellParams(boolean isNewSet)
private void	readCrystallographicCoords()
private void	readEnergy()
private boolean	readFragments()
private boolean	readFrequencies()
private boolean	readGradient()
private boolean	readHeader()
private boolean	readMagneticMoments()
private boolean	readPartialCharges()
private boolean	readPrimitiveMapping() create arrays that maps primitive atoms to conventional atoms in a 1:1 fashion.
private boolean	readShift()
private boolean	readSpins()
private boolean	readTotalAtomicCharges()
private void	readTransformationMatrix()
private boolean	readVolumePrimCell()
private void	setData(java.lang.String name, java.lang.String data, int pt, int dp)
private boolean	setDirect()
private void	setEnergy()
private void	setFreqValue(float freq, java.lang.String[] data)

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

addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokensAt, getTokensFloat, getTokensStr, initializeSymmetry, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseStringInfestedFloatArray, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, parseTrimmedAt, parseTrimmedRange, processBinaryDocument, processDOM, read3Vectors, readDataObject, readLine, readLines, RL, set2D, setAtomCoord, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFractionalCoordinates, setIsPDB, setLoadNote, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

isVersion3

private boolean isVersion3

isPrimitive

private boolean isPrimitive

isPolymer

private boolean isPolymer

isSlab

private boolean isSlab

isMolecular

private boolean isMolecular

haveCharges

private boolean haveCharges

isFreqCalc

private boolean isFreqCalc

inputOnly

private boolean inputOnly

isLongMode

private boolean isLongMode

getLastConventional

private boolean getLastConventional

havePrimitiveMapping

private boolean havePrimitiveMapping

isProperties

private boolean isProperties

atomCount

private int atomCount

atomIndexLast

private int atomIndexLast

atomFrag

private int[] atomFrag

primitiveToIndex

private int[] primitiveToIndex

nuclearCharges

private float[] nuclearCharges

vInputCoords

private JmolList<java.lang.String> vInputCoords

energy

private java.lang.Double energy

ptOriginShift

private P3 ptOriginShift

primitiveToCryst

private Matrix3f primitiveToCryst

directLatticeVectors

private V3[] directLatticeVectors

spaceGroupName

private java.lang.String spaceGroupName

Constructor Detail

CrystalReader

public CrystalReader()

Method Detail

initializeReader

protected void initializeReader()
                         throws java.lang.Exception

Overrides:

initializeReader in class AtomSetCollectionReader

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

finalizeReader

protected void finalizeReader()
                       throws java.lang.Exception

Description copied from class: AtomSetCollectionReader

optional reader-specific method run first.

Overrides:

finalizeReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

setDirect

private boolean setDirect()
                   throws java.lang.Exception

Throws:

java.lang.Exception

readTransformationMatrix

private void readTransformationMatrix()
                               throws java.lang.Exception

Throws:

java.lang.Exception

readShift

private boolean readShift()

fraction

private float fraction(java.lang.String f)

readGradient

private boolean readGradient()
                      throws java.lang.Exception

Throws:

java.lang.Exception

readVolumePrimCell

private boolean readVolumePrimCell()

readSpins

private boolean readSpins()
                   throws java.lang.Exception

Throws:

java.lang.Exception

readMagneticMoments

private boolean readMagneticMoments()
                             throws java.lang.Exception

Throws:

java.lang.Exception

setData

private void setData(java.lang.String name,
           java.lang.String data,
           int pt,
           int dp)
              throws java.lang.Exception

Throws:

java.lang.Exception

readHeader

private boolean readHeader()
                    throws java.lang.Exception

Throws:

java.lang.Exception

readCellParams

private void readCellParams(boolean isNewSet)
                     throws java.lang.Exception

Throws:

java.lang.Exception

readPrimitiveMapping

private boolean readPrimitiveMapping()
                              throws java.lang.Exception

create arrays that maps primitive atoms to conventional atoms in a 1:1 fashion. Creates: int[] primitiveToIndex -- points to model-based atomIndex

Returns:

TRUE

Throws:

java.lang.Exception

readAtoms

private boolean readAtoms()
                   throws java.lang.Exception

Throws:

java.lang.Exception

getAtomName

private java.lang.String getAtomName(java.lang.String s)

getAtomicNumber

private int getAtomicNumber(java.lang.String token)

readCrystallographicCoords

private void readCrystallographicCoords()
                                 throws java.lang.Exception

Throws:

java.lang.Exception

processInputCoords

private void processInputCoords()
                         throws java.lang.Exception

Throws:

java.lang.Exception

newAtomSet

private void newAtomSet()
                 throws java.lang.Exception

Throws:

java.lang.Exception

readEnergy

private void readEnergy()

setEnergy

private void setEnergy()

readPartialCharges

private boolean readPartialCharges()
                            throws java.lang.Exception

Throws:

java.lang.Exception

readTotalAtomicCharges

private boolean readTotalAtomicCharges()
                                throws java.lang.Exception

Throws:

java.lang.Exception

getAtomIndexFromPrimitiveIndex

private int getAtomIndexFromPrimitiveIndex(int iPrim)

readFragments

private boolean readFragments()
                       throws java.lang.Exception

Throws:

java.lang.Exception

readFrequencies

private boolean readFrequencies()
                         throws java.lang.Exception

Throws:

java.lang.Exception

setFreqValue

private void setFreqValue(float freq,
                java.lang.String[] data)

getPropertyTensors

private boolean getPropertyTensors()
                            throws java.lang.Exception

Throws:

java.lang.Exception