org.jmol.adapter.readers.xtal

Class CrystalReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.xtal.CrystalReader

All Implemented Interfaces:

javajs.api.GenericLineReader

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	ac
private int[]	atomFrag
private int	atomIndexLast
private javajs.util.V3[]	directLatticeVectors
private java.lang.Double	energy
private boolean	getLastConventional
private boolean	haveCharges
private boolean	havePrimitiveMapping
private boolean	inputOnly
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 float	primitiveDensity
private javajs.util.M3	primitiveToCryst
private int[]	primitiveToIndex
private float	primitiveVolume
private javajs.util.P3	ptOriginShift
private java.lang.String	spaceGroupName
private javajs.util.Lst<java.lang.String>	vCoords
private javajs.util.Lst<java.lang.String>	vPrimitiveMapping

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

addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors

Constructor and Description
CrystalReader()

Method Summary

Modifier and Type	Method and Description
protected boolean	checkLine()
private void	createAtomsFromCoordLines() Now create atoms from the coordinate lines.
protected void	finalizeSubclassReader() optional reader-specific method run first.
private static java.lang.String	fixAtomName(java.lang.String s) MN33 becomes Mn33
private int	getAtomicNumber(java.lang.String token)
private int	getAtomIndexFromPrimitiveIndex(int iPrim)
private boolean	getQuadrupoleTensors()
protected void	initializeReader()
private void	newAtomSet()
private boolean	readAtoms()
private boolean	readBornChargeTensors()
private void	readCoordLines() Read coordinates, either input or crystallographic, just saving their lines in a vector for now.
private boolean	readData(java.lang.String name, int nfields) For spin and magnetic moment data, read the data block and save it as property_spin or propert_magneticMoment.
private void	readEnergy()
private boolean	readFreqFragments() Select only specific atoms for frequency generation.
private boolean	readFrequencies()
private boolean	readGradient() Read minimization measures
private boolean	readHeader()
private void	readLatticeParams(boolean isNewSet) Read the lattice parameters.
private boolean	readPartialCharges()
private void	readPrimitiveMapping()
private boolean	readShift() Read the origin shift
private boolean	readTotalAtomicCharges()
private void	readTransformationMatrix() Read transform matrix primitive to conventional.
private boolean	setDirect()
private void	setEnergy()
private void	setFreqValue(float freq, java.lang.String[] data)
private boolean	setPrimitiveMapping() Create arrays that maps primitive atoms to conventional atoms in a 1:1 fashion.
private void	setPrimitiveVolumeAndDensity() Read the primitive cell volume and density.

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

addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassSymmetry, forceSymmetry, getElementSymbol, getFilter, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, processBinaryDocument, processDOM, processDSSR, rd, read3Vectors, readDataObject, readLines, readNextLine, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setModelPDB, 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

inputOnly

private boolean inputOnly

isLongMode

private boolean isLongMode

getLastConventional

private boolean getLastConventional

havePrimitiveMapping

private boolean havePrimitiveMapping

isProperties

private boolean isProperties

ac

private int ac

atomIndexLast

private int atomIndexLast

atomFrag

private int[] atomFrag

primitiveToIndex

private int[] primitiveToIndex

nuclearCharges

private float[] nuclearCharges

vCoords

private javajs.util.Lst<java.lang.String> vCoords

energy

private java.lang.Double energy

ptOriginShift

private javajs.util.P3 ptOriginShift

primitiveToCryst

private javajs.util.M3 primitiveToCryst

directLatticeVectors

private javajs.util.V3[] directLatticeVectors

spaceGroupName

private java.lang.String spaceGroupName

primitiveVolume

private float primitiveVolume

primitiveDensity

private float primitiveDensity

vPrimitiveMapping

private javajs.util.Lst<java.lang.String> vPrimitiveMapping

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

finalizeSubclassReader

protected void finalizeSubclassReader()
                               throws java.lang.Exception

Description copied from class: AtomSetCollectionReader

optional reader-specific method run first.

Overrides:

finalizeSubclassReader 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

Read transform matrix primitive to conventional.

Throws:

java.lang.Exception

readShift

private boolean readShift()

Read the origin shift

Returns:

true

setPrimitiveVolumeAndDensity

private void setPrimitiveVolumeAndDensity()

Read the primitive cell volume and density. Not sure why we are rounding here.

readHeader

private boolean readHeader()
                    throws java.lang.Exception

Throws:

java.lang.Exception

readLatticeParams

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

Read the lattice parameters.

Parameters:

isNewSet -

Throws:

java.lang.Exception

readPrimitiveMapping

private void readPrimitiveMapping()
                           throws java.lang.Exception

Throws:

java.lang.Exception

setPrimitiveMapping

private boolean setPrimitiveMapping()
                             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 if coordinates have been created

Throws:

java.lang.Exception

readAtoms

private boolean readAtoms()
                   throws java.lang.Exception

Throws:

java.lang.Exception

fixAtomName

private static java.lang.String fixAtomName(java.lang.String s)

MN33 becomes Mn33

Parameters:

s -

Returns:

fixed atom name

getAtomicNumber

private int getAtomicNumber(java.lang.String token)

readCoordLines

private void readCoordLines()
                     throws java.lang.Exception

Read coordinates, either input or crystallographic, just saving their lines in a vector for now.

Throws:

java.lang.Exception

createAtomsFromCoordLines

private void createAtomsFromCoordLines()
                                throws java.lang.Exception

Now create atoms from the coordinate lines.

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)

readFreqFragments

private boolean readFreqFragments()
                           throws java.lang.Exception

Select only specific atoms for frequency generation. (See freq_6for_001.out)

Returns:

true

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)

readGradient

private boolean readGradient()
                      throws java.lang.Exception

Read minimization measures

Returns:

true

Throws:

java.lang.Exception

readData

private boolean readData(java.lang.String name,
                         int nfields)
                  throws java.lang.Exception

For spin and magnetic moment data, read the data block and save it as property_spin or propert_magneticMoment.

Parameters:

name -

nfields -

Returns:

true

Throws:

java.lang.Exception

getQuadrupoleTensors

private boolean getQuadrupoleTensors()
                              throws java.lang.Exception

Throws:

java.lang.Exception

readBornChargeTensors

private boolean readBornChargeTensors()
                               throws java.lang.Exception

Throws:

java.lang.Exception