org.jmol.adapter.readers.xtal

Class GulpReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.xtal.GulpReader

public class GulpReader
extends AtomSetCollectionReader

Problems identified (Bob Hanson) -- -- Coordinates for the asymmetric unit are conventional. Default right now is to read conventional cell, not primitive celll -- Frequency data number of atoms does not correspond to initial atom count. It looks like there is a missing report of symmetry-generated atoms. see https://projects.ivec.org/gulp/

Version:

1.0

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 float	a
private float	alpha
private java.util.Map<java.lang.String,java.lang.Float>	atomCharges
private float	b
private float	beta
private boolean	bTest
private float	c
private boolean	coordinatesArePrimitive
private java.lang.String	energyUnits
private float	gamma
private boolean	isMolecular
private boolean	isPolymer
private boolean	isPrimitive
private boolean	isSlab
private float[]	primitiveData
private java.lang.String	sep
private java.lang.String	spaceGroup
private static java.lang.String[]	tags
private java.lang.Double	totEnergy

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, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer

Constructor Summary

Constructors

Constructor and Description
GulpReader()

Method Summary

Methods

Modifier and Type	Method and Description
void	applySymmetryAndSetTrajectory()
protected boolean	checkLine()
protected void	finalizeReader()
protected void	initializeReader()
private void	newAtomSet(boolean doSetUnitCell)
private static int	parameterIndex(java.lang.String key)
private void	readAtomicPos(boolean finalizeSymmetry)
private void	readCellParameters(boolean isLatticeVectors)
private boolean	readDimensionality()
private void	readEnergy()
private void	readFinalCell()
private void	readPartialCharges()
private void	readSpaceGroup()
private void	scalePrimitiveData(int i, float value)
private void	setEnergy()
private void	setModelParameters(boolean isPrimitive)
private void	setParameter(java.lang.String key, float value)

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

addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, 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

spaceGroup

private java.lang.String spaceGroup

isSlab

private boolean isSlab

isPolymer

private boolean isPolymer

isMolecular

private boolean isMolecular

isPrimitive

private boolean isPrimitive

sep

private java.lang.String sep

coordinatesArePrimitive

private boolean coordinatesArePrimitive

atomCharges

private java.util.Map<java.lang.String,java.lang.Float> atomCharges

bTest

private boolean bTest

a

private float a

b

private float b

c

private float c

alpha

private float alpha

beta

private float beta

gamma

private float gamma

primitiveData

private float[] primitiveData

tags

private static java.lang.String[] tags

totEnergy

private java.lang.Double totEnergy

energyUnits

private java.lang.String energyUnits

Constructor Detail

GulpReader

public GulpReader()

Method Detail

initializeReader

protected void initializeReader()
                         throws java.lang.Exception

Overrides:

initializeReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

finalizeReader

protected void finalizeReader()

Overrides:

finalizeReader in class AtomSetCollectionReader

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

readDimensionality

private boolean readDimensionality()
                            throws java.lang.Exception

Throws:

java.lang.Exception

readSpaceGroup

private void readSpaceGroup()
                     throws java.lang.Exception

Throws:

java.lang.Exception

parameterIndex

private static int parameterIndex(java.lang.String key)

setParameter

private void setParameter(java.lang.String key,
                float value)

newAtomSet

private void newAtomSet(boolean doSetUnitCell)

setModelParameters

private void setModelParameters(boolean isPrimitive)

readCellParameters

private void readCellParameters(boolean isLatticeVectors)
                         throws java.lang.Exception

Throws:

java.lang.Exception

readFinalCell

private void readFinalCell()
                    throws java.lang.Exception

Throws:

java.lang.Exception

scalePrimitiveData

private void scalePrimitiveData(int i,
                      float value)

applySymmetryAndSetTrajectory

public void applySymmetryAndSetTrajectory()
                                   throws java.lang.Exception

Overrides:

applySymmetryAndSetTrajectory in class AtomSetCollectionReader

Throws:

java.lang.Exception

readAtomicPos

private void readAtomicPos(boolean finalizeSymmetry)
                    throws java.lang.Exception

Throws:

java.lang.Exception

readPartialCharges

private void readPartialCharges()
                         throws java.lang.Exception

Throws:

java.lang.Exception

readEnergy

private void readEnergy()
                 throws java.lang.Exception

Throws:

java.lang.Exception

setEnergy

private void setEnergy()