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
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 |
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 |
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
GulpReader
public GulpReader()
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()