Package org.jmol.adapter.readers.xtal
Class VaspOutcarReader
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetCollectionReader
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- org.jmol.adapter.readers.xtal.VaspOutcarReader
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- All Implemented Interfaces:
javajs.api.GenericLineReader
public class VaspOutcarReader extends AtomSetCollectionReader
http://cms.mpi.univie.ac.at/vasp/- 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
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Field Summary
Fields Modifier and Type Field Description private int
ac
private java.lang.String[]
atomNames
private java.lang.Double
electronEne
private javajs.util.Lst<java.lang.String>
elementNames
private java.lang.Double
gibbsEnergy
private java.lang.Double
gibbsEntropy
private boolean
inputOnly
private boolean
isVersion5
private java.lang.Double
kinEne
private boolean
mDsimulation
private float
temp
private java.lang.Double
totEne
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Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors Constructor Description VaspOutcarReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected boolean
checkLine()
protected void
finalizeSubclassReader()
optional reader-specific method run first.private java.lang.String
fixMinus(java.lang.String line)
protected void
initializeReader()
private void
readAtomCountAndSetNames()
private void
readElementNames()
private void
readEnergy()
private void
readFrequency()
private void
readInitialCoordinates()
private void
readMdyn()
private void
readPOSITION()
private void
readUnitCellVectors()
private void
setAtomSetInfo()
private void
setAtomSetInfoMd()
private void
setSymmetry()
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Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, 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, 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
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Field Detail
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atomNames
private java.lang.String[] atomNames
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ac
private int ac
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inputOnly
private boolean inputOnly
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mDsimulation
private boolean mDsimulation
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isVersion5
private boolean isVersion5
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elementNames
private javajs.util.Lst<java.lang.String> elementNames
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gibbsEnergy
private java.lang.Double gibbsEnergy
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gibbsEntropy
private java.lang.Double gibbsEntropy
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electronEne
private java.lang.Double electronEne
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kinEne
private java.lang.Double kinEne
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totEne
private java.lang.Double totEne
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temp
private float temp
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Method Detail
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initializeReader
protected void initializeReader()
- Overrides:
initializeReader
in classAtomSetCollectionReader
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checkLine
protected boolean checkLine() throws java.lang.Exception
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
java.lang.Exception
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finalizeSubclassReader
protected void finalizeSubclassReader() throws java.lang.Exception
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classAtomSetCollectionReader
- Throws:
java.lang.Exception
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readElementNames
private void readElementNames() throws java.lang.Exception
- Throws:
java.lang.Exception
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readAtomCountAndSetNames
private void readAtomCountAndSetNames() throws java.lang.Exception
- Throws:
java.lang.Exception
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readUnitCellVectors
private void readUnitCellVectors() throws java.lang.Exception
- Throws:
java.lang.Exception
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fixMinus
private java.lang.String fixMinus(java.lang.String line)
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setSymmetry
private void setSymmetry() throws java.lang.Exception
- Throws:
java.lang.Exception
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readInitialCoordinates
private void readInitialCoordinates() throws java.lang.Exception
- Throws:
java.lang.Exception
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readPOSITION
private void readPOSITION() throws java.lang.Exception
- Throws:
java.lang.Exception
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readEnergy
private void readEnergy() throws java.lang.Exception
- Throws:
java.lang.Exception
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setAtomSetInfo
private void setAtomSetInfo()
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readMdyn
private void readMdyn() throws java.lang.Exception
- Throws:
java.lang.Exception
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setAtomSetInfoMd
private void setAtomSetInfoMd()
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readFrequency
private void readFrequency() throws java.lang.Exception
- Throws:
java.lang.Exception
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