Package org.jmol.adapter.readers.xtal

Class VaspOutcarReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.xtal.VaspOutcarReader

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

Field Summary

Fields

Modifier and Type	Field	Description
private int	ac
private String[]	atomNames
private Double	electronEne
private javajs.util.Lst<String>	elementNames
private Double	gibbsEnergy
private Double	gibbsEntropy
private boolean	inputOnly
private boolean	isVersion5
private Double	kinEne
private boolean	mDsimulation
private float	temp
private Double	totEne

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

addedData, addedDataKey, addVibrations, allow_a_len_1, 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, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors

Constructor	Description
VaspOutcarReader()

Method Summary

Modifier and Type	Method	Description
protected boolean	checkLine()
protected void	finalizeSubclassReader()	optional reader-specific method run first.
private String	fixMinus(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()

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

Methods inherited from class java.lang.Object

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

Field Detail

atomNames

private String[] atomNames

ac

private int ac

inputOnly

private boolean inputOnly

mDsimulation

private boolean mDsimulation

isVersion5

private boolean isVersion5

elementNames

private javajs.util.Lst<String> elementNames

gibbsEnergy

private Double gibbsEnergy

gibbsEntropy

private Double gibbsEntropy

electronEne

private Double electronEne

kinEne

private Double kinEne

totEne

private Double totEne

temp

private float temp

Constructor Detail

VaspOutcarReader

public VaspOutcarReader()

Method Detail

initializeReader

protected void initializeReader()

Overrides:

initializeReader in class AtomSetCollectionReader

checkLine

protected boolean checkLine()
                     throws Exception

Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

Exception

finalizeSubclassReader

protected void finalizeSubclassReader()
                               throws Exception

Description copied from class: AtomSetCollectionReader

optional reader-specific method run first.

Overrides:

finalizeSubclassReader in class AtomSetCollectionReader

Throws:

Exception

readElementNames

private void readElementNames()
                       throws Exception

Throws:

Exception

readAtomCountAndSetNames

private void readAtomCountAndSetNames()
                               throws Exception

Throws:

Exception

readUnitCellVectors

private void readUnitCellVectors()
                          throws Exception

Throws:

Exception

fixMinus

private String fixMinus(String line)

setSymmetry

private void setSymmetry()
                  throws Exception

Throws:

Exception

readInitialCoordinates

private void readInitialCoordinates()
                             throws Exception

Throws:

Exception

readPOSITION

private void readPOSITION()
                   throws Exception

Throws:

Exception

readEnergy

private void readEnergy()
                 throws Exception

Throws:

Exception

setAtomSetInfo

private void setAtomSetInfo()

readMdyn

private void readMdyn()
               throws Exception

Throws:

Exception

setAtomSetInfoMd

private void setAtomSetInfoMd()

readFrequency

private void readFrequency()
                    throws Exception

Throws:

Exception