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 Double

kinEne

private boolean

mDsimulation

private float

temp

private Double

totEne

private int

vaspVersion

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noPack, optimize2D, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, 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

readVersion()

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, checkAndRemoveFilterKey, 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, getFilterWithCase, 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 Details
- atomNames
  
  private String[] atomNames
- ac
  
  private int ac
- inputOnly
  
  private boolean inputOnly
- mDsimulation
  
  private boolean mDsimulation
- vaspVersion
  
  private int vaspVersion
- 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 Details
- VaspOutcarReader
  
  public VaspOutcarReader()
Method Details
- 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
- readVersion
  
  private void readVersion()
- 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

Class VaspOutcarReader

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Details

atomNames

ac

inputOnly

mDsimulation

vaspVersion

elementNames

gibbsEnergy

gibbsEntropy

electronEne

kinEne

totEne

temp

Constructor Details

VaspOutcarReader

Method Details

initializeReader

checkLine

readVersion

finalizeSubclassReader

readElementNames

readAtomCountAndSetNames

readUnitCellVectors

fixMinus

setSymmetry

readInitialCoordinates

readPOSITION

readEnergy

setAtomSetInfo

readMdyn

setAtomSetInfoMd

readFrequency