org.jmol.adapter.readers.xtal
Class VaspOutcarReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.xtal.VaspOutcarReader
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
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, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, 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 |
atomNames
private java.lang.String[] atomNames
elementNames
private java.util.ArrayList<java.lang.String> elementNames
atomCount
private int atomCount
inputOnly
private boolean inputOnly
mDsimulation
private boolean mDsimulation
isVersion5
private boolean isVersion5
unitCellData
private float[] unitCellData
gibbsEnergy
private java.lang.Double gibbsEnergy
gibbsEntropy
private java.lang.Double gibbsEntropy
electronEne
private java.lang.Double electronEne
kinEne
private java.lang.Double kinEne
totEne
private java.lang.Double totEne
temp
private float temp
VaspOutcarReader
public VaspOutcarReader()
initializeReader
protected void initializeReader()
- Overrides:
initializeReader
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
finalizeReader
protected void finalizeReader()
throws java.lang.Exception
- Overrides:
finalizeReader
in class AtomSetCollectionReader
- Throws:
java.lang.Exception
readElementNames
private void readElementNames()
throws java.lang.Exception
- Throws:
java.lang.Exception
readAtomCountAndSetNames
private void readAtomCountAndSetNames()
throws java.lang.Exception
- Throws:
java.lang.Exception
readUnitCellVectors
private void readUnitCellVectors()
throws java.lang.Exception
- Throws:
java.lang.Exception
setUnitCell
private void setUnitCell()
setSymmetry
private void setSymmetry()
throws java.lang.Exception
- Throws:
java.lang.Exception
readInitialCoordinates
private void readInitialCoordinates()
throws java.lang.Exception
- Throws:
java.lang.Exception
readPOSITION
private void readPOSITION()
throws java.lang.Exception
- Throws:
java.lang.Exception
readEnergy
private void readEnergy()
throws java.lang.Exception
- Throws:
java.lang.Exception
setAtomSetInfo
private void setAtomSetInfo()
readMdyn
private void readMdyn()
throws java.lang.Exception
- Throws:
java.lang.Exception
setAtomSetInfoMd
private void setAtomSetInfoMd()
readFrequency
private void readFrequency()
throws java.lang.Exception
- Throws:
java.lang.Exception