org.jmol.adapter.readers.xtal
Class VaspOutcarReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by 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

Field Summary
private  int atomCount
           
private  java.lang.String[] atomNames
           
private  java.lang.Double electronEne
           
private  java.util.ArrayList<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
           
private  float[] unitCellData
           
 
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
 
Constructor Summary
VaspOutcarReader()
           
 
Method Summary
protected  boolean checkLine()
           
protected  void finalizeReader()
           
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()
           
private  void setUnitCell()
           
 
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
 

Field Detail

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
Constructor Detail

VaspOutcarReader

public VaspOutcarReader()
Method Detail

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