org.jmol.adapter.readers.xtal

Class VaspPoscarReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.xtal.VaspPoscarReader

public class VaspPoscarReader
extends AtomSetCollectionReader

http://cms.mpi.univie.ac.at/vasp/

Version:

1.0

Author:

Pieremanuele Canepa, Wake Forest University, Department of Physics Winston Salem, NC 27106, canepap@wfu.edu

Field Summary

Fields

Modifier and Type	Field and Description
private int	atomCount
private JmolList<java.lang.String>	atomLabels

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

addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterAtomTypeStr, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, mustFinalizeModelSet, next, notionalUnitCell, os, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer

Constructor Summary

Constructors

Constructor and Description
VaspPoscarReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected void	initializeReader()
private void	readCoordinates()
private void	readJobTitle()
private void	readMolecularFormula()
private void	readUnitCellVectors()

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

addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReader, finalizeReaderASCR, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokensAt, getTokensFloat, getTokensStr, initializeSymmetry, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseStringInfestedFloatArray, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, parseTrimmedAt, parseTrimmedRange, processBinaryDocument, processDOM, read3Vectors, readDataObject, readLine, readLines, RL, set2D, setAtomCoord, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFractionalCoordinates, setIsPDB, setLoadNote, setPdb, 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

atomLabels

private JmolList<java.lang.String> atomLabels

atomCount

private int atomCount

Constructor Detail

VaspPoscarReader

public VaspPoscarReader()

Method Detail

initializeReader

protected void initializeReader()
                         throws java.lang.Exception

Overrides:

initializeReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

readJobTitle

private void readJobTitle()
                   throws java.lang.Exception

Throws:

java.lang.Exception

readUnitCellVectors

private void readUnitCellVectors()
                          throws java.lang.Exception

Throws:

java.lang.Exception

readMolecularFormula

private void readMolecularFormula()
                           throws java.lang.Exception

Throws:

java.lang.Exception

readCoordinates

private void readCoordinates()
                      throws java.lang.Exception

Throws:

java.lang.Exception