org.jmol.adapter.readers.xml

Class XmlVaspReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.xml.XmlReader

org.jmol.adapter.readers.xml.XmlVaspReader

public class XmlVaspReader
extends XmlReader

Vasp vasprun.xml reader

Author:

hansonr

Field Summary

Fields

Modifier and Type	Field and Description
(package private) float	a
(package private) float	alpha
private int	atomCount
(package private) String	atomName
(package private) String[]	atomNames
(package private) String	atomSym
(package private) String[]	atomSyms
(package private) float	b
(package private) float	beta
(package private) float	c
private javajs.util.SB	data
private String	enthalpy
(package private) float	gamma
private String	gibbsEnergy
(package private) boolean	haveUnitCell
private int	iAtom
private boolean	isE_fr_energy
private boolean	isE_wo_entrp
private String[]	myAttributes
private String	name

Fields inherited from class org.jmol.adapter.readers.xml.XmlReader

atom, atts, chars, domAttributes, keepChars, parent

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, filterHetero, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer

Constructor Summary

Constructors

Constructor and Description
XmlVaspReader()

Method Summary

Modifier and Type	Method and Description
protected String[]	getDOMAttributes()
(package private) void	processEndElement(String localName)
void	processStartElement(String localName)
protected void	processXml(XmlReader parent, Object saxReader)

Methods inherited from class org.jmol.adapter.readers.xml.XmlReader

applySymmetryAndSetTrajectory, initializeReader, processDOM, PX, setKeepChars

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

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

Methods inherited from class java.lang.Object

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

Field Detail

data

private javajs.util.SB data

name

private String name

atomCount

private int atomCount

iAtom

private int iAtom

isE_wo_entrp

private boolean isE_wo_entrp

isE_fr_energy

private boolean isE_fr_energy

enthalpy

private String enthalpy

gibbsEnergy

private String gibbsEnergy

myAttributes

private String[] myAttributes

haveUnitCell

boolean haveUnitCell

atomNames

String[] atomNames

atomSyms

String[] atomSyms

atomName

String atomName

atomSym

String atomSym

a

float a

b

float b

c

float c

alpha

float alpha

beta

float beta

gamma

float gamma

Constructor Detail

XmlVaspReader

XmlVaspReader()

Method Detail

getDOMAttributes

protected String[] getDOMAttributes()

Overrides:

getDOMAttributes in class XmlReader

processXml

protected void processXml(XmlReader parent,
                          Object saxReader)
                   throws Exception

Overrides:

processXml in class XmlReader

Throws:

Exception

processStartElement

public void processStartElement(String localName)

Overrides:

processStartElement in class XmlReader

processEndElement

void processEndElement(String localName)

Overrides:

processEndElement in class XmlReader