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

Nested Class Summary

Nested classes/interfaces inherited from class org.jmol.adapter.readers.xml.XmlReader

XmlReader.DummyResolver, XmlReader.JmolXmlHandler

Field Summary

Fields

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

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

atom, chars, implementedAttributes, 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, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, ptSupercell, reader, readerName, readMolecularOrbitals, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer

Constructor Summary

Constructors

Constructor and Description
XmlVaspReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected java.lang.String[]	getImplementedAttributes()
void	processEndElement(java.lang.String uri, java.lang.String localName, java.lang.String qName)
void	processStartElement(java.lang.String namespaceURI, java.lang.String localName, java.lang.String qName, java.util.Map<java.lang.String,java.lang.String> atts)
protected void	processXml(XmlReader parent, AtomSetCollection atomSetCollection, java.io.BufferedReader reader, java.lang.Object xmlReader, XmlReader.JmolXmlHandler handler)

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

applySymmetryAndSetTrajectory, getHandler, initializeReader, parseReaderXML, processXml, setKeepChars

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

addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, checkFilter, checkLastModel, checkLine, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processBinaryDocument, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setElementAndIsotope, 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

vaspImplementedAttributes

java.lang.String[] vaspImplementedAttributes

data

private java.lang.StringBuffer data

name

private java.lang.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 java.lang.String enthalpy

gibbsEnergy

private java.lang.String gibbsEnergy

haveUnitCell

boolean haveUnitCell

atomNames

java.lang.String[] atomNames

atomSyms

java.lang.String[] atomSyms

atomName

java.lang.String atomName

atomSym

java.lang.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

getImplementedAttributes

protected java.lang.String[] getImplementedAttributes()

Overrides:

getImplementedAttributes in class XmlReader

processXml

protected void processXml(XmlReader parent,
              AtomSetCollection atomSetCollection,
              java.io.BufferedReader reader,
              java.lang.Object xmlReader,
              XmlReader.JmolXmlHandler handler)

Overrides:

processXml in class XmlReader

processStartElement

public void processStartElement(java.lang.String namespaceURI,
                       java.lang.String localName,
                       java.lang.String qName,
                       java.util.Map<java.lang.String,java.lang.String> atts)

Overrides:

processStartElement in class XmlReader

processEndElement

public void processEndElement(java.lang.String uri,
                     java.lang.String localName,
                     java.lang.String qName)

Overrides:

processEndElement in class XmlReader