org.jmol.adapter.readers.xml.XmlVaspReader

All Implemented Interfaces:: javajs.api.GenericLineReader

public class XmlVaspReader extends XmlReader

Vasp vasprun.xml reader

Author:: hansonr

Field Summary

Fields

Modifier and Type

Field

Description

(package private) float

a

private int

ac

(package private) float

alpha

(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

name

Fields inherited from class org.jmol.adapter.readers.xml.XmlReader
atom, atts, bond, chars, keepChars, parent

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noPack, optimize2D, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
Constructor Summary

Constructors

Constructor

Description

XmlVaspReader()
Method Summary

Modifier and Type

Method

Description

(package private) void

processEndElement(String localName)

void

processStartElement(String localName, String nodeName)

protected void

processXml(XmlReader parent, Object saxReader)

Methods inherited from class org.jmol.adapter.readers.xml.XmlReader
applySymmetryAndSetTrajectory, createDomNodeJS, endDocument, finalizeSubclassReader, initializeReader, processDOM, processXml2, setKeepChars

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymTrajASCR, checkAndRemoveFilterKey, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, processBinaryDocument, rd, read3Vectors, readDataObject, readLines, readNextLine, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setModelPDB, 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 Details
- data
  
  private javajs.util.SB data
- name
  
  private String name
- ac
  
  private int ac
- 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
- 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 Details
- XmlVaspReader
  
  public XmlVaspReader()
Method Details
- processXml
  
  protected void processXml(XmlReader parent, Object saxReader) throws Exception
  
  Overrides:
  
  processXml in class XmlReader
  
  Throws:
  
  Exception
- processStartElement
  
  public void processStartElement(String localName, String nodeName)
  
  Overrides:
  
  processStartElement in class XmlReader
  
  nodeName - TODO
- processEndElement
  
  void processEndElement(String localName)
  
  Overrides:
  
  processEndElement in class XmlReader

Class XmlVaspReader

Field Summary

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

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

Constructor Summary

Method Summary

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

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

Methods inherited from class java.lang.Object

Field Details

data

name

ac

iAtom

isE_wo_entrp

isE_fr_energy

enthalpy

gibbsEnergy

haveUnitCell

atomNames

atomSyms

atomName

atomSym

a

b

c

alpha

beta

gamma

Constructor Details

XmlVaspReader

Method Details

processXml

processStartElement

processEndElement