Package org.jmol.adapter.readers.xml
Class XmlVaspReader
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetCollectionReader
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- org.jmol.adapter.readers.xml.XmlReader
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- org.jmol.adapter.readers.xml.XmlVaspReader
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- All Implemented Interfaces:
javajs.api.GenericLineReader
public class XmlVaspReader extends XmlReader
Vasp vasprun.xml reader- Author:
- hansonr
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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
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Fields inherited from class org.jmol.adapter.readers.xml.XmlReader
atom, atts, bond, chars, keepChars, parent
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Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors Constructor Description XmlVaspReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description (package private) void
processEndElement(String localName)
void
processStartElement(String localName, String nodeName)
protected void
processXml(XmlReader parent, Object saxReader)
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Methods inherited from class org.jmol.adapter.readers.xml.XmlReader
applySymmetryAndSetTrajectory, createDomNodeJS, endDocument, initCML, initializeReader, processDOM, processXml2, setKeepChars
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Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymTrajASCR, 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, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, 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
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Field Detail
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data
private javajs.util.SB data
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name
private String name
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ac
private int ac
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iAtom
private int iAtom
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isE_wo_entrp
private boolean isE_wo_entrp
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isE_fr_energy
private boolean isE_fr_energy
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enthalpy
private String enthalpy
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gibbsEnergy
private String gibbsEnergy
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haveUnitCell
boolean haveUnitCell
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atomNames
String[] atomNames
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atomSyms
String[] atomSyms
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atomName
String atomName
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atomSym
String atomSym
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a
float a
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b
float b
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c
float c
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alpha
float alpha
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beta
float beta
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gamma
float gamma
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Method Detail
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processXml
protected void processXml(XmlReader parent, Object saxReader) throws Exception
- Overrides:
processXml
in classXmlReader
- Throws:
Exception
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processStartElement
public void processStartElement(String localName, String nodeName)
- Overrides:
processStartElement
in classXmlReader
nodeName
- TODO
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processEndElement
void processEndElement(String localName)
- Overrides:
processEndElement
in classXmlReader
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