Package org.jmol.adapter.readers.xtal
Class VaspPoscarReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.xtal.VaspPoscarReader
- All Implemented Interfaces:
javajs.api.GenericLineReader
- Direct Known Subclasses:
AFLOWReader,VaspChgcarReader
adjusted for AFLOW options - adding element names, environment radius on atom line
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 (pcanepa@mit.edu), Bob Hanson
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected intprotected javajs.util.Lst<String>private booleanprotected String[]protected String[](package private) intprivate booleanprotected boolean(package private) intprivate floatprotected Stringprivate float[]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 -
Method Summary
Modifier and TypeMethodDescriptionprotected voidoptional reader-specific method run first.protected StringgetElement(String token) allow for any number of characters, for which the first one or two are an element symbol.protected voidprotected Stringrdline()protected voidprotected voidtry various ways to read the optional atom labels.protected voidreadStructure(String titleMsg) protected voidMethods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, 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, processDOM, 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 Details
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atomLabels
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haveAtomLabels
private boolean haveAtomLabels -
atomsLabeledInline
private boolean atomsLabeledInline -
scaleFac
private float scaleFac -
ac
protected int ac -
title
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quiet
protected boolean quiet -
defaultLabels
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unitCellData
private float[] unitCellData -
elementLabel
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radiusPt
int radiusPt -
elementPt
int elementPt
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Constructor Details
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VaspPoscarReader
public VaspPoscarReader()
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Method Details
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initializeReader
- Overrides:
initializeReaderin classAtomSetCollectionReader- Throws:
Exception
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readStructure
- Throws:
Exception
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finalizeSubclassReader
Description copied from class:AtomSetCollectionReaderoptional reader-specific method run first.- Overrides:
finalizeSubclassReaderin classAtomSetCollectionReader- Throws:
Exception
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readUnitCellVectors
- Throws:
Exception
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readMolecularFormula
try various ways to read the optional atom labels. There is no convention here.- Throws:
Exception
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readCoordinates
- Throws:
Exception
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getElement
allow for any number of characters, for which the first one or two are an element symbol.- Parameters:
token-- Returns:
- element symbol
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rdline
- Throws:
Exception
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