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 int
protected javajs.util.Lst
<String> private boolean
protected String[]
protected String[]
(package private) int
private boolean
protected boolean
(package private) int
private float
protected String
private 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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected void
optional reader-specific method run first.protected String
getElement
(String token) allow for any number of characters, for which the first one or two are an element symbol.protected void
protected String
rdline()
protected void
protected void
try various ways to read the optional atom labels.protected void
readStructure
(String titleMsg) protected void
Methods 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:
initializeReader
in classAtomSetCollectionReader
- Throws:
Exception
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readStructure
- Throws:
Exception
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finalizeSubclassReader
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in 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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