Package org.jmol.adapter.readers.xtal
Class VaspPoscarReader
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetCollectionReader
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- org.jmol.adapter.readers.xtal.VaspPoscarReader
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- All Implemented Interfaces:
javajs.api.GenericLineReader
- Direct Known Subclasses:
AFLOWReader
,VaspChgcarReader
public class VaspPoscarReader extends AtomSetCollectionReader
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
Fields Modifier and Type Field Description protected int
ac
protected javajs.util.Lst<java.lang.String>
atomLabels
private boolean
atomsLabeledInline
protected java.lang.String[]
defaultLabels
protected java.lang.String[]
elementLabel
(package private) int
elementPt
private boolean
haveAtomLabels
protected boolean
quiet
(package private) int
radiusPt
private float
scaleFac
protected java.lang.String
title
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Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, 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, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors Constructor Description VaspPoscarReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
finalizeSubclassReader()
optional reader-specific method run first.protected java.lang.String
getElement(java.lang.String token)
allow for any number of characters, for which the first one or two are an element symbol.protected void
initializeReader()
protected java.lang.String
rdline()
protected void
readCoordinates()
protected void
readMolecularFormula()
try various ways to read the optional atom labels.protected void
readStructure(java.lang.String titleMsg)
protected void
readUnitCellVectors()
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Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, 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, 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 Detail
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atomLabels
protected javajs.util.Lst<java.lang.String> atomLabels
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haveAtomLabels
private boolean haveAtomLabels
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atomsLabeledInline
private boolean atomsLabeledInline
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scaleFac
private float scaleFac
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ac
protected int ac
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title
protected java.lang.String title
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quiet
protected boolean quiet
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defaultLabels
protected java.lang.String[] defaultLabels
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elementLabel
protected java.lang.String[] elementLabel
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radiusPt
int radiusPt
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elementPt
int elementPt
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Method Detail
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initializeReader
protected void initializeReader() throws java.lang.Exception
- Overrides:
initializeReader
in classAtomSetCollectionReader
- Throws:
java.lang.Exception
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readStructure
protected void readStructure(java.lang.String titleMsg) throws java.lang.Exception
- Throws:
java.lang.Exception
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finalizeSubclassReader
protected void finalizeSubclassReader() throws java.lang.Exception
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classAtomSetCollectionReader
- Throws:
java.lang.Exception
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readUnitCellVectors
protected void readUnitCellVectors() throws java.lang.Exception
- Throws:
java.lang.Exception
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readMolecularFormula
protected void readMolecularFormula() throws java.lang.Exception
try various ways to read the optional atom labels. There is no convention here.- Throws:
java.lang.Exception
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readCoordinates
protected void readCoordinates() throws java.lang.Exception
- Throws:
java.lang.Exception
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getElement
protected java.lang.String getElement(java.lang.String token)
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
protected java.lang.String rdline() throws java.lang.Exception
- Throws:
java.lang.Exception
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