public class VaspOutcarReader extends AtomSetCollectionReader
Modifier and Type | Field and Description |
---|---|
private int |
ac |
private String[] |
atomNames |
private Double |
electronEne |
private javajs.util.Lst<String> |
elementNames |
private Double |
gibbsEnergy |
private Double |
gibbsEntropy |
private boolean |
inputOnly |
private boolean |
isVersion5 |
private Double |
kinEne |
private boolean |
mDsimulation |
private float |
temp |
private Double |
totEne |
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
Constructor and Description |
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VaspOutcarReader() |
Modifier and Type | Method and Description |
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protected boolean |
checkLine() |
protected void |
finalizeSubclassReader()
optional reader-specific method run first.
|
private String |
fixMinus(String line) |
protected void |
initializeReader() |
private void |
readAtomCountAndSetNames() |
private void |
readElementNames() |
private void |
readEnergy() |
private void |
readFrequency() |
private void |
readInitialCoordinates() |
private void |
readMdyn() |
private void |
readPOSITION() |
private void |
readUnitCellVectors() |
private void |
setAtomSetInfo() |
private void |
setAtomSetInfoMd() |
private void |
setSymmetry() |
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, 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
private String[] atomNames
private int ac
private boolean inputOnly
private boolean mDsimulation
private boolean isVersion5
private javajs.util.Lst<String> elementNames
private Double gibbsEnergy
private Double gibbsEntropy
private Double electronEne
private Double kinEne
private Double totEne
private float temp
protected void initializeReader()
initializeReader
in class AtomSetCollectionReader
protected boolean checkLine() throws Exception
checkLine
in class AtomSetCollectionReader
Exception
protected void finalizeSubclassReader() throws Exception
AtomSetCollectionReader
finalizeSubclassReader
in class AtomSetCollectionReader
Exception
private void setAtomSetInfo()
private void setAtomSetInfoMd()