public class VaspOutcarReader extends AtomSetCollectionReader
Modifier and Type | Field and Description |
---|---|
private int |
ac |
private java.lang.String[] |
atomNames |
private java.lang.Double |
electronEne |
private javajs.util.Lst<java.lang.String> |
elementNames |
private java.lang.Double |
gibbsEnergy |
private java.lang.Double |
gibbsEntropy |
private boolean |
inputOnly |
private boolean |
isVersion5 |
private java.lang.Double |
kinEne |
private boolean |
mDsimulation |
private float |
temp |
private java.lang.Double |
totEne |
private float[] |
unitCellData |
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, validation, vibrationNumber, vibsFractional, vwr
Constructor and Description |
---|
VaspOutcarReader() |
Modifier and Type | Method and Description |
---|---|
protected boolean |
checkLine() |
protected void |
finalizeSubclassReader()
optional reader-specific method run first.
|
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() |
private void |
setUnitCell() |
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassSymmetry, forceSymmetry, 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, processDSSR, 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 java.lang.String[] atomNames
private int ac
private boolean inputOnly
private boolean mDsimulation
private boolean isVersion5
private javajs.util.Lst<java.lang.String> elementNames
private float[] unitCellData
private java.lang.Double gibbsEnergy
private java.lang.Double gibbsEntropy
private java.lang.Double electronEne
private java.lang.Double kinEne
private java.lang.Double totEne
private float temp
protected void initializeReader()
initializeReader
in class AtomSetCollectionReader
protected boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
protected void finalizeSubclassReader() throws java.lang.Exception
AtomSetCollectionReader
finalizeSubclassReader
in class AtomSetCollectionReader
java.lang.Exception
private void readElementNames() throws java.lang.Exception
java.lang.Exception
private void readAtomCountAndSetNames() throws java.lang.Exception
java.lang.Exception
private void readUnitCellVectors() throws java.lang.Exception
java.lang.Exception
private void setUnitCell()
private void setSymmetry() throws java.lang.Exception
java.lang.Exception
private void readInitialCoordinates() throws java.lang.Exception
java.lang.Exception
private void readPOSITION() throws java.lang.Exception
java.lang.Exception
private void readEnergy() throws java.lang.Exception
java.lang.Exception
private void setAtomSetInfo()
private void readMdyn() throws java.lang.Exception
java.lang.Exception
private void setAtomSetInfoMd()
private void readFrequency() throws java.lang.Exception
java.lang.Exception