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 |
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, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, 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.
|
private java.lang.String |
fixMinus(java.lang.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, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, 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, 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, setupASCRprivate 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 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 AtomSetCollectionReaderprotected boolean checkLine()
throws java.lang.Exception
checkLine in class AtomSetCollectionReaderjava.lang.Exceptionprotected void finalizeSubclassReader()
throws java.lang.Exception
AtomSetCollectionReaderfinalizeSubclassReader in class AtomSetCollectionReaderjava.lang.Exceptionprivate void readElementNames()
throws java.lang.Exception
java.lang.Exceptionprivate void readAtomCountAndSetNames()
throws java.lang.Exception
java.lang.Exceptionprivate void readUnitCellVectors()
throws java.lang.Exception
java.lang.Exceptionprivate java.lang.String fixMinus(java.lang.String line)
private void setSymmetry()
throws java.lang.Exception
java.lang.Exceptionprivate void readInitialCoordinates()
throws java.lang.Exception
java.lang.Exceptionprivate void readPOSITION()
throws java.lang.Exception
java.lang.Exceptionprivate void readEnergy()
throws java.lang.Exception
java.lang.Exceptionprivate void setAtomSetInfo()
private void readMdyn()
throws java.lang.Exception
java.lang.Exceptionprivate void setAtomSetInfoMd()
private void readFrequency()
throws java.lang.Exception
java.lang.Exception