public class AFLOWReader extends VaspPoscarReader
| Modifier and Type | Field and Description |
|---|---|
private java.lang.String |
aabb |
private java.util.Map<java.lang.String,float[]> |
compositions |
private int |
fileModelNumber |
private float |
fracB |
private boolean |
getComposition |
private boolean |
havePRE |
private java.util.Map<java.lang.String,java.lang.String> |
keyMap |
private java.lang.String |
listKey |
private java.lang.String |
listKeyCase |
private boolean |
readPRE |
private java.lang.String |
titleMsg |
ac, atomLabels, defaultLabels, elementLabel, quiet, titleaddedData, 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 |
|---|
AFLOWReader() |
| Modifier and Type | Method and Description |
|---|---|
private void |
alignUnitCells() |
protected boolean |
checkLine() |
private java.lang.String |
cleanKey(java.lang.String key)
cleans key to just letters and digits
|
private void |
finalizeModel() |
protected void |
finalizeSubclassReader()
optional reader-specific method run first.
|
private boolean |
getData() |
protected void |
initializeReader() |
private void |
listCompositions() |
private void |
readElementLabelsOnly()
scan the AFLOWReader PRE structure for elements in coord section
|
private boolean |
readPrePost() |
getElement, rdline, readCoordinates, readMolecularFormula, readStructure, readUnitCellVectorsaddAtomXYZSymName, 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 aabb
private boolean readPRE
private float fracB
private java.util.Map<java.lang.String,float[]> compositions
private boolean getComposition
private java.lang.String listKey
private java.lang.String listKeyCase
private int fileModelNumber
private boolean havePRE
private java.lang.String titleMsg
private java.util.Map<java.lang.String,java.lang.String> keyMap
protected void initializeReader()
throws java.lang.Exception
initializeReader in class VaspPoscarReaderjava.lang.Exceptionprotected boolean checkLine()
throws java.lang.Exception
checkLine in class AtomSetCollectionReaderjava.lang.Exceptionprivate boolean readPrePost()
throws java.lang.Exception
java.lang.Exceptionprivate void finalizeModel()
throws java.lang.Exception
java.lang.Exceptionprivate void readElementLabelsOnly()
throws java.lang.Exception
java.lang.Exceptionprivate boolean getData()
throws java.lang.Exception
java.lang.Exceptionprivate java.lang.String cleanKey(java.lang.String key)
key - protected void finalizeSubclassReader()
throws java.lang.Exception
AtomSetCollectionReaderfinalizeSubclassReader in class VaspPoscarReaderjava.lang.Exceptionprivate void listCompositions()
private void alignUnitCells()