Package org.jmol.adapter.readers.more
Class AFLOWReader
- 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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- org.jmol.adapter.readers.more.AFLOWReader
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- All Implemented Interfaces:
javajs.api.GenericLineReader
public class AFLOWReader extends VaspPoscarReader
A reader for various AFLOW file types. For starters, we have output from the binaries page. see http://www.aflowlib.org/binary_alloys.php or, in Jmol, from: print load("http://aflowlib.mems.duke.edu/php/apool.php?POST?job=awrapper_apool&lattice=all&alloy=AgAu") Unit cells are centered. Selected compositions can be obtained using the filter "Ca=0.5" for example.- Version:
- 1.0
- Author:
- Bob Hanson
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Field Summary
Fields Modifier and Type Field 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
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Fields inherited from class org.jmol.adapter.readers.xtal.VaspPoscarReader
ac, atomLabels, defaultLabels, elementLabel, quiet, title
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Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterCased, 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, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noPack, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors Constructor Description AFLOWReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description private void
alignUnitCells()
protected boolean
checkLine()
private java.lang.String
cleanKey(java.lang.String key)
cleans key to just letters and digitsprivate 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 sectionprivate boolean
readPrePost()
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Methods inherited from class org.jmol.adapter.readers.xtal.VaspPoscarReader
getElement, rdline, readCoordinates, readMolecularFormula, readStructure, readUnitCellVectors
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Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkAndRemoveFilterKey, 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, getFilterWithCase, 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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aabb
private java.lang.String aabb
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readPRE
private boolean readPRE
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fracB
private float fracB
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compositions
private java.util.Map<java.lang.String,float[]> compositions
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getComposition
private boolean getComposition
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listKey
private java.lang.String listKey
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listKeyCase
private java.lang.String listKeyCase
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fileModelNumber
private int fileModelNumber
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havePRE
private boolean havePRE
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titleMsg
private java.lang.String titleMsg
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keyMap
private java.util.Map<java.lang.String,java.lang.String> keyMap
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Method Detail
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initializeReader
protected void initializeReader() throws java.lang.Exception
- Overrides:
initializeReader
in classVaspPoscarReader
- Throws:
java.lang.Exception
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checkLine
protected boolean checkLine() throws java.lang.Exception
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
java.lang.Exception
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readPrePost
private boolean readPrePost() throws java.lang.Exception
- Throws:
java.lang.Exception
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finalizeModel
private void finalizeModel() throws java.lang.Exception
- Throws:
java.lang.Exception
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readElementLabelsOnly
private void readElementLabelsOnly() throws java.lang.Exception
scan the AFLOWReader PRE structure for elements in coord section- Throws:
java.lang.Exception
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getData
private boolean getData() throws java.lang.Exception
- Throws:
java.lang.Exception
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cleanKey
private java.lang.String cleanKey(java.lang.String key)
cleans key to just letters and digits- Parameters:
key
-- Returns:
- cleaned key
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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 classVaspPoscarReader
- Throws:
java.lang.Exception
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listCompositions
private void listCompositions()
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alignUnitCells
private void alignUnitCells()
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