Package org.jmol.adapter.readers.more
Class AFLOWReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.xtal.VaspPoscarReader
org.jmol.adapter.readers.more.AFLOWReader
- All Implemented Interfaces:
javajs.api.GenericLineReader
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
-
Field Summary
FieldsModifier and TypeFieldDescriptionprivate String
private int
private float
private boolean
private boolean
private String
private String
private boolean
private String
Fields inherited from class org.jmol.adapter.readers.xtal.VaspPoscarReader
ac, atomLabels, defaultLabels, elementLabel, quiet, title
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, filterAllHetero, filterCased, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noPack, optimize2D, 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 -
Method Summary
Modifier and TypeMethodDescriptionprivate void
protected boolean
private String
cleans key to just letters and digitsprivate void
protected void
optional reader-specific method run first.private boolean
getData()
protected void
private void
private void
scan the AFLOWReader PRE structure for elements in coord sectionprivate boolean
Methods inherited from class org.jmol.adapter.readers.xtal.VaspPoscarReader
getElement, rdline, readCoordinates, readMolecularFormula, readStructure, readUnitCellVectors
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 Details
-
aabb
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readPRE
private boolean readPRE -
fracB
private float fracB -
compositions
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getComposition
private boolean getComposition -
listKey
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listKeyCase
-
fileModelNumber
private int fileModelNumber -
havePRE
private boolean havePRE -
titleMsg
-
keyMap
-
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Constructor Details
-
AFLOWReader
public AFLOWReader()
-
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Method Details
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initializeReader
- Overrides:
initializeReader
in classVaspPoscarReader
- Throws:
Exception
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checkLine
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
Exception
-
readPrePost
- Throws:
Exception
-
finalizeModel
- Throws:
Exception
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readElementLabelsOnly
scan the AFLOWReader PRE structure for elements in coord section- Throws:
Exception
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getData
- Throws:
Exception
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cleanKey
cleans key to just letters and digits- Parameters:
key
-- Returns:
- cleaned key
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finalizeSubclassReader
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classVaspPoscarReader
- Throws:
Exception
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listCompositions
private void listCompositions() -
alignUnitCells
private void alignUnitCells()
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