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

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

Field Summary

Fields

Modifier and Type	Field	Description
private String	aabb
private Map<String,float[]>	compositions
private int	fileModelNumber
private float	fracB
private boolean	getComposition
private boolean	havePRE
private Map<String,String>	keyMap
private String	listKey
private String	listKeyCase
private boolean	readPRE
private String	titleMsg

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, 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, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors

Constructor	Description
AFLOWReader()

Method Summary

Modifier and Type	Method	Description
private void	alignUnitCells()
protected boolean	checkLine()
private String	cleanKey(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()

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, 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, setupASCR

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

aabb

private String aabb

readPRE

private boolean readPRE

fracB

private float fracB

compositions

private Map<String,float[]> compositions

getComposition

private boolean getComposition

listKey

private String listKey

listKeyCase

private String listKeyCase

fileModelNumber

private int fileModelNumber

havePRE

private boolean havePRE

titleMsg

private String titleMsg

keyMap

private Map<String,String> keyMap

Constructor Detail

AFLOWReader

public AFLOWReader()

Method Detail

initializeReader

protected void initializeReader()
                         throws Exception

Overrides:

initializeReader in class VaspPoscarReader

Throws:

Exception

checkLine

protected boolean checkLine()
                     throws Exception

Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

Exception

readPrePost

private boolean readPrePost()
                     throws Exception

Throws:

Exception

finalizeModel

private void finalizeModel()
                    throws Exception

Throws:

Exception

readElementLabelsOnly

private void readElementLabelsOnly()
                            throws Exception

scan the AFLOWReader PRE structure for elements in coord section

Throws:

Exception

getData

private boolean getData()
                 throws Exception

Throws:

Exception

cleanKey

private String cleanKey(String key)

cleans key to just letters and digits

Parameters:

key -

Returns:

cleaned key

finalizeSubclassReader

protected void finalizeSubclassReader()
                               throws Exception

Description copied from class: AtomSetCollectionReader

optional reader-specific method run first.

Overrides:

finalizeSubclassReader in class VaspPoscarReader

Throws:

Exception

listCompositions

private void listCompositions()

alignUnitCells

private void alignUnitCells()