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, 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
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, 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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- 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 Details
- AFLOWReader
  
  public AFLOWReader()
Method Details
- 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()

Class AFLOWReader

Field Summary

Fields inherited from class org.jmol.adapter.readers.xtal.VaspPoscarReader

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Constructor Summary

Method Summary

Methods inherited from class org.jmol.adapter.readers.xtal.VaspPoscarReader

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Methods inherited from class java.lang.Object

Field Details

aabb

readPRE

fracB

compositions

getComposition

listKey

listKeyCase

fileModelNumber

havePRE

titleMsg

keyMap

Constructor Details

AFLOWReader

Method Details

initializeReader

checkLine

readPrePost

finalizeModel

readElementLabelsOnly

getData

cleanKey

finalizeSubclassReader

listCompositions

alignUnitCells