AFLOWReader

java.lang.Object
- org.jmol.adapter.smarter.AtomSetCollectionReader
- - org.jmol.adapter.readers.xtal.VaspPoscarReader
  - - org.jmol.adapter.readers.aflow.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 and 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, 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, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors
Constructor and Description

AFLOWReader()

Constructors
Constructor and Description
`AFLOWReader()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and 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, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, 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()
```

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 Detail

aabb

readPRE

fracB

compositions

getComposition

listKey

listKeyCase

fileModelNumber

havePRE

titleMsg

keyMap

Constructor Detail

AFLOWReader

Method Detail

initializeReader

checkLine

readPrePost

finalizeModel

readElementLabelsOnly

getData

cleanKey

finalizeSubclassReader

listCompositions

alignUnitCells