VaspPoscarReader

java.lang.Object
- org.jmol.adapter.smarter.AtomSetCollectionReader
- - org.jmol.adapter.readers.xtal.VaspPoscarReader

All Implemented Interfaces:

javajs.api.GenericLineReader

Direct Known Subclasses:

AFLOWReader, VaspChgcarReader
```
public class VaspPoscarReader
extends AtomSetCollectionReader
```
adjusted for AFLOW options - adding element names, environment radius on atom line http://cms.mpi.univie.ac.at/vasp/

Version:

1.0

Author:

Pieremanuele Canepa, Wake Forest University, Department of Physics Winston Salem, NC 27106, canepap@wfu.edu (pcanepa@mit.edu), Bob Hanson

Field Summary

Fields
Modifier and Type	Field and Description
`protected int`	`ac`
`protected javajs.util.Lst<String>`	`atomLabels`
`private boolean`	`atomsLabeledInline`
`protected String[]`	`defaultLabels`
`protected String[]`	`elementLabel`
`(package private) int`	`elementPt`
`private boolean`	`haveAtomLabels`
`protected boolean`	`quiet`
`(package private) int`	`radiusPt`
`private float`	`scaleFac`
`protected String`	`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

VaspPoscarReader()

Constructors
Constructor and Description
`VaspPoscarReader()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected void`	`finalizeSubclassReader()` optional reader-specific method run first.
`protected String`	`getElement(String token)` allow for any number of characters, for which the first one or two are an element symbol.
`protected void`	`initializeReader()`
`protected String`	`rdline()`
`protected void`	`readCoordinates()`
`protected void`	`readMolecularFormula()` try various ways to read the optional atom labels.
`protected void`	`readStructure(String titleMsg)`
`protected void`	`readUnitCellVectors()`

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, 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

atomLabels

protected javajs.util.Lst<String> atomLabels

haveAtomLabels
```
private boolean haveAtomLabels
```

atomsLabeledInline
```
private boolean atomsLabeledInline
```

scaleFac
```
private float scaleFac
```

ac
```
protected int ac
```

title
```
protected String title
```

quiet
```
protected boolean quiet
```

defaultLabels
```
protected String[] defaultLabels
```

elementLabel
```
protected String[] elementLabel
```

radiusPt
```
int radiusPt
```

elementPt
```
int elementPt
```

Constructor Detail
- VaspPoscarReader
```
public VaspPoscarReader()
```

Method Detail
- initializeReader
```
protected void initializeReader()
                         throws Exception
```
  Overrides:
  
  initializeReader in class AtomSetCollectionReader
  
  Throws:
  
  Exception
- readStructure
```
protected void readStructure(String titleMsg)
                      throws Exception
```
  Throws:
  
  Exception
- finalizeSubclassReader
```
protected void finalizeSubclassReader()
                               throws Exception
```
  Description copied from class: AtomSetCollectionReader
  
  optional reader-specific method run first.
  
  Overrides:
  
  finalizeSubclassReader in class AtomSetCollectionReader
  
  Throws:
  
  Exception
- readUnitCellVectors
```
protected void readUnitCellVectors()
                            throws Exception
```
  Throws:
  
  Exception
- readMolecularFormula
```
protected void readMolecularFormula()
                             throws Exception
```
  try various ways to read the optional atom labels. There is no convention here.
  
  Throws:
  
  Exception
- readCoordinates
```
protected void readCoordinates()
                        throws Exception
```
  Throws:
  
  Exception
- getElement
```
protected String getElement(String token)
```
  allow for any number of characters, for which the first one or two are an element symbol.
  
  Parameters:
  
  token -
  
  Returns:
  
  element symbol
- rdline
```
protected String rdline()
                 throws Exception
```
  Throws:
  
  Exception

Class VaspPoscarReader

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Detail

atomLabels

haveAtomLabels

atomsLabeledInline

scaleFac

ac

title

quiet

defaultLabels

elementLabel

radiusPt

elementPt

Constructor Detail

VaspPoscarReader

Method Detail

initializeReader

readStructure

finalizeSubclassReader

readUnitCellVectors

readMolecularFormula

readCoordinates

getElement

rdline