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

VaspPoscarReader()

Method Summary

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

haveAtomLabels
```
private boolean haveAtomLabels
```

atomsLabeledInline
```
private boolean atomsLabeledInline
```

scaleFac
```
private float scaleFac
```

ac
```
protected int ac
```

title
```
protected java.lang.String title
```

quiet
```
protected boolean quiet
```

defaultLabels

protected java.lang.String[] defaultLabels

elementLabel

protected java.lang.String[] elementLabel

radiusPt
```
int radiusPt
```

elementPt
```
int elementPt
```

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

Method Detail
- initializeReader
```
protected void initializeReader()
                         throws java.lang.Exception
```
  Overrides:
  
  initializeReader in class AtomSetCollectionReader
  
  Throws:
  
  java.lang.Exception
- readStructure
```
protected void readStructure(java.lang.String titleMsg)
                      throws java.lang.Exception
```
  Throws:
  
  java.lang.Exception
- finalizeSubclassReader
```
protected void finalizeSubclassReader()
                               throws java.lang.Exception
```
  Description copied from class: AtomSetCollectionReader
  
  optional reader-specific method run first.
  
  Overrides:
  
  finalizeSubclassReader in class AtomSetCollectionReader
  
  Throws:
  
  java.lang.Exception
- readUnitCellVectors
```
protected void readUnitCellVectors()
                            throws java.lang.Exception
```
  Throws:
  
  java.lang.Exception
- readMolecularFormula
```
protected void readMolecularFormula()
                             throws java.lang.Exception
```
  try various ways to read the optional atom labels. There is no convention here.
  
  Throws:
  
  java.lang.Exception
- readCoordinates
```
protected void readCoordinates()
                        throws java.lang.Exception
```
  Throws:
  
  java.lang.Exception
- getElement
```
protected java.lang.String getElement(java.lang.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 java.lang.String rdline()
                           throws java.lang.Exception
```
  Throws:
  
  java.lang.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