org.jmol.adapter.readers.xtal
Class AimsReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.xtal.AimsReader

public class AimsReader
extends AtomSetCollectionReader

FHI-aims (http://www.fhi-berlin.mpg.de/aims) geometry.in file format samples of relevant lines in geometry.in file are included as comments below

Version:
1.2
Author:
Joerg Meyer, FHI Berlin 2009 (meyer@fhi-berlin.mpg.de)

Field Summary
private  javax.vecmath.Vector3f[] latticeVectors
           
private  int nLatticeVectors
           
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCheckUnitCell, doProcessLines, filter, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, symmetry, templateAtomCount, vibrationNumber, viewer
 
Constructor Summary
AimsReader()
           
 
Method Summary
protected  boolean checkLine()
           
protected  void finalizeReader()
           
private  void setUnitCellFromLatticeVectors(javax.vecmath.Vector3f[] abc)
           
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, createSpaceGroup, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeReader, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readLine, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

nLatticeVectors

private int nLatticeVectors

latticeVectors

private javax.vecmath.Vector3f[] latticeVectors
Constructor Detail

AimsReader

public AimsReader()
Method Detail

checkLine

protected boolean checkLine()
Overrides:
checkLine in class AtomSetCollectionReader
Returns:
true if need to read new line

finalizeReader

protected void finalizeReader()
                       throws java.lang.Exception
Overrides:
finalizeReader in class AtomSetCollectionReader
Throws:
java.lang.Exception

setUnitCellFromLatticeVectors

private void setUnitCellFromLatticeVectors(javax.vecmath.Vector3f[] abc)