org.jmol.adapter.readers.xtal
Class AimsReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
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
modified (May 1, 2011, hansonr@stolaf.edu) to account for atom/atom_frac lines
and to bring it into compliance with other load options (such as overriding
file-based symmetry or unit cell parameters).
- Version:
- 1.3
- Author:
- Joerg Meyer, TU Muenchen 2011 (joerg.meyer@ch.tum.de)
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 |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, 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 |
globalDoApplySymmetry
private boolean globalDoApplySymmetry
isFractional
private boolean isFractional
nLatticeVectors
private int nLatticeVectors
AimsReader
public AimsReader()
initializeReader
protected void initializeReader()
- Overrides:
initializeReader
in class AtomSetCollectionReader
checkLine
protected boolean checkLine()
- Overrides:
checkLine
in class AtomSetCollectionReader
- Returns:
- true if need to read new line
finalizeReader
protected void finalizeReader()
throws Exception
- Overrides:
finalizeReader
in class AtomSetCollectionReader
- Throws:
Exception
readLatticeVector
private void readLatticeVector(String[] tokens)
readAtom
private void readAtom(String[] tokens,
boolean isFractional)
readMultipole
private void readMultipole(String[] tokens)