org.jmol.adapter.readers.more
Class AdfReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.more.AdfReader

public class AdfReader
extends AtomSetCollectionReader

A reader for ADF output. Amsterdam Density Functional (ADF) is a quantum chemistry program by Scientific Computing & Modelling NV (SCM) (http://www.scm.com/).

Molecular coordinates, energies, and normal coordinates of vibrations are read. Each set of coordinates is added to the ChemFile in the order they are found. Energies and vibrations are associated with the previously read set of coordinates.

This reader was developed from a small set of example output files, and therefore, is not guaranteed to properly read all ADF output. If you have problems, please contact the author of this code, not the developers of ADF.

Version:
1.0
Author:
Bradley A. Smith (yeldar@home.com)

Field Summary
(package private)  java.lang.String energy
           
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, doApplySymmetry, filter, getHeader, haveAtomFilter, havePartialChargeFilter, htParams, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isTrajectory, latticeCells, line, modelNumber, needToApplySymmetry, next, prevline, reader, readerName, spaceGroup, templateAtomCount
 
Constructor Summary
AdfReader()
           
 
Method Summary
 void readAtomSetCollection(java.io.BufferedReader reader)
          Read the ADF output.
private  void readCoordinates()
          Reads a set of coordinates
private  void readFrequencies()
          Reads a set of vibrations.
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, applySymmetryAndSetTrajectory, checkLineForScript, checkLineForScript, clearLatticeParameters, deducePdbElementSymbol, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, fillDataBlock, filterAtom, filterAtom, getElementSymbol, getStrings, getTokens, getTokens, getTokens, getTokensFloat, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readData, readLine, readLineTrimmed, setAtomCoord, setAtomCoord, setError, 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

energy

java.lang.String energy
Constructor Detail

AdfReader

public AdfReader()
Method Detail

readAtomSetCollection

public void readAtomSetCollection(java.io.BufferedReader reader)
Read the ADF output.

Specified by:
readAtomSetCollection in class AtomSetCollectionReader
Parameters:
reader - input stream

readCoordinates

private void readCoordinates()
                      throws java.lang.Exception
Reads a set of coordinates

Throws:
java.lang.Exception - if an I/O error occurs

readFrequencies

private void readFrequencies()
                      throws java.lang.Exception
Reads a set of vibrations.

Throws:
java.lang.Exception - if an I/O error occurs