org.jmol.adapter.readers.more
Class AdfReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
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, desiredModelNumber, desiredSpaceGroupIndex, doApplySymmetry, filter, getHeader, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveDesiredModel, iHaveSymmetryOperators, iHaveUnitCell, latticeCells, line, modelNumber, needToApplySymmetry, next, notionalUnitCell, prevline, primitiveLatticeVectors, ptLine, reader, readerName, spaceGroup |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, applySymmetry, checkLineForScript, checkLineForScript, clearLatticeParameters, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, fillDataBlock, filterAtom, getElementSymbol, getStrings, getTokens, getTokens, getTokens, getTokensFloat, initialize, initialize, initializeCartesianToFractional, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readLine, readLineTrimmed, setAtomCoord, setAtomCoord, setError, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setUnitCell, setUnitCellItem |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
energy
java.lang.String energy
AdfReader
public AdfReader()
readAtomSetCollection
public AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)
- Read the ADF output.
- Specified by:
readAtomSetCollection
in class AtomSetCollectionReader
- Parameters:
reader
- input stream
- Returns:
- a ChemFile with the coordinates, energies, and vibrations.
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