org.jmol.adapter.readers.quantum
Class AdfReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.quantum.BasisFunctionReader
org.jmol.adapter.readers.quantum.SlaterReader
org.jmol.adapter.readers.quantum.AdfReader
public class AdfReader
- extends SlaterReader
TODO: adf-2007.out causes failure reading basis functions
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.
Added note (Bob Hanson) -- 1/1/2010 --
Trying to implement reading of orbitals; ran into the problem
that the atomic Slater description uses Cartesian orbitals,
but the MO refers to spherical orbitals.
- Version:
- 1.0
- Author:
- Bradley A. Smith (yeldar@home.com)
Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader |
alphaBeta, CANONICAL_DC_LIST, CANONICAL_DS_LIST, CANONICAL_FC_LIST, CANONICAL_FS_LIST, dfCoefMaps, ignoreMOs, moData, nOrbitals, orbitals, shells |
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, 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, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
htSymmetries
private java.util.Map<java.lang.String,AdfReader.SymmetryData> htSymmetries
vSymmetries
private java.util.List<AdfReader.SymmetryData> vSymmetries
energy
private java.lang.String energy
nXX
private int nXX
symLine
private java.lang.String symLine
AdfReader
public AdfReader()
checkLine
protected boolean checkLine()
throws java.lang.Exception
- Overrides:
checkLine
in class AtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
java.lang.Exception
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
readSymmetries
private void readSymmetries()
throws java.lang.Exception
- Throws:
java.lang.Exception
readSlaterBasis
private void readSlaterBasis()
throws java.lang.Exception
- Throws:
java.lang.Exception
readMolecularOrbitals
private void readMolecularOrbitals(java.lang.String sym)
throws java.lang.Exception
- Throws:
java.lang.Exception
addMo
private void addMo(AdfReader.SymmetryData sd,
int moPt,
float occ,
float energy)