org.jmol.adapter.readers.quantum
public class AdfReader extends SlaterReader
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.
Modifier and Type | Class and Description |
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(package private) class |
AdfReader.SymmetryData |
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter
Modifier and Type | Field and Description |
---|---|
private String |
energy |
private Map<String,AdfReader.SymmetryData> |
htSymmetries |
private int |
nXX |
private String |
symLine |
private List<AdfReader.SymmetryData> |
vSymmetries |
slaterArray, slaters
alphaBeta, CANONICAL_DC_LIST, CANONICAL_DS_LIST, CANONICAL_FC_LIST, CANONICAL_FS_LIST, dfCoefMaps, ignoreMOs, moData, nOrbitals, orbitals, shells
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
Constructor and Description |
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AdfReader() |
Modifier and Type | Method and Description |
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private void |
addMo(AdfReader.SymmetryData sd,
int moPt,
float occ,
float energy) |
protected boolean |
checkLine() |
private void |
readCoordinates()
Reads a set of coordinates
|
private void |
readFrequencies()
Reads a set of vibrations.
|
private void |
readMolecularOrbitals(String sym) |
private void |
readSlaterBasis() |
private void |
readSymmetries() |
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, scaleSlater, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals
canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, isQuantumBasisSupported, setMO
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
private Map<String,AdfReader.SymmetryData> htSymmetries
private List<AdfReader.SymmetryData> vSymmetries
private String energy
private int nXX
private String symLine
protected boolean checkLine() throws Exception
checkLine
in class AtomSetCollectionReader
Exception
private void readCoordinates() throws Exception
Exception
- if an I/O error occursprivate void readFrequencies() throws Exception
Exception
- if an I/O error occursprivate void readMolecularOrbitals(String sym) throws Exception
Exception
private void addMo(AdfReader.SymmetryData sd, int moPt, float occ, float energy)