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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private class |
AdfReader.SymmetryData |
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter
BasisFunctionReader.MOEnergySorter
Modifier and Type | Field and Description |
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private java.lang.String |
energy |
private java.util.Map<java.lang.String,AdfReader.SymmetryData> |
htSymmetries |
private int |
nXX |
private java.lang.String |
symLine |
private javajs.util.Lst<AdfReader.SymmetryData> |
vSymmetries |
slaterArray, slaters
alphaBeta, CANONICAL_DC_LIST, CANONICAL_DS_LIST, CANONICAL_FC_LIST, CANONICAL_FS_LIST, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitals, shells
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, validation, vibrationNumber, vibsFractional, vwr
Constructor and Description |
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AdfReader() |
Modifier and Type | Method and Description |
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private void |
addMo(java.lang.String sym,
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(java.lang.String sym) |
private void |
readSlaterBasis() |
private void |
readSymmetries() |
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, scaleSlater, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals
canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getNewDfCoefMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, getElementSymbol, getFilter, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeReader, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, processBinaryDocument, processDOM, processDSSR, rd, read3Vectors, readDataObject, readLines, readNextLine, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setModelPDB, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR
private java.util.Map<java.lang.String,AdfReader.SymmetryData> htSymmetries
private javajs.util.Lst<AdfReader.SymmetryData> vSymmetries
private java.lang.String energy
private int nXX
private java.lang.String symLine
protected boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
private void readCoordinates() throws java.lang.Exception
java.lang.Exception
- if an I/O error occursprivate void readFrequencies() throws java.lang.Exception
java.lang.Exception
- if an I/O error occursprivate void readSymmetries() throws java.lang.Exception
java.lang.Exception
private void readSlaterBasis() throws java.lang.Exception
java.lang.Exception
private void readMolecularOrbitals(java.lang.String sym) throws java.lang.Exception
java.lang.Exception
private void addMo(java.lang.String sym, int moPt, float occ, float energy)