abstract class MopacSlaterReader extends SlaterReader
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter
BasisFunctionReader.MOEnergySorter
Modifier and Type | Field and Description |
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protected int[] |
atomicNumbers |
protected static float |
MIN_COEF |
private static int[] |
npqd |
private static int[] |
principalQuantumNumber |
private static int[] |
sphericalDValues |
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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MopacSlaterReader() |
Modifier and Type | Method and Description |
---|---|
protected void |
createSphericalSlaterByType(int iAtom,
int atomicNumber,
java.lang.String type,
float zeta,
float coef)
We have the type as a string and need to translate that
to exponents for x, y, z, and r.
|
private static int |
getNPQ(int atomicNumber) |
private static int |
getNPQd(int atomicNumber)
for D orbitals, MOPAC adds 1 to n for noble gases
but subtracts 1 from n for transition metals
|
private static int |
getNPQp(int atomicNumber)
for P orbitals, MOPAC adds 1 to n for helium only
|
private static int |
getNPQs(int atomicNumber)
for S orbitals, MOPAC adds 1 to n for noble gases other than helium
|
protected double |
scaleSlater(int ex,
int ey,
int ez,
int er,
double zeta)
overrides method in SlaterReader to allow for MOPAC's treatment of
the radial exponent differently depending upon position in
the periodic table -- noble gases and transition metals
and for the fact that these are spherical functions (5D, not 6D)
ignores any F orbitals.
|
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, 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, checkLine, 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
protected static final float MIN_COEF
protected int[] atomicNumbers
private static final int[] sphericalDValues
private static final int[] principalQuantumNumber
private static final int[] npqd
protected void createSphericalSlaterByType(int iAtom, int atomicNumber, java.lang.String type, float zeta, float coef)
iAtom
- atomicNumber
- type
- zeta
- coef
- protected double scaleSlater(int ex, int ey, int ez, int er, double zeta)
scaleSlater
in class SlaterReader
ex
- ey
- ez
- er
- zeta
- private static final int getNPQ(int atomicNumber)
private static final int getNPQs(int atomicNumber)
atomicNumber
- private static final int getNPQp(int atomicNumber)
atomicNumber
- private static final int getNPQd(int atomicNumber)
atomicNumber
-