Package org.jmol.adapter.readers.quantum
Class MopacSlaterReader
- 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.MopacSlaterReader
-
- All Implemented Interfaces:
javajs.api.GenericLineReader
- Direct Known Subclasses:
CsfReader
,MoldenReader
,MopacGraphfReader
,WebMOReader
abstract class MopacSlaterReader extends SlaterReader
- Author:
- hansonr
-
-
Nested Class Summary
-
Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.SlaterReader
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter
-
Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
BasisFunctionReader.MOEnergySorter
-
-
Field Summary
Fields Modifier and Type Field Description protected int[]
atomicNumbers
protected static float
MIN_COEF
private static int[]
npqd
private static int[]
principalQuantumNumber
private static int[]
sphericalDValues
-
Fields inherited from class org.jmol.adapter.readers.quantum.SlaterReader
slaterArray, slaters
-
Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shells
-
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
-
-
Constructor Summary
Constructors Constructor Description MopacSlaterReader()
-
Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method 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 metalsprivate static int
getNPQp(int atomicNumber)
for P orbitals, MOPAC adds 1 to n for helium onlyprivate static int
getNPQs(int atomicNumber)
for S orbitals, MOPAC adds 1 to n for noble gases other than heliumprotected 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.-
Methods inherited from class org.jmol.adapter.readers.quantum.SlaterReader
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals
-
Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, clearOrbitals, discardPreviousAtoms, enableShell, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO
-
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, 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, 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
-
-
-
-
Field Detail
-
MIN_COEF
protected static final float MIN_COEF
- See Also:
- Constant Field Values
-
atomicNumbers
protected int[] atomicNumbers
-
sphericalDValues
private static final int[] sphericalDValues
-
principalQuantumNumber
private static final int[] principalQuantumNumber
-
npqd
private static final int[] npqd
-
-
Method Detail
-
createSphericalSlaterByType
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. No F here.- Parameters:
iAtom
-atomicNumber
-type
-zeta
-coef
-
-
scaleSlater
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.- Overrides:
scaleSlater
in classSlaterReader
- Parameters:
ex
-ey
-ez
-er
-zeta
-- Returns:
- scaling factor
-
getNPQ
private static final int getNPQ(int atomicNumber)
-
getNPQs
private static final int getNPQs(int atomicNumber)
for S orbitals, MOPAC adds 1 to n for noble gases other than helium- Parameters:
atomicNumber
-- Returns:
- adjusted principal quantum number
-
getNPQp
private static final int getNPQp(int atomicNumber)
for P orbitals, MOPAC adds 1 to n for helium only- Parameters:
atomicNumber
-- Returns:
- adjusted principal quantum number
-
getNPQd
private static final int getNPQd(int atomicNumber)
for D orbitals, MOPAC adds 1 to n for noble gases but subtracts 1 from n for transition metals- Parameters:
atomicNumber
-- Returns:
- adjusted principal quantum number
-
-