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
- Direct Known Subclasses:
- CsfReader, MoldenReader, MopacGraphfReader, WebMOReader
abstract class MopacSlaterReader
- extends SlaterReader
- Author:
- hansonr
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, doCheckUnitCell, doProcessLines, filter, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, symmetry, templateAtomCount, vibrationNumber, viewer |
Method Summary |
protected void |
createSphericalSlaterByType(int iAtom,
int atomicNumber,
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. |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLine, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, discardLines, 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, readAtomSetCollectionFromDOM, readData, readLine, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
MopacSlaterReader
MopacSlaterReader()
createSphericalSlaterByType
protected void createSphericalSlaterByType(int iAtom,
int atomicNumber,
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 class SlaterReader
- 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