org.jmol.adapter.readers.quantum.GamessReader

All Implemented Interfaces:: GenericLineReader

Direct Known Subclasses:: GamessUKReader, GamessUSReader

public abstract class GamessReader extends MOReader

Nested Class Summary

Nested classes/interfaces inherited from class BasisFunctionReader
BasisFunctionReader.MOEnergySorter
Field Summary

Fields

Modifier and Type

Field

Description

protected static final double

_1_4pi

protected boolean

allowMopacDCoef

protected int[]

atomicNumbers

protected Lst<String>

atomNames

protected static final double[]

fact_2n

protected static final float

MIN_COEF

static final String

MOPAC_TYPES

protected float[][]

mopacBasis

GAMESS may need AM1, PMn, or RM1 zeta/coef data

protected boolean

scaleSlaters

Fields inherited from class MOReader
allowNoOrbitals, energyUnits, forceMOPAC, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, lastMoData, moTypes, orbitalsRead, shellCount

Fields inherited from class BasisFunctionReader
alphaBeta, dfCoefMaps, haveCoefs, ignoreMOs, moData, nCoef, nOrbitals, orbitals, shells, slaterArray, slaters

Fields inherited from class AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, CELL_TYPE_SUPER, cellSlop, centroidPacked, checkNearAtoms, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filteredPrecision, filterHetero, floatifyJavaDouble, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isSUPERCELL, isTrajectory, latticeCells, latticeScaling, latticeType, line, lowPrecision, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noMinimize, noPack, optimize2D, out, paramsCentroid, paramsLattice, precision, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
Constructor Summary

Constructors

Constructor

Description

GamessReader()
Method Summary

Modifier and Type

Method

Description

protected final SlaterData

addSlater(int iAtom, int a, int b, int c, int d, double zeta, double coef)

We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)

protected void

addSlater(SlaterData sd, int n)

protected void

addSlaterBasis()

When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS

void

createMopacSlaters(int iAtom, int atomicNumber, float[] values, boolean allowD)

protected void

createSphericalSlaterByType(int iAtom, int atomicNumber, String type, double zeta, float coef)

We have the type as a string and need to translate that to exponents for x, y, z, and r.

protected static double

fact(double f, double zeta, int n)

Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents.

protected static String

fixBasisLine(String line)

protected abstract String

fixShellTag(String tag)

static float[][]

getMopacAtomZetaSPD(String type)

Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number

protected static final double

getSlaterConstCartesian(int n, double zeta, int el, int ex, int ey, int ez)

scales slater using double factorials involving quantum number n, l, and xyz exponents.

protected Lst<SlaterData>

getSlaters()

protected void

initializeReader()

protected abstract void

readAtomsInBohrCoordinates()

protected void

readBasisInfo()

protected void

readControlInfo()

protected void

readEnergy()

protected void

readFrequencies()

protected void

readGaussianBasis(String initiator, String terminator)

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.

protected void

setAtom(Atom atom, int atomicNumber, String name, String id)

protected void

setCalculationType()

void

setMOData(boolean clearOrbitals)

protected final void

setMOs(String units)

protected final void

setSlaters(boolean doSort)

after the vectors intinfo and floatinfo are completed, we

protected void

sortOrbitalCoefficients(int[] pointers)

sorts coefficients by atomic number for speed later

protected void

sortOrbitals()

sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"

Methods inherited from class MOReader
addCoef, addMOData, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals

Methods inherited from class BasisFunctionReader
canonicalizeQuantumSubshellTag, clearOrbitals, discardPreviousAtoms, enableShell, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO

Methods inherited from class AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addMoreUnitCellInfo, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, applySymTrajASCR, checkAndRemoveFilterKey, 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, fixDoubleA, fixFloatA, fixFloatPt, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, getFortranFormatLengths, getInterface, getPackingRangeValue, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parsePrecision, 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, setPrecision, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR, warnSkippingOperation

Methods inherited from class Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- atomNames
  
  protected Lst<String> atomNames
- MIN_COEF
  protected static final float MIN_COEF
  
  See Also:
  
  Constant Field Values
- atomicNumbers
  
  protected int[] atomicNumbers
- mopacBasis
  
  protected float[][] mopacBasis
  
  GAMESS may need AM1, PMn, or RM1 zeta/coef data
- allowMopacDCoef
  
  protected boolean allowMopacDCoef
- MOPAC_TYPES
  public static final String MOPAC_TYPES
  
  See Also:
  
  Constant Field Values
- scaleSlaters
  
  protected boolean scaleSlaters
- _1_4pi
  protected static final double _1_4pi
  
  See Also:
  
  Constant Field Values
- fact_2n
  
  protected static final double[] fact_2n
Constructor Details
- GamessReader
  
  public GamessReader()
Method Details
- readAtomsInBohrCoordinates
  
  protected abstract void readAtomsInBohrCoordinates() throws Exception
  
  Throws:
  
  Exception
- initializeReader
  
  protected void initializeReader() throws Exception
  
  Overrides:
  
  initializeReader in class MOReader
  
  Throws:
  
  Exception
- setAtom
  
  protected void setAtom(Atom atom, int atomicNumber, String name, String id)
- readEnergy
  
  protected void readEnergy()
- readGaussianBasis
  
  protected void readGaussianBasis(String initiator, String terminator) throws Exception
  
  Throws:
  
  Exception
- fixShellTag
  
  protected abstract String fixShellTag(String tag)
- readFrequencies
  
  protected void readFrequencies() throws Exception
  
  Throws:
  
  Exception
- fixBasisLine
  
  protected static String fixBasisLine(String line)
- setCalculationType
  
  protected void setCalculationType()
- readControlInfo
  
  protected void readControlInfo() throws Exception
  
  Throws:
  
  Exception
- readBasisInfo
  
  protected void readBasisInfo() throws Exception
  
  Throws:
  
  Exception
- 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.
  
  Parameters:
  
  ex -
  
  ey -
  
  ez -
  
  er -
  
  zeta -
  
  Returns:
  
  scaling factor
- setMOData
  
  public void setMOData(boolean clearOrbitals)
  
  Overrides:
  
  setMOData in class MOReader
- addSlaterBasis
  
  protected void addSlaterBasis()
  
  When slater basis is referred to only by "AM1" "PM6" etc., as in GAMESS
  
  Overrides:
  
  addSlaterBasis in class MOReader
- createMopacSlaters
  
  public void createMopacSlaters(int iAtom, int atomicNumber, float[] values, boolean allowD)
- createSphericalSlaterByType
  
  protected void createSphericalSlaterByType(int iAtom, int atomicNumber, String type, double 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 -
- getMopacAtomZetaSPD
  
  public static float[][] getMopacAtomZetaSPD(String type)
  
  Retrieve the MOPAC zeta(1/bohr) [s,p,d] array by atom number
  
  Parameters:
  
  type -
  
  Returns:
  
  [[zs,zp,zd],[zs,zp,zd]...] where [1] is for hydrogen, [6] is for carbon, etc.
- addSlater
  
  protected final SlaterData addSlater(int iAtom, int a, int b, int c, int d, double zeta, double coef)
  
  We build two data structures for each slater: int[] slaterInfo[] = {iatom, a, b, c, d} float[] slaterData[] = {zeta, coef} where psi = (coef)(x^a)(y^b)(z^c)(r^d)exp(-zeta*r) Mopac: a == -2 ==> z^2 ==> (coef)(2z^2-x^2-y^2)(r^d)exp(-zeta*r) and: b == -2 ==> (coef)(x^2-y^2)(r^d)exp(-zeta*r)
  
  Parameters:
  
  iAtom - now 1-based
  
  a -
  
  b -
  
  c -
  
  d -
  
  zeta -
  
  coef -
- getSlaters
  
  protected Lst<SlaterData> getSlaters()
- addSlater
  
  protected void addSlater(SlaterData sd, int n)
- setSlaters
  
  protected final void setSlaters(boolean doSort)
  
  after the vectors intinfo and floatinfo are completed, we
  
  Parameters:
  
  doSort - TODO
- setMOs
  
  protected final void setMOs(String units)
- sortOrbitalCoefficients
  
  protected void sortOrbitalCoefficients(int[] pointers)
  
  sorts coefficients by atomic number for speed later
  
  Parameters:
  
  pointers -
- sortOrbitals
  
  protected void sortOrbitals()
  
  sorts orbitals by energy rather than by symmetry so that we can use "MO HOMO" "MO HOMO - 1" "MO LUMO"
- fact
  
  protected static double fact(double f, double zeta, int n)
  
  Sincere thanks to Miroslav Kohout (DGRID) for helping me get this right -- Bob Hanson, 1/5/2010 slater scaling based on zeta, n, l, and x y z exponents. sqrt[(2zeta)^(2n + 1) * f / 4pi / (2n)!] where f = (2 el + 1)!! / (2 ex - 1)!! / (2 ey - 1)!! / (2 ez - 1)!! The double factorials are precalculated.
  
  Parameters:
  
  f -
  
  zeta -
  
  n -
  
  Returns:
  
  scaled exponent
- getSlaterConstCartesian
  
  protected static final double getSlaterConstCartesian(int n, double zeta, int el, int ex, int ey, int ez)
  
  scales slater using double factorials involving quantum number n, l, and xyz exponents. fact2[x] is (2x - 1)!! Since x!! = 1 for x = 1, 0 or -1, we can just ignore this part for s and p orbitals, where x, y, and z are all 0 or 1. 7!! = 105 5!! = 15 3!! = 3 Numerators/4pi: all d orbitals: fact2[3] = (2*2 + 1)!! = 5!! = 15/4pi all f orbitals: fact2[4] = (2*3 + 1)!! = 7!! = 105/4pi Denominators: dxy, dyz, dxz all are 1 giving 15/4pi dx2, dy2, and dz2 all have one "2", giving 15/3!!/4pi or 5/4pi
  
  Parameters:
  
  n -
  
  zeta -
  
  el -
  
  ex -
  
  ey -
  
  ez -
  
  Returns:
  
  scaled exponent

Class GamessReader

Nested Class Summary

Nested classes/interfaces inherited from class BasisFunctionReader

Field Summary

Fields inherited from class MOReader

Fields inherited from class BasisFunctionReader

Fields inherited from class AtomSetCollectionReader

Constructor Summary

Method Summary

Methods inherited from class MOReader

Methods inherited from class BasisFunctionReader

Methods inherited from class AtomSetCollectionReader

Methods inherited from class Object

Field Details

atomNames

MIN_COEF

atomicNumbers

mopacBasis

allowMopacDCoef

MOPAC_TYPES

scaleSlaters

_1_4pi

fact_2n

Constructor Details

GamessReader

Method Details

readAtomsInBohrCoordinates

initializeReader

setAtom

readEnergy

readGaussianBasis

fixShellTag

readFrequencies

fixBasisLine

setCalculationType

readControlInfo

readBasisInfo

scaleSlater

setMOData

addSlaterBasis

createMopacSlaters

createSphericalSlaterByType

getMopacAtomZetaSPD

addSlater

getSlaters

addSlater

setSlaters

setMOs

sortOrbitalCoefficients

sortOrbitals

fact

getSlaterConstCartesian