Package org.jmol.adapter.readers.quantum
Class BasisFunctionReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.quantum.BasisFunctionReader
- All Implemented Interfaces:
GenericLineReader
- Direct Known Subclasses:
MOReader
,SpartanInputReader
,SpartanReader
- Author:
- hansonr invalid input: '<'hansonr@stolaf.edu>
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Nested Class Summary
Nested Classes -
Field Summary
FieldsModifier and TypeFieldDescriptionprotected String
protected int[][]
protected boolean
protected boolean
protected int
protected int
Lst
<int[]> protected SlaterData[]
protected Lst
<SlaterData> Fields inherited from class org.jmol.adapter.smarter.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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected static final String
protected void
protected void
protected void
enableShell
(int shellType) This flag must be explicitly set when a reader has been verified to properly sort G, H, I,...protected boolean
filterMO()
check line for filter optionsprotected int
fixSlaterTypes
(int typeOld, int typeNew) Only for 5D, 10F, 15G designations.int[][]
protected boolean
finds the position in the Jmol-required list of function types.static String
getQuantumShellTag
(int id) static int
static int
void
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, 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, initializeReader, 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
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Field Details
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shells
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slaters
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slaterArray
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moData
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orbitals
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nOrbitals
protected int nOrbitals -
ignoreMOs
protected boolean ignoreMOs -
alphaBeta
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dfCoefMaps
protected int[][] dfCoefMaps -
nCoef
protected int nCoef -
haveCoefs
protected boolean haveCoefs
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Constructor Details
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BasisFunctionReader
public BasisFunctionReader()
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Method Details
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filterMO
protected boolean filterMO()check line for filter options- Returns:
- true if a match
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setMO
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getDFMap
protected boolean getDFMap(String shell, String fileList, int shellType, String jmolList, int minLength) finds the position in the Jmol-required list of function types. This list is reader-dependent.- Parameters:
shell
- TODOfileList
-shellType
-jmolList
-minLength
-- Returns:
- true if successful
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enableShell
protected void enableShell(int shellType) This flag must be explicitly set when a reader has been verified to properly sort G, H, I,... orbitals.- Parameters:
shellType
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getDfCoefMaps
public int[][] getDfCoefMaps() -
canonicalizeQuantumSubshellTag
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fixSlaterTypes
protected int fixSlaterTypes(int typeOld, int typeNew) Only for 5D, 10F, 15G designations. Each time this method is run through, additional changes are made in the orbital count. So only the final reading is significant.- Parameters:
typeOld
-typeNew
-- Returns:
- the number of coefficients overall, for all orbital types
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getQuantumShellTagIDSpherical
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getQuantumShellTagID
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getQuantumShellTag
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discardPreviousAtoms
protected void discardPreviousAtoms()- Overrides:
discardPreviousAtoms
in classAtomSetCollectionReader
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clearOrbitals
protected void clearOrbitals()
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