Package org.jmol.adapter.readers.quantum
Class GamessReader
- java.lang.Object
-
- All Implemented Interfaces:
javajs.api.GenericLineReader
- Direct Known Subclasses:
GamessUKReader
,GamessUSReader
public abstract class GamessReader extends MopacSlaterReader
-
-
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 javajs.util.Lst<java.lang.String>
atomNames
private java.util.Map<java.lang.String,java.lang.String>
calcOptions
private boolean
isTypeSet
-
Fields inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
_AM1_C, allowMopacDCoef, atomicNumbers, MIN_COEF, MOPAC_TYPES, mopacBasis
-
Fields inherited from class org.jmol.adapter.readers.quantum.SlaterReader
scaleSlaters
-
Fields inherited from class org.jmol.adapter.readers.quantum.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 org.jmol.adapter.readers.quantum.BasisFunctionReader
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitalMaps, orbitals, shells, slaterArray, slaters
-
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, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterCased, 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, paramsCentroid, paramsLattice, 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
All Methods Static Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description protected static java.lang.String
fixBasisLine(java.lang.String line)
protected abstract java.lang.String
fixShellTag(java.lang.String tag)
protected void
initializeReader()
protected abstract void
readAtomsInBohrCoordinates()
protected void
readBasisInfo()
private void
readCalculationInfo(java.lang.String type)
protected void
readControlInfo()
protected void
readEnergy()
protected void
readFrequencies()
protected void
readGaussianBasis(java.lang.String initiator, java.lang.String terminator)
protected void
setAtom(Atom atom, int atomicNumber, java.lang.String name, java.lang.String id)
protected void
setCalculationType()
-
Methods inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
addSlaterBasis, createMopacSlaters, createSphericalSlaterByType, getMopacAtomZetaSPD, scaleSlater, setMOData
-
Methods inherited from class org.jmol.adapter.readers.quantum.SlaterReader
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, getSlaters, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals
-
Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addCoef, addMOData, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals
-
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, 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, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, 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
-
-
-
-
Method Detail
-
readAtomsInBohrCoordinates
protected abstract void readAtomsInBohrCoordinates() throws java.lang.Exception
- Throws:
java.lang.Exception
-
initializeReader
protected void initializeReader() throws java.lang.Exception
- Overrides:
initializeReader
in classMOReader
- Throws:
java.lang.Exception
-
setAtom
protected void setAtom(Atom atom, int atomicNumber, java.lang.String name, java.lang.String id)
-
readEnergy
protected void readEnergy()
-
readGaussianBasis
protected void readGaussianBasis(java.lang.String initiator, java.lang.String terminator) throws java.lang.Exception
- Throws:
java.lang.Exception
-
fixShellTag
protected abstract java.lang.String fixShellTag(java.lang.String tag)
-
readFrequencies
protected void readFrequencies() throws java.lang.Exception
- Throws:
java.lang.Exception
-
fixBasisLine
protected static java.lang.String fixBasisLine(java.lang.String line)
-
setCalculationType
protected void setCalculationType()
-
readControlInfo
protected void readControlInfo() throws java.lang.Exception
- Throws:
java.lang.Exception
-
readBasisInfo
protected void readBasisInfo() throws java.lang.Exception
- Throws:
java.lang.Exception
-
readCalculationInfo
private void readCalculationInfo(java.lang.String type) throws java.lang.Exception
- Throws:
java.lang.Exception
-
-