Class NWChemReader
- All Implemented Interfaces:
javajs.api.GenericLineReader
AtomSets will be generated for output coordinates in angstroms, energy gradients with vector information of the gradients, and frequencies with an AtomSet for every separate frequency containing vector information of the vibrational mode.
Note that the different modules give quite different formatted output so it is not certain that all modules will be properly interpreted. Most testing has been done with the SCF and DFT tasks.
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Nested Class Summary
Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
BasisFunctionReader.MOEnergySorter
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate javajs.util.Lst<String>
private boolean
private static String
private static String
private String
The type of energy last calculated.private String
The last calculated energy value.private int
The number of equivalent atom sets.private static String
private static String
private boolean
private boolean
private boolean
(package private) int
(package private) int
private boolean
private int
The number of the task begin interpreted.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, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noPack, optimize2D, 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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected boolean
private void
checkMOs()
protected void
optional reader-specific method run first.private String
Returns a modified identifier for a tag, so that the element can be determined from it in theAtom
.private void
init()
protected void
rd()
private void
Reads the output coordinates section into a new AtomSet.private void
private boolean
private void
Reads the AtomSet and projected frequencies in the frequency section.private boolean
readMOs()
(package private) void
Reads partial charges and assigns them only to the last atom set.private void
Read the symmetry information and set the property.private void
Interpret a line starting with a line with "Total" in it.private void
setEnergies
(String key, String value, int nAtomSets) private void
private void
private void
Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addCoef, addMOData, addSlaterBasis, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals, setMOData
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, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, 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, 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
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Field Details
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taskNumber
private int taskNumberThe number of the task begin interpreted.Used for the construction of the 'path' for the atom set.
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equivalentAtomSets
private int equivalentAtomSetsThe number of equivalent atom sets.Needed to associate identical properties to multiple atomsets
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energyKey
The type of energy last calculated. -
energyValue
The last calculated energy value. -
converged
private boolean converged -
haveEnergy
private boolean haveEnergy -
haveAt
private boolean haveAt -
inInput
private boolean inInput -
atomTypes
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htMOs
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nBasisFunctions
int nBasisFunctions -
DS_LIST
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FS_LIST
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DC_LIST
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FC_LIST
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moCount
int moCount -
purging
private boolean purging
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Constructor Details
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NWChemReader
public NWChemReader()
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Method Details
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initializeReader
protected void initializeReader()- Overrides:
initializeReader
in classMOReader
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checkLine
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
Exception
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finalizeSubclassReader
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classAtomSetCollectionReader
- Throws:
Exception
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init
private void init() -
setEnergies
- Parameters:
key
-value
-nAtomSets
- NOT USED
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setEnergy
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readSymmetry
Read the symmetry information and set the property.- Throws:
Exception
- If an error occurs.
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readTotal
private void readTotal()Interpret a line starting with a line with "Total" in it.Determine whether it reports the energy, if so set the property and name(s)
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readAtSign
- Throws:
Exception
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setProps
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setNames
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readAtoms
Reads the output coordinates section into a new AtomSet.- Parameters:
thisLine
-- Throws:
Exception
- If an error occurs.
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readFrequencies
Reads the AtomSet and projected frequencies in the frequency section.Attaches the vibration vectors of the projected frequencies to duplicates of the atom information in the frequency section.
- Throws:
Exception
- If an error occurs.
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readPartialCharges
Reads partial charges and assigns them only to the last atom set.- Throws:
Exception
- When an I/O error or discardlines error occurs
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fixTag
Returns a modified identifier for a tag, so that the element can be determined from it in theAtom
.The result is that a tag that started with Bq (case insensitive) will be renamed to have the Bq removed and '-Bq' appended to it.
A tag consisting only of Bq (case insensitive) will return X. This can happen in a frequency analysis.- Parameters:
tag
- the tag to be modified- Returns:
- a possibly modified tag
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readBasis
- Throws:
Exception
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readMOs
- Throws:
Exception
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checkMOs
- Throws:
Exception
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rd
- Overrides:
rd
in classAtomSetCollectionReader
- Throws:
Exception
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