java.lang.Object
- org.jmol.adapter.smarter.AtomSetCollectionReader
- - org.jmol.adapter.readers.quantum.BasisFunctionReader
  - - org.jmol.adapter.readers.quantum.MOReader
    - - org.jmol.adapter.readers.quantum.NWChemReader

All Implemented Interfaces:

javajs.api.GenericLineReader
```
public class NWChemReader
extends MOReader
```
A reader for NWChem 4.6 NWChem is a quantum chemistry program developed at Pacific Northwest National Laboratory. See http://www.nwchem-sw.org/index.php/NWChem_Documentation for orbital plotting, one needs to use the following switches: print "final vectors" "final vectors analysis"
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.

Nested Class Summary
- Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
  BasisFunctionReader.MOEnergySorter

Field Summary

Fields
Modifier and Type	Field	Description
`private javajs.util.Lst<java.lang.String>`	`atomTypes`
`private boolean`	`converged`
`private static java.lang.String`	`DC_LIST`
`private static java.lang.String`	`DS_LIST`
`private java.lang.String`	`energyKey`	The type of energy last calculated.
`private java.lang.String`	`energyValue`	The last calculated energy value.
`private int`	`equivalentAtomSets`	The number of equivalent atom sets.
`private static java.lang.String`	`FC_LIST`
`private static java.lang.String`	`FS_LIST`
`private boolean`	`haveAt`
`private boolean`	`haveEnergy`
`private java.util.Map<java.lang.String,javajs.util.Lst<java.lang.String>>`	`htMOs`
`private boolean`	`inInput`
`(package private) int`	`moCount`
`(package private) int`	`nBasisFunctions`
`private boolean`	`purging`
`private int`	`taskNumber`	The number of the task begin interpreted.

Fields inherited from class org.jmol.adapter.readers.quantum.MOReader
allowNoOrbitals, energyUnits, gaussianCount, gaussians, haveNboCharges, haveNboOrbitals, HEADER_GAMESS_OCCUPANCIES, HEADER_GAMESS_ORIGINAL, HEADER_GAMESS_UK_MO, HEADER_NONE, moTypes, orbitalsRead, shellCount

Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitals, shells

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors
Constructor Description

NWChemReader()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected boolean`	`checkLine()`
`private void`	`checkMOs()`
`protected void`	`finalizeSubclassReader()`	optional reader-specific method run first.
`private java.lang.String`	`fixTag(java.lang.String tag)`	Returns a modified identifier for a tag, so that the element can be determined from it in the `Atom`.
`private void`	`init()`
`protected void`	`initializeReader()`
`java.lang.String`	`rd()`
`private void`	`readAtoms()`	Reads the output coordinates section into a new AtomSet.
`private void`	`readAtSign()`
`private boolean`	`readBasis()`
`private void`	`readFrequencies()`	Reads the AtomSet and projected frequencies in the frequency section.
`private void`	`readGradients()`	Reads the energy gradients section into a new AtomSet.
`private boolean`	`readMOs()`
`(package private) void`	`readPartialCharges()`	Reads partial charges and assigns them only to the last atom set.
`private void`	`readSymmetry()`	Read the symmetry information and set the property.
`private void`	`readTotal()`	Interpret a line starting with a line with "Total" in it.
`private void`	`setEnergies(java.lang.String key, java.lang.String value, int nAtomSets)`
`private void`	`setEnergy(java.lang.String key, java.lang.String value)`
`private void`	`setNames(java.lang.String atomSetName, BS namedSets, int n)`
`private void`	`setProps(java.lang.String key, java.lang.String value, int n)`

Methods inherited from class org.jmol.adapter.readers.quantum.MOReader
addCoef, addMOData, checkAndRemoveFilterKey, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals, setMOData

Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, discardPreviousAtoms, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, 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

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

- Field Detail
  - taskNumber
```
private int taskNumber
```
    The number of the task begin interpreted.
    Used for the construction of the 'path' for the atom set.
  - equivalentAtomSets
```
private int equivalentAtomSets
```
    The number of equivalent atom sets.
    Needed to associate identical properties to multiple atomsets
  - energyKey
```
private java.lang.String energyKey
```
    The type of energy last calculated.
  - energyValue
```
private java.lang.String energyValue
```
    The last calculated energy value.
  - converged
```
private boolean converged
```
  - haveEnergy
```
private boolean haveEnergy
```
  - haveAt
```
private boolean haveAt
```
  - inInput
```
private boolean inInput
```
  - atomTypes
```
private javajs.util.Lst<java.lang.String> atomTypes
```
  - htMOs
```
private java.util.Map<java.lang.String,javajs.util.Lst<java.lang.String>> htMOs
```
  - nBasisFunctions
```
int nBasisFunctions
```
  - DS_LIST
```
private static java.lang.String DS_LIST
```
  - FS_LIST
```
private static java.lang.String FS_LIST
```
  - DC_LIST
```
private static java.lang.String DC_LIST
```
  - FC_LIST
```
private static java.lang.String FC_LIST
```
  - moCount
```
int moCount
```
  - purging
```
private boolean purging
```
- Constructor Detail
  - NWChemReader
```
public NWChemReader()
```
- Method Detail
  - initializeReader
```
protected void initializeReader()
```
    Overrides:
    
    initializeReader in class MOReader
  - checkLine
```
protected boolean checkLine()
                     throws java.lang.Exception
```
    Overrides:
    
    checkLine in class AtomSetCollectionReader
    
    Returns:
    
    true if need to read new line
    
    Throws:
    
    java.lang.Exception
  - finalizeSubclassReader
```
protected void finalizeSubclassReader()
                               throws java.lang.Exception
```
    Description copied from class: AtomSetCollectionReader
    
    optional reader-specific method run first.
    
    Overrides:
    
    finalizeSubclassReader in class AtomSetCollectionReader
    
    Throws:
    
    java.lang.Exception
  - init
```
private void init()
```
  - setEnergies
```
private void setEnergies(java.lang.String key,
                         java.lang.String value,
                         int nAtomSets)
```
    Parameters:
    
    key -
    
    value -
    
    nAtomSets - NOT USED
  - setEnergy
```
private void setEnergy(java.lang.String key,
                       java.lang.String value)
```
  - readSymmetry
```
private void readSymmetry()
                   throws java.lang.Exception
```
    Read the symmetry information and set the property.
    
    Throws:
    
    java.lang.Exception - If an error occurs.
  - 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)
  - readAtSign
```
private void readAtSign()
                 throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - setProps
```
private void setProps(java.lang.String key,
                      java.lang.String value,
                      int n)
```
  - setNames
```
private void setNames(java.lang.String atomSetName,
                      BS namedSets,
                      int n)
```
  - readAtoms
```
private void readAtoms()
                throws java.lang.Exception
```
    Reads the output coordinates section into a new AtomSet.
    
    Throws:
    
    java.lang.Exception - If an error occurs.
  - readGradients
```
private void readGradients()
                    throws java.lang.Exception
```
    Reads the energy gradients section into a new AtomSet.
    One could consider not adding a new AtomSet for this, but just adding the gradient vectors to the last AtomSet read (if that was indeed the same nuclear arrangement).
    
    Throws:
    
    java.lang.Exception - If an error occurs.
  - readFrequencies
```
private void readFrequencies()
                      throws java.lang.Exception
```
    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:
    
    java.lang.Exception - If an error occurs.
  - readPartialCharges
```
void readPartialCharges()
                 throws java.lang.Exception
```
    Reads partial charges and assigns them only to the last atom set.
    
    Throws:
    
    java.lang.Exception - When an I/O error or discardlines error occurs
  - fixTag
```
private java.lang.String fixTag(java.lang.String tag)
```
    Returns a modified identifier for a tag, so that the element can be determined from it in the Atom.
    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
  - readBasis
```
private boolean readBasis()
                   throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - readMOs
```
private boolean readMOs()
                 throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - checkMOs
```
private void checkMOs()
               throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - rd
```
public java.lang.String rd()
                    throws java.lang.Exception
```
    Overrides:
    
    rd in class AtomSetCollectionReader
    
    Throws:
    
    java.lang.Exception

Class NWChemReader

Nested Class Summary

Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

Field Summary

Fields inherited from class org.jmol.adapter.readers.quantum.MOReader

Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Constructor Summary

Method Summary

Methods inherited from class org.jmol.adapter.readers.quantum.MOReader

Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Methods inherited from class java.lang.Object

Field Detail

taskNumber

equivalentAtomSets

energyKey

energyValue

converged

haveEnergy

haveAt

inInput

atomTypes

htMOs

nBasisFunctions

DS_LIST

FS_LIST

DC_LIST

FC_LIST

moCount

purging

Constructor Detail

NWChemReader

Method Detail

initializeReader

checkLine

finalizeSubclassReader

init

setEnergies

setEnergy

readSymmetry

readTotal

readAtSign

setProps

setNames

readAtoms

readGradients

readFrequencies

readPartialCharges

fixTag

readBasis

readMOs

checkMOs

rd