org.jmol.adapter.readers.quantum
Class NWChemReader

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

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. no support yet for orbitals

Field Summary

private List<String>	atomTypes
private boolean	converged
private static String	DC_LIST
private static String	DS_LIST
private String	energyKey The type of energy last calculated.
private String	energyValue The last calculated energy value.
private int	equivalentAtomSets The number of equivalent atom sets.
private static String	FC_LIST
private static String	FS_LIST
private boolean	haveAt
private boolean	haveEnergy
private boolean	inInput
(package private) int	moCount
private Map<Integer,Map<String,Object>>	moInfo
(package private) int	nBasisFunctions
private boolean	purging
private boolean	readROHFonly
private int	taskNumber The number of the task begin interpreted.

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

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, CANONICAL_DC_LIST, CANONICAL_DS_LIST, CANONICAL_FC_LIST, CANONICAL_FS_LIST, dfCoefMaps, ignoreMOs, moData, nOrbitals, orbitals, shells

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

addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer

Constructor Summary

NWChemReader()

Method Summary

protected boolean	checkLine()
private String	fixTag(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()
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.
String	readLine()
private boolean	readMolecularOrbitalAnalysis(boolean doClear)
private boolean	readMolecularOrbitalVectors()
(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(String key, String value, int nAtomSets)
private void	setEnergy(String key, String value)

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

addMOData, checkNboLine, getMOHeader, getNboTypes, readMolecularOrbitals, setMOData, setMOType

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

canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, isQuantumBasisSupported, setMO

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

addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processBinaryDocument, processXml, read3Vectors, readData, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem

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 String energyKey

The type of energy last calculated.

energyValue

private 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 List<String> atomTypes

readROHFonly

private boolean readROHFonly

nBasisFunctions

int nBasisFunctions

DS_LIST

private static String DS_LIST

FS_LIST

private static String FS_LIST

DC_LIST

private static String DC_LIST

FC_LIST

private static String FC_LIST

moInfo

private Map<Integer,Map<String,Object>> moInfo

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 Exception

Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

Exception

init

private void init()

setEnergies

private void setEnergies(String key,
                         String value,
                         int nAtomSets)

Parameters:

key -

value -

nAtomSets - NOT USED

setEnergy

private void setEnergy(String key,
                       String value)

readSymmetry

private void readSymmetry()
                   throws Exception

Read the symmetry information and set the property.

Throws:

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 Exception

Throws:

Exception

readAtoms

private void readAtoms()
                throws Exception

Reads the output coordinates section into a new AtomSet.

Throws:

Exception - If an error occurs.

readGradients

private void readGradients()
                    throws 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:

Exception - If an error occurs.

readFrequencies

private void readFrequencies()
                      throws 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:

Exception - If an error occurs.

readPartialCharges

void readPartialCharges()
                  throws Exception

Reads partial charges and assigns them only to the last atom set.

Throws:

Exception - When an I/O error or discardlines error occurs

fixTag

private String fixTag(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 Exception

Throws:

Exception

readMolecularOrbitalAnalysis

private boolean readMolecularOrbitalAnalysis(boolean doClear)
                                      throws Exception

Throws:

Exception

readMolecularOrbitalVectors

private boolean readMolecularOrbitalVectors()
                                     throws Exception

Throws:

Exception

readLine

public String readLine()
                throws Exception

Overrides:

readLine in class AtomSetCollectionReader

Throws:

Exception