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java.lang.Objectorg.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.more.NWChemReader
public class NWChemReader
A reader for NWChem 4.6 NWChem is a quantum chemistry program developed at Pacific Northwest National Laboratory.
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.
Field Summary | |
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private boolean |
converged
|
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 boolean |
haveAt
|
private boolean |
haveEnergy
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private boolean |
inInput
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private int |
taskNumber
The number of the task begin interpreted. |
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
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ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, desiredModelNumber, desiredSpaceGroupIndex, doApplySymmetry, filter, getHeader, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveDesiredModel, iHaveSymmetryOperators, iHaveUnitCell, latticeCells, line, modelNumber, needToApplySymmetry, next, notionalUnitCell, prevline, primitiveLatticeVectors, ptLine, reader, readerName, spaceGroup |
Constructor Summary | |
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NWChemReader()
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Method Summary | |
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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()
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private void |
readAtoms()
Reads the output coordinates section into a new AtomSet. |
AtomSetCollection |
readAtomSetCollection(java.io.BufferedReader reader)
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private void |
readAtSign()
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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 void |
readNWChemLine()
|
(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)
|
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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private int taskNumber
Used for the construction of the 'path' for the atom set.
private int equivalentAtomSets
Needed to associate identical properties to multiple atomsets
private java.lang.String energyKey
private java.lang.String energyValue
private boolean converged
private boolean haveEnergy
private boolean haveAt
private boolean inInput
Constructor Detail |
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public NWChemReader()
Method Detail |
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public AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)
readAtomSetCollection
in class AtomSetCollectionReader
private void init()
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 readSymmetry() throws java.lang.Exception
java.lang.Exception
- If an error occurs.private void readNWChemLine()
private void readTotal()
Determine whether it reports the energy, if so set the property and name(s)
private void readAtSign() throws java.lang.Exception
java.lang.Exception
private void readAtoms() throws java.lang.Exception
java.lang.Exception
- If an error occurs.private void readGradients() throws java.lang.Exception
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).
java.lang.Exception
- If an error occurs.private void readFrequencies() throws java.lang.Exception
Attaches the vibration vectors of the projected frequencies to duplicates of the atom information in the frequency section.
java.lang.Exception
- If an error occurs.void readPartialCharges() throws java.lang.Exception
java.lang.Exception
- When an I/O error or discardlines error occursprivate java.lang.String fixTag(java.lang.String tag)
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.
tag
- the tag to be modified
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