org.jmol.adapter.readers.more
public class NWChemReader extends AtomSetCollectionReader
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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boolean | converged |
String | energyKey
The type of energy last calculated. |
String | energyValue
The last calculated energy value. |
int | equivalentAtomSets
The number of equivalent atom sets.
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boolean | haveAt |
boolean | haveEnergy |
boolean | inInput |
int | taskNumber
The number of the task begin interpreted.
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Method Summary | |
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String | fixTag(String tag)
Returns a modified identifier for a tag, so that the element can be determined
from it in the Atom.
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void | init() |
void | readAtoms()
Reads the output coordinates section into a new AtomSet. |
AtomSetCollection | readAtomSetCollection(BufferedReader reader) |
void | readAtSign() |
void | readFrequencies()
Reads the AtomSet and projected frequencies in the frequency section.
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void | readGradients()
Reads the energy gradients section into a new AtomSet.
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void | readNWChemLine() |
void | readPartialCharges()
Reads partial charges and assigns them only to the last atom set. |
void | readSymmetry()
Read the symmetry information and set the property. |
void | readTotal()
Interpret a line starting with a line with "Total" in it.
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void | setEnergies(String key, String value, int nAtomSets) |
void | setEnergy(String key, String value) |
Needed to associate identical properties to multiple atomsets
Used for the construction of the 'path' for the atom set.
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
Throws: Exception If an error occurs.
Attaches the vibration vectors of the projected frequencies to duplicates of the atom information in the frequency section.
Throws: Exception If an error occurs.
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.
Throws: Exception When an I/O error or discardlines error occurs
Throws: Exception If an error occurs.
Determine whether it reports the energy, if so set the property and name(s)