Rene wrote:
>> Q: Do these atomSets have both a vibrational
>> frequency and an energy?
>
> Yes. A vibrational analysis is done for a single
> particular nuclear arrangement which an electronic
< energy for the stationary system. The vibrations
> are energies above that electronic ground state
> associated with the fact that a molecule always vibrates.
Then perhaps our default atomSetNames should be something like:
{frequency} ({energy})
as in
123.45 Hz (250 watts)
using, of course, the appropriate units ;-)
>>> I noticed that there are still quite a few variables
>> and classes that still have the name Model in them.
>> I did not touch those...
>>
>> OK ... we should try to get those cleaned up tomorrow.
>
> Well, I was wondering since the class names that are
> still in the org/jmol/adapter directory are:
> CdkModelAdapter, ModelAdapter, ModelResolver,
> SmarterModelAdapter. changing the Model to
> AtomSetCollection, would make some of them pretty
> long. (I recall downloading a java project in my OS 9
> days and getting in trouble because the filenames where
> too long...)
> In some cases, the variable names in the Readers
> could indeed refer to a single structural model and
> therefor really a single AtomSet.
I agree that AtomSetCollectionAdapter would not be appropriate.
I believe I used the word 'Model' in part because I was thinking about
'data model', not a molecular model. But it was a poor choice.
If anyone has any suggestions for other terms, please make them now.
Otherwise, I suppose the other option would be to drop the 'Model' part
and simply call it either Adapter or JmolAdapter.
ModelResolver is not a problem. It is only used within the package. We can
just change it to Resolver.
You can make the change ModelResolver.java -> Resolver.java
> So I didn't do it exactly in an atomic fashion.
> Within BBEdit you can Add and Commit a file to put
> it in the repository, but to remove one you need to
> do a Remove and a Commit Parent Folder (of Commit
> Folder on the repository as a whole) to really have
> it removed from the repository.
OK
> In retrospect that actually makes sense (like some many
> other things do :-)
Yes :-)
Miguel
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