Miguel,
I reread your message below and after working some more on the Gaussian reader and trying out some calculation option combinations, I have come to the conclusion that it would not be preferable to just ignore the 'Input orientation'.
Depending on how the calculation is set up one can have one of the following cases, with an example (as just committed to the repository):
Z-Matrix only (H2O_NoSymm_G03_zopt.log in the optimization steps)
or
Input only (H2O_NoSymm_G03.log)
or
Z-Matrix and Standard (H2O_G03_zopt.log)
or
Input and Standard (H2O_G03.log)
(see also the javadoc for the readAtomSetCollection method in the GaussianReader class).
Thus ignoring the Input orientation would make it impossible to read the result of one type of calculation (which actually may be often performed).
Out of the 4 files above, Jmol version 9 had problems with:
* H2O_NoSymm_G03_zopt.log
* H2O_NoSymm_G03.log
Since that version was limited to only looking at Standard orientations (i.e., calculations in which symmetry was not turned on).
I think the current implementation of Jmol10 is better in that it can deal with all of them.
About the center of gravity problem.
If it is possible to 'tag' each AtomSet with a proper property, the viewer could determine which ones should have the same center of gravity and only calculate the center of gravity for that particular set (some kind of cgID, a center of gravity ID). The Properties are not implemented yet, but we are getting close to that.
Another solution would be present if the hierarchical information can be defined. That way the list of atomSets that are related would be inherently know and the center of gravity for that particular set could be maintained independently from others. I like the latter best, because it also allows for the selection of set of atomSets that could be animated (e.g., the optimization of one molecule without going into the animation of the optimization of the next molecule). This is probably quite a bit in the future.
Just my two cents on this.
Ren�
On Oct 22, 2004, at 10:55 AM, Miguel wrote:
I have uncovered a problem when dealing with Gaussian files.
Detail
------
Rene has been helping/encouraging work on Gaussian files (and all the
other 'computational' packages like Gaussian). One of the changes he did
was retain all the intermediate steps during optimizations.
That is a good thing.
Now, the file samples/gaussian/H2O_NoSymm.out does not contain a 'Standard
orientation:' ... it only contains an 'Input orientation:'
In the spirit of the work that Rene has done I thought that I would also
store the 'Input orientation:' so that it could be displayed in Jmol. That
was easily done.
However, it uncovered a problem ... a problem that has not raised its ugly
head in a long time.
The 'center of gravity' of the molecules is calculated across all of the
models/frames. This is then used as the center of rotation for all models.
You cannot calculate the cg of each frame independently because:
- in multi-frame animations the atoms are moving ... therefore the cg of
each frame is different ... therefore the center of the frames is not
stable ... therefore you must calculate the cg of the frame set as a
whole
- in multi-model .pdb files with more than one conformation you want the
majority of the atoms to line up ... that way you can switch from one
conformation to another and see the areas that are different ...
therefore all the frames must have the same cg cartesian point.
The problem is that this approach does not work well when the Input
orientation: is included with the Gaussian set. This is because the Input
orientation: can be off-centered. So the center-of-gravity of the Input
orientation: messes up all the other models.
For the present time I am going to leave this code in ... so that you eager Gaussian users can take a look at it.
In the short term we can just 'sweep this problem under the rug' by
removing support for the 'Input orientation:' ... but in the longer term
we are going to have to come up with some solution.
Miguel
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