Out of curiousity, why did you puy the plot widget go into the
animation extension? I’d always envisioned this in the conformer
dialog.
I think Tim also imports MD trajectories, which go directly into the animations. Also, the conformer dialog is currently to generate conformers, not necessarily animate them.
It’s worth thinking about design / best use here. How would you want to use some of these features?
Cheers,
-Geoff
On Sun, Feb 21, 2010 at 8:24 PM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:
Out of curiousity, why did you puy the plot widget go into the
animation extension? I’d always envisioned this in the conformer
dialog.I think Tim also imports MD trajectories, which go directly into the animations. Also, the conformer dialog is currently to generate conformers, not necessarily animate them.
It’s worth thinking about design / best use here. How would you want to use some of these features?
I had just planned on having a plot to supplement the table, clicking
on a point would load the conformer and highlight the entry on the
table. The plot would be Energy vs. Conformer number, but that could
be modified to something else (not sure what…) if desired by a
couple of combo boxes.
If it’s more useful in Animation I have no objection to putting it
there, it just struck me as an odd location.
Dave
Hi,
On Mon, Feb 22, 2010 at 2:28 AM, David Lonie loniedavid@gmail.com wrote:
On Sun, Feb 21, 2010 at 8:24 PM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:Out of curiousity, why did you puy the plot widget go into the
animation extension? I’d always envisioned this in the conformer
dialog.I think Tim also imports MD trajectories, which go directly into the animations. Also, the conformer dialog is currently to generate conformers, not necessarily animate them.
It’s worth thinking about design / best use here. How would you want to use some of these features?
I had just planned on having a plot to supplement the table, clicking
on a point would load the conformer and highlight the entry on the
table. The plot would be Energy vs. Conformer number, but that could
be modified to something else (not sure what…) if desired by a
couple of combo boxes.If it’s more useful in Animation I have no objection to putting it
there, it just struck me as an odd location.
The reason why I put it in the animation dialog was because that was
the place I would go to if I wanted to see the results of my mopac
calculations. The animation extension’s time line changed together
with the selected conformer in the plot. It just seemed a logic place.
There might have been a practical reason too: If placed outside the
animation extension, there is no easy way to find out if the current
conformer has changed. A quick inspection of Molecule::setConformer
doesn’t seem to emit any signal. It might be possible using just
molecule’s update signal + Molecule::currentConformer()…
However, perhaps it’s even better to give this a separate dialog
called “Energy plot” or something. This would make sense when reading
in QM/MD trajectories right? Clicking the points would change the
displayed conformer.
Cheers,
Tim
Dave
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On Feb 21, 2010, at 10:12 AM, Geoffrey Hutchison wrote:
Forces can be stored, much like the optimizations and conformers in Avogadro. In principal, if the OB formats stored them, they would “magically” work in Avogadro.
So if you have latest trunk of OB an my “master” from GitHub, you can read conformers from Gaussian, including energies. I haven’t yet added forces.
It’s not quite automatic – we need some support in Molecule::setOBMol() but it’s not hard code.
Cheers,
-Geoff
On Feb 23, 2010, at 6:54 PM, Geoffrey Hutchison wrote:
So if you have latest trunk of OB an my “master” from GitHub, you can read conformers from Gaussian, including energies. I haven’t yet added forces.
Oh, I also haven’t checked yet if there’s an an “off-by-one” error between geometries and energies.
-Geoff
Is it possible to assign several ConformerData entries to OBMol for storage of multiple geometry optimizations?
23.02.10, 18:54, “Geoffrey Hutchison” geoff.hutchison@gmail.com:
On Feb 21, 2010, at 10:12 AM, Geoffrey Hutchison wrote:
Forces can be stored, much like the optimizations and conformers in Avogadro. In principal, if the OB formats stored them, they would “magically” work in Avogadro.
So if you have latest trunk of OB an my “master” from GitHub, you can read conformers from Gaussian, including energies. I haven’t yet added forces.
It’s not quite automatic – we need some support in Molecule::setOBMol() but it’s not hard code.
Cheers,
-Geoff
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proactively, and fine-tune applications for parallel performance.
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–
Regards,
Konstantin
Also, it’s needed to destinguish conformer data from optimization and other conformer data entries (e.g., if some file format contains several molecules in one file)
23.02.10, 18:54, “Geoffrey Hutchison” geoff.hutchison@gmail.com:
On Feb 21, 2010, at 10:12 AM, Geoffrey Hutchison wrote:
Forces can be stored, much like the optimizations and conformers in Avogadro. In principal, if the OB formats stored them, they would “magically” work in Avogadro.
So if you have latest trunk of OB an my “master” from GitHub, you can read conformers from Gaussian, including energies. I haven’t yet added forces.
It’s not quite automatic – we need some support in Molecule::setOBMol() but it’s not hard code.
Cheers,
-Geoff
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
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Regards,
Konstantin
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On Wed, Feb 24, 2010 at 02:55:34PM +0300, Konstantin Tokarev wrote:
Also, it’s needed to destinguish conformer data from optimization and
other conformer data entries (e.g., if some file format contains
several molecules in one file)
Yes, I think this would be something useful. For example, it would not
necessarily make much sense for the GUI to display the geometry change
between one conformer and the next for a random search or a MD
calculation; however it is useful information for geometry optimizations
(where the geometry change is one of the parameters to be optimized).
Michael
Added initial support for optimization import from gamess (also without forces)
–
Regards,
Konstantin