To Do projects for 1.1.x and 1.2

A while ago, Annulen asked about release plans for 1.x and 1.2. I created a page for this:
http://avogadro.openmolecules.net/wiki/To_Do_for_1.1

I added a few projects I’m working on – I think an important point is that we should think carefully about any tasks which need improvements in Open Babel. For example, support for following geometry optimizations or energy scans in QM codes will need improved import code in OB. My suggestion is to discuss both on the wiki and the mailing list.

Perhaps David and Konstantin could fill in some of the work they’ve already finished? :slight_smile:

Cheers,
-Geoff

A while ago, Annulen asked about release plans for 1.x and 1.2. I created a page for this:
http://avogadro.openmolecules.net/wiki/To_Do_for_1.1
I added a few projects I’m working on – I think an important point is that we should think carefully about any tasks which need improvements in Open Babel. For example, support for following geometry optimizations or energy scans in QM codes will need improved import code in OB. My suggestion is to discuss both on the wiki and the mailing list.

Is this plan for 1.1.0 or 1.2?


Regards,
Konstantin

On Feb 21, 2010, at 6:09 AM, Konstantin Tokarev wrote:

Is this plan for 1.1.0 or 1.2?

Both. Just like we had multiple “development” releases of 0.9.x leading up to the stable 1.0 release, we will have multiple “development” releases of 1.1.x leading up to 1.2.0.

This policy seemed to work fairly well for 0.9.x – users interested in unstable releases could grab them. I think it will be more useful now, since we can point users at the latest stable releases while we experiment a bit leading up to 1.2.

-Geoff

21.02.10, 07:28, “Geoffrey Hutchison” geoff.hutchison@gmail.com:

On Feb 21, 2010, at 6:09 AM, Konstantin Tokarev wrote:

Is this plan for 1.1.0 or 1.2?
Both. Just like we had multiple “development” releases of 0.9.x leading up to the stable 1.0 release, we will have multiple “development” releases of 1.1.x leading up to 1.2.0.
This policy seemed to work fairly well for 0.9.x – users interested in unstable releases could grab them. I think it will be more useful now, since we can point users at the latest stable releases while we experiment a bit leading up to 1.2.

Maybe it’s worth to divide todo for 1.1.0 and 1.2.0? to know, what’s likely to be finished in 1.1.0


Regards,
Konstantin

For example, I’m very interested in geometry optimization support, which you stated in TODO. What’s going on this front (I also mean OB)?

Regards,
Konstantin

For example, I’m very interested in geometry optimization support, which you stated in TODO. What’s going on this front (I also mean OB)?

Each input format just needs some additional code. I’d be happy to work out an example for you – say with Gaussian in the next day or so.

-Geoff

On Sun, Feb 21, 2010 at 08:19:20AM -0500, Geoffrey Hutchison wrote:

For example, I’m very interested in geometry optimization support,
which you stated in TODO. What’s going on this front (I also mean
OB)?

Each input format just needs some additional code. I’d be happy to
work out an example for you – say with Gaussian in the next day or
so.

I could pick up a couple of formats to convert, however, I am not sure
on what the status for OB is? How are geometry optimizations going to
be implemented?

Michael

I could pick up a couple of formats to convert, however, I am not sure
on what the status for OB is? How are geometry optimizations going to
be implemented?

There’s already implementation – geometry optimizations or reaction coordinates would be stored as conformers. OB will have a set of coordinates and corresponding energies.

Hope that helps,
-Geoff

On Saturday, February 20, 2010, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

Perhaps David and Konstantin could fill in some of the work they’ve already finished? :slight_smile:

I’ve not done much since 1.0 except work on my extensions, so I’m
afraid there’s not much I can add at the moment. I remember Tim
mentioning something about a plot of conformer energies – Has any
code been added for this? I may work on that if it’s not already in
the works.

Dave

21.02.10, 08:19, “Geoffrey Hutchison” geoff.hutchison@gmail.com:

For example, I’m very interested in geometry optimization support, which you stated in TODO. What’s going on this front (I also mean OB)?
Each input format just needs some additional code.

Of course

I’d be happy to work out an example for you – say with Gaussian in the next day or so.

Can you give more details? Will you add optimization steps as conformers?
I’m also inrested in relaxed scans (don’t know if they are supported by Gaussian, I only used this feature in PCGamess). Relaxed scan looks like several geometry optimizations in one run with one of internal coordinates (e.g., dihedral angle of internal rotation) fixed in every optimization and changed on given value in the next one.Also, such programs as Molpro or NWChem support multiple optimizations in single run. So, list of step lists is also needed to get them displayed separately


Regards,
Konstantin

On Sun, Feb 21, 2010 at 08:33:35AM -0500, Geoffrey Hutchison wrote:

I could pick up a couple of formats to convert, however, I am not sure
on what the status for OB is? How are geometry optimizations going to
be implemented?

There’s already implementation – geometry optimizations or reaction
coordinates would be stored as conformers. OB will have a set of
coordinates and corresponding energies.

What about forces, step sizes etc.? Will those be stored as well, or
just the energy?

Michael

On Sun, Feb 21, 2010 at 9:56 AM, Michael Banck mbanck@gmx.net wrote:

On Sun, Feb 21, 2010 at 08:33:35AM -0500, Geoffrey Hutchison wrote:

I could pick up a couple of formats to convert, however, I am not sure
on what the status for OB is? How are geometry optimizations going to
be implemented?

There’s already implementation – geometry optimizations or reaction
coordinates would be stored as conformers. OB will have a set of
coordinates and corresponding energies.

What about forces, step sizes etc.? Will those be stored as well, or
just the energy?

Forces in particular would be fantastic for me as well…

21.02.10, 15:56, “Michael Banck” mbanck@gmx.net:

On Sun, Feb 21, 2010 at 08:33:35AM -0500, Geoffrey Hutchison wrote:

I could pick up a couple of formats to convert, however, I am not sure
on what the status for OB is? How are geometry optimizations going to
be implemented?

There’s already implementation – geometry optimizations or reaction
coordinates would be stored as conformers. OB will have a set of
coordinates and corresponding energies.
What about forces, step sizes etc.? Will those be stored as well, or
just the energy?

Geoff: maybe some new API is needed, not just conformers?

Regards,
Konstantin

I’ve not done much since 1.0 except work on my extensions, so I’m
afraid there’s not much I can add at the moment.

Could you at least document what you’ve added so far in your extensions? IIRC, you’ve added crystallographic coordinate editing, CD, UV/Vis, and DOS spectra graphing?

I remember Tim mentioning something about a plot of conformer energies – Has any
code been added for this?

No, that hasn’t been added yet, but would be greatly appreciated, I’m sure.

-Geoff

On Feb 21, 2010, at 10:00 AM, David Lonie wrote:

What about forces, step sizes etc.? Will those be stored as well, or
just the energy?

Forces in particular would be fantastic for me as well…

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.

Cheers,
-Geoff

On Sunday, February 21, 2010, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

I’ve not done much since 1.0 except work on my extensions, so I’m
afraid there’s not much I can add at the moment.

Could you at least document what you’ve added so far in your extensions? IIRC, you’ve added crystallographic coordinate editing, CD, UV/Vis, and DOS spectra graphing?

The wiki should be pretty up to date as far as spectra are concerned
– Konstantin has been working on some new features in spectra lately,
when those get merged with cryos/master we can update the spectra
page.

Are we including the new coordinate editor in these releases? The
crystallographic editor functionality is only in the new one.

Other than that, all my time has been going into the xtalopt
extension, which will be pretty well documented when it goes public :smiley:

I remember Tim mentioning something about a plot of conformer energies – Has any
code been added for this?

No, that hasn’t been added yet, but would be greatly appreciated, I’m sure.

Ok. If I get some free time or need to escape writing this paper at
some point I’ll put that in :wink:

Dave

On Feb 21, 2010, at 9:56 AM, Michael Banck wrote:

What about forces, step sizes etc.? Will those be stored as well, or
just the energy?

I don’t know exactly what you mean by “step sizes”, but many things can be stored in OBConformerData records:
http://openbabel.org/api/2.2.0/classOpenBabel_1_1OBConformerData.shtml

On Feb 21, 2010, at 8:54 AM, Konstantin Tokarev wrote:

I’m also inrested in relaxed scans (don’t know if they are supported by Gaussian, I only used this feature in PCGamess). Relaxed scan looks like several geometry optimizations in one run with one of internal coordinates (e.g., dihedral angle of internal rotation) fixed in every optimization and changed on given value in the next one.Also, such programs as Molpro or NWChem support multiple optimizations in single run. So, list of step lists is also needed to get them displayed separately

Well, I think the end question is how you’d want this to appear in Avogadro. My guess is that a relaxed scan might look like a large set of conformers, but storing the list of step lists – that could be done, for example in the OBConformerData::_vData vector.

Hope that helps,
-Geoff

I’m also inrested in relaxed scans (don’t know if they are supported by Gaussian, I only used this feature in PCGamess). Relaxed scan looks like several geometry optimizations in one run with one of internal coordinates (e.g., dihedral angle of internal rotation) fixed in every optimization and changed on given value in the next one.Also, such programs as Molpro or NWChem support multiple optimizations in single run. So, list of step lists is also needed to get them displayed separately
Well, I think the end question is how you’d want this to appear in Avogadro.

Like this: http://avogadro.openmolecules.net/wiki/Chemcraft
i.e., use tree view
I don’t think it’s necessary to put vibrations to the same tree view, as it’s done in Chemcraft, but they could be in different tabs of the same (“computational”) dock with vibrations

Regards,
Konstantin

On Sun, Feb 21, 2010 at 2:54 PM, David Lonie loniedavid@gmail.com wrote:

On Saturday, February 20, 2010, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

Perhaps David and Konstantin could fill in some of the work they’ve already finished? :slight_smile:

I’ve not done much since 1.0 except work on my extensions, so I’m
afraid there’s not much I can add at the moment. I remember Tim
mentioning something about a plot of conformer energies – Has any
code been added for this? I may work on that if it’s not already in
the works.

I have experimented with this by adding a plot widget to the animate
dialog so that looping through the frames would update the plot widget
by selecting the associated point. However, this code is on the hard
drive in my desktop which has a broken main board. I returned it to
the shop since it was only 6 months old but it might take up to 2
months before I get a replacement :frowning:

Should I make a new attempt at implementing this again? I’m also on
IRC in case someone wants to give this a try and needs help…

Tim

Dave


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On Sun, Feb 21, 2010 at 3:31 PM, Tim Vandermeersch
tim.vandermeersch@gmail.com wrote:

On Sun, Feb 21, 2010 at 2:54 PM, David Lonie loniedavid@gmail.com wrote:

On Saturday, February 20, 2010, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

Perhaps David and Konstantin could fill in some of the work they’ve already finished? :slight_smile:

I’ve not done much since 1.0 except work on my extensions, so I’m
afraid there’s not much I can add at the moment. I remember Tim
mentioning something about a plot of conformer energies – Has any
code been added for this? I may work on that if it’s not already in
the works.

I have experimented with this by adding a plot widget to the animate
dialog so that looping through the frames would update the plot widget
by selecting the associated point. However, this code is on the hard
drive in my desktop which has a broken main board. I returned it to
the shop since it was only 6 months old but it might take up to 2
months before I get a replacement :frowning:

Should I make a new attempt at implementing this again? I’m also on
IRC in case someone wants to give this a try and needs help…

Out of curiousity, why did you puy the plot widget go into the
animation extension? I’d always envisioned this in the conformer
dialog.

Dave
Dave