Animate anything other than xyz files

Is it possible to use Avogadro to animate anything other than xyz format
files? I’m particularly interested in anything that allows crystal
structures.


Rick Muller
rpmuller@gmail.com

Is it possible to use Avogadro to animate anything other than xyz format files? I’m particularly interested in anything that allows crystal structures.

I think it also animates GROMACS “xtc” files. But I can probably cook something up with the Open Babel “free form fractional” format, if that works:
http://openbabel.org/wiki/Free_Form_Fractional

Are you willing to try a development version?

-Geoff

Geoff,

Absolutely willing to use a dev version. Didn’t know about the OB freeform
fractional format.

I was wondering whether CML could do anything like this. Is something like
this valid CML?

Water Water

Avogadro can read this, but only displays the first geometry. Can obviously
also put fields in to make this periodic as well.

On Sat, Sep 11, 2010 at 5:36 PM, Geoffrey Hutchison <
geoff.hutchison@gmail.com> wrote:

Is it possible to use Avogadro to animate anything other than xyz format
files? I’m particularly interested in anything that allows crystal
structures.

I think it also animates GROMACS “xtc” files. But I can probably cook
something up with the Open Babel “free form fractional” format, if that
works:
http://openbabel.org/wiki/Free_Form_Fractional

Are you willing to try a development version?

-Geoff


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rpmuller@gmail.com
505-750-7557

Absolutely willing to use a dev version. Didn’t know about the OB freeform fractional format.

Actually, the original Babel had it too. I just adopted it before OB had support for CIF. I mentioned it, because it’s as close to XYZ as possible, and should support animations, just like XYZ.

(Hmm, I just checked, and there’s a filter in the “Animate…” dialog. I’ll fix that.)

I was wondering whether CML could do anything like this. Is something like this valid CML?

Not quite. XML documents have to have a root element. So you’d have to do something like:

... ...

Avogadro can read this, but only displays the first geometry. Can obviously also put fields in to make this periodic as well.

Weird. As I said, the Avogadro code which reads files has code to detect identical atom lists. I should have a bit of time tomorrow evening to take a look.

Thanks for the report!
-Geoff

Thanks, Geoff. Let me know, and I’ll check out the dev version.

On Sun, Sep 12, 2010 at 7:20 PM, Geoffrey Hutchison <
geoff.hutchison@gmail.com> wrote:

Absolutely willing to use a dev version. Didn’t know about the OB
freeform fractional format.

Actually, the original Babel had it too. I just adopted it before OB had
support for CIF. I mentioned it, because it’s as close to XYZ as possible,
and should support animations, just like XYZ.

(Hmm, I just checked, and there’s a filter in the “Animate…” dialog. I’ll
fix that.)

I was wondering whether CML could do anything like this. Is something
like this valid CML?

Not quite. XML documents have to have a root element. So you’d have to do
something like:

... ...

Avogadro can read this, but only displays the first geometry. Can
obviously also put fields in to make this periodic as well.

Weird. As I said, the Avogadro code which reads files has code to detect
identical atom lists. I should have a bit of time tomorrow evening to take a
look.

Thanks for the report!
-Geoff


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and start using them to simplify application deployment and
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Rick Muller
rpmuller@gmail.com
505-750-7557

Geoff,

Just downloaded the 9/14 nightly build, but it still looks like the filter
is in the Animate dialog. Have you had time to look at this yet? I’ve
corrected my animated CML file with the root element.

On Mon, Sep 13, 2010 at 9:02 AM, Rick Muller rpmuller@gmail.com wrote:

Thanks, Geoff. Let me know, and I’ll check out the dev version.

On Sun, Sep 12, 2010 at 7:20 PM, Geoffrey Hutchison <
geoff.hutchison@gmail.com> wrote:

Absolutely willing to use a dev version. Didn’t know about the OB
freeform fractional format.

Actually, the original Babel had it too. I just adopted it before OB had
support for CIF. I mentioned it, because it’s as close to XYZ as possible,
and should support animations, just like XYZ.

(Hmm, I just checked, and there’s a filter in the “Animate…” dialog.
I’ll fix that.)

I was wondering whether CML could do anything like this. Is something
like this valid CML?

Not quite. XML documents have to have a root element. So you’d have to do
something like:

... ...

Avogadro can read this, but only displays the first geometry. Can
obviously also put fields in to make this periodic as well.

Weird. As I said, the Avogadro code which reads files has code to detect
identical atom lists. I should have a bit of time tomorrow evening to take a
look.

Thanks for the report!
-Geoff


Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing
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Rick Muller
rpmuller@gmail.com
505-750-7557


Rick Muller
rpmuller@gmail.com
505-750-7557

Just downloaded the 9/14 nightly build, but it still looks like the filter is in the Animate dialog. Have you had time to look at this yet? I’ve corrected my animated CML file with the root element.

No, sorry, things have been crazy here. I should be able to give that a try tomorrow morning and I’ll send you an e-mail. I probably need a fix in the reading code too – it’s not just changing the filter.

Best regards,
-Geoff

No worries. Let me know when to check the code. If I get bored, I’ll learn
how to build from source.

On Wed, Sep 15, 2010 at 3:50 PM, Geoffrey Hutchison <
geoff.hutchison@gmail.com> wrote:

Just downloaded the 9/14 nightly build, but it still looks like the
filter is in the Animate dialog. Have you had time to look at this yet? I’ve
corrected my animated CML file with the root element.

No, sorry, things have been crazy here. I should be able to give that a try
tomorrow morning and I’ll send you an e-mail. I probably need a fix in the
reading code too – it’s not just changing the filter.

Best regards,
-Geoff


Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
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Rick Muller
rpmuller@gmail.com
505-750-7557

Just downloaded the 9/14 nightly build, but it still looks like the filter is in the Animate dialog. Have you had time to look at this yet? I’ve corrected my animated CML file with the root element.

Give the unstable 9/16 nightly build a try. Don’t worry about the “load file” filter in the Animate dialog. This is a hack and needs a deeper fix. If you open your CML file, it should have the frames as conformers. The animation interface should know what to do from there.

(The bug was in the code which attempted to read conformers in a file like yours – it read the conformers and the the GUI threw them away. Oops.)

Thanks and best regards,
-Geoff

Didn’t work for me, but I downloaded the 9/17 build. Going to retry with the
9/16 build, just in case that was a one-off…

FYI, here’s is the file I’m trying to load. It’s a two-frame version of my
earlier example with a proper root element. Only loads the first frame.

Water Water

On Thu, Sep 16, 2010 at 3:39 PM, Geoffrey Hutchison <
geoff.hutchison@gmail.com> wrote:

Just downloaded the 9/14 nightly build, but it still looks like the
filter is in the Animate dialog. Have you had time to look at this yet? I’ve
corrected my animated CML file with the root element.

Give the unstable 9/16 nightly build a try. Don’t worry about the “load
file” filter in the Animate dialog. This is a hack and needs a deeper fix.
If you open your CML file, it should have the frames as conformers. The
animation interface should know what to do from there.

(The bug was in the code which attempted to read conformers in a file like
yours – it read the conformers and the the GUI threw them away. Oops.)

Thanks and best regards,
-Geoff


Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
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Rick Muller
rpmuller@gmail.com
505-750-7557

Didn’t work for me, but I downloaded the 9/17 build. Going to retry with the 9/16 build, just in case that was a one-off…

Try http://avogadro.openmoleules.net/nightly/mac/unstable/Avogadro-nightly.dmg.zip

This is the latest unstable daily build. I can confirm both 9/16 and 9/17 work for me. The stable build (of 1.0.x) doesn’t have the fix – we’re very conservative in backporting fixes.

Hope that helps,
-Geoff

Yep, that worked. Thanks!

I really appreciate how conservative you are about the builds. It’s a very
professionally run project.

On Sat, Sep 18, 2010 at 10:59 AM, Geoffrey Hutchison <
geoff.hutchison@gmail.com> wrote:

Didn’t work for me, but I downloaded the 9/17 build. Going to retry with
the 9/16 build, just in case that was a one-off…

Try http://avogadro.openmoleules.net/nightly/mac/unstable/
Avogadro-nightly.dmg.ziphttp://avogadro.openmolecules.net/nightly/mac/unstable/Avogadro-nightly.dmg.zip

This is the latest unstable daily build. I can confirm both 9/16 and 9/17
work for me. The stable build (of 1.0.x) doesn’t have the fix – we’re very
conservative in backporting fixes.

Hope that helps,
-Geoff


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Rick Muller
rpmuller@gmail.com
505-750-7557