Saving with more significant figures

General Discussion
1

Dear Avogadro users,

I would like to save my molecules as a .xyz file, but this only gives me xyz
coordinates with up to 5 decimal places. Is there any way that I can
increase the number of decimal places outputted by Avogadro? Thank you!

Benjamin

2

I would like to save my molecules as a .xyz file, but this only gives me xyz coordinates with up to 5 decimal places. Is there any way that I can increase the number of decimal places outputted by Avogadro? Thank you!

I think my main question is why? You really need accuracy beyond 0.00001 (i.e., 1/100 000 Angstrom)? I guess that’s 1 fm?

Are you running into some problem with geometry convergence? The Open Babel code (used by Avogadro) trims coordinates to 5 decimal places for XYZ files to save disk space.

It’s certainly possible to change Open Babel to output more decimals, but I’d be curious what problem you’re encountering.

Thanks,
-Geoff

3

Dear Avogadro users, I would like to save my molecules as a .xyz file, but this only gives me xyz coordinates with up to 5 decimal places. Is there any way that I can increase the number of decimal places outputted by Avogadro? Thank you! Benjamin

4

I’m pretty sure I answered this previously (on 9/14):

I think my main question is why? You really need accuracy beyond 0.00001 (i.e., 1/100 000 Angstrom)? I guess that’s 1 fm?

Are you running into some problem with geometry convergence? The Open Babel code (used by Avogadro) trims coordinates to 5 decimal places for XYZ files to save disk space.

It’s certainly possible to change Open Babel to output more decimals, but I’d be curious what problem you’re encountering.

Thanks,
-Geoff

Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/

5

Dear Geoff,

Thanks for your reply. I ask this question because I have noticed some
differences in energy after I have taken the coordinates of my system from
the output of my program, imported it into Avogadro, saved it as an xyz file
(without any changes made) and run it in my program again. As some atoms of
my system are fixed, re-optimization of the system will not fix the small
discrepancies in atomic positions caused by the small losses in accuracy
when saving. The differences in energy are not large (~1kJ mol-1 for my
system) but still noticeable.

In addition, I have found that when I take differences in charge density,
the coordinates of the fixed atoms have to be exactly in the same position
for the two charge density files, or there will be artefacts in the charge
density difference.

Thus I was hoping that one could save in more significant figures, since I
have noticed that the Cartesian editor is much more accurate, and thought it
might be possible to transfer that accuracy into the output xyz files. Hope
this makes my argument clearer. Thank you!

Best wishes,
Benjamin

-----Original Message-----
From: Geoffrey Hutchison [mailto:geoff.hutchison@gmail.com]
Sent: Friday, 19 September 2014 11:13 AM
To: avogadro-discuss@lists.sourceforge.net
Subject: Re: [Avogadro-Discuss] Saving with more significant figures

I’m pretty sure I answered this previously (on 9/14):

I think my main question is why? You really need accuracy beyond 0.00001
(i.e., 1/100 000 Angstrom)? I guess that’s 1 fm?

Are you running into some problem with geometry convergence? The Open
Babel code (used by Avogadro) trims coordinates to 5 decimal places for XYZ
files to save disk space.

It’s certainly possible to change Open Babel to output more decimals, but
I’d be curious what problem you’re encountering.

Thanks,
-Geoff

Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/

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