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:geo...@pitt.edu] 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: geo...@pitt.edu web: http://hutchison.chem.pitt.edu/ ---------------------------------------------------------------------------- -- Slashdot TV. Video for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg.clktrk _______________________________________________ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss ------------------------------------------------------------------------------ Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk _______________________________________________ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
