From: Noel O'B. <bao...@gm...> - 2007-11-28 14:33:20
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Geoff is interested in point group symmetry code... ---------- Forwarded message ---------- From: Geoffrey Hutchison <ge...@pi...> Hi guys, I've been toying around with the point group symmetry code that was GPL'ed by Dr. Serguei Patchkovskii http://www.cobalt.chem.ucalgary.ca/ps/symmetry/ I've found that while it looks like it has great capabilities (strange higher-order symmetry like C7 and S7 rotations), it doesn't work very well. For example, I drew benzene in Avogadro, ran an optimization and saved it. The molecule is in the Z=0 plane, but slightly out of center and not aligned to the X or Y axes. (In short, a typical aromatic benzene with equal bond lengths.) All it finds is the mirror plane along Z=0. So I'm curious to ask you two: as part of the cclib work, whether you've come across some *robust* point group symmetry recognition code? Thanks, -Geoff ------------------------------------------- Geoff Hutchison Assistant Professor University of Pittsburgh, Department of Chemistry 219 Parkman Avenue Pittsburgh, PA 15260 |
From: Noel O'B. <bao...@gm...> - 2007-11-28 14:38:56
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I was hoping that Sergei's code would do the job as this would be a really useful capability. My only suggestion is to trawl through known open source codes, e.g.: http://www.google.com/codesearch?q=C2v+D3h&hl=en&btnG=Search+Code :-/ Noel On 28/11/2007, Noel O'Boyle <bao...@gm...> wrote: > Geoff is interested in point group symmetry code... > > ---------- Forwarded message ---------- > From: Geoffrey Hutchison <ge...@pi...> > > Hi guys, > > I've been toying around with the point group symmetry code that was > GPL'ed by Dr. Serguei Patchkovskii > http://www.cobalt.chem.ucalgary.ca/ps/symmetry/ > > I've found that while it looks like it has great capabilities (strange > higher-order symmetry like C7 and S7 rotations), it doesn't work very > well. For example, I drew benzene in Avogadro, ran an optimization and > saved it. The molecule is in the Z=0 plane, but slightly out of center > and not aligned to the X or Y axes. (In short, a typical aromatic > benzene with equal bond lengths.) > > All it finds is the mirror plane along Z=0. > > So I'm curious to ask you two: as part of the cclib work, whether > you've come across some *robust* point group symmetry recognition code? > > Thanks, > -Geoff > > ------------------------------------------- > Geoff Hutchison > Assistant Professor > University of Pittsburgh, Department of Chemistry > 219 Parkman Avenue > Pittsburgh, PA 15260 > |
From: Noel O'B. <bao...@gm...> - 2007-11-28 14:41:11
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In GaussView there is a setting for how 'strict' the point group detection software is. Is there some similar 'epsilon' value you can set for Sergei's code? On 28/11/2007, Noel O'Boyle <bao...@gm...> wrote: > I was hoping that Sergei's code would do the job as this would be a > really useful capability. My only suggestion is to trawl through known > open source codes, e.g.: > > http://www.google.com/codesearch?q=C2v+D3h&hl=en&btnG=Search+Code > > :-/ > > Noel > > On 28/11/2007, Noel O'Boyle <bao...@gm...> wrote: > > Geoff is interested in point group symmetry code... > > > > ---------- Forwarded message ---------- > > From: Geoffrey Hutchison <ge...@pi...> > > > > Hi guys, > > > > I've been toying around with the point group symmetry code that was > > GPL'ed by Dr. Serguei Patchkovskii > > http://www.cobalt.chem.ucalgary.ca/ps/symmetry/ > > > > I've found that while it looks like it has great capabilities (strange > > higher-order symmetry like C7 and S7 rotations), it doesn't work very > > well. For example, I drew benzene in Avogadro, ran an optimization and > > saved it. The molecule is in the Z=0 plane, but slightly out of center > > and not aligned to the X or Y axes. (In short, a typical aromatic > > benzene with equal bond lengths.) > > > > All it finds is the mirror plane along Z=0. > > > > So I'm curious to ask you two: as part of the cclib work, whether > > you've come across some *robust* point group symmetry recognition code? > > > > Thanks, > > -Geoff > > > > ------------------------------------------- > > Geoff Hutchison > > Assistant Professor > > University of Pittsburgh, Department of Chemistry > > 219 Parkman Avenue > > Pittsburgh, PA 15260 > > > |
From: Geoffrey H. <ge...@ge...> - 2007-11-28 15:33:09
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On Nov 28, 2007, at 9:41 AM, Noel O'Boyle wrote: > In GaussView there is a setting for how 'strict' the point group > detection software is. Is there some similar 'epsilon' value you can > set for Sergei's code? Yes. There are a variety of options, including how many "optimization" steps you can make. The problem seems to be in the initial recognition phase. I'm going to continue to play with it, but I'm worried when benzene shows up as Cs and it doesn't even find any plausible C2 axes or other mirror planes. A Google search this morning did turn up some code in GAMGI, which I'll examine. Cheers, -Geoff |