Dear Geoff, Thanks a lot for you help and your patience. Im very sorry for my delay in this mail. I would like to know if possible to see the ferroelectric behavior of 1, 2, n molecules up to form a unit cell. One example of what I would like to model is the croconic acid (Horiuchi) in just one molecule and "apply" an electric field and the same with the crystal unit cell. I know for instance HyperChem can do this easily. I would like to try Avogadro or other free software (I accept kind suggestions ;) ). In the other hand, about the mineralogy of polymorphs I work with biominerals and FTIR. For the model Im interested in CaCO3 in shells (aragonite, calcite) and in this case, I would like to know the environment when a molecule "feels" the most stable conformation. I mean, beginning from one molecule of CaCO3 up to the formation of the CaCO3 polymorph unit cell. I would like to develop this two ideas by using Avogadro...having a difficulty. Nobody in my environment works with modeling and I just used HyperChem before. Anyhow Im always very glad to know new methods and suggestions as to publish nice results.
Kindest Regards, Alex (Horiuchi) http://www.physorg.com/wire-news/29836312/discovery-of-ferroelectricity-of-croconic-acid-a-low-molecular-w.html Message: 7 Date: Wed, 02 Nov 2011 10:28:09 -0400 From: Geoff Hutchison <[email protected]> Subject: Re: [Avogadro-Discuss] Electric field and stability of a unit cell To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=us-ascii Dear Alex, > My name is Alejandro Heredia Barbero and I try to measure the effect > of an electric field in organic molecules. I'm not quite sure what you mean here. There are many possible effects of an electric field on an organic molecule -- not the least of which is a change in the electron density due to polarizability (and non-linear effects). Most of these effects are best treated with various quantum chemistry packages, like MOPAC or Gaussian. (Although not all quantum packages can treat electric fields.) This is one area of my research, so if you can be a bit more specific, I'm sure we can help you. > this. Additionally to this, I would like to do an insight in stability > of molecules when are in polymorphs. Your help would be very important > for my professional activities. Again, I'm not sure I completely understand what you wish to learn. Do you wish to find different polymorphs for a given compound? Or do you have different polymorph crystal structures and you wish to calculate which is the most stable form? The latter is definitely easier, but also requires a quantum package, for example ABINIT or VASP. Hope that helps, -Geoff On 17 November 2011 17:18, <[email protected]> wrote: > Send Avogadro-Discuss mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/avogadro-discuss > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Avogadro-Discuss digest..." > > > Today's Topics: > > 1. Re: Status of PyQt signals (Noel O'Boyle) > 2. problems to visualize molecules (leonardo espinosa) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 17 Nov 2011 17:10:48 +0100 > From: "Noel O'Boyle" <[email protected]> > Subject: Re: [Avogadro-Discuss] Status of PyQt signals > To: [email protected] > Message-ID: > <CAOC-GK22J8yV309m=wfoyw4lvqk-hahguswxqms_3lbaap4...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Actually it seems to be working now :-) My only problem is that I > can't figure out exactly why it was failing before... > > - Noel > > On 17 November 2011 15:55, Noel O'Boyle <[email protected]> wrote: >> Hi all, >> >> I've been successfully usnig basic Signals from PyQt (Avo 1.0.1+Python >> on Windows) but I'm ready to throw in the towel on using signals with >> parameters: >> >> I have a QTableWidget and am trying to catch the signal when someone >> clicks on a cell: >> >> ? ?QObject.connect(self.allpharmas, >> ? ? ? ? ? ? ? ? ? ?SIGNAL("currentCellChanged(int, int, int, int)"), >> ? ? ? ? ? ? ? ? ? ?self, SLOT("selectPharmacophore(int,int,int,int)")) >> >> The signal never arrives at selectPharmacophore: >> ?@pyqtSignature("int,int,int,int") >> ?def selectPharmacophore(self, a, b, c, d): >> ? ?self.debug("select pharmacophore") >> >> Does anyone know whether I am doing something wrong here? If these >> signals aren't usable it really limits the possibilities of extending >> Avo through Python. >> >> - Noel >> > > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Nov 2011 17:00:42 +0100 > From: leonardo espinosa <[email protected]> > Subject: [Avogadro-Discuss] problems to visualize molecules > To: [email protected] > Message-ID: > <cacqbx0z5rndo3oyeqonvf1vsnng7kimbmbmfbbqsttjjjxr...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear avogadro users, > > I've been using avogadro since a couple of months ago, it worked perfectly > on the last Ubuntu versions (10.04 and 10.10), > a couple of weeks ago I upgrade to 11.04 and since this I have problems > opening xyz and pdb files, I attached you a > snapshot of the screen and the terminal message: > > QStackedLayout::setCurrentWidget: Widget 0x18d3750 not contained in stack > libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area > Gtk-Message: (for origin information, set GTK_DEBUG): failed to retrieve > property `GtkWidget::visited-link-color' of type `GdkColor' from rc file > value "((GString*) 0x24b22e0)" of type `GString' > > All the best, > > -- > =============================================== > Leonardo Andr?s Espinosa Leal > PhD student of PNAM (Physics of Nanostructures and Advanced Materials) > Nano-Bio Spectroscopy Group (web: http://nano-bio.ehu.es/) > University of the Basque Country / Euskal Herriko Unibertsitatea (UPV/EHU) > Materials Physics Center (http://cfm.ehu.es/) > Donostia-San Sebasti?n, Gip?zkoa (Spain) > _____________________________________________________ > European Theoretical Spectroscopy Facility (ETSF), Spanish node > web: http://www.etsf.es/ > Joxe Mari Korta building, Av. de Tolosa, 72, 20018. ETSF rooms > Donostia-San Sebasti?n, Gipuzkoa (Spain). > _____________________________________________________ > Contact: > Phone: +34 943018820 Fax: +34 943018390 > Mobile:+34 655731411 > *alternative emails*: > email1: laespinosa001 [at] ikasle [dot] ehu [dot] es > email2: espinosa [dot] leal [at] gmail [dot] com > skype: espinosa [dot] leal > ================================================ > -------------- next part -------------- > An HTML attachment was scrubbed... > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: avogadro-bug.png > Type: image/png > Size: 180946 bytes > Desc: not available > > ------------------------------ > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. 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