Dear Geoff, Dear Avogadro Forum, Sorry that I was not clear in my question. I want to model the ferroelectric behavior in the croconic acid and its FTIR. I want to publish using avogadro and for this collaborations are very welcome. Additionally to that I have a crash in the avogadro 1.0.3.
Thanks a lot, Alex Problem signature: Problem Event Name: APPCRASH Application Name: avogadro.exe Application Version: 0.0.0.0 Application Timestamp: 4db4b9a7 Fault Module Name: openbabel-2.dll Fault Module Version: 0.0.0.0 Fault Module Timestamp: 4db1fa94 Exception Code: c0000005 Exception Offset: 00006414 OS Version: 6.0.6002.2.2.0.768.3 Locale ID: 1033 Additional Information 1: fd00 Additional Information 2: ea6f5fe8924aaa756324d57f87834160 Additional Information 3: fd00 Additional Information 4: ea6f5fe8924aaa756324d57f87834160 Read our privacy statement: http://go.microsoft.com/fwlink/?linkid=50163&clcid=0x0409 On 25 November 2011 18:09, <[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: problems to visualize molecules (Geoff Hutchison) > 2. Drawing from GAMESS ([email protected]) > 3. Re: [SPAM] Drawing from GAMESS (Jan Halborg Jensen) > 4. Re: Avogadro-Discuss Digest, Vol 28, Issue 3 (Alejandro Heredia) > 5. atomic charges on each atom (Victor Eduardo Bahamonde Padilla) > 6. Re: atomic charges on each atom (David Lonie) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 18 Nov 2011 16:22:51 -0500 > From: Geoff Hutchison <[email protected]> > Subject: Re: [Avogadro-Discuss] problems to visualize molecules > To: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset=iso-8859-1 > >> 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' > > There are warning messages, but not indicators of errors. I suspect that > upgrading has given you a lousy OpenGL driver. These types of artifacts are > typical of driver issues on Windows and Linux. > > -Geoff > > > > > ------------------------------ > > Message: 2 > Date: Mon, 21 Nov 2011 14:31:45 +0100 > From: [email protected] <[email protected]> > Subject: [Avogadro-Discuss] Drawing from GAMESS > To: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset="utf-8" > > > Good morning, > > How can I draw molecular densities from GAMESS output? > > Thanks > > > > ------------------------------------------------------- > @@@@@@@@@@@@@@@@@@@@@ > "It is said that mathematics is the language of nature. If so, then physics > is its poetry" > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 3 > Date: Mon, 21 Nov 2011 13:47:27 +0000 > From: Jan Halborg Jensen <[email protected]> > Subject: Re: [Avogadro-Discuss] [SPAM] Drawing from GAMESS > To: "<[email protected]>" > <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="us-ascii" > > Here is a short description: > http://molecularmodelingbasics.blogspot.com/2009/11/electron-density-reloaded.html > > Best regards, Jan > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- > Jan H. Jensen Professor > Department of Chemistry [email protected] **NEW** > University of Copenhagen Phone: +45 35 32 02 39 > Universitetsparken 5 FAX: +45 35 32 02 14 > 2100 Copenhagen Denmark > http://tinyurl.com/jhjensen > http://molecularmodelingbasics.blogspot.com > http://proteinsandwavefunctions.blogspot.com/ > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- > > > On Nov 21, 2011, at 2:31 PM, [email protected] wrote: > >> >> Good morning, >> >> How can I draw molecular densities from GAMESS output? >> >> Thanks >> >> >> >> ------------------------------------------------------- >> @@@@@@@@@@@@@@@@@@@@@ >> "It is said that mathematics is the language of nature. If so, then physics >> is its poetry" >> >> ------------------------------------------------------------------------------ >> 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. IT sense. And common sense. >> http://p.sf.net/sfu/splunk-novd2d_______________________________________________ >> Avogadro-Discuss mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/avogadro-discuss > > > > > > ------------------------------ > > Message: 4 > Date: Tue, 22 Nov 2011 12:49:59 +0000 > From: Alejandro Heredia <[email protected]> > Subject: Re: [Avogadro-Discuss] Avogadro-Discuss Digest, Vol 28, Issue > 3 > To: [email protected], [email protected] > Message-ID: > <CAMOwbg=-akg+eoocgeyp0bctdvznpcksn9n8yowuuybrho4...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > 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. IT sense. And common sense. >> http://p.sf.net/sfu/splunk-novd2d >> >> ------------------------------ >> >> _______________________________________________ >> Avogadro-Discuss mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/avogadro-discuss >> >> >> End of Avogadro-Discuss Digest, Vol 28, Issue 3 >> *********************************************** >> > > > > ------------------------------ > > Message: 5 > Date: Fri, 25 Nov 2011 10:46:21 -0300 > From: Victor Eduardo Bahamonde Padilla <[email protected]> > Subject: [Avogadro-Discuss] atomic charges on each atom > To: avogadro-mail-list <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > > Hello > Is there any way to see the value of the atomic charges on each atom of the > molecule displayed as gaussview? > > Thanks in advance > > V?ctor E. Bahamonde Padilla > Laboratorio Fisicoquimica Molecular > Departamento de Qu?mica > Facultad de Ciencias > Universidad de Chile > Phone: 562-978-7443 > [email protected] > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 6 > Date: Fri, 25 Nov 2011 13:09:03 -0500 > From: David Lonie <[email protected]> > Subject: Re: [Avogadro-Discuss] atomic charges on each atom > To: [email protected] > Message-ID: > <cabzw8w9rasjwsuskncgakrcv7efst91qlvkpbzos7lje6lh...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Fri, Nov 25, 2011 at 8:46 AM, Victor Eduardo Bahamonde Padilla > <[email protected]> wrote: >> Hello >> Is there any way to see the value of the atomic charges on each atom of the >> molecule displayed as gaussview? > > Click "Display Settings" and check "Label", then open the label > configuration dialog. In Atom Labels --> Text there are Formal Charge > and Partial Charge options. However, I don't see an way to set the > formal charges, other than to read them in from a calculation or enter > them manually under View --> Properties --> Atom Properties. > > Does anyone know of a way to perceive them? This sounds like something > OpenBabel should be able do. > > Dave > > > > ------------------------------ > > ------------------------------------------------------------------------------ > 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. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > > ------------------------------ > > _______________________________________________ > Avogadro-Discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/avogadro-discuss > > > End of Avogadro-Discuss Digest, Vol 28, Issue 4 > *********************************************** ------------------------------------------------------------------------------ Learn Windows Azure Live! Tuesday, Dec 13, 2011 Microsoft is holding a special Learn Windows Azure training event for developers. It will provide a great way to learn Windows Azure and what it provides. You can attend the event by watching it streamed LIVE online. Learn more at http://p.sf.net/sfu/ms-windowsazure _______________________________________________ Avogadro-Discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
