I was compiling/installing avogadro-squared with git
According to the page
"If you have Git and CMake installed, you can use the new "Avogadro Squared" build to fetch and build any needed dependencies."
But it failed.
Here is my pastebin 
http://pastebin.com/baMS0sgA


Is there another easy way to install avogadro 1.1.0 on ubuntu 12.04 ????


On Tue, May 21, 2013 at 8:18 AM, avogadro-discuss-request@lists.sourceforge.net wrote:
Send Avogadro-Discuss mailing list submissions to avogadro-discuss@lists.sourceforge.net 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 avogadro-discuss-request@lists.sourceforge.net You can reach the person managing the list at avogadro-discuss-owner@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than "Re: Contents of Avogadro-Discuss digest..." Today's Topics: 1. Re: The defect site changes place after rotation! (David Lonie) 2. Re: The defect site changes place after rotation! (???) 3. Re: The defect site changes place after rotation! (David Lonie) 4. Re: The defect site changes place after rotation! (???) ---------------------------------------------------------------------- Message: 1 Date: Tue, 21 May 2013 07:57:32 -0400 From: David Lonie <david.lonie@kitware.com> Subject: Re: [Avogadro-Discuss] The defect site changes place after rotation! To: avogadro-discuss@lists.sourceforge.net Message-ID: <CA+=e1osNoSfY+nyjnYY-zXvk2VEhoL6_2vjZgaqeaNWeAJKkLw@mail.gmail.com> Content-Type: text/plain; charset=UTF-8 On Tue, May 21, 2013 at 5:58 AM, ??? <limurphy1985@gmail.com> wrote:
Dear Avogadro users, I am visualizing a supercell containing two defect sites, but after rotating the cell, the defect site changes place! It is really terrifying as I can not determine the exact defect site by viewing it. As shown in the attached files, in POSCAR.jpg, the defect at the right-up side is located at the second top atomic layer, but after I rotate the cell, as shown in POSCAR2.jpg, the defect site shifts to the first top layer. Is this problem related to periodic boundary condition? Does anyone know the reason of this problem and how to determine the defect site by Avogadro? Thank you very much, and very much looking forward to your help!
It looks like it might be related to periodic boundaries and wrapping the atoms back into the unit cell. What do you mean by "rotating the cell"? Are you just moving the camera, or are you modifying the structure? Dave ------------------------------ Message: 2 Date: Tue, 21 May 2013 14:05:38 +0200 From: ??? <limurphy1985@gmail.com> Subject: Re: [Avogadro-Discuss] The defect site changes place after rotation! To: avogadro-discuss@lists.sourceforge.net Message-ID: <CAJB5uaz=iw6r-0Lw11p4vfLTs_xxGWZDzkbRWqH9iY2w1Zu9Rg@mail.gmail.com> Content-Type: text/plain; charset="big5" Dear Dave, Thank you for your follow-up. For "rotation", I mean I drag the cell (pressing the right bottom of my mouse), so it can be rotated around certain axis. If it is due to PBC, then how could I fix the defect position? Thank you again! Sincerely, Murphy 2013/5/21 David Lonie <david.lonie@kitware.com>
On Tue, May 21, 2013 at 5:58 AM, ??? <limurphy1985@gmail.com> wrote: > Dear Avogadro users, > > I am visualizing a supercell containing two defect sites, but after rotating > the > cell, the defect site changes place! It is really terrifying as I can not > determine > the exact defect site by viewing it. As shown in the attached files, in > POSCAR.jpg, > the defect at the right-up side is located at the second top atomic layer, > but after I rotate the > cell, as shown in POSCAR2.jpg, the defect site shifts to the first top > layer. > > Is this problem related to periodic boundary > condition? Does anyone know the reason of this problem and how to determine > the defect > site by Avogadro? > > Thank you very much, and very much looking forward to your help! It looks like it might be related to periodic boundaries and wrapping the atoms back into the unit cell. What do you mean by "rotating the cell"? Are you just moving the camera, or are you modifying the structure? Dave ------------------------------------------------------------------------------ Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may _______________________________________________ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
-------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ Message: 3 Date: Tue, 21 May 2013 08:19:17 -0400 From: David Lonie <david.lonie@kitware.com> Subject: Re: [Avogadro-Discuss] The defect site changes place after rotation! To: avogadro-discuss@lists.sourceforge.net Message-ID: <CA+=e1otm5rcJsMuiO+QEKTSeHiGG9dPm0VmfwKQFUY6pzan_Dg@mail.gmail.com> Content-Type: text/plain; charset=UTF-8 On Tue, May 21, 2013 at 8:05 AM, ??? <limurphy1985@gmail.com> wrote:
Dear Dave, Thank you for your follow-up. For "rotation", I mean I drag the cell (pressing the right bottom of my mouse), so it can be rotated around certain axis.
The right mouse button doesn't perform rotations, it will either translate the camera (in navigation) or delete an atom (in draw). It looks like the defect is still in the same corner of the cell, but there is an atom missing in the top layer of atoms. Is it possible that an atom was accidentally deleted while manipulating the view? Can you reproduce this consistently? If so, can you save and send a copy of the structure with the steps to reproduce the behavior? Thanks, Dave ------------------------------ Message: 4 Date: Tue, 21 May 2013 15:18:01 +0200 From: ??? <limurphy1985@gmail.com> Subject: Re: [Avogadro-Discuss] The defect site changes place after rotation! To: avogadro-discuss@lists.sourceforge.net Message-ID: <CAJB5uawKkk0GVQH36m9JDGGWRPGvLbL8iN8hsA4hjZVdvgD86g@mail.gmail.com> Content-Type: text/plain; charset="big5" My apology, it is the left bottom of the mouse... Please find attached the POSCAR file. I do reproduce the problem, but currently I did not find the way to reproduce it regularly. Basically, what I did was just keeping pressing the left mouse bottom and rotate the cell around different axes (Originally I just wanted to investigate the structure). It should be worthy to mention, that this problem also occurs for VESTA! Hope this helps you to solve the problem! Sincerely, Murphy 2013/5/21 David Lonie <david.lonie@kitware.com>
On Tue, May 21, 2013 at 8:05 AM, ??? <limurphy1985@gmail.com> wrote: > Dear Dave, > > Thank you for your follow-up. > > For "rotation", I mean I drag the cell (pressing the right bottom of my > mouse), > so it can be rotated around certain axis. The right mouse button doesn't perform rotations, it will either translate the camera (in navigation) or delete an atom (in draw). It looks like the defect is still in the same corner of the cell, but there is an atom missing in the top layer of atoms. Is it possible that an atom was accidentally deleted while manipulating the view? Can you reproduce this consistently? If so, can you save and send a copy of the structure with the steps to reproduce the behavior? Thanks, Dave ------------------------------------------------------------------------------ Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may _______________________________________________ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
-------------- next part -------------- An HTML attachment was scrubbed... -------------- next part -------------- A non-text attachment was scrubbed... Name: POSCAR.avogadro Type: application/octet-stream Size: 3785 bytes Desc: not available ------------------------------ ------------------------------------------------------------------------------ Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may ------------------------------ _______________________________________________ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss End of Avogadro-Discuss Digest, Vol 46, Issue 4 ***********************************************