Re: [Avogadro-Discuss] Problem Compiling Avogadro v-1.2.0

[Patrick Avery]

One factor is that you probably don't want to use
github.com/cryos/avogadro-squared

The main avogadro repo is here: https://github.com/cryos/avogadro

You might want to try compiling it again with that one instead. Just make
sure openbabel and the other dependencies are found.

Patrick

On Tue, Nov 15, 2016 at 9:55 AM, Stephen P. Molnar 
wrote:

> I attempting a build of Avogadro v-1.2.0 in Debian v-8.5.0 using:
>
>
>
> git clone --recursive git://github.com/cryos/avogadro-squared.git
>
> mkdir avogadro-build
>
> cd avogadro-build
>
> cmake ../avogadro-squared
>
>
>
> All seemed to go well until the very end of the build process when I got:
>
>
>
> [0mlconvert: could not exec '/usr/lib/x86_64-linux-gnu/qt4/bin/lconvert':
> No such file or directory
>
> libavogadro/src/CMakeFiles/avogadro.dir/build.make:488: recipe for target
> 'libavogadro/src/libavogadro_zh_CN.qm' failed
>
> make[5]: *** [libavogadro/src/libavogadro_zh_CN.qm] Error 1
>
> make[5]: *** Waiting for unfinished jobs
>
> CMakeFiles/Makefile2:134: recipe for target 
> 'libavogadro/src/CMakeFiles/avogadro.dir/all'
> failed
>
> make[4]: *** [libavogadro/src/CMakeFiles/avogadro.dir/all] Error 2
>
> Makefile:137: recipe for target 'all' failed
>
> make[3]: *** [all] Error 2
>
> CMakeFiles/avogadro.dir/build.make:110: recipe for target
> 'avogadro-prefix/src/avogadro-stamp/avogadro-build' failed
>
> make[2]: *** [avogadro-prefix/src/avogadro-stamp/avogadro-build] Error 2
>
> CMakeFiles/Makefile2:62: recipe for target 'CMakeFiles/avogadro.dir/all'
> failed
>
> make[1]: *** [CMakeFiles/avogadro.dir/all] Error 2
>
> Makefile:76: recipe for target 'all' failed
>
> make: *** [all] Error 2
>
> ]0;comp@inga: 
> ~/Downloads/Avogadro/avogadro-buildcomp@inga:~/Downloads/Avogadro/avogadro-build$
> exit
>
>
>
> Apparently lconvert is missing.  How do I solve this problem?
>
>
>
> I have attached the complete make.log to this email.
>
>
>
> The Debian distribution version of Avogadro installed and runs with no
> problems.
>
>
>
> Thanks in advance.
>
>
>
> Stephen P. Molnar, Ph.D.   Life is a fuzzy set
>
> www.molecular-modeling.net Stochastic and Multivariate
>
> s.mol...@sbcglobal.net
>
> (614)312-7528(c)
>
> Skype:  smolnar1
>
>
>
> 
> --
>
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Re: [Avogadro-Discuss] AutoOptimization

[Patrick Avery]

My best guess is that when you open a Gaussian file by double clicking it,
it results in Avogadro's runtime location being in that directory (which
means it won't find the force field files).

For now, I'd always open Avogadro by using the shortcut, and then open the
Gaussian file using the "Open" dialog, and it should work. I will try to
figure out how to fix that sometime sooner or later...

On Sunday, October 23, 2016, Željko M. Svedružić <zsved...@biol.pmf.hr>
wrote:

> Michael,
>
> most of the molecular modeling software does not tolerate "Program Files"
> in the path name. The code for all those programs is written for Linux and
> just adapted to windows. Linux does not recognize empty space, i.e.
> "Program Files" should be "Program_Files". Thus, when I have to work on
> windows I install all my modeling software in C:\\ directory, and
> everything works fine. Alternatively stick with Linux.
>
> Hope this helps,
>
> Best of luck in your work, Cheers,
>
> www.svedruziclab.com
>
> On 2016-10-23 4:32, Michael Morgan wrote:
>
> Dear Patrick,
>
>
>
> Thank you for your kind help! The problem is solved with your help.
>
>
>
> 1)  If I run Avogadro.exe from the \bin folder, then open files, I
> can use the force fields.
>
> 2)  If I created a shortcut link in the desktop and run it, I can use
> the force fields.
>
> 3)  I have assigned “C:\Program Files (x86)\Avogadro\bin\avogadro.exe”
> to open the Gaussian output files by default. If I open an output
> file using Avogadro by directly clicking the file, I cannot use the force
> fields. Not sure what is wrong.
>
>
>
> Cheers,
>
> Michael
>
>
>
> *From:* Patrick Avery [mailto:psav...@buffalo.edu
> <javascript:_e(%7B%7D,'cvml','psav...@buffalo.edu');>]
> *Sent:* Saturday, October 22, 2016 9:35 AM
> *To:* avogadro-discuss@lists.sourceforge.net
> <javascript:_e(%7B%7D,'cvml','avogadro-discuss@lists.sourceforge.net');>
> *Subject:* Re: [Avogadro-Discuss] AutoOptimization
>
>
>
> Hi Michael,
>
>
>
> This usually means the force field files were not found. These are the
> files at this location: https://github.com/openbabel/openbabel/tree/
> master/data
>
>
>
> I can think of two likely scenarios. Either
>
>
>
> 1: you don't have the files. Check your install location (probably
> C:\Program Files (x86)\Avogadro). Open the bin folder and see if the force
> field files are there.
>
>
>
> 2: if you do have the files, the force field files may not be loading if
> Avogadro's runtime location is not in C:\Program Files (x86)\Avogadro\bin.
> You can double click the Avogadro executable in C:\Program Files
> (x86)\Avogadro\bin
>
> And the force fields should work then. If you are using a shortcut, right
> click it and select "properties" and make sure it says it is starting in 
> C:\Program
> Files (x86)\Avogadro\bin and not C:\Program Files (x86)\Avogadro.
>
>
>
> I tried setting it up to make sure we wouldn't run into either of those
> problems. Perhaps I missed something, though. Did you create your own
> shortcut?
>
>
>
> Thanks,
>
> Patrick
>
>
> On Friday, October 21, 2016, Michael Morgan <michaelmorgan...@gmail.com
> <javascript:_e(%7B%7D,'cvml','michaelmorgan...@gmail.com');>> wrote:
>
> Dear All,
>
>
>
> My Avogadro’s AutoOptimization stopped working. When I clicked “Start”, it
> showed “AutoOpt: Could not setup force field…”. I have tried most simple
> molecules, as well as choosing different force field. All the same. Any
> idea what is wrong?
>
>
>
> My Avogadro version is most recent one (1.2.0). Windows 10.
>
>
>
> Thank you very much.
>
>
>
> Best
>
> Michael
>
>
>
>
>
>
>
> --
> **address file***
> Željko Svedružić ph.d.zsved...@biol.pmf.hr 
> <javascript:_e(%7B%7D,'cvml','zsved...@biol.pmf.hr');>
> web:https://profiles.google.com/106720515809875304148#106720515809875304148/about
> **
>
>
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[Avogadro-Discuss] GSoC 2016

[Patrick Avery]

Hey Avogadro community!

Just wanted to provide an update for GSoC. I was fortunately able to pass!

I added a lot of features to Avogadro 2 that will probably be helpful for
materials science groups. Here is a list of the primary features I was able
to add:


   - Added POSCAR (from Vienna Ab Initio Simulation Package) format reader
   and writer. This is used by a lot of computational materials science groups.
   - Added an "Import Crystal from Clipboard" feature. This was present in
   Avogadro 1 and allows the user to copy a crystal file to their clipboard
   and import it from there. It is particularly useful for POSCAR format due
   to the way files are named.
   - Added a supercell builder. This is helpful for visualization and
   situations that require a supercell.
   - Added spglib to Avogadro2. Spglib is a library written in C that
   allows for many useful crystal operations related to symmetry and space
   groups.
   - Added space group perception using spglib.
   - Added functions using spglib that allow users to primitive reduce a
   crystal, conventionalize a crystal, and symmetrize a crystal.
   - Added functions to fill a unit cell by using symmetry operations for a
   space group, and added functions to reduce a unit cell to its asymmetric
   unit.


They're all very interesting and useful features! More detailed information
with pictures can be found in my blog posts:

http://avogadro2crystals.blogspot.com/2016/06/recently-those-of-us-in-google-summer.html

http://avogadro2crystals.blogspot.com/2016/08/end-of-gsoc.html


On the GSoC website, my project is here:

https://summerofcode.withgoogle.com/organizations/6290185763422208/#6428631593123840

and my final submission was this blog post here:

http://avogadro2crystals.blogspot.com/2016/08/gsoc-summary.html

I want to thank Marcus and the Avogadro team for letting me participate
this summer! Looking forward to seeing where Avogadro goes next!

Patrick
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[Avogadro-Discuss] Yaehmop Additions

[Patrick Avery]

Hello Avogadro community!

I've been working on implementing some extended Huckel theory calculations
into Avogadro through YAeHMOP. It's pretty exciting what you can do with it!

I've mostly been implementing band structures, but I'm moving to density of
states next. Molecular orbitals should come along sometime sooner or later
as well.

I link a ~14 min video here where I demonstrate (with verbal commentary) a
band structure calculation for diamond using YAeHMOP. If anyone has a
better idea for implementing some of the GUI, you can let me know. Here is
the link!

https://drive.google.com/open?id=0B0keOob3eAJgVGJOTEdfTEF5UXc

Like I mention in the video. I should be adding other features soon.

Let me know if you have any feedback.

Thanks,
Patrick
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Re: [Avogadro-Discuss] How to use Avogadro from terminal?

[Patrick Avery]

Hi there Ana,

If you just need a file translator, you might want to consider using Open
Babel directly: http://openbabel.org/wiki/Main_Page

Avogadro uses Open Babel for a lot of its file translations. After you
compile/install open Babel and get the executables, you just need to run
something like:

obabel -icml -osmi -OoutputFilename

Whatever after -i is the input file type. After -o is output file type, and
I believe after -O is output file name.

https://openbabel.org/docs/dev/Command-line_tools/babel.html

You would be able to write a python script and use subprocess to run this
command multiple times.

Patrick

On Tuesday, June 28, 2016, Anastasya Karchevskaya  wrote:

>
> I wish I could use Avogadro from the terminal, either Windows or Linux. I
> don’t need GUI and actually need to use Avogadro as a file translator for
> 100K files (approximately), avogadro reads my file properly and is able to
> save it as smiles (as the test has shown), but I need somewhat like:
>
> for file in folder…
>
>
> I can write Python scripts as well, but I just don’t get it from the
> instructions: a) how to start python console in Avogadro b) How to open
> file and save it?
>
> If it is a Python script I would do somewhat like:
>
> import os
>
> folderInp = “blablabla1”
> folderOutp = “blablabla2”
>
> for fileMol2 in os.listdir(folderInp):
>
> file = Avogadro.open(folderInp + fileMol2)
> newPath = folderOutp + fileMol2.split(‘.mol2’)[0] + ‘.smi'
> fileSave = Avogadro.save(“.smi”, file, newPath)
>
> But I don’t know how to do that in Avogadro/with Avogadro?
>
> Here is what I have ion settings:
>
>
> And here’s what I have in the toolbox:
>
>
> So there’s no Python Console. O_O
>
> Thank you,
>
> Regards,
>
> Ana
>
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Re: [Avogadro-Discuss] XTALOPT hangs if server connection lost

[Patrick Avery]

Hi Ron,

We did actually fix this issue for the new update that is coming soon. Let
me know if you have any issues with your fix and I can give you the updated
version of that file.

Thanks,
Patrick

On Friday, August 21, 2015, Cohen, Ronald rco...@carnegiescience.edu
wrote:

 I think the attached code I edited fixes this problem.

 Ron
 ---
 Ronald Cohen
 Geophysical Laboratory
 Carnegie Institution
 5251 Broad Branch Rd., N.W.
 Washington, D.C. 20015
 rco...@carnegiescience.edu javascript:;
 office: 202-478-8937
 skype: ronaldcohen
 https://twitter.com/recohen3
 https://www.linkedin.com/profile/view?id=163327727


 On Fri, Aug 21, 2015 at 12:08 PM, Cohen, Ronald
 rco...@carnegiescience.edu javascript:; wrote:
  Unfortunately the CLI is not correct! I get:
 
  Warning:  Optimizer::Update: Error loading structure at
  /home/ucfbcoh/XTALOPT/C12H12/200GPa//3x00051/
 
  and when I look at that directory I find on the client:
 
  ls /home/ucfbcoh/XTALOPT/C12H12/200GPa//3x00051/
  3x00051  job.sh  structure.state  xtal.in
  ucfbcoh@tomcat:~/src/xtalopt2/build$ ls
  /home/ucfbcoh/XTALOPT/C12H12/200GPa//3x00051/3x00051/
  job.sh  pwscf.save  xtal.in  xtal.out
 
  I had fixed this also long ago, but it is back again. It is storing
  one directory down.
 
  Ron
 
  ---
  Ronald Cohen
  Geophysical Laboratory
  Carnegie Institution
  5251 Broad Branch Rd., N.W.
  Washington, D.C. 20015
  rco...@carnegiescience.edu javascript:;
  office: 202-478-8937
  skype: ronaldcohen
  https://twitter.com/recohen3
  https://www.linkedin.com/profile/view?id=163327727
 
 
  On Fri, Aug 21, 2015 at 1:48 AM, Ronald Cohen
  rco...@carnegiescience.edu javascript:; wrote:
  I switched to the CLI ssh and so far no problems! I guess it is a
 problem
  with sshlib.
  Ron
  Sent from my iPad
 
  On Aug 17, 2015, at 9:41 AM, David Lonie david.lo...@kitware.com
 javascript:; wrote:
 
  On Fri, Aug 14, 2015 at 4:35 PM, Cohen, Ronald 
 rco...@carnegiescience.edu javascript:;
  wrote:
 
  I had fixed this in an earlier version but don't remember how.
  Sometimes the connection to the server or nameserver goes down (about
  once a day) and I see an error like:
 
  SSHConnectionLibSSH::isConnected(): server timeout.
  SSH error:  Failed to resolve hostname legion.rc.ucl.ac.uk (Name or
  service not known)
  Cannot connect to ssh server ucfb...@legion.rc.ucl.ac.uk:22
  Warning:  Cannot connect to ssh server
 
 
  If you're having issues resolving hosts, there's not much that can be
 done
  about that from the XtalOpt side of things. Might be VPN related?
 
  Dave
 
 
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