Re: [Avogadro-Discuss] [Avogadro-devel] Workflow Scripts (for Avo2)

2016-12-28 Thread Marcus D. Hanwell 
On Wed, Dec 28, 2016 at 3:04 PM, Gary Kedziora  wrote:

> Have you looked at pymatgen?  It has a lot of useful features for crystal
> structures and some also for molecules as well.
>
> I have been looking at pymatgen, but hadn't thought about it in this
context. We should take another look at it, I think coupled with the
workflows it could be reused with minimal effort.

Thanks,

Marcus
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Re: [Avogadro-Discuss] paid modeling work and/or tutor

2016-11-10 Thread Marcus D. Hanwell 
On Thu, Nov 10, 2016 at 12:34 PM, Tim Potter  wrote:
> Thank you so much for your offer to help.  I'm happy to help user document
> avogadro when you get to that point.  I started trying avogadro 2 because
> avogadro 1 was not saving double bonds, and was also not aware that avogadro
> 1 had these extension capabilities.  I saved the file in CML which solved
> both issues - I was able to open the file in avogadro 2 and also the double
> bond information that was created in avogadro 1 displayed in avogadro 2.

I am glad this helped, CML saves bonding information whereas PDB has
only limited support.
>
> Great, thank you for offering guidance.  I used avogadro 1 to calculate the
> energy at [Energy = 9,515.9 kJ/mol].  The wiki does not detail exactly what
> is meant by this figure.  What is the context for the kJ/mol figure?
>
I think that is the energy calculated by Open Babel using a molecular
mechanics force field. You would need to use an input generator, and
run a quantum code if you wanted to get a more accurate number (that
would also be slower in general).

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Re: [Avogadro-Discuss] paid modeling work and/or tutor

2016-11-09 Thread Marcus D. Hanwell 
On Tue, Nov 8, 2016 at 12:44 PM, Tim Potter  wrote:
> Hello
>
> I'm very slowly working through making avogadro2 functional to calculate
> electron density, bond strain, and total energy for a new carbon molecule.

Avogadro 1 and 2 provide a method of generating input for quantum
codes, such as NWChem, Gaussian, MOPAC, etc. They do not do the
calculation directly, but can read a number of these outputs.
>
> It's been a few days now and I've still not gotten the openbabel plugin to
> optimize geometry properly for a simple benzene molecule, nor have I been
> able to open PDB files that were made in avogadro1.  I see a wiki for
> avogadro1 but there seems to be almost no documentation for avogadro2.

There is sparse documentation, and some features are simply missing at
this stage. I am working on some updates, and hope to have more merged
in the near future so that we can make an updated release. At this
stage knowing a little more about what you are having trouble with
would be helpful.

I would recommend saving structures from Avogadro 1 as CML, but PDB
should probably work too. There is not any user documentation at this
stage, it is something I would like to put some time into once we are
closer to having a final release - is there a reason you don't simply
use Avogadro 1 at this stage?
>
> I would prefer to hire someone who is experienced with the software and can
> perform at least one of these three calculations with relative ease.
>
We can offer help on this list, the company I work for has consulting
rates but for such a small task I think I could provide some guidance,
and even write up a post going through the steps as it would be of
interest to the wider community.

Marcus

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Re: [Avogadro-Discuss] AutoOptimization

2016-10-24 Thread Marcus D. Hanwell 
It would be good to do some verification on this, because in my testing
this was consistently the location of the executable. We could add some
code to print out what it sees, or try to reproduce this locally.

There is quite a bit of work in several projects I work on where we
successfully rely upon this, and on Windows the executable needs the DLLs
in system paths or the same directory (which is why it is packaged the way
it is).

On Sun, Oct 23, 2016 at 11:55 AM, Patrick Avery  wrote:

> Indeed. I think that is BABEL_DATADIR. For Windows, I believe that is set
> here:
>
> https://github.com/cryos/avogadro/blob/2a98712f24506d023aa4b84c984136
> a913017e81/avogadro/src/main.cpp#L106
>
> Perhaps that is what we should change that setup for the next release.
>
>
> On Sunday, October 23, 2016, Marcos Verissimo Alves <
> marcos_veriss...@id.uff.br> wrote:
>
>> What if path variables with the location of the force fields are set? If
>> I'm not mistaken, Windows has those too.
>>
>> Best,
>>
>> Marcos
>>
>> Em domingo, 23 de outubro de 2016, Patrick Avery 
>> escreveu:
>>
>>> 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 
>>> 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]
 *Sent:* Saturday, October 22, 2016 9:35 AM
 *To:* 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/o
 penbabel/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 
 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







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Re: [Avogadro-Discuss] Issue building from source (undefined reference to symbol 'XInitThreads')

2016-03-29 Thread Marcus D. Hanwell 
On Tue, Mar 29, 2016 at 1:58 PM, Miro Moman  wrote:
> Hello,
>
> I am struggling to build Avogadro 1.1.1 from source in Ubuntu 15.10 x86-64.
>
> I run
>
> cmake ../
> -DEIGEN2_INCLUDE_DIR=/home/administrator/Downloads/avogadro/eigen-eigen-b23437e61a0
>
> followed by make
>
> Everything seems to compile fine but there is an issue at linking stage:
>
> [100%] Building CXX object
> avogadro/src/CMakeFiles/avogadro-app.dir/qrc_avogadro.cxx.o
> Linking CXX executable ../../bin/avogadro
> /usr/bin/ld: CMakeFiles/avogadro-app.dir/main.cpp.o: undefined reference to
> symbol 'XInitThreads'
> /usr/lib/x86_64-linux-gnu/libX11.so.6: error adding symbols: DSO missing
> from command line
> collect2: error: ld returned 1 exit status
> avogadro/src/CMakeFiles/avogadro-app.dir/build.make:1552: recipe for target
> 'bin/avogadro' failed
> make[2]: *** [bin/avogadro] Error 1
> CMakeFiles/Makefile2:2925: recipe for target
> 'avogadro/src/CMakeFiles/avogadro-app.dir/all' failed
> make[1]: *** [avogadro/src/CMakeFiles/avogadro-app.dir/all] Error 2
> Makefile:136: recipe for target 'all' failed
> make: *** [all] Error 2
>
> The reason for compiling from source is that Avogadro depends on
> libopenbabel but that conflicts with my OpenBabel 2.3.90 installation.
>
I fixed something similar in GLEW compile recently, it would appear
the Linux distros have changed linker behavior/library layouts in
recent releases. I will see if I can reproduce and come up with a
patch, I think this is transitive linking that used to work fine and
you must now explicitly call out libraries you use symbols from.

Thanks,

Marcus

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Re: [Avogadro-Discuss] importing molecule by name

2015-11-20 Thread Marcus D. Hanwell 
On Thu, Nov 19, 2015 at 10:35 AM, Steven Wathen
 wrote:
> Hello,
>
> For some reason the Import - Fetch by chemical name function in Avogadro is 
> not working today.  When I try I get en error message:  Specified molecule 
> could not be loaded: toluene.sdf
>
> I takes a minute or two before this error message appears.

What version of Avogadro are you using, what platform is this on?
>
> I tried importing from the protein data bank and got the same type of message.
>
> Does anyone know what would cause this?  Is it on my end, or is the problem 
> with the server that Avogadro fetches the structures from?
>
The upstream service looks like it is working, we should add some more
explicit messages to the code for when this fails as it can be a
little too mysterious. It could be your end if the service was blocked
for some reason.

Marcus

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Re: [Avogadro-Discuss] [Avogadro-devel] New Avogadro Manual

2015-09-02 Thread Marcus D. Hanwell 
On Mon, Aug 31, 2015 at 4:51 PM, Geoffrey Hutchison
 wrote:
> Thanks to support from the University of Pittsburgh Department of Chemistry, 
> there is a new manual for Avogadro:
> http://ghutchis.gitbooks.io/avogadro/
>
> You can find the images and Markdown on GitHub, of course, which should make 
> it fairly easy to edit, patch, and/or translate into other languages:
> https://github.com/avogadro/manual
>
That is great, thanks for putting this together!

Marcus

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Re: [Avogadro-Discuss] orbital visualisation with Gaussian formatted checkpoint files

2015-06-23 Thread Marcus D. Hanwell 
On Sat, Jun 20, 2015 at 10:38 AM, Jose A Gamez joseantonio.ga...@uam.es wrote:
 Hi everybody,

 I have a organometallic complex whose wave function I’ve calculated with G09 
 (UDFT, as it’s a quintet, TPSSh/def2-SVP). I open Gaussian's formatted 
 checkpoint with Avogadro to draw the orbitals.

 First thing. According to Avogadro, the HOMO is orbital no. 182, but it is 
 indeed orbital 184. Is the HOMO simply assigned as number of electrons/2?

It is at present.

 Second thing. Just alpha orbitals are showed. Is it possible to visualise 
 beta orbitals as well?

It is not, although that is something being added in Avogadro 2.
Previously we only really handled closed shell, and should have
possibly been stricter on warning about other files.

Marcus

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Re: [Avogadro-Discuss] docking small molecule againt a small molecule

2015-04-20 Thread Marcus D. Hanwell 
Hi,

On Thu, Apr 9, 2015 at 9:36 AM, mirko busato mirko.bus...@gmail.com wrote:
 Dear all,

 Is there a way with Avogadro to perform a small molecule/small molecule
 docking?

I see papers citing Avogadro that do docking, but I think they often
use it for the small molecule piece. This is something I have wanted
to add to Avogadro in a more formal way, but there is only so much
time in a day.

I am not aware of an extension targeted to this area as yet. Please
speak up if anyone out there has more information I am missing.

Best,

Marcus

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Re: [Avogadro-Discuss] Windows / Ubuntu Avogadro Differences

2015-04-20 Thread Marcus D. Hanwell 
Hi Darren,

On Thu, Apr 16, 2015 at 4:43 AM, darren.rhodes darren.rho...@gmail.com wrote:
 Hi All

 I have Avogadro at home (Ubuntu) and at work (Windows).  They are both
 the same version but the Windows Avogadro allows for conformer
 searching (Extensions/Molecular Mechanics/Conformer Search) but this
 isn't present in the Ubuntu Avogadro version.  In the latter the
 Extensions drop down does not have Molecular Mechanics.

 Both are Avogadro 1.1.1.

 Can any suggest a remedy for my problem?

This is odd, is the Ubuntu version built by you or packaged by Ubuntu?
I have Ubuntu 14.04, and so can take a look on there if you give me a
little more detail. These extensions are provided by Open Babel, you
may need to install more pieces of Open Babel.

Thanks,

Marcus

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Re: [Avogadro-Discuss] avogadro crashes X on ubuntu 14 under vnc

2015-04-20 Thread Marcus D. Hanwell 
Hi Ron,

What VNC server/client are you trying to use? I have Ubuntu 14.04 and
could try to replicate, I would expect this to work with VNC, the
major complication is often getting a good OpenGL context but VNC
usually does rendering on the server-side and simplifies this.

Thanks,

Marcus

On Fri, Apr 17, 2015 at 9:19 AM, Cohen, Ronald
rco...@carnegiescience.edu wrote:
 It runs fine under nomachine, but the enterprise version of nomachine
 needed to have virtual desktops is very expensive. Thanks,

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


 On Thu, Apr 16, 2015 at 11:56 PM, Cohen, Ronald
 rco...@carnegiescience.edu wrote:
 This is driving me crazy, and maybe someone has seen it. I have tried
 everything. I have a new ubuntu 14 machine and I built everthing with
 no errors, and avogadro runs fine on the console and ssh -X , but when
 I try to run it under vnc it always crashes the X server. I have tried
 every xserver I could find and every version of xstartup I could find.
 The whole vnc client crashes when I try just avogadro.

 After a crash the vnc log file shows:

 Thu Apr 16 23:46:04 2015
  Connections: accepted: 0.0.0.0::51330
  SConnection: Client needs protocol version 3.8
  SConnection: Client requests security type VncAuth(2)
  VNCSConnST:  Server default pixel format depth 16 (16bpp) little-endian 
 rgb565
  VNCSConnST:  Client pixel format depth 16 (16bpp) little-endian rgb565
 XIO:  fatal IO error 11 (Resource temporarily unavailable) on X server :16
   after 172 requests (172 known processed) with 0 events remaining.

 If I run avogadro -h under vnc I see (and it does not crash the server):

 avogadro -h
 Xlib:  extension XInputExtension missing on display :16.
 Avogadro version: 1.1.1 Git: 5e4d1f7
 LibAvogadro version: 1.1.1 Git: 5e4d1f7
 Locale:  en_GB
 Translation successfully loaded.
 Usage: avogadro [options] [files]

 Avogadro - Advanced Molecular Editor (version 1.1.1)

 Options:
   -h, --help Show help options (this)
   -v, --version Show version information

 So there are too symptoms--the XIO crash and the
 Xlib:  extension XInputExtension missing on display :16.

 Neither of these happen on the console or a regular sh -X session.

 I really need to get this working under vnc, so if anyone has any
 ideas or experience with this I would greatly appreciate it!

 Thank you!

 Sincerely,

 Ron

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Re: [Avogadro-Discuss] New CP2K input generator in Avogadro,

2015-03-23 Thread Marcus D. Hanwell 
On Mon, Mar 23, 2015 at 6:14 PM, Željko M. Svedružić
zsved...@biol.pmf.hr wrote:
 For those of you who like to work with CP2K, we are happy to tell you that
 we have prepared an input generator in Avogadro

 http://cp2k.org/tools

This looks great, I will try to get it tested and make sure we
distribute this in a future release. Thanks for sharing!

Marcus

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Re: [Avogadro-Discuss] Avagadro-lammps

2014-06-24 Thread Marcus D. Hanwell 
On Tue, Jun 24, 2014 at 8:31 PM, S Arun Srikant Sridhar
ss3...@drexel.edu wrote:
 Can some body please tell me whether avagadro can create lammps input data
 file

It cannot at this time - I have been looking into LAMMPS, and how we
might produce input for MD codes in general but we don't have anything
working yet (that I am aware of at least). I did add some support for
XYZ trajectories, GROMACS files, and am hoping to add some more in the
future but this has mainly been limited to the output from MD codes.

Marcus

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Re: [Avogadro-Discuss] How do I access the Z-matrix tool?

2014-04-07 Thread Marcus D. Hanwell 
Hi Rick,

On Mon, Apr 7, 2014 at 12:46 PM, Rick Muller rpmul...@gmail.com wrote:
 I'm interested in using the Z-matrix tool in Avogadro. I'm currently using
 Avogadro v1.1.1, and the tool does not appear in the toolbar or the menus.
 Can I enable it, or do I need to download a newer build to get it?

It is not enabled by default because I never got it working in a
robust way. It is enabled by a build flag, I could enable it in the
next release builds by default (and would like to revisit this as it
would be great to get working).

Thanks,

Marcus

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Re: [Avogadro-Discuss] How do I access the Z-matrix tool?

2014-04-07 Thread Marcus D. Hanwell 
Rick,

It is the former (to/from Cartesian, corner cases), it was also in
progress as I moved between positions and I never got around to it. I
would welcome input on robust implementations, and can handle the
Avogadro side. I would gladly update the Avogadro 1.1 version, and am
eager to port this to Avogadro 2.

Thanks,

Marcus

On Mon, Apr 7, 2014 at 4:36 PM, Rick Muller rpmul...@gmail.com wrote:
 Marcus,

 Thanks for the reply. What's the probably getting the zmatrix robust? Is it
 the conversion to cartesian coordinates, or the interaction with the rest of
 Avogadro? I might be able to help with the former, but probably not the
 latter.

 Rick


 On Mon, Apr 7, 2014 at 10:51 AM, Marcus D. Hanwell
 marcus.hanw...@kitware.com wrote:

 Hi Rick,

 On Mon, Apr 7, 2014 at 12:46 PM, Rick Muller rpmul...@gmail.com wrote:
  I'm interested in using the Z-matrix tool in Avogadro. I'm currently
  using
  Avogadro v1.1.1, and the tool does not appear in the toolbar or the
  menus.
  Can I enable it, or do I need to download a newer build to get it?
 
 It is not enabled by default because I never got it working in a
 robust way. It is enabled by a build flag, I could enable it in the
 next release builds by default (and would like to revisit this as it
 would be great to get working).

 Thanks,

 Marcus


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Re: [Avogadro-Discuss] Python terminal

2014-04-03 Thread Marcus D. Hanwell 
On Thu, Apr 3, 2014 at 2:23 PM, G M jakm...@yahoo.it wrote:
 Hi all,
 I would like to use python terminal, I followed the tutorial in the
 documentation page but there is no Python terminal option in my Avogadro
 1.1.0 or 1.1.1. I'm in a MacOX mountain lion, I've tried to begin a
 discussion in the documentation page but seems that I can't.

I don't think the Mac version is built with Python enabled. This has
always been a packaging challenge for us due to different versions of
Python on different Mac OS X versions, if you build it yourself then
it should work (enable Python in the build), but this is far from
ideal admittedly.

Marcus

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Re: [Avogadro-Discuss] can I get removed form this list?

2014-04-03 Thread Marcus D. Hanwell 
If you follow the link below (included in every email to the list) you
can unsubscribe there.

https://lists.sourceforge.net/lists/listinfo/avogadro-discuss

On Thu, Apr 3, 2014 at 2:24 PM, Andy Engelkemier
andy.engelkem...@gmail.com wrote:
 thanks

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Re: [Avogadro-Discuss] Delete some atoms in a supercell

2013-10-01 Thread Marcus D. Hanwell 
On Tue, Oct 1, 2013 at 2:07 PM, Sara Yzdn saray...@gmail.com wrote:

 Hi,

 I have generated a supercell in avogadro. I want to remove some of the
 atoms. Is there a way I can remove them by the aid of the gui and not
 guessing their position in the Cartesian built?

You can use the selection tool, and then either hit the delete key or
use edit-clear should remove any selected atoms (and bonds).

Marcus

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Re: [Avogadro-Discuss] cube files

2013-09-30 Thread Marcus D. Hanwell 
Do you know if the full data set can be downloaded, and what license
they applied to the data? It looks like it could be a useful data set,
but from the site I didn't see clear licensing or a data download
link. We are working on a demo with Avogadro, web services, and
chemical data and I am certainly interested in finding useful open
datasets (I realize this might be useful for teaching if their terms
are acceptable to whoever is teaching).

Marcus

On Mon, Sep 30, 2013 at 7:23 AM, Noel O'Boyle baoille...@gmail.com wrote:
 Might I suggest the CSD teaching set?
 http://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/CSDTeachingDatabase.aspx

 This would save a lot of legwork, and I imagine they would be happy to
 have the added value.

 - Noel

 On 30 September 2013 04:36, Geoffrey Hutchison geo...@pitt.edu wrote:
 if there are open source cube files for common molecules?

 I echo the suggestion of NWChem. OpenMOPAC is also available free to 
 academic users, which I believe applies to high school teachers. 
 (http://openmopac.net/)

 As for the common molecules question. I've been thinking hard about this 
 exact problem for some time. Let's just say the biggest problem is 
 generating a list of common molecules. If people would like to suggest how 
 to come up with say 100 or 1,000 or 10,000 molecules for teaching use .. I 
 think the University of Pittsburgh will gladly donate the CPU time using 
 MOPAC and/or NWChem.

 So my big question (to the community).. how do we generate such a list 
 and/or take genuine requests?

 Cheers,
 -Geoff

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Re: [Avogadro-Discuss] Error message in saving animations

2013-06-30 Thread Marcus D. Hanwell 
On Sat, Jun 29, 2013 at 6:52 PM, MD MAHBUBUL ISLAM mmi...@psu.edu wrote:
 Hello,

 I am trying to make animation using Avogadro 1.1.0 version. When I intend to
 'save as .avi' it gives an error message of 'could not run povray'. I
 installed povray in my laptop, but I don't understand- how I can set up the
 PATH of povray for saving animation. I am using Avogadro in windows 7. I
 would highly appreciate- If anyone would help me. Thanks in advance.

This was not as well tested on Windows, I will try to take a look at
this and see if we can ensure it works for the next release. I am not
sure if we exposed a way of changing the POV-Ray path, it has been a
while since I looked at this code.

Thanks for the report.

Marcus

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Re: [Avogadro-Discuss] read gaussian input file?

2013-05-14 Thread Marcus D. Hanwell 
Hi,

On Sun, May 12, 2013 at 9:55 AM, Randy Bin Lin mumuwe...@gmail.com wrote:

 hi all

 I noticed that avogadro is able to read in gaussian output file. can it read 
 in its input file or is there a plan to do that? it will be very helpful with 
 preparing a gaussian job.

I have never liked the asymmetry, but we have no current plans to add
readers. One of the issues is the variability of the input files,
although it wouldn't be that hard to add a reader to parse simple
input files. I remember speaking with Geoff about this many years ago
when I was a postdoc in his group about this - he may be able to
elaborate further.

Marcus

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Re: [Avogadro-Discuss] segfault or reading ABINIT file

2013-04-30 Thread Marcus D. Hanwell 
On Mon, Apr 29, 2013 at 2:12 PM, Cohen, Ron rco...@carnegiescience.edu wrote:
 The reproducible error is:

snip

 Program received signal SIGSEGV, Segmentation fault.
 [Switching to Thread 0x40602940 (LWP 17304)]
 OpenBabel::ABINITFormat::ReadMolecule (this=optimized out,
 pOb=optimized out, pConv=0x40601b50)
 at /home/rcohen/SRC/openbabel/src/formats/abinitformat.cpp:188
 188   atom-SetAtomicNum(atomicNumbers[type]);
 The abinit output file is attached. Ron

This looks like a bug in the Open Babel format, and would need to be
fixed there.

Marcus

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[Avogadro-Discuss] First Avogadro 2 beta release

2013-04-11 Thread Marcus D. Hanwell 
Hi,

I wanted to let people on these lists know that we just made our first
beta release of Avogadro 2, along with MoleQueue and MongoChem. Please
see the blog post here,

http://blog.cryos.org/archives/265-First-Open-Chemistry-Beta-Release.html

We have created binary installers for Windows and Mac OS X, along with
regular source releases,

http://www.openchemistry.org/OpenChemistry/resources/software.html

These are not feature complete, and we intend to make regular releases
as new features land in master. There are several exciting new
features, along with some missing pieces that will be brought back as
we can get to them. I will work on making a screen cast highlighting
how the three applications can be used together soon, and discussing
some of the new features in more detail.

We have automated as much of the testing and release process as
possible, and will continue to streamline things. Binaries are
uploaded nightly to the dashboards for Windows and Mac, and API
documentation is updated nightly,

http://cdash.openchemistry.org/
http://doc.openchemistry.org/avogadrolibs/api/

Avogadro 2 also uses a different binary name, and library names,
meaning that there should be no problems in installing Avogadro 1 and
2 on the same system in the same prefixes. There is lots more to do
before, so I will get back to it, but I hope you will check out what
we have been working on. I will see if I can get some more of the
features you have grown to expect back in Avogadro 2.

Thanks,

Marcus

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Re: [Avogadro-Discuss] Avogadro to lammps

2013-03-12 Thread Marcus D. Hanwell 
On Wed, Mar 6, 2013 at 3:02 PM, Ibrahim (Ibrahim Awad) Awad
iea...@crimson.ua.edu wrote:
 I've built my structure on avogadro and i want to create lammps data file
 that contains atoms, bonds and angles. How can i do that please

LAMMPS is something David Lonie worked on recently in Avogadro 2, with
a very early prototype in this topic,

http://review.source.kitware.com/#/t/2206/

We never added MD generators in version 1, and we are still figuring
out the required steps in Avogadro 2 to usefully generate input. We
would appreciate help if there are LAMMPS users out there that could
take us through there needs and current workflows.

Thanks,

Marcus

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Re: [Avogadro-Discuss] Problem loading files through a python extension

2013-03-12 Thread Marcus D. Hanwell 
Hi,

On Thu, Mar 7, 2013 at 3:20 PM, Mason, Nicholas
nicholas.maso...@imperial.ac.uk wrote:
 Hello,

 I have been writing a python extension to add ORCA support to Avogadro. The
 extension so far consists of a input generator, which works nicely, and an
 output-file reader, which I can't seem to get to work satisfactorily.

 The dialog for the output reader is working nicely, but I have become a bit
 stuck when it comes to making the extracted molecular geometries visible in
 the GLWidget.

 Initially my approach was to extract the coordinates into lists, where the
 first item was a string that acted as a title for that set of coordinates
 (for example, OPT CYCLE 5 or SINGLE POINT), followed by a list for every
 atom, consisting of its atomicNumber as an int and x, y, z coordinates as
 floats.

 This was then translated into Avogadro with the function below:

 @pyqtSignature()
 def renderCartesians(self):
 molecule = Avogadro.molecules.addMolecule()
 atom_index = 0
 for info in self.cartesians[-1][1:]:
 molecule.addAtom()
 molecule.atom(atom_index).atomicNumber = info[0]
 molecule.atom(atom_index).pos = numpy.array(info[1:])
 atom_index += 1
 self.glwidget.molecule = molecule


 This seemed to work, except that the molecule only consists of atoms (no
 bonds), and does not seem to be recognised by any of avogadro's other
 extensions or plugins.

 To avoid using the openbabel python bindings, my solution to the bond
 problem was to extract the coordinates and format them as a string in the
 .xyz format; then create a temporary .xyz file, write the coordinates to the
 file and read them back into Avogadro using MoleculeFile.readMolecule():

 @pyqtSignature()
 def renderCartesians(self):
 tempxyz = tempfile.NamedTemporaryFile(suffix=.xyz)
 tempxyz.write(self.cartesians_xyz[-1])
 tempxyz.seek(0)
 molecule = Avogadro.MoleculeFile.readMolecule(tempxyz.name)
 tempxyz.close()
 self.glwidget.molecule = molecule


 This procedure seemed to work when I tried it in the avogadro python
 terminal (although the molecule is still not recognised by the other
 plugins) but when implemented, as shown above, through my Extension script,
 Avogadro just crashes when the line self.glwidget.molecule = molecule is
 executed.

This is just using Open Babel under the covers to read and perceive bonds.

 I feel like I should be using setMolecule(), but I am not sure how to use
 it.

 I have also been reading about Avogadro::Extension::moleculeChanged, but
 this does not seem to be included in the python Extension class.

This is what I added to allow for extensions to read molecules, the
problem was that we needed to be able to inform the GUI there was a
new molecule and emitting a signal was the best solution I found. I
never thought, or got around to, adding this to the Python wrapping.

 Does anyone have any tips on how to render a molecule object and have it
 recognised by the other avogadro plugins (Such as ViewPropertiesMolecular
 properties..)? I am using Avogadro 1.1.0 on Mac OS X 10.8.

Either writing the extension in C++, or we could look at extending the
Python API to support this signal. It has been a while, but I might be
able to find some time to take a look at extending (although I never
did much of the work on the SIP layer that this needs - I think that
was Tim).

Marcus

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Re: [Avogadro-Discuss] installation problems

2013-03-12 Thread Marcus D. Hanwell 
On Wed, Mar 6, 2013 at 6:06 PM, Cohen, Ron rco...@carnegiescience.edu wrote:
 I built avogadro but get a segfault when I try to run. Is the problem that
 it is not finding the translations? Any suggestions? Thanks,

Could you run this from gdb and post the backtrace? I haven't seen
this, and there is nothing obvious in the output you posted. Linux
version/distro and compiler would be great as Geoff requested.

Marcus

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Re: [Avogadro-Discuss] installation problems

2013-03-12 Thread Marcus D. Hanwell 
On Tue, Mar 12, 2013 at 2:19 PM, Cohen, Ron rco...@carnegiescience.edu wrote:
 I finally got it to run. The problem was in my openbabel installation, as I
 found by gdb. The problem was multiple versions of libraries and or trying
 to use the intel compilers. I switched to gnu and made sure openbabel worked
 OK before installing avogadro, and that worked. Thank you for your help.

That is great news, please let us know if you hit any further issues.

Marcus

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Re: [Avogadro-Discuss] Where to click on a hydrogen

2013-03-05 Thread Marcus D. Hanwell 
On Tue, Mar 5, 2013 at 4:24 AM, Noel O'Boyle baoille...@gmail.com wrote:
 Hey there,

 I used an automated GUI tester to investigate where Avogadro accepts
 clicks on a hydrogen:
 http://baoilleach.blogspot.co.uk/2013/03/avogadro-hydrogen-clicking-craziness.html
 (see comments there also for a discussion of the issues).

 I would argue that the centre of the hydrogen is the logical place,
 but it seems that the sweet spot has been pushed towards the end of
 the bond.

I see Geoff's comments on the post already, and he added this to
Avogadro. It never felt right to me either, but it was hard to gauge
how many people were wanting to click on a hydrogen to do stuff (such
as change element type to build up a larger molecule with add
hydrogens). I would argue that for many structures drawing the
backbone and adding hydrogens at the end is the quickest way, but we
obviously want to be as flexible as we can here and many people like
the addition of hydrogens as they go.

It looks to me like the center is just pushed to where the center of
the sphere is, with a smaller radius, due to the perspective
projection. I once changed the code a little to look at rendered
versus picking, it wouldn't be hard to render that to show more
clearly what is happening and perhaps at least tweak if not remove
this. It probably wouldn't take much to add an option to turn this on
and off, as we did for the navigation rendering you didn't like.

Marcus

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Re: [Avogadro-Discuss] cut-n-paste in Avogadro running on Ubuntu

2013-01-19 Thread Marcus D. Hanwell 
Hi,

On Sat, Jan 19, 2013 at 10:52 AM, fredrik haeffner
jfhaeff...@hotmail.com wrote:
 Hi!

 Avogadro's cut-n-paste doesn't work for me running on Ubuntu. Yes, you can
 copy a XYZ-file from a terminal window and paste it into Avogadro. However,
 say, you select 3 atoms in Avogadro and copy-n-paste it in the same Avogadro
 window, it keeps pasting what was orginally stored (from the Terminal
 window). Otherwise it seems to work great.

Could you let me know what version of Avogadro and Ubuntu this is on?
I don't use Ubuntu myself, but there are a few people in the office
who do so I could likely take a look. It works fine here on Linux
using Avogadro's master from today (Arch Linux 64 bit). That code has
not changed very much, but I know Ubuntu is probably still on Avogadro
1.0.3 or so.

 I have been using Avogadro for years on Mac OS-X and the program is very
 unstable, that's why I decided to give Ubuntu a go.

 It would be great to hear from someone about this!

We have tried to reduce crashes, and with Avogadro 2 rewrite that is
something I am focusing on - a stable and well tested core. Work is
progressing well there, but it is not ready to replace Avogadro 1 yet.
The copy/paste code has not changed much, and I use that functionality
quite regularly on Linux.

Marcus

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Re: [Avogadro-Discuss] Inability to calculate carbon dioxide dipole moment?

2013-01-19 Thread Marcus D. Hanwell 
On Sat, Jan 19, 2013 at 12:31 PM, Steven Petrovic petro...@sou.edu wrote:
 Hello,
 Despite how wonderful I think Avogadro is for molecular modeling and its
 potential for educational purposes, I hesitate to use Avogadro in the
 chemistry laboratory when there seems to be such glaring issues as
 predicting the dipole moment for simple inorganic molecules such as carbon
 dioxide. When I build carbon dioxide using either 1.0.3 (in Ubuntu) or 1.1.0
 (on a PC) and optimize the geometry using MMFF94, the bond lengths are the
 same (1.197 angstroms for each C=O bond) and the bond angle is 180 degrees,
 just as you would predict with VSEPR theory. Yet, the dipole moment is a
 robust 9.72 Debye, not 0 Debye as would be predicted by VSEPR theory. In
 addition, if you build carbon dioxide in 1.0.3 by selecting double bonds and
 turning off adjust hydrogens, the partial charge on the carbon and oxygen
 atoms remains zero, and not 0.37 for C and -0.19 for each O. Unfortunately,
 Ubuntu has not put the latest version of Avogadro in its repository.
 I cannot explain why such discrepancies exist in the software and so I'm
 calling on the users and developers of Avogadro for some help on explaining
 or overcoming such discrepancies.
 Thank you for your assistance,

I think all of these numbers come from Open Babel, and the force
fields we use that were implemented by the Open Babel team. Perhaps
posing this question on the Open Babel list, or looking at other open
source implementations we could integrate would make sense.

I think Geoff and Tim would be more qualified to comment on how much
work it would be to correct some of these issues in Open Babel, we
also integrate with many third party quantum codes and using third
party MD packages might be another viable route to more accurate
numbers.

Marcus

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Re: [Avogadro-Discuss] cut-n-paste in Avogadro running on Ubuntu

2013-01-19 Thread Marcus D. Hanwell 
On Sat, Jan 19, 2013 at 1:23 PM, Marcus D. Hanwell
marcus.hanw...@kitware.com wrote:
 Hi,

 On Sat, Jan 19, 2013 at 10:52 AM, fredrik haeffner
 jfhaeff...@hotmail.com wrote:
 Hi!

 Avogadro's cut-n-paste doesn't work for me running on Ubuntu. Yes, you can
 copy a XYZ-file from a terminal window and paste it into Avogadro. However,
 say, you select 3 atoms in Avogadro and copy-n-paste it in the same Avogadro
 window, it keeps pasting what was orginally stored (from the Terminal
 window). Otherwise it seems to work great.

 Could you let me know what version of Avogadro and Ubuntu this is on?
 I don't use Ubuntu myself, but there are a few people in the office
 who do so I could likely take a look. It works fine here on Linux
 using Avogadro's master from today (Arch Linux 64 bit). That code has
 not changed very much, but I know Ubuntu is probably still on Avogadro
 1.0.3 or so.

 I have been using Avogadro for years on Mac OS-X and the program is very
 unstable, that's why I decided to give Ubuntu a go.

 It would be great to hear from someone about this!

 We have tried to reduce crashes, and with Avogadro 2 rewrite that is
 something I am focusing on - a stable and well tested core. Work is
 progressing well there, but it is not ready to replace Avogadro 1 yet.
 The copy/paste code has not changed much, and I use that functionality
 quite regularly on Linux.

Another point I just remembered about Ubuntu - they tend to break the
Open Babel package up, I have looked at other people's systems where
installing all of the Open Babel packages made several features work
(I think missing data files is one culprit). This may have improved,
if not we should try and get in touch with the Ubuntu developer to get
them to adjust the dependencies of the Avogadro package.

Marcus

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Re: [Avogadro-Discuss] Configure Avogadro on Cent OS

2012-09-19 Thread Marcus D. Hanwell 
On Sat, Sep 15, 2012 at 5:21 PM, Ismail, Mohd F. fa...@ou.edu wrote:
 As a solution, I managed to compile Avogadro using avogadro-squared, as
 mentioned on Avogadro this
 (http://avogadro.openmolecules.net/wiki/Compiling_on_Linux_and_Mac_OS_X)
 Avogadro wiki page.

 Hopefully it'll help saves some one's time and hair.

If more people find this useful (I use it quite a bit myself), then we
could even start tagging releases in the git repository with the Open
Babel, Avogadro etc versions used in that particular release. Great to
hear it was of help, it can be a little tricky getting all of our
dependencies set up.

Marcus

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