Re: [Avogadro-Discuss] Conformer search

[David Lonie]

On Mon, Dec 19, 2011 at 2:17 PM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
 Is there currently a GUI-based method to generate and view
 conformations of a molecule? Using the forcefield extension, I appear
 to be generating the conformers, but in View  Properties  Conformer
 Properties, only a single entry shows up.

 What conformer search are you using? The weighted search will just give you 
 the lowest energy conformer, not generate new ones. Systematic searching 
 should give you a set.

Even with systematic and random search, I only get a single conformer
in the properties dialog. Is this a bug or am I missing a step?
(avogadro master and OB trunk)

 We would like to do this as part of a lab, so we need a GUI-based,
 student-friendly way to generate and compare conformations. Does
 anyone know if such a workflow is possible using existing tools?

 Without much coding, yes. Open Babel has a new (v2.3) conformer search 
 framework, which should probably replace the weighted search and will 
 generate multiple conformations. Better yet, you can either pick low-energy 
 conformers, or a diverse set (i.e., maximizing RMSD differences).

 I just haven't had time to splice the new framework into the forcefield 
 extension.

I should be able to spend some time on this, since it will be related
to my PI's lab course. I saw a GA search heuristic go into trunk, is
this the one you mean? I can replace the current weighted search in
the forcefield extension with that. Are the different fitness options
already incorporated into OB, or can it take a user supplied fitness
function callback? I can add some of these in if there's time.

 I also have some ideas about manual dihedral scans, but that will need 
 someone with more programming time.

Check out the RotateSelection extension example
(libavogadro/examples/thirdPartyExtensions/04-RotateSelection), I
think it should be able to do dihedral scans without too much trouble,
you might be able to modify that for a quick version.

Dave

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Re: [Avogadro-Discuss] error during conformational search

[David Lonie]

On Thu, Mar 15, 2012 at 11:52 AM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
 I'm a Phd student and I'll have to do 'systematic research of rotors' even 
 for much larger molecules.

 You may want to investigate the genetic-algorithm and Monte Carlo weighted 
 search options in Open Babel (which are used by Avogadro). These can be 
 accessed from the babel command-line and GUI.

 http://openbabel.org/docs/dev/Command-line_tools/babel.html#generating-conformers-for-structures

I agree with Geoff -- that molecule would generate quite a few
conformers, at least 10,000 (the GUI cuts off there -- there are
probably many more potential conformers for this flexible of a
molecule). I started the search and within seconds the search had
consumed over 2GB of RAM to store the conformer data. This is probably
what caused your crash -- if I had not stopped avogadro on my system,
I would have quickly run out of memory and crashed, too.

Unfortunately Avogadro doesn't currently have any utilities to
generate this many conformers in a memory efficient way, which would
require writing to disk as more conformers generated. Your options
here are to use a different search algorithm (random/Monte Carlo or
GA) to try just sampling some of the conformational space, or try to
find a computer with an enormous RAM reserve.

If you really do need to generate all 10,000+ conformers, you'll
probably need to use the commandline openbabel interface. The Avogadro
interface is only capable of generating 10,000 conformers. I doubt
that the raw babel CLI interface has such a restriction, but I'm not
100% sure on that.

Hope this helps,

Dave

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Re: [Avogadro-Discuss] Binary RPM for CentOS 5.8 ... ??

[David Lonie]

On Fri, Feb 1, 2013 at 4:42 PM, Richard Walsh richard.wa...@csi.cuny.eduwrote:

  After a frustrating day of trying to install everything required
 for Avogadro 1.1.0 (Babel, Eigen, Qt, cmake, wxWidgets) on
 a CentOS 5.8 system (although with no issues specific to CentOS)
 I am wondering if there is an Binary RPM.  I looked around
 in the first instance and did not see anything.  What do you
 recommend as a low-risk should work alternative.

  I manage to get all the support packages installed, but
 Avogadro itself is failing in the Make phase after CMake.


I'm not aware of any CentOS specific builds. Can you attach the build error
you're getting? We can help you with the build configuration.

Dave
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Re: [Avogadro-Discuss] Avogadro 1.1.0 cannot deal with files with certain names?

[David Lonie]

On Fri, Feb 1, 2013 at 5:40 PM, Xing xi...@pitt.edu wrote:

 Dear all,

 The attached pdbs are two identical files from Protein Data Bank. The one
with the original name 2K4G.pdb will cause Avogadro 1.1.0 to crash (see
2K4G.log) and just changing the name from 2K4G.pdb to 2K4G_avo.pdb will
prevent the software from crashing. Avogadro 1.0.3 does not have this
problem. Maybe it's related to the new Open Babel version (2.3.1) ?
Actually this happens to various files containing large molecules and the
error messages are usually different from one to another.

 I can reproduce the bug on both Windows 7 and OpenSUSE 12.2 platforms. Am
I the only one facing the problem or maybe it is really a bug?


Definitely an odd bug, one that I cannot reproduce here.

But, digging through the sources, I find the error message at the end of
the .log file in the openqube mopac .aux file reader. Are there any files
in the directory with 2K4G.pdb that have a .aux (or similar) extension? Or
have you done any MOPAC calculations on it?

Does it work if you move the pdb file to another directory?

I don't see this particular error message anywhere else in openbabel or
avogadro, so it definitely seems to be because of a bad .aux file.

If you still see this issue with the pdb file in another directory, we'll
need to get a backtrace of the crash to really track this down.

 Department of Chemistry
 University of Pittsburgh

Perhaps Dr. Hutchison could help with the debug build/backtrace if needed
;-)

Dave
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Re: [Avogadro-Discuss] Avogadro 1.1.0 cannot deal with files with certain names?

[David Lonie]

On Sun, Feb 3, 2013 at 10:26 AM, Xing Yin xi...@pitt.edu wrote:

  Wow, I do have 2K4G.aux (generated by MOPAC2012) in the same directory
 as 2K4G.pdb. Once I copy 2K4G.pdb into a new folder, it can be read by
 Avogadro 1.1.0 without a problem just like 2K4G_avo.pdb. Simply symlink
 2K4G.pdb to another directory cannot solve the problem.

 Thanks very much! Now I know what is the problem and how to avoid it. ;)
 But still, is Avogadro supposed to read an aux file while loading a pdb
 file? If so, can Avogadro continue to load the pdb if something is wrong in
 the aux file?


It should, but there seems to be an issue in the mopac aux file reader. Can
you attach the .aux file? I'd like to see what's causing the crash.

Dave
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Re: [Avogadro-Discuss] Avogadro 1.1.0 cannot deal with files with certain names?

[David Lonie]

This patch should fix it in the next release:

http://review.source.kitware.com/#/t/2057/

Thanks for the report!

Dave


On Sun, Feb 3, 2013 at 11:01 AM, Xing Yin xi...@pitt.edu wrote:

  It's attached in my previous reply. Here it is again. ;)

 Sincerely yours
 Xing Yin
 Department of Chemistry, Univ Pittsburgh
 G-3 Chevron Science Center
 219 Parkman Ave
 Pittsburgh, PA 15260

 On 02/03/2013 10:58 AM, David Lonie wrote:

  On Sun, Feb 3, 2013 at 10:26 AM, Xing Yin xi...@pitt.edu wrote:

  Wow, I do have 2K4G.aux (generated by MOPAC2012) in the same directory
 as 2K4G.pdb. Once I copy 2K4G.pdb into a new folder, it can be read by
 Avogadro 1.1.0 without a problem just like 2K4G_avo.pdb. Simply symlink
 2K4G.pdb to another directory cannot solve the problem.

 Thanks very much! Now I know what is the problem and how to avoid it. ;)
 But still, is Avogadro supposed to read an aux file while loading a pdb
 file? If so, can Avogadro continue to load the pdb if something is wrong in
 the aux file?


  It should, but there seems to be an issue in the mopac aux file reader.
 Can you attach the .aux file? I'd like to see what's causing the crash.

  Dave


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Re: [Avogadro-Discuss] crash loading GAMESS log files

[David Lonie]

Hi Blake,

I tried using the 1.1.0 version on the sourceforge site, and also saw the
crash with this log file. I built a new version from the 1.1.0 git tag
against an up-to-date openbabel, and the new version works. I've uploaded
an installer here:

http://xtalopt.openmolecules.net/misc/Avogadro-1.1.0-win32-no-python-inchi-or-ffs.exe

As you may have guessed from the filename, this build doesn't have python,
inchi, or forcefield support, but it should open your log file.

Dave


On Fri, Feb 8, 2013 at 5:02 PM, Blake Mertz blake.me...@mail.wvu.eduwrote:

 Hello,

 Was hoping to get some help from someone -- I'm running a geometry
 optimization on ammonia at RHF level using GAMESS, and when I go to
 load the log file, Avogadro crashes with the following report:

 Problem signature:
   Problem Event Name:   BEX
   Application Name: avogadro.exe
   Application Version:  0.0.0.0
   Application Timestamp:50450db5
   Fault Module Name:MSVCR90.dll
   Fault Module Version: 9.0.30729.6161
   Fault Module Timestamp:   4dace5b9
   Exception Offset: 0006ccd5
   Exception Code:   c417
   Exception Data:   
   OS Version:   6.1.7601.2.1.0.768.3
   Locale ID:1033
   Additional Information 1: 05ca
   Additional Information 2: 05ca81ad486f92904cbfa8d569982719
   Additional Information 3: dcc8
   Additional Information 4: dcc8d3719fc561987a655fb4871d918b

 This is avogadro win32 version 1.1.0, using a GAMESS log file from
 version 11-64. I'm attaching the ammonia log file if that helps.
 Thanks, you guys have a great piece of software, hope I can help with
 some of the bug issues I've encountered now and in the past.

 Blake

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Re: [Avogadro-Discuss] Unit cell builder

[David Lonie]

On Wed, Feb 27, 2013 at 2:21 PM, Richard Overstreet 
reoverstre...@catamount.wcu.edu wrote:

 Hello all,

 I have a problem with the unit cell builder. I am able to successfully
 build a unit cell where a = b = c = 2 and alpha = beta = gamma = 108
 with NH3BH3. However, when I go to export the unit cell to NWChem
 format, or save as .xyz or .pdb none of the atoms created with the unit
 cell builder appear in the input file only the original or starting
 molecule coordinates appear. Additionally, the new atom coordinates do
 not show up in the Cartesian coordinate editor and labels do not appear
 on the constructed crystal lattice molecules in Avogadro. I am using
 Avogadro application version 1.0.3, library version 1.0.3, and openbabel
 version 2.3.0 on ubuntu 12.04 LTS x64.


Can you try to reproduce this with Avogadro 1.1.0? There are a lot of new
crystallography features and unit cell creation has been rewritten.

Also, do you have the cell repeat options set? The cell repeat feature only
draws extra unit cells, but does not modify the actual crystal data. Use
the supercell builder if you want to add repeat cells to the crystal data.

Dave
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Re: [Avogadro-Discuss] rotating a bond

[David Lonie]

Hi,

The easiest way is to use the bond-centric manipulation tool. See the icon
for the tool and instructions on this page:

http://avogadro.openmolecules.net/wiki/Bond_Centric_Manipulate_Tool

Hope this helps,

Dave


On Sat, Mar 2, 2013 at 6:54 AM, Isidoro A. Gómez Parrales ian...@us.eswrote:

 **

 Hello, I'm new in this list and I'd like to know if is possible to rotate
 a bond in Avogador, and how can I make it?

 Thenk you


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Re: [Avogadro-Discuss] building slab with avogadro

[David Lonie]

On Thu, Mar 14, 2013 at 5:51 PM, Rupashree Shyama Ray
shyama@gmail.comwrote:

 Hi,

 While building input files for quantum espresso, certain atoms are
 duplicated in avogadro.
 Can anyone suggest how to deal with the problem within avogadro?
 It's terrible to do a trial and error to remove certain edge atoms to get
 the structure correct.


Can you describe what you mean more clearly? What steps are you taking to
produce the structure? Which atoms are duplicated?

Dave
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Re: [Avogadro-Discuss] problem with libpng(no atom display)

[David Lonie]

On Thu, Apr 18, 2013 at 12:31 PM, Ganesh, Panchapakesan
gane...@ornl.gov wrote:
 I believe I am having the same problem.  While I could get avogadro working 
 nicely on my mac, an ubuntu 12.04 installation either from the ubuntu-repo or 
 compiling from source-code from https://github.com/dlonie/avogadro.

I didn't catch this earlier, but those instructions were a bit out of
date. Can you try installing from https://github.com/cryos/avogadro?
My fork is probably out of date -- I've updated the instructions to
point at cryos's repo.

Dave

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Re: [Avogadro-Discuss] Reg- compiling error Avogadro

[David Lonie]

On Tue, Apr 23, 2013 at 1:11 PM, Dr. Amar Bahadur amar.b@gmail.com wrote:
 Dear Users,
   While compiling AVOGADRO, in Fedora-17, I got following
 error message:

 [dramarbahadur@dramarbahadur build]$ cmake ../
 snip
 -- checking for module 'openbabel-2.0=2.3.0'
 --   package 'openbabel-2.0=2.3.0' not found
 CMake Error at cmake/modules/FindOpenBabel2.cmake:69 (message):
   Could NOT find OpenBabel 2.3 or later

Do you have openbabel installed? See the installation instruction at
http://avogadro.openmolecules.net/wiki/Compiling_on_Linux_and_Mac_OS_X.

Dave

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

[David Lonie]

Hi Ron,

Thanks for the report. Is this issue fixed by the patch you sent, or
is this a separate issue?

Dave

On Mon, Apr 29, 2013 at 2:12 PM, Cohen, Ron rco...@carnegiescience.edu wrote:
 The reproducible error is:

 New Thread 0x40200940 (LWP 14602)]
 Settings are missing for the next engines: ()
 QStackedLayout::setCurrentWidget: Widget 0x1086190 not contained in stack
 dev warning: Extension GAMESS is using a deprecated DockWidget
 loading method. See Extension::dockWidgets() documentation.
 dev warning: Extension Orbitals is using a deprecated DockWidget
 loading method. See Extension::dockWidgets() documentation.
 dev warning: Extension Vibration is using a deprecated DockWidget
 loading method. See Extension::dockWidgets() documentation.
 No matching basis set file found:  /home/rcohen/untitled.cml
 GLWidget initialisation...
 GLWidget initialised...
 createObjects()
 [New Thread 0x40401940 (LWP 15450)]
 [New Thread 0x40602940 (LWP 15451)]
 [Thread 0x40401940 (LWP 15450) exited]
 [Thread 0x40602940 (LWP 15451) exited]
 [New Thread 0x40602940 (LWP 17304)]

 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

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Re: [Avogadro-Discuss] The defect site changes place after rotation!

[David Lonie]

On Tue, May 21, 2013 at 5:58 AM, 李文凡 limurphy1...@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

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Re: [Avogadro-Discuss] The defect site changes place after rotation!

[David Lonie]

On Tue, May 21, 2013 at 8:05 AM, 李文凡 limurphy1...@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

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Re: [Avogadro-Discuss] creating *.mol file

[David Lonie]

Hi Brent,

Did you try:
File  Save as  mymolecule.mol?

Best,
Dave


On Wed, May 29, 2013 at 2:28 PM, Brent Friesen ochemonl...@gmail.comwrote:

 I would like to use Avogadro as a way to create energy-minimized molecular
 conformations for an NMR prediction platform called PERCH.
 PERCH will only accept 3D structure files in *.mol or *.mms format.
 How can I save the Avogadro-generated 3 structure as a *.mol file?
 Thanks


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Re: [Avogadro-Discuss] About nanotube builder in Avogadro

[David Lonie]

On Thu, Aug 8, 2013 at 12:48 PM, Hyun-seok Kim roite...@snu.ac.kr wrote:
 Hi, I’m Hyun-seok Kim a graduate student at Seoul National University in
 South Korea.

 While using the ‘nanotube builder’ included in Avogadro I’ve noticed that
 (n,m) specification of nanotube is restricted maximum up to 9.

 Is there a particular reason?

The nanotube builder uses the TubeGen code to generate the nanotube
geometry, and the algorithm used can be very slow for large chirality
indices. We've clamped the values to produce structures that can be
built in a reasonable amount of time.

Why 9? Probably because it's the largest single digit number :)

We could increase the limit if people are regularly working with larger tubes.

 Furthermore, it will be nice to know how can I draw a nanotube with (n,m)
 indexes over 9.

 Such as (12, 0) or (12,1).

At this time, you'd need to modify the Avogadro source code and
recompile the executable, but that is a complicated task unless you're
familiar with software development.

For now, I'd recommend just using TubeGen through the author's web interface:

http://turin.nss.udel.edu/research/tubegenonline.html

IIRC, it will produce a .xyz file that can be opened in Avogadro.

Hope this helps,
Dave

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

[David Lonie]

Hi Sara,

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 delete atoms by right-clicking on them with the Draw tool.

Hope this helps,

Dave
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Re: [Avogadro-Discuss] Avogadro 2 0.7.0 Released

[David Lonie]

On Tue, Dec 3, 2013 at 11:14 AM, Stephen P. Molnar
s.mol...@sbcglobal.netwrote:

 Thank you for your note.  I tried all of the force fields on cyclohexane
 with no change in the structure.


Bear in mind that the conformer resulting from a computational geometry
optimization depends heavily on the starting structure. If the starting
structure is closer to boat, the optimization will follow the gradients to
the stationary point on the PES that corresponds to the boat structure, and
if the starting point is closer to chair, you will get chair. Try moving
some of the atoms to roughly form the chair, and then apply the
optimization. Note that this will happen with Avogadro 1 (or any other
computational code) as well.

Hope this helps,
Dave



 Stephen P. Molnar, Ph.D.Life is a fuzzy
 set
 Foundation for Chemistry   Stochastic and
 multivariate
 www.FoundationForChemistry.com
 (614)312-7528 (c)
 Skype:  smolnar1


 -Original Message-
 From: Marcus D. Hanwell [mailto:marcus.hanw...@kitware.com]
 Sent: Tuesday, December 03, 2013 10:49 AM
 To: avogadro-discuss@lists.sourceforge.net
 Cc: Avogadro-devel Devel
 Subject: Re: [Avogadro-Discuss] Avogadro 2 0.7.0 Released

 On Tue, Dec 3, 2013 at 8:25 AM, Stephen P. Molnar s.mol...@sbcglobal.net
 wrote:
  I must say that, in my opinion, this release is premature. I
  appreciate the comment ' lacks features present in Avogadro 1', but
  the new version appears to be incapable of rendering benzene as a planar
 molecule at this point.
  Although the optimized geometry of cyclohexane approximates the less
  stable boat conformer, the 1.0 version will generate the more stable
  chair conformer on optimization.

 I would disagree, and think that 'release early, release often' is a useful
 mantra in closing the loop between development and use that is employed by
 many open source projects (including Avogadro in the past, and now). We
 worked hard to ensure you could install Avogadro 1 and 2 on the same
 machine, removing any requirement to choose one or the other. Perhaps this
 article will fill add some of the motivation you appear to be inquiring
 about,

 http://www.kitware.com/source/home/post/113

 When you say 'incapable of rendering' is this referring to the forcefield
 optimization as your second point about cyclohexane is? I am not sure I see
 any reason why a planar benzene would not render, but could see the
 forcefield defaults giving issues. They both use the same forcefields
 underneath (the ones developed by the Open Babel project), and I can look
 into modifying our defaults as I had noticed version 2 generally didn't
 optimize the structures as well.
 
  Is it possible that I am missing something in the new, more convoluted
  directory and subdirectory structure of the gui?
 
 It is, but you would have to be more specific for me to hope to answer your
 question. If you are just interested in using the Avogadro application I am
 not sure why this would concern you. Thank you for your feedback, if you
 find Avogadro 2 unsuitable then certainly continue using 1.1 for now - we
 have an update planned for that shortly too.

 Sincerely,

 Marcus
 
  -Original Message-
  From: Marcus D. Hanwell [mailto:marcus.hanw...@kitware.com]
  Sent: Monday, December 02, 2013 2:14 PM
  To: Avogadro-devel Devel; avogadro-discuss@lists.sourceforge.net
  Subject: [Avogadro-Discuss] Avogadro 2 0.7.0 Released
 
  We are very proud to announce the availability of Avogadro 2 0.7.0.
 
  Avogadro 2 is a free, open source, cross-platform molecular editor
  designed for flexible use in computational chemistry, molecular
  modeling, bioinformatics, materials science, and related areas.
  Packages are available for Windows, Linux and Mac OS X. The source
  code source is available under the 3-clause BSD license.
 
  Avogadro 2 is a rewrite of Avogadro, and still lacks features present
  in Avogadro 1. Both packages can be installed on the same system, and
  so it is possible to try the latest without losing access to the
  previous version. We will be making occasional releases of Avogadro
  1.x too, along with migrating functionality to Avogadro 2. We value
  your feedback, and hope that you will find the improvements made in
 version 2 useful.
 
  What does Avogadro 2 do?
  * We've tried to make the best, most intuitive builder
  * Interfaces to many common computational packages
  * Designed to help both educational users and advanced research
  * Plugins that allow it to be extended and customized
  * Can be extended with simple Python scripts for file IO and input
  generation
  * Well defined public API, libraries and modular design
 
  Download:
  https://sourceforge.net/projects/avogadro/files/avogadro2/0.7.0/
 
  What's new? See the Release Notes:
  http://wiki.openchemistry.org/Avogadro2_0.7.0
 
  For more information: http://wiki.openchemistry.org/Avogadro
 
  If you use Avogadro or Avogadro 2, 

Re: [Avogadro-Discuss] Output/Viewable/Zoom question

[David Lonie]

I'm not aware of a way to do this directly in avogadro, but exporting to
svg / ps / pdf or some other vector graphics format will produce a
resizeable image, which could then be rasterized to higher resolution
raster image using something like imagemagick.

Hope this helps,
Dave

On Sat, Jun 13, 2015 at 11:38 AM, Rebecca Veitch revei...@gmail.com wrote:

 anyway to save a molecule output in a larger zoomed in aspect?  My
 molecule is huge and since Avogadro wil only output what is viewable in the
 window, it will not fit in an output file without being super small and
 unusuable.

 Is there a way to make that work?


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Re: [Avogadro-Discuss] XTALOPT hangs if server connection lost

[David Lonie]

On Fri, Aug 14, 2015 at 4:35 PM, Cohen, Ronald rco...@carnegiescience.edu
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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Re: [Avogadro-Discuss] xtalopt not digesting pwscf (quantum espresso) output

[David Lonie]

On Thu, Jul 30, 2015 at 8:46 AM, Ronald Cohen rco...@carnegiescience.edu
wrote:

 I can try to fix myself. Will let you know. Thanks!  Ron


That's be awesome! I'm away from my main development computer at the
moment, so you can probably get to it faster than me :)

The parsing code is in the OpenBabel project, at
src/formats/pwscfformat.cpp, if I remember correctly.

Thanks,
Dave
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Re: [Avogadro-Discuss] Regarding the execution of gamess input file

[David Lonie]

This looks like an issue with GAMESS itself. I'd suggest contacting them as
they'll be able to better help you.

Dave

On Tue, Mar 22, 2016 at 5:43 AM, Rajat Gupta  wrote:

> Dear sir,
>
> I am generating an input file for the calculation of energy of a cluster
> for gamess using avagadro but in that always following  error is coming:
>
> ddikick.x: application process 0 quit unexpectedly.
>  ddikick.x: Sending kill signal to DDI processes.
>  ddikick.x: Execution terminated due to error(s).
>
>
> Can you please suggest some solutions for that.
>
> Regards,
>
> Rajat Gupta
>
>
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Re: [Avogadro-Discuss] Yaehmop Additions

[David Lonie]

Very cool -- this is a nice addition for crystallographers!

On Sun, Sep 4, 2016 at 11:13 PM, Patrick Avery  wrote:
> 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] [Avogadro-devel] GSoC 2016

[David Lonie]

On Sun, Sep 11, 2016 at 9:26 PM, Patrick Avery  wrote:

> 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!
>

I just got caught up on all this -- great work! It's nice to see these
features make it into Avogadro 2!
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