Re: [Avogadro-devel] Plugin Repositories & Archives

CMake just internally includes libarchive, zlib, and libbzip2 here: https://github.com/Kitware/CMake/tree/master/Utilities and makes API calls into them as needed. Nothing fancy :) Dave On Thu, Nov 17, 2016 at 9:48 AM, Geoffrey Hutchison < geoff.hutchi...@gmail.com> wrote: > > The problem,

Re: [Avogadro-devel] GSoC 2016

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

Re: [Avogadro-devel] [Avogadro-Discuss] Yaehmop Additions

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

Re: [Avogadro-devel] Build Avogadro in Windows from source. MinGW or MSVC?

On Mon, Nov 16, 2015 at 7:13 AM, Carlos Salgado < carlos.salgado@gmail.com> wrote: > Dear all, > > I am trying to build the developer version of Avogadro in Windows, but I > am not sure if I have to use MSVC or MinGW, and the corresponding version > of Qt. I have build it in UNIX with

Re: [Avogadro-devel] New Avogadro Manual

That looks really great Geoff! I took a look through it and it's a great resource. Thanks to you and your group for putting the time in on this. BTW, if any of the features I added, particularly the crystal stuff, need some explanation let me know. Some of those features/options were rather

Re: [Avogadro-devel] [Avogadro-Discuss] Qt errors in xtalopt

Hi Ron, Can we move XtalOpt related discussions to the xtalopt-devel mailing list? http://lists.openmolecules.net/listinfo.cgi/xtalopt-devel-openmolecules.net Otherwise it might cause some confusion, as these warnings are unrelated to Avogadro ;) As for these warnings, I recall tracking them

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

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():

Re: [Avogadro-devel] subclass QColumnView

Have you tried using QtDesigner to add it as a promoted widget, instead of modifying the ui file directly? I suggest that approach as there may be some non-obvious bits of the ui file that need to change as well. On Wed, Jun 3, 2015 at 10:55 AM, Defusco III, Albert A defu...@pitt.edu wrote: Hi

Re: [Avogadro-devel] OpenID authentication for wiki?

It wouldn't hurt. Most sites I'm familiar with use that these days. I'm all for it. Dave On Thu, Feb 6, 2014 at 5:06 PM, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: Hi everyone, I've been doing some long-overdue tuning and wiki cleanup. One thing that comes up with anti-spam is

Re: [Avogadro-devel] Some symmetry operations fail to honor spacegroup setting

Hi Jure, Thanks for offering to fix up some of the rough edges here, any contributions are greatly appreciated! The eigen fix looks reasonable, but surprising that it didn't get inherited from a higher level directory. For now, you might be better off basing your work off of master. The

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

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

Re: [Avogadro-devel] Tenure Thanks

Congrats, Geoff! It's great news that your tenure has been accepted! :-) Dave On Wed, Oct 30, 2013 at 4:10 PM, Geoffrey Hutchison geo...@pitt.edu wrote: Dear everyone, My department voted recently to recommend me for tenure here at Pitt. While this still needs approval from the Dean, it’s

Re: [Avogadro-devel] Rép : superclasses and subclasses

Oops, I missed this -- apparently GMail doesn't recognize the Rép prefix as a reply ;-) static_cast will work, but it's less safe. It doesn't do any checking to see if the pointee is actually the type you're attempting to convert it to -- it just does the conversion. See this page for more info:

Re: [Avogadro-devel] First Avogadro 2 beta release

Hi Jens, On Fri, Apr 12, 2013 at 5:00 AM, Jens linuck...@gmail.com wrote: Really great to hear that avogadro2 is now on the scene and I'm excited to see how it develops in the future. It's already looking very impressive - I read in some pretty big molecules and the performance and

Re: [Avogadro-devel] The Hello World Example

On Tue, Nov 20, 2012 at 8:25 AM, Dubois Marc-André ma.dub...@umontreal.ca wrote: Hi everyone, I have a pretty beginner question regarding the development of an extension for Avogadro. I am trying to build the Hello World extension given as a example but I face this

Re: [Avogadro-devel] Deploying a version of Avogadro

On Tue, Aug 14, 2012 at 5:27 PM, Sexton, Thomas tsex...@mail.smu.edu wrote: I have an altered version of Avogadro which compiles and runs on my computer. However, when I share Avogadro.app with other users, the application crashes on launch. The trouble is that other computers do not have the

Re: [Avogadro-devel] [ avogadro-Bugs-3530802 ] Extensions-Molecular Orbitals... is a no-op

On Wed, May 30, 2012 at 9:57 AM, Michael Banck mba...@gmx.net wrote: (replying here again cause I think it is a more fundamental issue) On Wed, May 30, 2012 at 06:26:40AM -0700, SourceForge.net wrote: You're right -- it's a dead menu item, the extension launches itself automatically, as

[Avogadro-devel] Building on Windows

Hi list, The instructions for building on MSVC 2010 reference a file scripts/cmake-msvc2010.bat, but my tree only has the 2008 version. Does anyone have the missing file? Dave -- Live Security Virtual Conference

Re: [Avogadro-devel] [OpenBabel-Devel] OBConformerSearch undefined references, missing vtable

these days, are there any distros that are hold this back? Dave On Thu, May 3, 2012 at 9:43 AM, Noel O'Boyle baoille...@gmail.com wrote: If OB is not built with Eigen these classes are missing. On 3 May 2012 11:42, David Lonie david.lo...@kitware.com wrote: I'm having an issue compiling

Re: [Avogadro-devel] Periodic bond rendering

Hi Tuukka, On Sun, Apr 15, 2012 at 1:58 PM, Tuukka Verho tuukka.ve...@aalto.fi wrote: Hi Dave, Your algorithm for finding the shortest bond vector doesn't work right for unit cells with angles other than 90deg. You're right! I saw that method in a patch that went into openbabel and thought

Re: [Avogadro-devel] Periodic bond rendering

Hi Tuukka, On Mon, Apr 16, 2012 at 9:59 AM, Tuukka Verho tuukka.ve...@aalto.fi wrote: I tidied it up a bit more and changed some of the variable names to better ones. I think this version is also more efficient if you count the function calls. I managed to compile this time, thanks... The

Re: [Avogadro-devel] Periodic bond rendering

On Mon, Apr 16, 2012 at 12:56 PM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: Is this going into a specialized plugin, or straight into bsdyengine? I didn't look at the code, but it seems pretty specialized and I wondered what (if any) impact this would have where there is no periodic

Re: [Avogadro-devel] Periodic bond rendering

On Mon, Apr 16, 2012 at 2:11 PM, Tuukka Verho tuukka.ve...@aalto.fi wrote: No I meant the ones I changed in my patch: sqNormDifference - minLengthSq curSqDist - lengthSq Ok, done. Dave -- For Developers, A Lot Can

Re: [Avogadro-devel] Periodic bond rendering

On Mon, Apr 16, 2012 at 2:42 PM, Tuukka Verho tuukka.ve...@aalto.fi wrote: David Lonie kirjoitti 16.4.2012 kello 20.19: My only concern with this approach is that it won't close off the cylinders, leading to odd backface culling artifacts. No, you can also close the cylinders. First you draw

[Avogadro-devel] WmAvo patch

Hi everyone, A patch that would add support for the WiiMote to avogadro was submitted to Gerrit last November: http://review.source.kitware.com/#/c/3225/ It sounds like an interesting development, but IMO should be maintained and released as an external plugin due to it's limited audience

Re: [Avogadro-devel] Avogadro and SPGLIB

On Tue, Mar 27, 2012 at 11:35 AM, Albert DeFusco defu...@pitt.edu wrote: David, After some playing around I was able to determine that SPGlib will generate the primitive lattice and basis atoms correctly for use in PWScf.  The avospg method reduceToPrimitive appears to work correctly only

Re: [Avogadro-devel] Avogadro and SPGLIB

Hi Albert, On Wed, Mar 14, 2012 at 1:40 PM, Albert DeFusco defu...@pitt.edu wrote: I am working on writing an input generator for PWScf.  The input requires that user knows the atomic lattice basis and the Bravais lattice or the exact primitive lattice vectors. I have been playing with

Re: [Avogadro-devel] How to turn off graphics?

Hi Divya, On Tue, Mar 13, 2012 at 11:27 AM, Divya Neelagiri divne...@umail.iu.edu wrote: I need avogadro to perform minimization and some other operations on proteins. I'm not sure how you would perform any operations without the GUI, as there is no real command line interface to Avogadro. I

Re: [Avogadro-devel] How to turn off graphics?

On Fri, Mar 9, 2012 at 1:28 PM, Ray Sheppard rshep...@indiana.edu wrote: Hello Avogadro Development folks,   I recently installed Avogadro on a supercomputer for the School of Pharmacology. These machines work within a batch job environment.  I was asked: can you please tell me the command  

Re: [Avogadro-devel] Insert crystal missing

, David Lonie lonieda...@gmail.com wrote: Hi Geoff, I noticed today that the BuildInsertCrystal option is missing from master. Can you reproduce this? Thanks, Dave -- Virtualization Cloud Management Using Capacity

[Avogadro-devel] Insert crystal missing

Hi Geoff, I noticed today that the BuildInsertCrystal option is missing from master. Can you reproduce this? Thanks, Dave -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of

[Avogadro-devel] Adjust hydrogens crash

Hi List, I'm going through the bug tracker today, and came across a crash in the draw command/adjust hydrogen code. I'm not very familiar with this code, and the bug is rather unusual, so I'd like to see if anyone here has any ideas before I dig too deeply. The bug is here:

[Avogadro-devel] Avogadro minimum requirements

Hi everyone, I'm closing this (rather old...) bug report: http://sourceforge.net/tracker/?func=detailaid=3458927group_id=165310atid=835077 and moving it to this list. Do we have any minimum specifications for graphics hardware? Dave Original bug: Hey Names Peter, pet...@gmail.com. Just

Re: [Avogadro-devel] Adjust hydrogens crash

On Sat, Feb 18, 2012 at 12:26 PM, David Lonie lonieda...@gmail.com wrote: I set a breakpoint in AdjustHydrogensPreCommand::AdjustHydrogensPreCommand(Molecule*, uint atomId) to try to see what was happening, and found something very odd:        atomId  19      unsigned long        molecule

Re: [Avogadro-devel] Compile failures on the dashboard

On Mon, Feb 13, 2012 at 4:16 PM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: I think it would be great to get a 1.1.0 release out sometime in the near future. I was looking at a couple of compilation failures on the dashboards, and have addressed some of them here,

Re: [Avogadro-devel] OpenQube, Avogadro and Eigen 3

On Mon, Feb 13, 2012 at 6:27 PM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: I wanted to let the list know that I just uploaded a patch porting OpenQube to use Eigen 3. Avogadro maintains a snapshot of it, and can optionally build against the system installed version. In the new work

Re: [Avogadro-devel] Replace qt4_automoc with qt4_wrap_cpp

Marcus, Could you skim through the CMake changes here? I'll throw this up on Gerrit if everything looks ok to you. Dave On Tue, Nov 29, 2011 at 3:43 PM, Andrea Scarpino and...@archlinux.org wrote: Hi Avogadro team, I'm the avogadro maintainer in Arch Linux. We are updating boost to 1.48.0,

Re: [Avogadro-devel] [Avogadro-Discuss] Heuristic for Reading CIF / Crystal Structures?

On Tue, Nov 8, 2011 at 3:40 PM, Geoffrey Hutchison ge...@geoffhutchison.net wrote: Is the problem with a filled molecular crystal cell just that it's difficult to see what's going on (too much info)? That's part of it, but also users often just want the experimentally-derived molecular

Re: [Avogadro-devel] Carbon Nanotube Builder

On Tue, Oct 11, 2011 at 11:32 AM, Geoff Hutchison ge...@geoffhutchison.net wrote: My group has developed a need for a carbon nanotube builder, ... does anyone have any existing code tucked away that I could use as a starting point? I don't have the Avogadro code, but I *do* have the

Re: [Avogadro-devel] How to add an extension to avogadro

Hi Gina, On Thu, Sep 29, 2011 at 4:59 AM, Elena-Gina CRACIUN ginasv2...@yahoo.com wrote: So, after construct the extension (for example the hello world) I've obtained the library which I copy in the avogadro lib directory (for example C:\Program

Re: [Avogadro-devel] Create a package

Hi Mickaël, I do something similar for my XtalOpt extension, which supports both linux and Windows. On Tue, Sep 20, 2011 at 5:38 AM, Mickaël Gadroy mickael.gad...@gmail.com wrote:   - For Linux, I don't understand how to. Konstantin built some linux installers, and there are also the avopkg

[Avogadro-devel] Deprecated install rules

Hi Marcus, I've been working on some windows builds, and I noticed that the portion of the build system that install openbabel-2.dll, etc has been disabled by default (option ENABLE_DEPRECATED_INSTALL_RULES in AvoCPack.cmake). I just enabled it and the packages are working correctly, but I'm

Re: [Avogadro-devel] Review Backlog

On Thu, Jul 28, 2011 at 2:47 PM, Geoffrey Hutchison geo...@pitt.edu wrote: I'd like to get through the review backlog as part of the push-to-1.1 release. Right now, I'd like to merge: http://review.source.kitware.com/2031 http://review.source.kitware.com/1733

Re: [Avogadro-devel] How can I call the optimize geometry method ?

Hi Mickaël, I've needed to do this myself at some point, but I ended up using the OpenBabel forcefield code directly (this is actually how the ForceField extension works). AFAIK, there is no way to access an extension's members from within another extension. See 

Re: [Avogadro-devel] Crystal Builder

On Wed, Mar 23, 2011 at 11:42 AM, Geoffrey Hutchison geo...@pitt.edu wrote: Here's a resource for some common crystals and builder code: http://vimes.svn.sourceforge.net/viewvc/vimes/trunk/Vimes/CrystalBuilder.py?revision=38content-type=text%2Fplain It doesn't have as many oxides that I'd

[Avogadro-devel] Molecule signals

Hi all, While working on some extensions, I started getting annoyed with the signals currently used by Molecule -- there is no easy way to trigger a slot when *something* about the molecule changes without creating connections to each of atomAdded, atomRemoved, atomUpdated, bondAdded... etc. I

Re: [Avogadro-devel] Crystallography extension ready for review

On Mon, Mar 21, 2011 at 4:48 PM, Geoffrey Hutchison ge...@geoffhutchison.net wrote: I've now added all the features I can think of to the builder, and I'll stop constantly pushing updates, I promise ;-) Ooh, ooo, I can think of a few features. :-) * Library of standard crystal structures?