Re: [Avogadro-devel] Building avogadrolibs "core" only

[Marcus D. Hanwell]

On Sun, Sep 16, 2018 at 3:33 PM Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:

> Hi Marcus,
>
> I'm working along on the force field code - and wondering if there's
> documentation on building the "core" parts of avogadrolibs.
>
> I have the sense that you do something like this for the Python interfaces
> - that you build everything except the Qt GUI? This seems like it would be
> a nice approach for the force field calculations - to enable people to use
> a "headless" non-GUI tool to run geometry optimizations in addition to the
> GUI. Also, it would give some ability for the Python notebooks to run force
> field minimizations.
>
> How do you set up a build for "core-only"? Or put another way, how do you
> build the Python components and maybe I can extrapolate that to core +
> forcefield.
>

As Patrick pointed out we have a Dockerfile building core with Python
bindings, and that is what we are using in our server component. We test it
pretty regularly, and we are actively adding relevant API to our RESTful
interface for the server plugin. I have designs on creating a binary wheel
so that we could pip install core at least.

Hope that helps,

Marcus
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Re: [Avogadro-devel] Working as a programmer on Avagadro

[Marcus D. Hanwell]

Hi,

I updated http://wiki.openchemistry.org/Build#Building with a little more
detail on my Windows build, locating the Qt5_DIR location from a binary. In
front of the machine if more is needed.

Thanks,

Marcus

On Sun, 15 Jul 2018 at 15:31, Marcus D. Hanwell  wrote:

> Hi,
>
> I recently build a fresh tree on Windows using Visual Studio 2017. You can
> download the binary Qt package for VS 2015/2017, and just use that to link
> to/build against. I can try and write up each step as I do it fresh
> tomorrow once I am in front of that machine, but it really didn't take too
> long.
>
> You should never have to build Qt, it is a pain to build, and takes quite
> some time. I normally use the offline installers that are a little hidden,
> but the online installers work fine too,
>
> https://www1.qt.io/offline-installers/
>
> The tricky thing is navigating into the installation to find the correct
> Qt5_DIR location as they layer it a little for different compilers. Let me
> see if I can find some more concrete details for you tomorrow if no one
> else has all the answers to hand.
>
> Thanks,
>
> Marcus
>
> On Sun, 15 Jul 2018 at 15:09, Geoffrey Hutchison <
> geoff.hutchi...@gmail.com> wrote:
>
>> Dave,
>>
>> I'm cc'ing the avogadro-devel mailing list as well as Patrick Avery and
>> Marcus on this. I'm quite sure you don't need to build Qt for Windows
>> before compiling OpenChemistry on Windows, but I don't use Visual Studio.
>> (I install a binary version on Mac, which saves loads of time.)
>>
>> Patrick, Marcus, and anyone else.. Dave would like to contribute to
>> Avogadro2 development and has offered to help me with the new force field
>> framework. He's building with Visual Studio, but has had some trouble
>> getting everything compiled. I had pointed him at
>> http://wiki.openchemistry.org/Build but that doesn't cover much.
>>
>> Yes, the mini project involves simply allowing users to set the two
>> tolerances (i.e., making them parameters in the method first, eventually to
>> allow a  small dialog for the GUI to set them). No, not terribly complex,
>> but a lot of features turn out this way. "Oh, you want X.. okay, I guess
>> that makes sense."
>>
>> Once we get things building for you, I can point you at the new
>> forcefield code - I'm hoping you can help with a new type of minimizer
>> that's based on concepts from MD. (As in, it uses the gradients as forces,
>> uses the masses to compute acceleration and velocities, then heads
>> "downhill".)
>>
>> Thanks,
>> -Geoff
>>
>>
>> On Jul 15, 2018, at 10:37 AM, Dave Wertz 
>> wrote:
>>
>> Geoff:
>>
>> I am having a lot of trouble getting QT to build.  I keep getting syntax
>> and similar errors when I run nmake.  The download I got from the QT
>> website has 4 different releases in it.  I have tried two of them and got
>> similar errors in both.  I am now testing the hypothesis that the errors
>> are in unit tests that aren't needed in the release version.
>>
>> The build process takes hours so I have had time to look at your mini
>> project.  After looking at the code is appears that the code already has
>> two default tolerances.  An upper bound called tolerance which is set to
>> 0.45 at line 714 and a lower bound of 0.1 used in the if statement at line
>> 740.  If I understand you correctly, you want these two tolerances to be
>> user settable.  Is my understanding correct?
>>
>> Thanks,
>>
>> Dave
>>
>>
>>
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Re: [Avogadro-devel] Working as a programmer on Avagadro

[Marcus D. Hanwell]

Hi,

I recently build a fresh tree on Windows using Visual Studio 2017. You can
download the binary Qt package for VS 2015/2017, and just use that to link
to/build against. I can try and write up each step as I do it fresh
tomorrow once I am in front of that machine, but it really didn't take too
long.

You should never have to build Qt, it is a pain to build, and takes quite
some time. I normally use the offline installers that are a little hidden,
but the online installers work fine too,

https://www1.qt.io/offline-installers/

The tricky thing is navigating into the installation to find the correct
Qt5_DIR location as they layer it a little for different compilers. Let me
see if I can find some more concrete details for you tomorrow if no one
else has all the answers to hand.

Thanks,

Marcus

On Sun, 15 Jul 2018 at 15:09, Geoffrey Hutchison 
wrote:

> Dave,
>
> I'm cc'ing the avogadro-devel mailing list as well as Patrick Avery and
> Marcus on this. I'm quite sure you don't need to build Qt for Windows
> before compiling OpenChemistry on Windows, but I don't use Visual Studio.
> (I install a binary version on Mac, which saves loads of time.)
>
> Patrick, Marcus, and anyone else.. Dave would like to contribute to
> Avogadro2 development and has offered to help me with the new force field
> framework. He's building with Visual Studio, but has had some trouble
> getting everything compiled. I had pointed him at
> http://wiki.openchemistry.org/Build but that doesn't cover much.
>
> Yes, the mini project involves simply allowing users to set the two
> tolerances (i.e., making them parameters in the method first, eventually to
> allow a  small dialog for the GUI to set them). No, not terribly complex,
> but a lot of features turn out this way. "Oh, you want X.. okay, I guess
> that makes sense."
>
> Once we get things building for you, I can point you at the new forcefield
> code - I'm hoping you can help with a new type of minimizer that's based on
> concepts from MD. (As in, it uses the gradients as forces, uses the masses
> to compute acceleration and velocities, then heads "downhill".)
>
> Thanks,
> -Geoff
>
>
> On Jul 15, 2018, at 10:37 AM, Dave Wertz 
> wrote:
>
> Geoff:
>
> I am having a lot of trouble getting QT to build.  I keep getting syntax
> and similar errors when I run nmake.  The download I got from the QT
> website has 4 different releases in it.  I have tried two of them and got
> similar errors in both.  I am now testing the hypothesis that the errors
> are in unit tests that aren't needed in the release version.
>
> The build process takes hours so I have had time to look at your mini
> project.  After looking at the code is appears that the code already has
> two default tolerances.  An upper bound called tolerance which is set to
> 0.45 at line 714 and a lower bound of 0.1 used in the if statement at line
> 740.  If I understand you correctly, you want these two tolerances to be
> user settable.  Is my understanding correct?
>
> Thanks,
>
> Dave
>
>
>
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Re: [Avogadro-devel] Design for Charges and Force Fields in avogadrolibs

[Marcus D. Hanwell]

On Wed, Apr 25, 2018 at 10:51 AM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:

> I'm working on an implementation of force field plugins for avogadrolibs
> but I have some conceptual questions on where to put some of the code.
>
> Initially, I'd just put the bits into qtplugins directories, like the
> "workflow" scripts. (Some of the force fields will be in C++ and others can
> be loaded as Python scripts.)
>

I think this is ideal when developing something new.

>
> But I can imagine wanting charges and force field energies in lots of
> places - particularly charges. For example, it would be great to have popup
> menus listing all charge models in multiple places in the UI:
>
> - Properties -> Atom (partial charges in a table)
> - Surfaces -> Electrostatic Potential (partial charges to color the
> surface)
> - Properties -> Dipole Moment (or something like this)
>
> There seems to be a need for these in core classes, or at least qtgui
>
> Thus, I can imagine developing a PythonScriptLoader class that finds
> scripts of different types (generators, workflows, charges, forcefields,
> etc.) and stores them as lists/hashes. Right now, interfacescript.h and
> pythonscript.h live in qtgui.


> Does it make sense for chargemodel.h and/or forcefield.h to live in qtgui
> as well? (This suggests that inputgenerator files should be moved there
> too.)
>

This sounds reasonable, I was thinking about the molequeue library, and I
didn't want to add an extra dependency to Avogadro's GUI stuff. The
MoleQueue client code is in a couple of classes we could pull in, they just
depend on QtCore/QtNetwork. I think defaulting to adding a few new data
structures to the qtgui library would be good, and we could look at whether
any of that would be useful in core later, i.e. so that it is accessible to
file IO, server code, etc.

If we are OK with adding the QtNetwork dependency we could fold in the
MoleQueue integration classes, otherwise we could just ensure the network
code is kept separate from the input generation. I think this is the better
option, it has been a while but I can look at how much work that will be.
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Re: [Avogadro-devel] PubChem QC in Avogadro

[Marcus D. Hanwell]

On Tue, Jul 25, 2017 at 3:34 PM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:

> > This sounds great, we can get the optimized structure, and some
> properties, but I don't see mention of orbital data - is that possible at
> this stage? This sounds like a great resource, and something we should
> integrate.
>
> If you have the PubChem CID number, it’s possible to access the
> XZ-compressed raw output file:
> http://pubchemqc.riken.jp/Compound_1_25000/
> 1/1.b3lyp_6-31g(d).log.xz
>
> Ah, that is great,  1 is the PubChem CID repeated in the three
locations? Great resource, thanks for the pointers.

Marcus
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Re: [Avogadro-devel] cannot load PDB into avogadro

[Marcus D. Hanwell]

On Tue, Jun 6, 2017 at 12:18 PM, Chitrak Gupta  wrote:

> Dear avogadro users,
>
> I am relatively new to Avogadro. I am facing problem loading PDB file into
> avogadro.
>
> I created a PDB file using the build feature of Avogadro, but when I try
> to load the same file, I am getting the following error:
>
> No matching basis set file found: "filename.pdb"
> HOMO at: -1
>
>
> I have tried loading it from the GUI as well as drag-and-drop, both gives
> the same error. Any clue how to fix this?
>
> Which version of Avogadro are you using? If you can send the file to me
offlist I can take a look at it, and try it locally. I don't recognize the
error.

Thanks,

Marcus
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Re: [Avogadro-devel] Conda builds?

[Marcus D. Hanwell]

On Wed, Apr 19, 2017 at 7:17 AM, Rick Muller  wrote:

> I took the easy way out and just uninstalled numpy and boost from my build
> environment, so that python wasn't autoconfigured by cmake. The build just
> completed successfully. I'll test it out when I get into work this
> afternoon. If all goes well, I'll post the recipe here. It's pretty easy.
>
> I am pleased to hear it worked out, and would appreciate a copy of the
build script. I will see if I can take a look at Conda soon as I would like
to get more familiar with it.

Marcus
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Re: [Avogadro-devel] Conda builds?

[Marcus D. Hanwell]

On Tue, Apr 18, 2017 at 7:09 AM, Rick Muller  wrote:

> Hi,
>
> Long time user, first time caller ;-). I'm interested in building avogadro
> under conda, but I haven't found any existing projects under the usual
> channels. Has anyone started anything like this with either avogadro or
> avogadro2? Any suggestions for getting started?
>

Welcome, I have been meaning to get more familiar with Conda, but I  am not
aware of any existing  work to build either with it. As I understand it
Conda provides Qt, Open Babel, and several other libraries. If they are in
a common prefix you could pass in CMAKE_PREFIX_PATH (or even a list of
them). I could likely help, and wrote a large portion of the build
system/have built it in many places.

>
> One thing I've had a hard time finding in the documentation is a list of
> all of the cmake variables I have to set. Many of these I can find out by
> having ccmake fail, and then playing around with the variables that it asks
> me to set, but others (openbabel??) I haven't been able to find. Does
> anyone have a well-filled in cmake build.sh file, or a pointer to some
> useful documentation on this?
>
> We try to follow the standard CMake patters, keeping the cache variables
as advanced, with reasonable defaults. There isn't a complete list that I
am aware of, the closest would be
https://github.com/OpenChemistry/openchemistry/blob/master/cmake/External_avogadrolibs.cmake
which uses a variable to pass in paths for third party libraries
(dependencies).


> Thanks for a great project!
>
> Thanks, let us know how it goes.

Marcus
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Re: [Avogadro-devel] Avo2: List of Plugin Repositories

[Marcus D. Hanwell]

> On Jan 10, 2017, 11:18 PM -0500, Geoffrey Hutchison
> , wrote:
> I met with Ethan today and he has a working version of the plugin
> downloader.
>
> What’s your thought on a source for the list of repositories? We have the
> avogadro.cc domain - but I’d like to make sure that there’s an easy way
> (e.g., git) to update the list.
>
From my perspective I think we want to make sure it uses SSL, and I
would have thought some sort of static generation would be ideal in
the short to medium term, even long term it could be generated from a
Git repo we control, and pushed to something like GitHub pages (offers
SSL, but not easily with CNAME), or FireBase (it actually offers a
JSON database feature that might prove useful in future, but is great
for deploying static content to).

I have been experimenting with static site generation, and found
Firebase to be nice and it supports custom domains well with SSL
certificates. I think having Git, and the history that comes with it,
would be needed to ensure we can all see and verify the history. I
would like to see signed tags/commits, but using a controlled
repository would be sufficient.

Marcus

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Re: [Avogadro-devel] CJSON in Open Babel

[Marcus D. Hanwell]

On Sat, Jan 7, 2017 at 2:56 PM, Geoffrey Hutchison
 wrote:
> As we continue to develop the workflow idea, one obvious help would be to 
> integrate CJSON into Open Babel. I'm willing to do some of the work, since 
> there's already other JSON formats (src/formats/json).
>
> I'm curious about multiple coordinate sets and/or conformers. Right now, 
> there don't seem to be examples with multiple coordinate sets, nor docs in 
> the CJSON repository.
>
> Do you have one? (There must be, since there's the animation tool.)
>
The animation tool work was mostly focused on existing trajectories in
xyz format. I have some code on my machine back home that added
support, but I never got around to fixing it up and merging it.

I am out of the country until Friday, and amazingly tired right now
after flying through the night, but can see about getting something
for you. It would be great to flesh this and a few other additions
out, and get some working code - especially if that helps get more
data via Open Babel.

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

[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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[Avogadro-devel] Avogadro 1.90.0 released

[Marcus D. Hanwell]

We are pleased to announce the release of Avogadro 1.90.0, our latest
release as we finish up features for a final Avogadro 2.0 release.
This release has a lot of new work completed over the last year,
including the results of our first Google Summer of Code where two
students worked on projects under the program. The binaries were build
against Qt 5.7.0 (latest Qt at the time of release), an updated Open
Babel, and using Visual Studio 2015 on Windows.

Avogadro 1.90.0 was tagged last week, and the latest binaries can be
downloaded from http://openchemistry.org/downloads/, I made this the
first release on GitHub as the downloads are a lot cleaner from there
- let me know if you have any trouble downloading them
(https://github.com/OpenChemistry/avogadroapp/releases/tag/1.90.0 is
the GitHub page).

I intend to bump the CMake minimum, require C++11, and remove some now
redundant code falling back to Boost when C++11 was not available (and
code that is now in CMake/updates to CMake logic due to improvements
in CMake upstream). I want to make another release either very late
this year or early next year, and I think there is some great stuff
that is just about ready to be merged.

Thanks to everyone who contributed, gave us feedback, and funded our
development work.

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Re: [Avogadro-devel] 1.90 release..

[Marcus D. Hanwell]

Geoff,

On Tue, Nov 29, 2016 at 4:04 PM, Geoffrey Hutchison  wrote:
>
> You had mentioned spinning the 1.90 release tomorrow. While I have a few 
> things moving along, they're clearly not ready for 1.90 - I'll target them at 
> mid-December.

Sounds great, the selection code is moving along, locally I have it
rendering a selection box on mouse move too, but need to add code for
finding the planes, and then detecting if primitives are within it as
all of that is deprecated GL 1.x code that was used in Avogadro 1. Is
it worth merging basic selection of individual atoms as a preview do
you think?

I think it would be good to tag a release, make sure binaries work,
and then start just using C++11, and updating the CMake build system a
little. Hopefully that makes sense, I am happy to do a quieter
release, but for those interested make binaries available.

Marcus

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Re: [Avogadro-devel] Selection tool progress

[Marcus D. Hanwell]

On Mon, Nov 21, 2016 at 9:47 AM, Geoffrey Hutchison
 wrote:
>> is much nicer than how we did it before, and it seems like it would be
>> simple to add to CJSON.
>
> I think it's a good idea to add selection to CJSON for a few reasons. One, 
> the concept of "named selections" was in Avo1 but never really used. For 
> example, an enhanced QM (or other) generator could allow you to mark a 
> particular selection as QM/MM or support automatic fragment calculations, etc.
>
> Also, the "run" scripts could mark selected atoms in CJSON, e.g., build a 
> carbon nanotube and then allow the user to move it.

I am totally sold on adding support for it in CJSON, I can see a
number of use cases would clearly benefit.
>
>> I was going to look at adding a selection box next, and deletion of
>> selected atoms. I also need to add undo/redo support, if anyone is
>> interested in the half-working version I can share it on my fork of
>> avogadrolibs,
>
> I'd be happy to help with some of this.
>
What I have has been on my fork since last night, should get back to
some of it later, start cleaning up the branch and rounding out
initial features.

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Re: [Avogadro-devel] Roadmap for 1.91?

[Marcus D. Hanwell]

On Mon, Nov 21, 2016 at 12:01 AM, Geoffrey Hutchison
 wrote:
> You mentioned previously wanting to get out a new release fairly soon (1.91). 
> Do you have a target date? Dec. 1st?
>
I would like to tag 1.90 pretty soon, and then move to C++11/14 being
required. I added a deadline of 30 November for that, and then a 1.91
tentatively at 29 December that I felt was more likely to slip.

> Should we be clear about the roadmap for the release as well as post-1.91 
> release plans?
>
I began adding some issues, and looking at what was possible. I was
hoping basic cleanup for 1.90, happy to tag sooner, but I would really
like to move on soon.

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Re: [Avogadro-devel] CJSON format proposal

[Marcus D. Hanwell]

On Sun, Nov 20, 2016 at 11:57 AM, Boone, Paul  wrote:
> Can you explain more how BSON fits in here? If CJSON were supposed to be a
> file format for internal interchange, then I have nothing against storing
> coords as one array and then processing them when you read it in or out.

BSON is used by MongoDB, and it is one of the things that motivated
the development of CJSON - it was useful to be able to move to/from
BSON with a fairly compact format, which also matched our in-memory
layout. Frankly I feel like this is all a matter of interpretation,
one array is convenient in a number of settings, and the meaning is
quite clear, tuples within arrays can also be convenient (in C++ you
can have the best or both worlds when using flat arrays cast to Eigen
fixed size vectors for example)

CJSON was quite clearly originally developed out of a need for a
simple format for getting data in and out of Avogadro 2. We wanted
something efficient, based on existing  parsers, that could easily be
extended. It has been developed in an ad-hoc way to satisfy that need,
in the last year or two we have been looking at standardizing the
format for wider use. It has always embedded a key-value pair to allow
for breaking changes, with the ability to retain code to continue
working with legacy data.
>
> For the python interface though, we were going to use CJSON as a public
> interchange format, and for a public interface, I’d be adamant about
> sticking to the principles of (1) readability (i.e. the format making sense
> to somebody just reading the text format) and (2) and explicitness (i.e. the
> structure of the file should represent the underlying data, without needing
> to interpret it in any way). Otherwise, we’re letting our internal
> implementation determine the structure of the format, when we want the
> semantics of the underlying data to determine the format.

I understand what you are saying. I think it is just as readable
whether stored as tuples or a flat array, and don't see any ambiguity.
I guess this is why others have begun using this as an interchange
format in some places, I have used it in C++, Python and JavaScript
without issue.
>
> I specifically wouldn’t worry about space considerations of the sub-arrays,
> but I don’t ever worry about space for JSON since it just wasn’t intended
> for that. Right now I think the biggest CJSON file we’re testing with for
> the python interface is about 117k, which I don’t think of as large. But I
> have no insight into how this format is being used elsewhere… Are you using
> it for really large structures?

There are a few test cases at a few million, in the case of bonds and
BSON your proposed format would nearly double storage for little gain
from my perspective.
>
> So the fundamental question for me that I’m sure you all can provide some
> insight on is:
>
> - are there really two formats here: (1) a format designed for internal use,
> ease of importing / exporting straight to/from avogadro internal structures,
> and optimized for minimal size, likely using BSON and (2) a public format
> designed for readablity and semantic explicitness?
> - or, is the public format sufficient for both purposes?

I would say that for most uses the existing format is useful for
public interchange, you are adamant it is not for your use case. There
are some existing projects that are making use of the current layout
in multiple languages, I would like to continue supporting them at
least in the short term. I think semantic explicitness would likely be
better achieved in a JSON-LD based format mentioned below.

You obviously have strong feelings on what you want the Python
interchange format to look like, and in the short term a good
direction might be to simply develop that, do as you wish, develop the
API you want, and the public interchange format you want, and not
worry about the CJSON format (or use it as a starting point). I think
we can live with some duplication, this seems like a very focused
effort on Python - Avogadro exchange at this point, and you would like
to take advantage of language features between JSON and Python that
seems fair enough.
>
> You also mention some additional changes you were thinking of making. Can
> you tell me about those?
>
There is an NWChem JSON format we have been developing as part of a
collaborative project with Berkeley Lab. That has explored another
layout that uses more objects, and push further into electronic
structure. There was also a workshop at the EPA, and we have been
looking at developing a JSON-LD format that actually has some semantic
meaning. There is also the GSoC project, and I am fixing up a few
remaining warnings, to get electronic structure from cclib into
Avogadro via an extended CJSON representation.

Hopefully this makes my thinking more transparent to you. The Python
integration is not the only user of this exchange format. When I
started working on this it was clear there were a number of ways to

Re: [Avogadro-devel] Plugin Repositories & Archives

[Marcus D. Hanwell]

Stuck on a plane most of the day traveling back from a conference, but
like Dave said CMake just reuses several libraries and adds a little
API on top. Very limited access to Internet, but I would rather not
make CMake a runtime dependency. If we need to add a new dependency
let's keep it as simple as we can - building dependencies is one of
the biggest pains for packaging/making installers.

On 17 November 2016 at 10:02, David Lonie  wrote:
> 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
>  wrote:
>>
>> > The problem, though, is that it looks like you may have to add cmake as
>> > a runtime dependency with this setup, and I know you may not want to do
>> > that…
>>
>> No, not necessarily. It would be a matter of asking Marcus if he can point
>> us to the CMake code that handles decompression and including that in
>> Avogadro2. :-)
>>
>> Thanks,
>> -Geoff
>>
>>
>>
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Re: [Avogadro-devel] Avogadro2 Tool Priorities

[Marcus D. Hanwell]

The current default is navigate when loading a molecule, and edit when
the molecule is empty. I think that should be preserved, and merging
the toolbars back together with priority ordering is the right way to
go.

On Wed, Nov 16, 2016 at 4:25 PM, Jens  wrote:
>
> I agree. I've always found that somewhat counterintuitive and would 
> definitely prefer navigate to be the default.
>
> Best wishes,
>
> Jens
>
> On 16 November 2016 at 19:47, Patrick Avery  wrote:
>>
>> Sounds reasonable to me! I think I like having navigate as the first tool.
>>
>> On Wed, Nov 16, 2016 at 1:56 PM, Geoffrey Hutchison 
>>  wrote:
>>>
>>> I'm currently doing some user interface clean-up in Avogadro2.
>>>
>>> One thing I want to revisit is tool order/priority. In Avogadro1, the 
>>> default tool was the draw/edit tool, then navigate, etc.
>>>
>>>
>>> Do we want "draw" to be the default or "navigate / view?"
>>>
>>> I'm actually leaning towards switching:
>>> - Navigate (tool 1)
>>> - Draw (tool 2) - becomes active in new document
>>> - Manipulate (tool 3)
>>> - Bond Manipulate (tool 4)
>>> - Select (tool 5)
>>> - Measure (tool 6)
>>> - Align (tool 7)
>>>
>>> The auto-opt tool is actually going to become a command / mode, not a tool.
>>>
>>> Thoughts?
>>>
>>> -Geoff
>>>
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Re: [Avogadro-devel] VS2015 Build

[Marcus D. Hanwell]

On Thu, Nov 10, 2016 at 1:14 PM, Marcus D. Hanwell
<marcus.hanw...@kitware.com> wrote:
> On Tue, Nov 8, 2016 at 1:47 PM, Marcus D. Hanwell
> <marcus.hanw...@kitware.com> wrote:
>> On Wed, Oct 12, 2016 at 10:22 AM, Marcus D. Hanwell
>> <marcus.hanw...@kitware.com> wrote:
>>> On Sun, Oct 9, 2016 at 5:39 PM, Pavolik, Ethan Thomas <et...@pitt.edu> 
>>> wrote:
>>>> I was wondering if you'd made any progress getting VS2015 up and running on
>>>> your machine. I'm still stuck with the previous link errors when trying to
>>>> build Avogadro-libs. This week I tried rebuilding QT5 from source and have
>>>> been digging through and comparing symbols in relevant .lib files trying to
>>>> figure out why they won't link for me, but I haven't been able to make any
>>>> progress.
>>>>
>>> I need to get back to this, I know we have seen a VS2015 issue around
>>> jsoncpp in another project. We have also confirmed that PyBind11 needs
>>> VS2015 as its minimum version on Windows.
>>
>> I am working my way through issues on this now, I fixed the spglib
>> find call, and am looking at symbol visibility. I want to have all
>> this building by the end of the week, hopefully sooner.
>>
> So I didn't do very much yesterday, but today spotted a few typos. I
> have all of AvogadroLibs compiling now, just working on cleaning up
> the patch a little. I also have the app compiling, but need to take a
> look at the packaging issues. Looking close, should have patches
> pretty soon.
>
> This is not attempting Open Babel and its dependencies yet, not sure
> if Geoff has had success there or if Windows is back on an older
> compiler. I remember libxml2 and some of the other Open Babel
> dependencies being difficult, I think you mentioned having used
> prebuilt binaries compiled with older Visual Studio for the C only
> libs.

So, I have it to the point where I can build this on Windows with
Visual Studio 2015. I need to move the submodules forward, but
everything builds and links. So that is great, and some progress. I do
this by typing,

cmake --build . --target avogadroapp --config Release

Pointing Qt5_DIR to the place where Qt5 is installed (within there
lib/cmake/Qt5). The next thing I need to figure out is why the
rendering context does not seem to be getting initialized correctly -
blank only on 64 bit build, and crashing on startup on the 32 bit
build.

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Re: [Avogadro-devel] VS2015 Build

[Marcus D. Hanwell]

On Tue, Nov 8, 2016 at 1:47 PM, Marcus D. Hanwell
<marcus.hanw...@kitware.com> wrote:
> On Wed, Oct 12, 2016 at 10:22 AM, Marcus D. Hanwell
> <marcus.hanw...@kitware.com> wrote:
>> On Sun, Oct 9, 2016 at 5:39 PM, Pavolik, Ethan Thomas <et...@pitt.edu> wrote:
>>> I was wondering if you'd made any progress getting VS2015 up and running on
>>> your machine. I'm still stuck with the previous link errors when trying to
>>> build Avogadro-libs. This week I tried rebuilding QT5 from source and have
>>> been digging through and comparing symbols in relevant .lib files trying to
>>> figure out why they won't link for me, but I haven't been able to make any
>>> progress.
>>>
>> I need to get back to this, I know we have seen a VS2015 issue around
>> jsoncpp in another project. We have also confirmed that PyBind11 needs
>> VS2015 as its minimum version on Windows.
>
> I am working my way through issues on this now, I fixed the spglib
> find call, and am looking at symbol visibility. I want to have all
> this building by the end of the week, hopefully sooner.
>
So I didn't do very much yesterday, but today spotted a few typos. I
have all of AvogadroLibs compiling now, just working on cleaning up
the patch a little. I also have the app compiling, but need to take a
look at the packaging issues. Looking close, should have patches
pretty soon.

This is not attempting Open Babel and its dependencies yet, not sure
if Geoff has had success there or if Windows is back on an older
compiler. I remember libxml2 and some of the other Open Babel
dependencies being difficult, I think you mentioned having used
prebuilt binaries compiled with older Visual Studio for the C only
libs.

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Re: [Avogadro-devel] VS2015 Build

[Marcus D. Hanwell]

On Wed, Oct 12, 2016 at 10:22 AM, Marcus D. Hanwell
<marcus.hanw...@kitware.com> wrote:
> On Sun, Oct 9, 2016 at 5:39 PM, Pavolik, Ethan Thomas <et...@pitt.edu> wrote:
>> I was wondering if you'd made any progress getting VS2015 up and running on
>> your machine. I'm still stuck with the previous link errors when trying to
>> build Avogadro-libs. This week I tried rebuilding QT5 from source and have
>> been digging through and comparing symbols in relevant .lib files trying to
>> figure out why they won't link for me, but I haven't been able to make any
>> progress.
>>
> I need to get back to this, I know we have seen a VS2015 issue around
> jsoncpp in another project. We have also confirmed that PyBind11 needs
> VS2015 as its minimum version on Windows.

I am working my way through issues on this now, I fixed the spglib
find call, and am looking at symbol visibility. I want to have all
this building by the end of the week, hopefully sooner.

Marcus

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Re: [Avogadro-devel] Chemical JSON Spec

[Marcus D. Hanwell]

On Wed, Oct 19, 2016 at 9:20 PM, Geoffrey Hutchison
 wrote:
> I know as part of the GSOC project there were some questions about a more 
> formal spec for CJSON. Considering that I'd like to start adding pieces into 
> Open Babel (and maybe RDKit?) it would be really helpful if there was a more 
> formal write-up.
>
We started the Chemical JSON GitHub repository, and there are a few
people interested in developing a more formalized spec. I would say
that this is a good place to organize a spec,

https://github.com/OpenChemistry/chemicaljson

There is also https://github.com/OpenChemistry/avogadrodata/tree/master/data
that has a number of examples, several of which are used in the unit
tests. There is the original wiki page,
http://wiki.openchemistry.org/Chemical_JSON and I think that should
point to the repository once we have fleshed things out.

If we need to add things then I would favor adding
examples/specifications to the chemicaljson repository, or discussing
them here. It has been pretty informal so far, I am still working on
getting the unit cell stuff to read correctly before I will merge the
GSoC code - hoping to take another look later today, and there was a
fragment suggestion that looked good and I would like to add.

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Re: [Avogadro-devel] Avo2 - Paste & Python Dialogs

[Marcus D. Hanwell]

On Wed, Oct 12, 2016 at 1:21 PM, Geoffrey Hutchison
 wrote:
>>> - I'm going to take the InputGeneratorWidget out of avogadrolibs / 
>>> molequeue and put it into qtgui/ as InterfaceWidget. It will handle both 
>>> input generators and the new action scripts (i.e., parsing the JSON from 
>>> the scripts) - I will probably add small subclasses to handle the two 
>>> different types, e.g., the preview text in the input generators, etc.
>
>> I would not like to lose all the MoleQueue integration due to a Sierra
>> build issue, I am sure we can get to the bottom of it.
>
> That’s not what I’m implying. The InputGeneratorWidget code has no need to 
> live in molequeue - it simply takes some JSON and creates a Qt form. That’s a 
> simple refactor that will be used by the new action scripts. The new class 
> will be called InterfaceWidget (e.g., JSON -> form).

Sounds good, I misunderstood what you meant.
>
> The MoleQueue integration will live - the InputGeneratorDialog (which already 
> is there) will handle the integration as it does now.
>
> I’m not sure whether some widgets will go into the InputGeneratorDialog 
> (e.g., the preview text, etc.) or there will be a new InputGeneratorWidget 
> that’s a subclass of the InterfaceWidget.
>
Sounds good, thanks for clarifying what I wasn't clear on. I should
finally have some decent chunks of time to work on improvements. I
already made a few updates to the CMake code for finding Qt5, and have
been working on getting the CJSON branch from the cclib GSoC to a
place where it can be merged. The unit cell part is failing, but it
looks about ready once I get to the bottom of that.

In another project we have been using PyBind11, and for the most part
is has been really nice. That project was using VS2013, and we found
we needed VS2015 but the Linux and Mac builds seemed very smooth.

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Re: [Avogadro-devel] Make Package for Avogadro

[Marcus D. Hanwell]

On Wed, Oct 12, 2016 at 1:09 PM, Geoffrey Hutchison
 wrote:
>> Geoff has some custom scripts he runs that are not in the build
>> system, I wasn't able to generate a DMG last time I tried in Avogadro
>> 1, but as Geoff always made the DMG I didn't look into it much more
>> deeply.
>
> On Mac, with v1 I simply run “make install” and then have a script that 
> copies to a DMG. I’m happy to share the DMG template, although it uses a 
> non-free tool called “DMG Canvas” (http://www.araelium.com/dmgcanvas) to 
> install the pictures, etc. That’s the only reason I haven’t shared - it 
> doesn’t seem like a good idea to force people to use that tool.
>
This post was just put up too, needs very recent CMake but the
installer looks good and I think it can all be done with make package.

https://blog.kitware.com/creating-mac-os-x-packages-with-cmake/

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Re: [Avogadro-devel] Make Package for Avogadro

[Marcus D. Hanwell]

On Tue, Oct 11, 2016 at 4:01 PM, Patrick Avery  wrote:
> Hi there,
>
> I've been working on adding yaehmop features to Avogadro. The work for Dr.
> Jochen Autschbach's class is pretty much complete (they are going to be
> trying it out), and I wanted to package the program on Windows, Mac, and
> Linux. Fortunately, I already know how to do it on Windows.

Windows is the one I know pretty well, and that should work for the most part.
>
> For Linux, after compiling avogadro, you can type "make package" and it will
> create several packages (including a shell script) that can be used to get
> avogadro on your system. Unfortunately, this package does not come with the
> OpenBabel shared libraries, so any action that requires them will fail on a
> system that does not have OpenBabel installed and its resources in the
> $PATH. There isn't some kind of command that will include the OpenBabel
> shared libraries when making the package, is there? I have tried just
> copying the shared object libraries into the directory, and it fixes some
> problems but not all (it doesn't crash saying that it failed to find
> external library functions, but the functions don't exactly work - for
> example, when reading a cif file, it fails and prints that it failed to read
> it).

We never invested any time in getting Linux packaging to work, so I
would be surprised if it worked. We mainly worked with packagers to
try and ensure it was widely packaged.
>
> For Mac (Geoff, you might be able to answer this), you can use the "make
> package" command as well. However, I fear this has the same issue as the
> Linux "make package." I noticed that we have .dmg files that we release for
> Mac builds. How are those created? I assume they include the OpenBabel
> shared libraries and .txt files that are needed for OpenBabel operations.
>
Geoff has some custom scripts he runs that are not in the build
system, I wasn't able to generate a DMG last time I tried in Avogadro
1, but as Geoff always made the DMG I didn't look into it much more
deeply. In Avogadro 2 I got this working within the build system, and
if you turn the flags on it will ensure obabel et al are packaged.

Marcus

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Re: [Avogadro-devel] Avo2 - Paste & Python Dialogs

[Marcus D. Hanwell]

On Wed, Oct 12, 2016 at 11:52 AM, Geoffrey Hutchison
 wrote:
> Hi Marcus,
>
> As I've mentioned before, I'm working with Paul Boone here at Pitt on a new 
> script interface in Avogadro 2. Scripts (not just Python) will have a similar 
> API to the input generators, but will hand back a modified molecule to 
> Avogadro. Eventually, we'll implement a download-from-GitHub feature.
>
> I'm trying to do the least amount of refactoring:
> - Right now it seems like "Paste" doesn't actually modify the molecule - 
> instead, a new one is created. I'd like to adapt the paste command to work 
> like Avogadro v1 -- add more atoms and bonds to the current molecule

Sounds good.
>
> - I still have no idea how the UI for the molecule list is supposed to work. 
> I realize this is a Mac bug, but it seems like there should be a way to 
> "merge" or "split" those entries. However, since the undo stack is maintained 
> by the RWMolecule, I'm unclear on how you would implement undo/redo for those 
> concepts.

I would paste in the molecule being merged in, add that as an undoable
step, but not try to preserve the old undo/redo from the molecule
being merged.
>
> - I'm going to add selection to the RWMolecule and CJSON (i.e., which atoms 
> are currently selected). This will enable "regular paste" by including an 
> append() method with undo/redo support. Selections will also have undo/redo 
> support (i.e., the before and after bit vectors of selected atoms).

Sounds reasonable.
>
> - I'm going to take the InputGeneratorWidget out of avogadrolibs / molequeue 
> and put it into qtgui/ as InterfaceWidget. It will handle both input 
> generators and the new action scripts (i.e., parsing the JSON from the 
> scripts) - I will probably add small subclasses to handle the two different 
> types, e.g., the preview text in the input generators, etc.
>
I would not like to lose all the MoleQueue integration due to a Sierra
build issue, I am sure we can get to the bottom of it. I don't see any
issue refactoring a little, but to be honest, worst case we should
just import the MoleQueue client classes into Avogadro, that would
remove the dependency, and it would keep the functionality. There
would be some code duplication, but that isn't the end of the world.

We still don't have a Sierra machine for me to test that out on,
should hopefully get something soon.

Marcus

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Re: [Avogadro-devel] VS2015 Build

[Marcus D. Hanwell]

On Sun, Oct 9, 2016 at 5:39 PM, Pavolik, Ethan Thomas  wrote:
> I was wondering if you'd made any progress getting VS2015 up and running on
> your machine. I'm still stuck with the previous link errors when trying to
> build Avogadro-libs. This week I tried rebuilding QT5 from source and have
> been digging through and comparing symbols in relevant .lib files trying to
> figure out why they won't link for me, but I haven't been able to make any
> progress.
>
I need to get back to this, I know we have seen a VS2015 issue around
jsoncpp in another project. We have also confirmed that PyBind11 needs
VS2015 as its minimum version on Windows.

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Re: [Avogadro-devel] CMake Error building MoleQueue on OSX 10.9.5

[Marcus D. Hanwell]

On Tue, Oct 11, 2016 at 10:44 PM, Geoffrey Hutchison
 wrote:
> I've installed Qt (5.6.0) and Cmake (3.3.1) using anaconda, and followed the
> instructions here:
>
>
> That may be the problem. I've had trouble with anaconda (or homebrew)
> versions of the Qt packages.
>
> I'd highly recommend Mac users go for the binary distribution:
> http://download.qt.io/official_releases/online_installers/qt-unified-mac-x64-online.dmg
>
> It'll ask for an account, but skip that step - it's for commercial Qt
> licenses.
>
> Then, before running cmake (i.e., /path/to/your/Qt/5.6 …)
> export CMAKE_PREFIX_PATH=/Users/ghutchis/Qt/5.6/clang_64/lib/cmake
>
Never used Anaconda, good to know, I didn't know they packaged things
like Qt. I have used homebrew quite successfully, but will look out
for issues. With some of the recent updates you can continue using
CMAKE_PREFIX_PATH, but Qt5 should only need Qt5_DIR to be defined.

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Re: [Avogadro-devel] CMake error (Avo2)

[Marcus D. Hanwell]

On Sun, Oct 9, 2016 at 11:33 AM, Marcus D. Hanwell
<marcus.hanw...@kitware.com> wrote:
> On Sun, Oct 9, 2016 at 11:32 AM, Marcus D. Hanwell
> <marcus.hanw...@kitware.com> wrote:
>> On Sun, Oct 9, 2016 at 12:04 AM, Geoffrey Hutchison
>> <geoff.hutchi...@gmail.com> wrote:
>>>
>>> > people. For now I am guessing you can turn it off and build or does it
>>> > fail later when AvogadroApp tries to find the libs?
>>>
>>> I can turn it off and complete the build. Unfortunately that entirely turns 
>>> off the python input generators. I'll work around that a bit.
>>>
>> That is weird, it shouldn't just turn off the automatic submission via
>> MoleQueue. I will take a look, maybe some of the logic isn't quite
>> right. The Mac paths are all different, and have quite a few extra
>> levels.
>>
> I meant "it should just turn off the submission via MoleQueue", the
> input generators should still be there, but it is using relative paths
> that might be incorrect.
>
I remember now, sorry for any confusion, the generators do have a hard
dependency on MoleQueue. That could probably be fixed, but we didn't
want to do the work at the time. It would need some refactoring as we
kept all the logic in a single generator class for building the UI,
and the submit job buttons.

I have been trying to reproduce this locally but it works fine
locally. I do not have a machine upgraded to Sierra at this point
though, and it is quite possibly specific to that OS. The file should
be in 'prefix/lib/cmake'.

I will see if I can get access to a machine that has been updated. My
Mac laptop is pretty ancient, and I will likely retire it soon, but
may try an update to see if it will take it.

Marcus

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Re: [Avogadro-devel] CMake error (Avo2)

[Marcus D. Hanwell]

On Wed, Oct 5, 2016 at 10:10 PM, Geoffrey Hutchison
 wrote:
> I upgraded my laptop to Mac OS Sierra and the new Xcode. I'm now having 
> trouble getting AvogadroApp to compile. I get a weird CMake error when 
> BUILD_MOLEQUEUE is enabled:
>
> CMake Error at 
> /Users/ghutchis/Devel/build/openchemistry/prefix/MoleQueue.app/Contents/Resources/MoleQueueConfig.cmake:20
>  (include):
>   include could not find load file:
>
> 
> /Users/ghutchis/Devel/build/openchemistry/prefix/MoleQueue.app/Contents/lib/cmake/molequeue/MoleQueueTargets.cmake
> Call Stack (most recent call first):
>   avogadro/molequeue/CMakeLists.txt:2 (find_package)
>
> There's no prefix/MoleQueue.app/Contents/lib/cmake directory. Where is this 
> supposed to be created / copied?
>
> If I look into molequeue/lib then I also don't see a cmake directory.
>
That is weird, I am guessing you already tried simply creating a new
build tree. I can take a look on my Mac (probably some time tomorrow),
but it is not Sierra. We haven't really upgraded any machines, or made
a CMake release since Sierra was updated. I will try to dig around a
little and see if I can spot anything, and ask our Mac-based CMake
people. For now I am guessing you can turn it off and build or does it
fail later when AvogadroApp tries to find the libs?

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Re: [Avogadro-devel] VS 2015 Progress

[Marcus D. Hanwell]

On Tue, Sep 20, 2016 at 8:38 PM, Pavolik, Ethan Thomas  wrote:
> I'm (bravely) trying to build Avogadro 2 using Visual Studio 2015 and I
> wanted to post on some issues I've resolved so far as well as try to get
> some help on the issues I'm currently facing.
>
Thanks for posting a summary of your progress.
>
> I've been working on a Windows 10 PC that I reset/wiped and completely
> reinstalled VS2015 and the Windows SDK version 10.0.10586.0 to cross out any
> errors being due to my install.
>
> Some things I've noticed and changed so far:
>
>
> zlib- zlib seems to build fine, however there is a post-build instruction
> that is defined somewhere in the cmake files that renames zlib.lib - >
> zlib1.lib. I'm not sure if this is a problem building on other platforms,
> but when I build in debug mode, VS produces zlibd.lib. Then when it attempts
> to do the renaming step, it will say the build failed despite zlibd.lib
> being correctly generated. Building as release seems to work fine.
>
I have never put the time in to get a working debug build on Windows,
this is likely true with VS2010 that I was using too.
>
> libxml2- At the time of this message, libxml 2.9.1 is being used as a
> dependency. After much frustration it turns out that they introduced a fix
> for VS2015 in version 2.9.2 involving a macro definition of "snprintf". I've
> since changed it to use version 2.9.4 on my machine. While that has allowed
> me to compile fine, I'm currently facing unresolved external errors during
> linking which I have yet to look into.
>
I actually had to push libxml2 back in order to get it to build with
VS2010, I am all in favor of moving this forward. It is mainly there
for Open Babel at this point, Avogadro 2 doesn't use it directly.
>
> boost- Attempting to build boost resulted in a single toolset error, which I
> was able to fix by adding
>
> "elseif(MSVC14)
>
> set(_toolset "msvc-14.0")"
> to cmake/External_boost.cmake.

For VS2015 and Avogadro 2/MoleQueue there should be no need for Boost
as far as I know.
>
> HDF5- They recently changed where they were hosting their 1.8.12 source. If
> you don't already have it in your downloads folder you will get a 404 error
> when trying to download the source. After changing the download location and
> version to 1.8.17 I still was not able to compile, but luckily they offer a
> binary compiled on VS2015 which seemed to work fine.

If you have the new location I would love to fix that, if you want to
make a pull request, or I can update it in the superbuild.
>
> Molequeue- Setting "CMAKE_PREFIX_PATH" was required for the required QT
> files to be located.

I have a couple of patches, where CMAKE_PREFIX_PATH will continue to
work, but Qt5_DIR should work and be passed down. I had been using
prefix path as it was the simplest solution.
>
> avogadrolibs- VS2015 wasn't able to recognize the type "uint" so I had to
> add "typedef unsigned int uint" at the top of poscarformat.cpp in order for
> this project to compile.

That is a mistake, I must have missed it in review. It should be
changed to unsigned int, I can patch that.
>
> These are the changes I've made so far in order to build most of the
> solution. Hopefully my notes so far can help some people in a similar
> situation, as well as bring up some issues that may affect others too (such
> as the HDF5 download location).

I will turn HDF5 off by default, the support was experimental and we
don't want to make builds harder unless they are actually using the
library.
>
> Right now my build is being stopped by unresolved externals in both the
> libxml2 and avogadrolibs projects. I'm focusing on solving my issues with
> avogadrolibs right now. The issue seems to be between AvogadroQuantumIo +
> Json::Value (http://pastebin.com/nG4YYRXj)  and AvogadroMoleQueue +
> Avogadro::QtGui::GenericHighlighter (http://pastebin.com/XDbDfAhA).

They are news to me, I will see if I can take a look. Thanks for
posting detailed notes, I can create a few patches for the simpler
fixes, and will see if I can get VS2015 up and running on my machine.

Marcus

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Re: [Avogadro-devel] Progress this Week

[Marcus D. Hanwell]

On Fri, Sep 9, 2016 at 9:28 AM, Geoffrey Hutchison
 wrote:
>
> I have an undergrad student, who will be working on some features in Avogadro 
> v2. Has there been success at VS2015 compilation?

I haven't even tried VS 2015, I thought you had a student who had
managed to get it building with 2015, I was working on 2013 but was
hoping to see some of what that student had done. I think we need to
get 2015 working, and will take a look when I get a chance.

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Re: [Avogadro-devel] Extending Avo2 "Input Generators" to "Modify" scripts

[Marcus D. Hanwell]

On Tue, Aug 2, 2016 at 5:52 PM, Geoffrey Hutchison
 wrote:
> I’ve been talking with Paul Boone, an experienced Python programmer on staff
> here at Pitt (and soon to be PhD student) about the Python interface to
> Avo2.
>
> Short message - we think it's easy to add script support for a *lot* of use
> cases without much work.
> - Scripts could pop up an options dialog, receive a cjson molecule, and pass
> back a new cjson and optionally some messages.
>
> Consider the case of a script (Python or not) that modifies the molecule
> somehow. Maybe it scales the bonds. Maybe it generates a crystal structure…
> That script probably wants an options dialog in Avogadro and then a “run”
> script that passes back the modified molecule in cjson format. Avogadro adds
> an undo/redo between the two structures.
>
> The beauty is that it's really easy to write this kind of script, either for
> personal use, or to distribute and it's powerful. Imagine a "stack" script
> that replicates the molecule X times along the x/y/z axis after translating
> by Y Angstroms.
>
Sounds good.
>
> Much of the code we want is already there in the input generators - building
> the dialog GUI.
> - Except the input generators currently don’t allow floating point #s
> - They don’t (always) receive the current molecule when asked to create the
> input dialog JSON
> - They don’t have any sort of language / localization
> - They don't allow multiple tabs/panels
>
> My suggestion here is to refactor the InputDialog class to OptionsDialog
> - Allow floating point numbers (with constraints on precision and range)
> - Add a --language=en flag to the script to load different JSON depending on
> the user's default language
> - Always pass the molecule as CJSON (and drop the CML version) - allowing
> the dialog to change based on the molecule

I think for big molecules there is value in not passing the molecule
when the script won't do anything, but this seems like a simple flag
in the JSON to specify whether the molecule is desired or not.

>   .. for example maybe showing a different interface if a unit cell is
> present, or filtering basis sets based on atoms
> - Add a syntax for multiple panels, e.g.
> "Basic" : [ .. ],
> "Advanced": [ .. ]
>
> I'd also suggest that to better support an "installer" feature, that we
> change the scripts to live in separate directories:

What would the installer feature do? It isn't clear what install
means, but the package.json, and run.py etc seem to make sense.
>
> gaussian/
>  .. run
>  .. install
>  .. package.json
> qchem/
>  .. run
>  .. install
>  .. package.json
>
> This means that while we'd encourage Python, in principal, users could write
> their plugin scripts in *any* language as long as it meets the minimal API
> (i.e., pass back JSON for the dialog).
>
This feature was designed from the start to support any language, but
we never went beyond Python. The input/output is language agnostic,
but there is value in knowing that this package is Python, and that we
can use the Python interpreter path to run it. On Windows I don't
think the executable Python stuff works at all for example, but a
binary would of course work without issue.

I think it totally makes sense to pull the JSON stuff into a separate
file, most of what we wrote so far has no use for an install script as
far as I can tell, but maybe I am missing something. I think using
file endings/embedding in the JSON file the type of script would help
us use the appropriate interpreter when needed.

To make it easier to implement I wonder if we want to explore adding
this more dynamic scripting interface as a new feature, then port the
input generators if it looks general enough for them too, and allowing
us to merge an earlier version that perhaps doesn't have everything
working. There are also the file format scripts, that could be in any
language too but are currently hardwired for Python.

Slicer has some work that has gone in this direction, see the command
line modules, 
https://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Developers/Modules
for some brief details. For the Tomviz project we have Python modules
that are currently hardwired in the application, and we are looking at
a very similar setup where these are all designed to operate on a cube
using Python, SciPy, NumPy, ITK, VTK etc. They are loaded into the
application's interpreter in the same memory space in the Tomviz case
though, whereas Slicer has executed command line interfaces.

I think this would be great, and I was hoping to find time to move our
Python stuff over to this style of layout to make installation/sharing
easier. We should also add support for running from home directory as
well as the system paths where the application gets installed.

Marcus

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Re: [Avogadro-devel] Avogadrolibs Roadmap

[Marcus D. Hanwell]

On Wed, Jun 15, 2016 at 3:44 PM, Geoffrey Hutchison
 wrote:
>
> - Are there general or specific “loose threads” in the code? It seems like 
> there are some needs for batch undo/redo in RWMolecule, for example.

I would like to investigate grouping commands, and naming them.
Batches/larger commands would be good for efficiency, and achieve much
the same. I could see both being useful.
>
> - You mentioned implementing selections.. where should selections "live"? 
> Does the molecule track this? Does the widget? For example, should selections 
> be a special type of molecular fragment?

I was working on making some additions to molecule, and think that is
a natural place. I could see some argument for attaching them to
widgets, but would prefer to keep it simple for now.
>
> - Implementing fragments and residues.. this seems like it needs to live in 
> both Molecule and RWMolecule with the current class scheme. How do changes to 
> fragments coalesce? For example, does there need to be a mechanism to 
> invalidate a residue name when an edit occurs?

Nothing really lives in RWMolecule, it simply references data in
Molecule, and provides undo/redo functionality. Anything in RWMolecule
that is not in Molecule should be to facilitate undo/redo. Those are
my thoughts at least, and by layering RWMolecule on Molecule it allows
much of the cost for undo/redo to live in that class too.
>
> - Rendering options? Right now, there's no way to change atom sizes or bond 
> sizes.. where would this code live?

I would say the view configuration, in much the same way it did in
Avogadro 1. The ball and stick plugin features a configuration widget,
and offers multiple bonds/hydrogen visibility as two options. I meant
to go back and add bond/atom radius multipliers - it shouldn't be too
hard.
>
> - Settings in general.. Do we need to go add QSettings read/write to plugins 
> like in Avo1? How should this work with the Python scripts like input 
> generators?

QSettings is a good question - is that still supported as the Qt
community was talking about deprecating the INI file stuff, and
QSettings I thought. I would love to wrap more of this in JSON, and
have a JSON settings file, along with JSON data files. This could then
be passed to Python even, or combined. That is a good question on
persistent settings and input generators - I hadn't looked into that.
>
> - How / when will volume rendering show up? (i.e., what's the barrier for 
> that to be possible?)

VTK changed quite a bit, I would like to resurrect it. I know know the
code to edit the color maps much better too, and so could add the user
interface for it more easily than back then. This was the big missing
piece. I will see if I can take a look at where that is on the weekend
- it was crashing which is why I removed the option, but I really want
to get it back in there.

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Re: [Avogadro-devel] Avo2 - Downloading from GitHub

[Marcus D. Hanwell]

On Thu, Jun 9, 2016 at 1:25 PM, Geoffrey Hutchison
 wrote:
>> GNU Octave can download and compile its C++ packages automatically.
>> Perhaps it can serve as an example?
>
> My concern is this requires a C++ compiler from the end-user. On Mac and 
> Windows in particular, that’s not very common.
>
> Moreover, while we've offered nice C++ APIs for Avo1, I think the pool of 
> Python programmers is greater in science than those who know C++.
> (Indeed, the APIs in Avo2 could probably be ported to other languages too - 
> we're mostly running scripts as separate processes.)
>
Yes, my vision was to go beyond prescribing the language they wrote
extensions in. Python is a great start, but anything is acceptable as
they execute in their own process.

I wonder if we might either use the GitHub APIs, or simply call the
git command line to clone/update. This is what Qt Creator does, and we
would simply need to ask the user to install git/point us at it. We
call obabel like that too.

Marcus

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Re: [Avogadro-devel] Avo2 - Downloading from GitHub

[Marcus D. Hanwell]

On Thu, Jun 9, 2016 at 1:57 PM, Geoffrey Hutchison
 wrote:
>> I wonder if we might either use the GitHub APIs
>
> We can definitely use the GitHub API via HTTP. The catch is this ties us to 
> GitHub a bit more, while using Git directly makes it easier to point at 
> multiple repositories.
>
> It's pretty easy to walk the JSON from the API, e.g.
> https://api.github.com/repos/cryos/avogadro/contents/crystals?ref=master

It also makes it pretty easy to add other RESTful endpoints, and they
can be backed by whatever people choose. Calling git or other tools
from the command line would let us clone/update without committing
entirely to git.

I feel like expanding out interaction with RESTful services is a good
general direction, GitHub provides one endpoint but it is not the only
one.

My $0.02 on it...

Marcus

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Re: [Avogadro-devel] Getting an Atom from an RWAtom (Avo2)

[Marcus D. Hanwell]

On Fri, May 27, 2016 at 11:22 AM, Marcus D. Hanwell
<marcus.hanw...@kitware.com> wrote:
> On Tue, May 24, 2016 at 11:54 AM, Geoffrey Hutchison
> <geoff.hutchi...@gmail.com> wrote:
>>> I thought that ideally HydrogenTools would operate on the RWMolecule,
>>> but RWMolecule is now a lightweight class. There is not currently a
>>> way to get the Atom from an RWAtom, but the code would be very simple
>>> so if we want to add it we can.
>>
So I was just taking another look, and I think all you need assuming
you have the QtGui::Molecule, and the Atom object you want to access:

RWAtom rwAtom = molecule->undoMolecule()->atom(atom.index());

If you have an example where that doesn't seem to work I can take a
better look. The call to undoMolecule on molecule is cheap, no object
creation/destruction, and the rwAtom object creation should also be
really cheap. There is also atomByUniqueId if you want it, but the
index version should be faster and safe in the context you want it.

Marcus

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Re: [Avogadro-devel] Getting an Atom from an RWAtom (Avo2)

[Marcus D. Hanwell]

On Tue, May 24, 2016 at 11:54 AM, Geoffrey Hutchison
 wrote:
>> I thought that ideally HydrogenTools would operate on the RWMolecule,
>> but RWMolecule is now a lightweight class. There is not currently a
>> way to get the Atom from an RWAtom, but the code would be very simple
>> so if we want to add it we can.
>
> Just a follow-up.. Can you point me in the direction here?
>
Sorry, I knew I owed you something. I will take a look at it, too much travel...

Marcus

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Re: [Avogadro-devel] avogadro-super custom targets?

[Marcus D. Hanwell]

Hi Geoff,

On Wed, May 25, 2016 at 2:51 PM, Geoffrey Hutchison  wrote:
> Hi Marcus,
>
> There was a request for an “uninstall” target for openbabel. So I added one.
>
> Now, the avogadro-super build fails because there are duplicate custom 
> targets..
>
> Any suggestions to resolve this?
>
You would need to use avogadro-squared, which uses the more modern
approach of external projects. Then each project has its own build
tree, and so you don't have the issue of duplicate targets. Otherwise
I don't think it is possible to resolve in an old-style combining all
projects in one CMake project approach as you cannot have duplicate
target names.

Marcus

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Re: [Avogadro-devel] Avo2 - no POVRay menu item?

[Marcus D. Hanwell]

On Thu, May 12, 2016 at 2:51 PM, Geoffrey Hutchison
 wrote:
> We're trying to port some of the VMRL export code to Avogadro 2 - so I 
> thought we should start with the POV-Ray export plugin: qtplugins/povray/
>
> But it doesn't appear in the interface, at least on Mac?! Any ideas?
>
I am at the airport, visiting somewhere all day tomorrow. I think I
got most of the basics working, but hadn't quite finished off the
POV-Ray exporter. I will see if I can take a look when I get to my
hotel room later and see where it was at, but I possibly didn't add
the menu item as it wasn't working properly for me (camera stuff
needed more work, possibly other stuff).

Marcus

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Re: [Avogadro-devel] Avogadro 2 release number simplification/jump

[Marcus D. Hanwell]

On Wed, May 11, 2016 at 3:49 PM, Michael Banck <mba...@debian.org> wrote:
> On Wed, May 11, 2016 at 03:43:19PM -0400, Marcus D. Hanwell wrote:
>> So I had one or two queries recently that made me realize I should
>> have done a better job on less ambiguous version numbering for
>> Avogadro 2 releases. I would like to make the next Avogadro 2 release
>> 1.90, and then after that 1.91, 1.92, 1.93, etc until we feel good
>> with sticking a 2.0 release out.
>
> What's the plan after 1.99?
>
> I assume it won't get to there, but it makes sense to plan for it.
> Calling it 1.100 wouldn't be a problem in my opinion, but if you don't
> like it now, maybe 1.90 isn't the best starting point.

I am fine with 1.100, but hope not to get there. I think it gives us a
good amount of space, I can start at 80 if people have feelings either
way. I am fine going up to 1.1000, but sincerely doubt we need that
many release numbers.

Marcus

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[Avogadro-devel] Avogadro 2 release number simplification/jump

[Marcus D. Hanwell]

Hi,

So I had one or two queries recently that made me realize I should
have done a better job on less ambiguous version numbering for
Avogadro 2 releases. I would like to make the next Avogadro 2 release
1.90, and then after that 1.91, 1.92, 1.93, etc until we feel good
with sticking a 2.0 release out.

This avoids repeating previous Avogadro release numbers, such as
0.8.0, 0.9.0, etc. It is also in line with several other projects that
use .90+ for releases before the next major version increment, and it
makes it clear that there are API changes in each release. Not much to
be done about previous releases.

I hope with our Google Summer of Code students, and general energy
around landing features we can get a few good releases out over the
summer. I would like to promote Avogadro 2 as a tool, and achieve
parity where features/polish are missing.

Thanks,

Marcus

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Re: [Avogadro-devel] "Active" Molecules Emit Interface Updates?

[Marcus D. Hanwell]

On Thu, May 5, 2016 at 2:13 PM, Barry Moore  wrote:
> All,
>
> I have been thinking about upgrades to the surfaces interface in Avogadro 2,
> but it brought me back to the "Molecules" widget (bottom left). Currently,
> it doesn't really do much but I think this would be a great interface to
> beef up. For example, it would be helpful if one could click a molecule to
> make it "active" then emit a signal for all other interfaces which are
> Molecule centric. Nearly all of the interfaces are linked to the current
> molecule and this would make it a lot easier to design interfaces. What do
> you guys think? Worth spending time on?
>
> In the future, one could open up multiple molecules and look at multiple
> properties, cubes, etc. all at the same time.
>
This is the design I was working towards there, and agree beefing it
up to make plugins more aware of active molecule changes would be
good. We should also let tools be aware of multiple molecules, and
look at what is needed to support that. I need to read through some of
what is there to remember how far I got with some of that.

Marcus

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Re: [Avogadro-devel] GitHub issue import test

[Marcus D. Hanwell]

On Sun, Apr 24, 2016 at 10:27 AM, Geoffrey Hutchison
 wrote:
> I started a test run of importing the Avogadro SourceForge bugs and feature 
> requests to GitHub issues:
> https://github.com/ghutchis/sfimporttest/issues
>
> * It's very difficult to script importing the milestone versions - but it 
> should be easy to make some batch changes (e.g., find the v_1_0 label and 
> assign a 1.0 milestone)
> * I think the "auto-migrated" and "source forge" labels are redundant. Which 
> one should I kill? (I'd keep the "auto-migrated" and kill the "source forge" 
> tag)

How many have contact details/any recent activity? So long as they
have a tag we can filter on I think either one works. Tougher job is
going through them and figuring out which are still relevant, and
whether is is possible to follow up with the reporters at all.

Thanks for working on this, what you have in the test looks good to
me. Not sure how much I would worry about historical milestones but if
it is easy it would be nice.

Best,

Marcus

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Re: [Avogadro-devel] Avogadro v2 Roadmap

[Marcus D. Hanwell]

On Wed, Mar 16, 2016 at 4:01 PM, Geoffrey Hutchison
 wrote:
> Since there's more interest in pushing for an Avogadro v2 "full" release in 
> 2016 (e.g., fall?) I wanted to start a roadmap.
> http://wiki.openchemistry.org/Avogadro_Roadmap
>
> The text came from some discussions that Marcus and I had previously, and was 
> hosted on GitHub, but no one actually edited it. :-)
>
> The roadmap will obviously be influenced by potential Summer of Code projects 
> (and progress) and some people contributing here at Pitt.
>
> Thoughts? Missing pieces? Better ways to host the list?
>
I think the wiki is fine for now, and it is good to get something up
in a generally accessible spot. I will be spending some time getting
the selection working, and have some basics working now.

My focus is going to be on carving out enough time to make progress on
missing features that prevent people from using Avogadro 2 over one,
but I am sure I will continue to be distracted by shiny things and
other work.

I tagged and released 0.9.0, I will put out a general announcement. It
was delayed a fair bit by packaging issues. Now that Qt 5.6.0 is out I
would like to get an updated release built against that, and hopefully
at least have selection working in it.

Best,

Marcus

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Re: [Avogadro-devel] Hello GSoC-2016

[Marcus D. Hanwell]

On Mon, Mar 14, 2016 at 10:01 AM, Reinis Danne  wrote:
> Two questions came up (Python binding project).
>
> 1. Is it ok to relay on C++11 compiler? A search showed that
> there was this discussion before and it was decided that it is ok
> to rely on the presence of C++11 compiler. But in the same time
> I saw some recent commits specifically removing reliance on C++11
> features (e.g., auto).

I think C++11 will be OK, when we removed them we hadn't decided to
make C++11 a hard requirement. I think we have good agreement now, but
I need to update the dependencies for Windows at least to build with a
more recent Visual Studio with C++11 support, several of the current
dependencies do not build.
>
> 2. Is tight integration with QML a strict requirement for the
> chosen solution? As far as I can see QML is not used in the
> current codebase. I'm interested in a solution which currently
> doesn't have QML support (might get added sometime later).
>
I don't think it is, personally I would rather see Python support over
QML, but see value in both. I think we are reasonably open to looking
at different proposals in this area.

Best,

Marcus

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Re: [Avogadro-devel] Hello GSoC-2016

[Marcus D. Hanwell]

On Mon, Mar 7, 2016 at 9:58 AM, Geoffrey Hutchison
 wrote:
>> I'm interested in the project "Python script bindings in Avogadro
>> 2". I see that there is already a boost-python branch for
>> avogadrolibs. Are you already settled on boost-python or are
>> other solutions still considered?
>
> Other solutions are definitely open. Indeed, that’s the key question for this 
> project. There are multiple technologies for scripting bindings in Qt apps, 
> but not all of them are ideal for Avogadro2 (PySide is not updated for Qt5, 
> SWIG, boost.python, and PyQt are also possible.)
>
To add a little more from my side, Qt-based solutions are great, and I
could see a good GSoC project developing them, but Avogadro 2's
libraries are more than just Qt now. I developed the Boost Python
based bindings to serve the needs of a web-based project, where we
needed to use Avogadro 2 API in a headless web server, so Qt, OpenGL,
X, etc were not available.

The requirements for server-based and desktop-based are quite
different, the core APIs can be used in more batch-oriented contexts,
whereas the desktop needs to align more closely with Qt's signal-slot
mechanism, etc.

Marcus

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Re: [Avogadro-devel] Windows Build for v1.2

[Marcus D. Hanwell]

Hi Geoff,

On Wed, Jan 13, 2016 at 2:21 PM, Geoffrey Hutchison
 wrote:
> Hi Marcus,
>
> My undergrad this term is working on a Windows build (using VS 2015). He's 
> had some problems with variable length array declarations and with linking.

Some of the topics merged were big, this has been a common theme when
getting Windows builds.
>
> I'd like to get a v1.2 build finalized - do you still have the CDash build 
> bot for Windows on v1.x master?
>
I can take a look at resurrecting the builder, that machine had its
hard drive die so I would need to add it back in.

> Assuming we can get everything built, I'd like to add a crash reporter to the 
> Windows build to debug some of the hard-to-understand random crashes people 
> mention. While Breakpad is used in lots of apps (e.g., Mozilla, Chrome, 
> Mendeley) getting the server running might be tricky.
>
> https://en.wikipedia.org/wiki/Crash_reporter
>
> Crashrpt / Crashfix Server (now completely open source under BSD)
> * http://crashrpt.sourceforge.net
> * http://crashfix.sourceforge.net
>
> Breakpad / Server (multiple forks at this point)
> * https://github.com/Mendeley/breakpad
> * https://github.com/atom/mini-breakpad-server
> * https://github.com/mozilla/socorro
>
Totally in favor, thanks for the extra info. Who is going to work on
that? Sounds like things have improved.

Marcus

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Re: [Avogadro-devel] Discourse and Translations

[Marcus D. Hanwell]

On Fri, Jan 1, 2016 at 1:06 PM, Geoffrey Hutchison
 wrote:
> Happy New Year!
>
> I'm looking into forum options (e.g., Discourse vs. Biostar). Seems like both 
> can import mbox archives, so I think a key question would be setting up the 
> Docker instance for Discourse, which can be deployed to Digital Ocean easily. 
> So I sent a message to Digital Ocean asking if they have deals for open 
> source projects - my current web host doesn't support Docker.

We talked about Discourse at a session during the GSoC mentor summit
last year, and it sounds like a number of communities have had great
results. From what they said you can use it as a mailing list
replacement if desired, but it has a number of options that they made
use of. I was hoping to look into this more soon as it sounds like it
is maturing really well.
>
> I'm also curious about an alternative to Launchpad for translations. Bazaar 
> doesn't support submodules, so the automatic git import-and-export is broken 
> for v.1.x (and also for v2).
>
> Two alternatives are Transifex (https://www.transifex.com) and Pootle 
> (http://pootle.translatehouse.org)
>
> Both are open source and used by different projects (Discourse is translated 
> using Transifex):
> http://www.worddelights.com/blog/gnome-outreach-program-for-women/translation-management-tools-transifex-pootle-and-launchpad-a-comparison-of-features
> * Transifex: Fedora, Tor, VLC
> * Pootle: LXDE, LibreOffice
>
> I'd be open to other suggestions - particularly if they natively support Qt's 
> .ts files (Launchpad still doesn't.)
>
Yeah, it would be great to look at translations for v2, although we
don't really need to worry about submodule support for v2. The libs
and app repositories have no submodules, they are within the
openchemistry superbuild repo that gathers them. I personally prefer
that method, it keeps third party code in a higher level module, that
looks more like system libraries. Still, very much open to looking at
new approaches for translation.

Happy New Year.

Best,

Marcus

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

[Marcus D. Hanwell]

On Mon, Nov 16, 2015 at 7:13 AM, Carlos Salgado
 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 ccmake-2.8.11 and it works like a charm. I
> have introduced modifications to the Gaussian calculation interface, for
> example. Avogadro is a very nice project.
>
> Could sombody, please, tell me which version of Qt in windows to use, and if
> I need to build it using MinGW or MSVC? I would really appreciate it.
>
I have been building Avogadro 1.1.x on Windows with MSVC 2008, and I
think 2010 more recently, using the latest Qt 4.8 binaries at the
time. That should work, my hard drive failed on that machine so I need
to get this spun up again. For Avogadro 2 I use Qt (5.3 I think last
time, want to try with 5.5) using MSVC 2010.

They both have superbuilds that can make it easier to get all of the
dependencies, or you can get them for yourself.

Hope that helps.

Marcus

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Re: [Avogadro-devel] [Openchemistry-developers] avogadrolibs UHF calculation representation

[Marcus D. Hanwell]

Adding Avogadro developers list to CC, this is probably most appropriate there.

On Mon, Sep 14, 2015 at 9:14 AM, Bryce Anderson
 wrote:
> First of all I should state my motivations: what I want is proper plotting
> of UHF wave functions including being able to select the spin and get the
> correct HOMO/LUMO if that is a 'automatic' feature. If things go well, I'd
> like to see support for more interesting features (not necessarily UHF
> related) such as Charge Decomposition Analysis (CDA) and visualizing the
> results of TD-DFT calculations, but those are distant future dreams.

Sounds great.
>
> The current state of avogadrolibs master branch on GitHub (currently at
> commit 65141530f6831c6364b71230512097b9d1de95ae) has poor support for
> unrestricted (UHF) calculations. My concerns are the lack of plotting
> features for UHF (the plotting interface is completely unaware of UHF) and
> the partial/broken parsing of quantum output. Functions like `lumo()` are
> completely unaware of UHF and can return incorrect results in UHF
> calculations.

It has some beginnings, but it honestly has no exposed support for any
open shell calculations at this point. There is some API that Albert
added, and we have bounced some ideas around, but it was not completed
and no user interface elements are present so that a user could
visualize the beta MOs.
>
> I have made a PR that is a work in progress, #38 on Github, that more or
> less addresses my concerns. Part of it is removing default arguments for
> many of the functions that have a different meaning for RHF and UHF
> calculations which turns out to be controversial.
> A few examples of functions that drop defaults are
>
> `virtual unsigned int molecularOrbitalCount(ElectronType type) = 0;`
> `unsigned int electronCount(ElectronType type);`
> in the `BasisSet` class.
>
Not controversial, but we have already thought about some of this and
I think there are better solutions in this case. We also have some
conventions used in the API, and I would like to keep things as
consistent as possible. I think we could verify correctness with some
additional asserts that can be triggered at runtime based upon the
input type for example.

>  Less controversial (I assume) is correcting a few of the quantumio parsers
> (I believe they are corrected: I don't have first hand experience with many
> of the packages that generate the results in the avogadrodata repository, if
> the examples exists at all) to either emit the UHF information they already
> parsed or to actually parse it. I doubt they are complete but I believe they
> are moving in the right direction. They really need examples and testing for
> both RHF and UHF calculations.

Agreed, building up examples of both types, and improving verification
of results would be extremely useful for us all. I would really like
to add the capability to display this class of calculations, and am
more actively working on this part of the code now as I have a project
to develop improved integration with NWChem output too.
>
> I have brought up some suggestions as to refining the type model to drop
> some of the features from `BasisSet` that are are not actually basis set
> related. I think the current representation would be more aptly named
> `WaveFunction`. I have made an initial attempt to separate the concepts of
> 'wave function' and 'basis set' but the combinations of Rhf/Uhf with STO/GTO
> make that abstraction very repetitive at best. The idea was to create a new
> type `WaveFunction` that contains a basis, the energies and coefficients. It
> would have subtypes `RhfWaveFunction` and `UhfWaveFunction`. The problem is
> that setting the MO coefficients for STO and GTO would require further type
> refinement to classes `StoRhfWaveFunction` etc. or shifting the point of
> representation duplication to an even less desirable position. Ultimately,
> I'm inclined to abandon this effort unless someone has a good suggestion
> about how to avoid the excessive duplication.

I remember Albert and I going down a similar path, and becoming
concerned about duplication and questioning if it was worth it. I
would love to focus on a minimum viable product in terms of user
interface for open shell, and how we expose that in an intuitive way
in the graphical interface. We could then look at what API is missing
- and you pointed out several bits in the calculation of the cubes for
example.

These classes have undergone some refactoring already, where the data
structure is now (mostly at least) separate from the algorithms that
act upon them. As a first step do we literally just need a drop down
for alpha/beta when the calculation is open shell for example?

Thanks for looking at this, and providing examples.

Best wishes,

Marcus

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Re: [Avogadro-devel] New Avogadro Manual

[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-devel] Symmetry element rendering

[Marcus D. Hanwell]

On Wed, Aug 19, 2015 at 11:26 AM, Marcus Johansson mcode...@gmail.com wrote:

 Hi

 Was wondering if anyone has some input on rendering symmetry elements in 
 Avogadro v2. There is a need for “disc” (mirror plane) and “vector” (rotation 
 axis) geometries as well as alpha in order to make things look good. Im 
 currently using the “cylinder” and “sphere” geometries, but as you can see 
 they are not well suited for the job.

For some of the other display types we added factories to create
triangle geometry. Many things can be represented by triangle meshes,
we made the special cases for spheres because we were using impostors
and cylinders because there are lots of them and might want to use
impostors in the future.

It would be great to consider what primitives might be missing, and
either add factories that simply create meshes, or boost them to new
primitive types if that makes more sense. I also need to dig into an
issue with text rendering on Windows where it appears to be causing
crashes in the latest release.

It would be great to get symmetry elements in Avogadro 2, thanks for
working on this!

Thanks,

Marcus

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Re: [Avogadro-devel] Require C++11/dropping Boost fallback

[Marcus D. Hanwell]

On Wed, Jun 3, 2015 at 6:50 PM, Michael Banck mba...@debian.org wrote:
 On Wed, Jun 03, 2015 at 01:20:01PM -0400, Geoffrey Hutchison wrote:
  Debian stable (jessie) ahs GCC 4.8 and 4.9, but it got released very
  recently and many are still on oldstable (wheezy) with GCC 4.7.

 I guess your impression agrees with Marcus - that probably everything
 we would use soon is fine and we can target anything supported by GCC
 4.7.x.

 As far as important Debian/Ubuntu releases are concerned, yes, (if 4.7
 really implements all the features), RHEL/CentOS/SL 6 might be an
 important target as well (or not, dunno), and AFAIK it only ships GCC
 4.4 (but might have some C++ features backpatched).

Closing the loop on this, I feel pretty comfortable in bumping this. I
think tagging before making a hard dependency on C++11 features would
be good in case people wanted that, but see no reason not to start
using modern C++ functionality.

Compiler support seems reasonable, building new compilers on older
machines is also possible, I know Ubuntu 12.04 still has a few years
of support left and that may present some issues but there is already
a new LTS people can move to (I think they get five years).

Marcus

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Re: [Avogadro-devel] Volume Rendering

[Marcus D. Hanwell]

On Thu, Jun 11, 2015 at 1:12 PM, Barry Moore moore0...@gmail.com wrote:
 Dear All,

 I recently saw Volume Rendering in the Getting Avo2 to release email and
 wanted to start some discussion. I recently exposed the Gaussian Cube file
 type to render MOs (pull request was submitted, including an example to
 avogadrodata) and I had some ideas for improvements:

 1) Is there a good place to submit improvements (not issues), and possibly
 rank the importance of such an improvement? I would like to help with
 important issues instead of just issues I am particularly interested in.

In the issue tracker, but tag them as enhancements. Bugs should be
tagged as bugs.

 2) Instead of Set background color in View tab, it might be better to
 have a Color Preferences where one could set many different colors
 (including opacity etc).

Sounds reasonable.

 3) Alignment tool, click two atoms, align to some axis (for exporting images
 mainly)

I had been meaning to port this from Avogadro 1 - it is a simple tool
I wrote for similar purposes (including QM with electric fields).

 4) I have suggested this to Marcus previously, but exporting graphics in
 vector formats for publications. The PNG images generated currently are
 lackluster. I dug into this a little, but I lack experience with Qt and the
 concepts were a bit over my head at the moment (working on that!).

Vector graphics is tougher, I would like to finish off some of my work
on bringing back POV-Ray/ray tracing export. For a scene of any
complexity even when you export the vector it can often be too much
for the rendering engine in Adobe Reader for example. After having
done this in Avogadro, and seen results from VTK I would say you are
best off rasterizing the 3D and exporting text, lines, etc.

We are pretty focused on getting some essentials finished up, as per
Geoff's post, but if you have time and want to develop some of these
features I would be interested in what you come up with.

Best,

Marcus

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Re: [Avogadro-devel] Getting Avo2 to release

[Marcus D. Hanwell]

On Thu, Jun 4, 2015 at 4:07 PM, Geoffrey Hutchison
geoff.hutchi...@gmail.com wrote:
 Selection and residues, along with some rendering features seem most 
 critical to me (we have stick but it has a rendering bug I need to dig into).

 I'd put selection slightly above residues because I think it's critical for 
 copy/paste/clear and moving fragments. (Which I guess also means that 
 inserting fragments is a needed piece.) Indeed, I think selection affects a 
 *lot* of tools and extensions, so that's my preference.

Agreed - wasn't really ranking, but selection is certainly more
critical than residues. I really don't think we are that far apart,
and value the input on priorities. If others have feelings it would be
great to have them.

I will do selection first, but would like to follow that quite quickly
with fragments, residues, monomers, etc.

Marcus

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Re: [Avogadro-devel] subclass QColumnView

[Marcus D. Hanwell]

On Wed, Jun 3, 2015 at 10:55 AM, Defusco III, Albert A defu...@pitt.edu wrote:
 Hi everyone,

 I am nearing completion of my space group dialog. You can see the current 
 state on GitHub

 https://github.com/AlbertDeFusco/avogadrolibs/tree/spg-rw

 The next thing I need to do is remove the final preview widget from my 
 QColumnView. I believe I can subclass it as follows in spacegroupdialog.cpp.

 class spgColumnView : public QColumnView
 {
   public:
 spgColumnView(QWidget* p) : QColumnView(p) {}
 QAbstractItemView * createColumn ( const QModelIndex  index )
 {
   Avogadro::QtPlugins::SpaceGroupItem *thisItem = 
 static_castAvogadro::QtPlugins::SpaceGroupItem*(index.internalPointer());
   QAbstractItemView *view = 0;
   if(thisItem-childCount() == 0)
 return view;
   else
 return QColumnView::createColumn(index);
 }
 };

 I then change QColumnView to spgColumnView in spacegroupdialog.ui. When I try 
 to build it I get the following error.

 /Users/albert/Development/oc-clean/build/avogadrolibs/avogadro/qtplugins/crystal/ui_spacegroupdialog.h:26:10:
  fatal error: 'spgcolumnview.h' file not found
 #include spgcolumnview.h
  ^
It looks like you are using the wrong include, should be  as this is
a local header, not  for system headers. The compiler will then
search the same directory automatically, as it knows that is the most
likely/default location.

 I was using the FileComboBox class, which is a subclass of QComboBox, in 
 qtplugins/clientserver as an example. Is there something I have to do in 
 CMake to get this to build? I tried setting SKIP_AUTOMOC to true for these 
 source files, but it didn’t seem to work.

You don't want to skip automoc.

Marcus

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Re: [Avogadro-devel] Getting Avo2 to release

[Marcus D. Hanwell]

On Wed, May 27, 2015 at 3:55 PM, Geoffrey Hutchison
geoff.hutchi...@gmail.com wrote:
 Thoughts? Concerns? Something I've missed?

 Oh, I forgot color schemes and custom colors. My feeling is that can fall to 
 nice to have for v2.1?

I have some time this next couple of weeks to take a stab at some
pieces. I think the critical and nice to have may vary a little
depending on person. I will make a new release soon (0.8) as I would
like to get more people testing stuff. Selection and residues, along
with some rendering features seem most critical to me (we have stick
but it has a rendering bug I need to dig into). I would like to expose
the transfer function editor from VTK, and finish off the volume
rendering piece but would put that firmly in nice to have.

This has languished more than I would like, so apologies from me for
not having as much time as I had hoped. There are some great features
in there, but UI polish is needed to make it more accessible. It is
orders of magnitude faster loading initial data, and rendering it, for
large systems, but the interface is missing some key pieces (some
already fixed) which led to me delaying 0.8.

I think your list is a good yard stick, and just like with 1.0 we will
possibly wait too long, but know it when we see it. I had hoped to
have it a year ago, and am determined to make it happen. I think a
test run on Qt 5 deployment will be valuable (it was working for me on
Mac and Windows when I tried it last time.

I am blown away by over 600,000 downloads since our first release of
Avogadro, and over 400 citations of our paper. I want to get some
momentum going again, and hope we have even more ideas to put into a
Google Summer of Code proposal next year.

Best,

Marcus

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Re: [Avogadro-devel] Avogadro2 Extensions Priorities

[Marcus D. Hanwell]

On Thu, May 21, 2015 at 3:43 PM, Geoffrey Hutchison
geoff.hutchi...@gmail.com wrote:
 I'd like to ask about Avogadro2 extensions and priorities.

 In Avogadro 1, plugins were loaded in alphabetical order (sorted by the 
 filesystem) and then the extension provided an ordered list of commands. This 
 meant that the extension basically was responsible for building out a menu 
 in-order. (I'm thinking for example of the Molecular Mechanics submenu.)

They were sorted by the 'usefulness', which was global for that
plugin. That allowed us to go beyond simple alphabetical sorting, but
only offered one global 'usefulness' per extension, and modulated the
position of all entries provided.

 In Avogadro v2, it's *very* hard to do this. Menu items are sorted 
 alphabetically and/or by priority. But since *nothing* has priority set right 
 now, things jump to the top.

I don't think it is very hard to do it, but maybe we failed to add the
right prorities. The intent was to order things with priority, and
fallback to alphabetical. We could add a convenience to increment
priority by 1 for each action if that is desired.

 I'm thinking for example of cut/copy/paste.

 Every OS has standardized on the order of cut-copy-paste. Of course this 
 isn't in alphabetical order.

 So right now, in Avogadro v2, you get Copy - Cut - Paste.

I can fix that, it was something we missed (and I admit that I tend to
use the keyboard shortcuts).

 I'm happy to patch the behavior (and revert back to Avogadro v1 strategy of 
 each plugin providing an ordered list). Was there a reason for this design?

It was a desire to go beyond some of the hardwired separators, so
every 100 a separator would be interted, and the menu items from
multiple plugins can be blended together/put in the same section, or
separated sections.

The menus need to be tidied, and maybe the menu ordering code needs
some refinement, but I would like to keep the additional flexibility.
I found it limiting in v1, hence the work to build something a little
more flexible, may be the API needs a bit more work (I would hate to
scrap it though as I think it has some real value).

We could simply call a second virtual, ordered, and usefulness, if we
wanted to offer a more global method as was done before. This could be
mapped into the new ordering by applying the number, and incrementing
each action by 1.

Marcus

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Re: [Avogadro-devel] Google Summer of Code

[Marcus D. Hanwell]

Hi,

To update the list, we were not selected this year. I got feedback
from Google which was very positive and encouraged us to apply again
next year. They only accepted 137 organizations this year (down from a
high of 190 last year). We had some great ideas, and we will continue
to work on links with other open source chemistry projects to put
together an even stronger proposal next year.

Thanks for everyone's interest, disappointed we didn't make it this
year but encouraged to try again next year. Working on some patches
and hopefully a release soon...more threads on that soon.

Marcus

On Wed, Dec 17, 2014 at 11:18 PM, Karol Langner karol.lang...@gmail.com wrote:
 Hi guys,

 I would definitely be happy to help out from the cclib side of things. I
 don't think I would manage the time to mentor, but could help generally
 organize things as well. I have been trying to make some time to get into
 Avogadro and openbabel, and this would be a good pretext.

 I have participated in GSOC in the past (as a student), in a project
 unrelated to chemistry.

 Cheers,
 Karol


 On Fri, Dec 12, 2014 at 12:41 PM, Geoffrey Hutchison
 geoff.hutchi...@gmail.com wrote:

 Here are some of the questions for mentoring organizations. I would hope
 that KDE and/or VTK/Kitware could vouch for us as an organization?



 In addition to anything else your organization would like to submit a
 proposal, Google will be asking (at least) the following questions as part
 of the proposal process:

 • Describe your organization.
 • Why is your organization applying to participate in Google
 Summer of Code 2015? What do you hope to gain by participating?
 • Has your organization participated in past Google Summer of
 Codes? (yes/no)
 • If you answered “yes” to the question above, please summarize
 your involvement and the successes and challenges of your participation.
 Please also list your pass/fail rate for each year.
 • If your organization has not previously participated in Google
 Summer of Code, have you applied in the past? If so, for what year(s)?
 • What Open Source Initiative approved license(s) does your
 project use?
 • What is the URL for your Ideas list? This is the most important
 part of your proposal. Please make sure we can access it and it is complete
 when you submit this proposal. “Placeholder” or inaccessible ideas pages
 will be grounds for an automatic rejection for participation in Google
 Summer of Code2015.
 • What is the main development mailing list for your organization?
 • What is the main IRC channel for your organization?
 • Who will be your backup organization administrator?
 • What criteria did you use to select the mentors? Please be as
 specific as possible.
 • What is your plan for dealing with disappearing students? Please
 be as specific as possible.
 • What is your plan for dealing with disappearing mentors? Please
 be as specific as possible.
 • What steps will you take to encourage students to interact with
 your project's community before, during and after the program?
 • Are you a new organization who has a Googler or other
 organization to vouch for you? If so, please list their name(s) here.
 • Are you an established or larger organization who would like to
 vouch for a new organization applying this year? If so, please list their
 name(s) here.
 • What will you do to encourage that your accepted students stick
 with the project afterGoogle Summer of Code concludes?

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[Avogadro-devel] Editing, viewing, and making things more fluid again

[Marcus D. Hanwell]

Hi,

So I slacked off a lot over the Christmas break, but have been working
on a few patches and thinking about the overall data architecture in
the Avogadro 2 application. We spent quite a while thinking about the
design, and I looked at a lot of what went well and not so well in
Avogadro 1. I thought now might be a good time to explain some of
those decisions (after a little prompting from Geoff), and
improvements I am working on to improve the (unfortunately)
non-intuitive interaction in the current application.

Overly general mega-classes were a source of many
bugs/crashes/inefficiencies in Avogadro. Several design decisions work
to improve that situation in Avogadro 2, including the use of
copy-on-write arrays, storing most molecular data in these arrays, use
of proxy classes for atom/bond/other lightweight objects, and
specializing an editable molecule with scalable undo/redo support,
signals, slots, etc.

If we have a specialized editable molecule we can focus on only the
things that can/should be editable. We can add the necessary
infrastructure to support scalable undo/redo - i.e. record
addition/removal of an atom rather than make many copies of the entire
molecule before and after an edit. The signals fired for each change,
along with the undo/redo objects created, do not scale when adding
millions of atoms though, and so having a view-focused molecule offers
a more scalable option for I/O.

Using copy-on-write arrays also offers very efficient copying from
each molecule type - these arrays do not copy any underlying data
unless a non-const method is called. So reading into a view molecule,
copying to an editable molecule, deleting the view molecule, and
editing the editable actually only ever creates one copy of the bulk
of the data - the array will only be duplicated if a non-const method
is called and its internal reference count is greater than 1.

What doesn't work at all well is the edit/view GL widget, and the
tough/hard line between editing a molecule/viewing it. I am working on
merging the two widgets together, and reflecting the fluidity of
moving between the two types in the interface so that it will be far
less/barely noticeable that you went from viewing to editing a
structure. I had hoped to get this merged sooner, I think I am pretty
close to having it resolved now.

I have also been experimenting with templating more of the algorithms,
like hydrogen addition/removal, bond perception, etc. This would make
it easy to use a command-line version with no undo/redo support (or Qt
dependency), and build the same algorithm using the editable molecule.
An added benefit would be the potential reuse by any other
library/application using its own molecule class if they implement an
adaptor that offers the expected API. I would love to avoid forcing
everyone into virtuals and using the same base class/API.

For the render widgets I was also hoping to move to the new OpenGL
classes added in Qt 5.4 soon. This email got very long, and I haven't
necessarily covered everything but would be happy to talk more on
IRC/Skype/Hangouts/on this thread. If this generates a lot of
additional work we should talk, and one thing I was never all that
sold on was not having a common base class for the view/edit molecule
- I have been weighing up if that would make things simpler/easier.

I was hoping to start posting more details/discussions as things have
become very quiet. I really want to get a new release out, but have
been delaying until the edit/view problems are resolved, and apologize
for the delays in getting this sorted - last year was pretty tough and
featured very little spare time. This year is looking much better, and
I really want to get this right while maintaining the speed and
efficiency improvements made.

Sincerely,

Marcus

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Re: [Avogadro-devel] Editing, viewing, and making things more fluid again

[Marcus D. Hanwell]

On Tue, Jan 6, 2015 at 12:03 PM, Michael Banck mba...@gmx.net wrote:
 On Tue, Jan 06, 2015 at 11:05:15AM -0500, Marcus D. Hanwell wrote:
 What doesn't work at all well is the edit/view GL widget, and the
 tough/hard line between editing a molecule/viewing it. I am working on
 merging the two widgets together, and reflecting the fluidity of
 moving between the two types in the interface so that it will be far
 less/barely noticeable that you went from viewing to editing a
 structure. I had hoped to get this merged sooner, I think I am pretty
 close to having it resolved now.

 Are you talking about how the user should do this with respect to mouse
 button-drag and modifier keys?  If so, it would be interesting to this
 disucss this, but I have no idea how it does (not) work currently, how
 it was supposed to work, and how you plan to fix it, based on your
 information above.

Referring to the need to close the edit widget, open the view widget,
or vice-versa. That will go away, and the switch between the two modes
will be pretty seamless. It is currently quite painful, but should be
fixed up soon.

 For the render widgets I was also hoping to move to the new OpenGL
 classes added in Qt 5.4 soon.

 Any good reason for doing this?  Is any major distribution shipping Qt
 5.4 already?

Yes, that is where I was hesitating... I may see if the API is close
enough that we can detect the version and use the latest when
available. I know how irritating it can be to require the latest
release of a major library. QGLWidget is deprecated, the OpenGL
variants already have more features and will be supported going
forward.

Marcus

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Re: [Avogadro-devel] Avogadro-devel Digest, Vol 90, Issue 2

[Marcus D. Hanwell]

Albert,

I think CML will continue to be very much a first class citizen too.
JSON feels much easier to change/augment, and Python support for JSON
is very good - it would be great to add it, but I don't think it is
critical. We could add some simple Python glue too, the format is
super-simple. With Open Babel we ended up using CML, MDL and XYZ to
get data into Avogadro 2.

Marcus

On Thu, Dec 18, 2014 at 9:59 AM, Defusco III, Albert A defu...@pitt.edu wrote:
 Hi Karol,

 It looks Avogadro2 will be using Chemical JSON whenever possible to transfer 
 data. Do you think this would be possible with cclib?

 http://wiki.openchemistry.org/Chemical_JSON



 Albert



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 On Dec 17, 2014, at 11:22 PM, Karol Langner karol.lang...@gmail.com wrote:

 One of the things I want to do soon is give cclib the ability to output CML. 
 That would be an easy way to communicate between programs in a standard 
 format.

 Karol

 On Fri, Dec 12, 2014 at 12:33 PM, Geoffrey Hutchison 
 geoff.hutchi...@gmail.com wrote:
  It sounds like you think of these things as exclusive, and I don't see
  why they should be.

 The current state of the code is 
 https://github.com/OpenChemistry/avogadrolibs/tree/master/avogadro/quantumio

 That is, these things are *separate* from “regular” IO. Reading files and 
 finding quantum data are currently in different parts of the code.

 Now, one may question whether “regular” and quantum IO *should* be separate. 
 But I’m not talking about throwing away existing code - I believe Albert was 
 saying that rather than adding X new implementations to 
 avogadrolibs/avogadro/quantumio, it would be helpful to have an interface to 
 cclib for parsing quantum data.

  is demonstrably much more efficient than going through Open Babel for
  regular input for example. We can certainly tweak defaults, so the

 I certainly wasn’t talking about changing the current pattern for regular 
 IO, although I’d certainly suggest that the interface could merge “import” 
 and “open” commands. In the case of CML or other formats that Avogadro 
 directly handles, preference can go to the internal implementation, and 
 other formats could be handled through Open Babel.

 I’d be happy to make that change.

 I thought the discussion was about Summer of Code projects, and certainly 
 improving quantum IO would be great. (Adding features to read and visualize 
 other “cube” formats would be nice too.)

 -Geoff


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Re: [Avogadro-devel] Avogadro-devel Digest, Vol 90, Issue 2

[Marcus D. Hanwell]

On Thu, Dec 11, 2014 at 11:36 PM, Geoffrey Hutchison
geoff.hutchi...@gmail.com wrote:
 I think Albert was talking about a glue layer for quantum io, not for
 regular input. Regular input is probably best handled through Open Babel,
 since that already handles bond perception, typing, etc.

 Right now, Avogadro v1 and v2 have separate code for reading basis set and
 MO information from various formats. Instead, such information (which is
 only performed when computing orbitals, etc) could be handled through a
 python call and cclib parsing.

It sounds like you think of these things as exclusive, and I don't see
why they should be. Maybe we just need to chat, and flesh out what is
meant a little more. If what was done for Open Babel is considered a
glue layer for regular input, then what I meant in my reply was
that it sounded like a great idea and that we even have a template for
such a layer.

We could certainly expand what can be brought in by such a layer, but
I have some motivation to keep some of the other IO work present as it
is demonstrably much more efficient than going through Open Babel for
regular input for example. We can certainly tweak defaults, so the
richest approach would be offered automatically.

Marcus

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Re: [Avogadro-devel] Avogadro-devel Digest, Vol 90, Issue 2

[Marcus D. Hanwell]

On Thu, Dec 11, 2014 at 4:14 PM, Defusco III, Albert A defu...@pitt.edu wrote:
 Hi guys,

 Would good project be to re-wire Avogadro to use cclib instead of relying on 
 the quantumio in Avogadro2? I'm very much in favor of adding visualization 
 capabilities for QuantumEspresso and CP2K.

You don't need to rewire, the Open Babel plugin reuses all of the
readers/writers advertised. That pattern could be used to reuse the
cclib readers/writers, offering the option of what reader to use if
there is more than one. I think it would be great to add that
capability.

Marcus

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Re: [Avogadro-devel] Google Summer of Code

[Marcus D. Hanwell]

On Mon, Dec 8, 2014 at 3:00 PM, Michael Banck mba...@gmx.net wrote:
 On Mon, Dec 08, 2014 at 10:53:50AM -0500, Geoffrey Hutchison wrote:
 The deadline for applying to be a mentoring organization for Google
 Summer of Code is fast approaching.

 I'm not sure precisely where to hang our hat (e.g., Avogadro alone,
 general open-source chemistry like Blue Obelisk, or through another
 group like the University of Pittsburgh) but I'd really like to see
 Avogadro apply and get a student or three funded again.

 Personally, I'd like to see more interoperability between the
 open-source chemistry apps, including avogadro, openbabel and cclib
 growing support for open source quantum chemistry packages like PSI4,
 NWchem, CP2K, Quantum ESPRESSO (Avogadro might support a few already),
 and I'd probably be willing to mentor.  However, I did think that Blue
 Obelisk might be the better umbrella organization for that.  In general,
 if there is enough good proposals etc. I'd say Blue Obelisk might have
 a better shot at being accepted as Avogadro alone.  On the other hand,
 if nobody else is pushing this...

I would vote for Blue Obelisk, but it has been hard in previous years
to get any momentum around it. I would be interested in mentoring, it
is hard to tell what Google is looking for and so I think we would
have a shot as Avogadro or Blue Obelisk - they certainly accept a
number. We could also talk to KDE, and see about doing it in their
umbrella as we did in previous years.

Marcus

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Re: [Avogadro-devel] Migrating Wiki to GitHub Pages

[Marcus D. Hanwell]

On Thu, Oct 16, 2014 at 4:33 PM, Geoffrey Hutchison geo...@pitt.edu wrote:
 Hi everyone,

 Despite the low level of action, I’ve been spending a lot of time *thinking*
 about Avogadro and the future. There are quite a few exciting things,
 although it may take a while before they fully appear.

 One thing I can talk about is pushing for tutorials and manuals.

 The University of Pittsburgh is putting money and student-power towards
 improving tutorials and manuals for Avogadro. We’re converting from a
 proprietary program to Avogadro over the next two years. So we’ll be putting
 up workflows, learning exercises, etc.

 One thing I'm considering is moving away from MediaWiki. It's insecure and
 spammy. The whole point was to let people easily edit the pages, and that
 doesn't work now.

 I'm open to suggestions, but I'd like to suggest GitHub pages. These are
 generated from a repo, so it's easy to add a pull request to modify them,
 translate, etc. As static pages, they're easier to package and distribute
 too.

 One catch is converting from MediaWiki to Jekyll, so if someone can help
 with that, eg parsing the XML dump, please let me know.

 Thoughts? Better alternatives?

This sounds good to me, I think being able to issue pull requests
would be useful along with easier packaging, offline editing.

Marcus

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Re: [Avogadro-devel] Migrating Wiki to GitHub Pages

[Marcus D. Hanwell]

I turned on wiki and issues for the repo if that helps. The GitHub
wikis are backed by git, and have editing facilities built in, so that
might be the easiest (I haven't used the GitHub wikis much, but
willing to give it a try).

Marcus

On Fri, Oct 17, 2014 at 1:47 PM, Patrick Fuller patrickful...@gmail.com wrote:
 To reiterate what Ian said, I think that pandoc + maybe a shell script will
 get you most of the way there. If you have the XML, you can try (untested):

 pandoc -f mediawiki -t markdown file.xml

 (f is “from”, t is “to) I also just tried parsing a URL directly and it’s
 not bad. This works decently well:

 pandoc -f html -t markdown http://avogadro.cc/wiki/Tutorials:Getting_started

 Regarding Jekyll / Liquid, I don’t think the AvogadroChem.github.io approach
 is the way to go. There’s a little wiki button to the right of any github
 repo (ex. d3’s wiki). My vote is to start with an official avogadro git repo
 (https://github.com/cryos/avogadro maybe?), git clone
 cryos/avogadro.wiki.git, dump in pandoc markdown, and then review the
 contents.

 Regards,
 Pat


 On Fri, Oct 17, 2014 at 12:30 PM, Geoffrey Hutchison
 geoff.hutchi...@gmail.com wrote:

 OK, a first pass is here:

 https://github.com/AvogadroChem/AvogadroChem.github.io
 e.g.

 https://github.com/AvogadroChem/AvogadroChem.github.io/blob/master/features.md

 This includes all the images I could grab, although I'm sure there are
 errors. It's not a functioning site yet, but if someone has worked with
 Jekyll or GitHub Pages before, please send me an e-mail so we can get
 something up and running.

 Also, thanks to those who wrote off-list about educational use. I might
 start a separate e-mail list for that, but I think we can coordinate to get
 some really nice exercises up for everyone to use.

 -Geoff

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Re: [Avogadro-devel] Discourse / Forum Interface

[Marcus D. Hanwell]

On Tue, Oct 7, 2014 at 12:46 PM, Geoffrey Hutchison
geoff.hutchi...@gmail.com wrote:
 I've been looking around at web forums, since I see a lot of current 
 undergrads and grad students (i.e., users) don't use e-mail much (much less 
 mailing lists).

 There are multiple packages and I'm open to suggestions. One that seems to 
 pop up a lot recently is Discourse (http://www.discourse.org) which looks 
 pretty slick. The feature set is nice, plus multi-language support 
 (http://v1.discourse.org/about/)

 The one caveat is that I don't have anywhere to host it (i.e., it uses 
 Postgres, .. Docker). They recommend Digital Ocean, for an extra $10/month..

 I know Ubuntu uses Discourse. Any feedback? Advantages or disadvantages?

I have played with Discourse, and it looks pretty nice but I haven't
really used it seriously in any sense. I wouldn't object to giving it
a try, but don't have anywhere I could host it right now either.

Marcus

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Re: [Avogadro-devel] Switching to GitHub pull requests for review/merge?

[Marcus D. Hanwell]

On Mon, Oct 6, 2014 at 10:34 PM, Marcus D. Hanwell
marcus.hanw...@kitware.com wrote:
 Hi,

 Would there be any objections to switching to GitHub pull requests for
 development? The Kitware instance of Gerrit will be upgraded at some
 point, removing the topic branch functionality. Gerrit feels a little
 heavy/clunky, and I feel like GitHub has come a long way since we made
 the switch to Gerrit.

Geoff gave me a +10 off-list, I will work on clearing the Gerrit
backlog, planning to move to GitHub pull requests unless I hear
objections. We are looking at a project called GitLab for several
Kitware projects that are considering moving from Gerrit (they are
also considering GitHub). This may be interesting, but it effectively
mirrors much of the functionality of GitHub.

Thanks,

Marcus

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Re: [Avogadro-devel] Avogadro2 Edit/View Molecule - Code and Interface

[Marcus D. Hanwell]

So the weekend resulted in no code being written, mostly ended up
having to fix some stuff in the house I was behind on due to all the
travel :-/ I did manage to get Windows reinstalled on the machine I
was using to create binaries (it suffered a hard drive failure a month
or two back - new, bigger hard drive too). I will have some time to
actually work on this in the coming days though, apologies on the
delay - I hadn't factored in spending so much time on real life
stuff...

Marcus

On Thu, Sep 4, 2014 at 9:31 PM, Marcus D. Hanwell
marcus.hanw...@kitware.com wrote:
 Hi Geoff,

 Sorry, crazy travel schedule, so didn't get this finished as soon as I
 had hoped. I am working on some changes to make the conversion much
 simpler, and to alleviate the UI issue. As I said at the time -
 totally agree, and not pushing to keep the current UI. I think it was
 a necessary step as I fleshed it out, but hope to make this much
 smoother.

 I think any of the edit functionality can convert to an editable
 molecule, they use implicitly shared arrays and so the copy cost is
 minimal with only the coordinates triggering a real copy when the
 forcefield kicks in. I would love to see what you are thinking for the
 auto-optimize, I just spent a few days at Daresbury Lab last week
 talking about some of these features (along with QMMM, how we might
 define regions, residues, etc).

 Let me see what I can get done on the weekend to make it clearer, and
 sketch out what I thought would work. Happy to iterate on this, and
 yes it is better to put more of these discussions on the mailing list.
 Measurement is a tool that I think we make work with edit and view
 molecules to be honest - so no need to switch at all.

 Marcus

 On Wed, Sep 3, 2014 at 10:44 PM, Geoffrey Hutchison
 geoff.hutchi...@gmail.com wrote:
 Hi Marcus,

 I wanted to follow-up about an off-list discussion with Avogadro v2. Between 
 v0.7, and the current git master (0.8?) there's now a clear UI division 
 between edit and view molecules.

 Can you outline some of the real reasons for this behind the scenes, 
 particularly on the UI side? I think this is currently a usability nightmare 
 and I'd like to make sure we can work past this or write up conversion code 
 that allows tools, extensions, etc. to convert back and forth.

 My big use-case concern is the Auto Optimize tool, which I'm trying to 
 design for Avogadro v2's very different architecture. For example, let's say 
 a user wants to set a measurement between two atoms (view). Then they switch 
 to the Auto Optimize tool (edit) and start pushing atoms around.

 In Avogadro v1, this wasn't a problem. The measurements would update while 
 the optimization occurred in a different thread.

 How can this work in Avogadro v2?

 Thanks,
 -Geoff

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Re: [Avogadro-devel] Avogadro2 Edit/View Molecule - Code and Interface

[Marcus D. Hanwell]

On Mon, Sep 8, 2014 at 10:14 AM, Defusco III, Albert A defu...@pitt.edu wrote:
 Good morning,

 Let me add a bit to this discussion as well. I've been working on the 
 crystallography extension in Avogadro2 and I find it exceeding difficult to 
 use the CrystalTools while editing or creating molecules.

 1. It takes several clicks in and out of view mode along with renaming the 
 molecule before the Crystal QT plugin recognizes that there is even a 
 molecule present. From what I can tell in edit mode the following check 
 returns false for a new molecule.

 crystal.cpp:
 if (m_molecule)

 2. Once a unit cell has been added it is not visible in edit mode. The 
 following appears to return false.

 3. Crystal operations, like filling a unit cell, show nothing in edit mode. 
 They appear to work and the output is present once the user changes to view 
 mode.

 All of these operations just worked in the 0.7 release and it didn't care if 
 the user had selected an edit tool or a view tool. One of the great features 
 of Avogadro is that the molecule was always editable and the programmer 
 didn't have to make many, or even any, special considerations when writing 
 tools.

Like I said, please give me a little time to finish it up, perhaps I
committed the feature too soon. Many of these issues are rendering
artifacts, along with some issues around certain editing features not
being ported to use the right structure. I am not pushing to keep it
this way, but like I said when I was over in Pittsburgh this can be
made intuitive with a little more work - I will see if I can get that
finished up soon so that things are easier, and we can make a release.

Thanks for your patience, I am thankfully done with travel for a
while, and should be able to focus on finishing this up. Major
advantages are a scalable undo/redo (with some rough edges
admittedly), and I honestly think it will be worth it to reduce
confusion about properties that are simply no longer valid after
editing. In the UI the difference between editing and viewing should
be fluid, but I hope to create a much clearer model in the API so that
we focus on doing one or the other well in most cases.

If by some chance it doesn't work out I can back out some of the changes.

Marcus

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Re: [Avogadro-devel] Avogadro2 Edit/View Molecule - Code and Interface

[Marcus D. Hanwell]

Hi Geoff,

Sorry, crazy travel schedule, so didn't get this finished as soon as I
had hoped. I am working on some changes to make the conversion much
simpler, and to alleviate the UI issue. As I said at the time -
totally agree, and not pushing to keep the current UI. I think it was
a necessary step as I fleshed it out, but hope to make this much
smoother.

I think any of the edit functionality can convert to an editable
molecule, they use implicitly shared arrays and so the copy cost is
minimal with only the coordinates triggering a real copy when the
forcefield kicks in. I would love to see what you are thinking for the
auto-optimize, I just spent a few days at Daresbury Lab last week
talking about some of these features (along with QMMM, how we might
define regions, residues, etc).

Let me see what I can get done on the weekend to make it clearer, and
sketch out what I thought would work. Happy to iterate on this, and
yes it is better to put more of these discussions on the mailing list.
Measurement is a tool that I think we make work with edit and view
molecules to be honest - so no need to switch at all.

Marcus

On Wed, Sep 3, 2014 at 10:44 PM, Geoffrey Hutchison
geoff.hutchi...@gmail.com wrote:
 Hi Marcus,

 I wanted to follow-up about an off-list discussion with Avogadro v2. Between 
 v0.7, and the current git master (0.8?) there's now a clear UI division 
 between edit and view molecules.

 Can you outline some of the real reasons for this behind the scenes, 
 particularly on the UI side? I think this is currently a usability nightmare 
 and I'd like to make sure we can work past this or write up conversion code 
 that allows tools, extensions, etc. to convert back and forth.

 My big use-case concern is the Auto Optimize tool, which I'm trying to design 
 for Avogadro v2's very different architecture. For example, let's say a user 
 wants to set a measurement between two atoms (view). Then they switch to the 
 Auto Optimize tool (edit) and start pushing atoms around.

 In Avogadro v1, this wasn't a problem. The measurements would update while 
 the optimization occurred in a different thread.

 How can this work in Avogadro v2?

 Thanks,
 -Geoff

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Re: [Avogadro-devel] Avogadro 1.1.x and Linux Distributions

[Marcus D. Hanwell]

On Fri, Aug 29, 2014 at 6:58 PM, Michael Banck mba...@debian.org wrote:
 Hi,

 On Fri, Aug 29, 2014 at 04:51:49PM -0400, Geoffrey Hutchison wrote:
  Any progress on this?  The Debian freeze is approaching in a couple of
  months, so I it would be nice to include Avogadro-1.2.0 into the next
  version.

 I think we should probably fix as many bugs as possible and push out
 1.1.x as 1.2, even though it'll be missing a few features. Is there a
 date for the freeze? When do you want something?

 The hard freeze is early November, but early October would be
 appreciated to leave some time for integration etc.

Sounds like something we could work towards.

 The relative quiet is that Marcus came to visit Pittsburgh and we've
 been assembling a hit list to get as many things ready for an
 Avogadro v2 release. The new rendering architecture is a huge
 improvement, but day-to-day usability needs a bit of work.

 If avogadro2 is out by then, I can see about getting it packaged, but it
 might be premature to replace avogadro1 with it for the Debian release.

Avogadro 2 is totally compatible with being installed in the same
prefix as Avogadro 1, would it be reasonable to package it as as well
as Avogadro 1 rather than replacing? The executable is avogadro2, the
libraries have different names, share directory etc.

Just a thought, if not then I am fine with holding off but I think it
would be nice to consider. Thanks for pushing us on this - it would be
great to get what we can in before the freeze.

Marcus

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

[Marcus D. Hanwell]

On Tue, Feb 4, 2014 at 5:39 AM, Jure Varlec jure.var...@ki.si wrote:
  Also, I had to add an include path for Eigen to  fix building, do I have
  to make a separate branch for that single commit?
 I'm not sure why that (adding an Eigen include path) would be necessary.
 That should be covered by CMake. Why don't you comment on your problems
 with Eigen and we'll see if it can be fixed outside of a patch.

 Well, CMake finds both Eigen2 and Eigen3, but build fails with 'fatal error:
 Eigen/Core: No such file or directory' unless I patch it with

 diff --git a/libavogadro/src/colors/CMakeLists.txt
 b/libavogadro/src/colors/CMakeLists.txt
 index a967516..c0836a8 100644
 --- a/libavogadro/src/colors/CMakeLists.txt
 +++ b/libavogadro/src/colors/CMakeLists.txt
 @@ -6,7 +6,7 @@ ADD_DEFINITIONS(-DQT_SHARED)

  set(DESTINATION_DIR ${Avogadro_PLUGIN_INSTALL_DIR}/colors)

 -include_directories(${CMAKE_CURRENT_BINARY_DIR})
 +include_directories(${CMAKE_CURRENT_BINARY_DIR} ${EIGEN_INCLUDE_DIR})

  set(LINK_LIBS avogadro)
  set(PLUGIN_LABEL colors)

Are you building with Eigen 2 or 3? I just looked at master, and
libavogadro/src/CMakeLists.txt adds it to the include directories, the
same is not true for Eigen 3. There are still a number of rough edges
with the Eigen 3 support, we should take a pass at getting that to
build consistently. A lot of people (myself included) have Eigen
installed and can miss this.

I also don't see anything that defines EIGEN_INCLUDE_DIR, both
variants have the major version number. Hope that helps.

Marcus

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

[Marcus D. Hanwell]

On Tue, Feb 4, 2014 at 10:45 AM, Jure Varlec jure.var...@ki.si wrote:
 On Tuesday 04 of February 2014 09:56:01 Marcus D. Hanwell wrote:
 Are you building with Eigen 2 or 3? I just looked at master, and
 libavogadro/src/CMakeLists.txt adds it to the include directories, the
 same is not true for Eigen 3. There are still a number of rough edges
 with the Eigen 3 support, we should take a pass at getting that to
 build consistently. A lot of people (myself included) have Eigen
 installed and can miss this.

 I also don't see anything that defines EIGEN_INCLUDE_DIR, both
 variants have the major version number. Hope that helps.

 I'm building with both. Although Eigen is a header-only library, I'm running
 Gentoo so both versions need to be installed as build-time dependencies of
 various packages, they are at /usr/include/eigen{2,3}

 Actually, when I touched one of CMakeLists and caused a reconfiguration, the
 problem popped out elsewhere, then disappeared later. It seems that, starting
 with an empty build directory, I have to run CMake twice, then it builds
 successfully. This behaviour seems to be consistent.

It is, I will see if I can reproduce. I don't even see where
EIGEN_INCLUDE_DIR would get defined, and how it would solve any
problem. A git grep for it in the source tree turns up nothing, and we
should consistently choose Eigen 2 or 3 - mixing the two would not end
well.

Thanks for your feedback, I will try to dig a little deeper when I
have some time and see if we can clean things up a little more.

Marcus

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Re: [Avogadro-devel] avogadro 1.1.1: Building with Eigen3 fails

[Marcus D. Hanwell]

On Tue, Dec 31, 2013 at 8:55 AM, Daniel Leidert daniel.leid...@wgdd.de wrote:

 Hi there,

 I'm speaking as part of the Debian package maintainers of avogadro. The
 latest release 1.1.1 fails to build with Eigen3. The reason is, that
 Eigen2 is still required, e.g. in
 libavogadro/src/extensions/surfaces/openqube/CMakeLists.txt. Also
 cmake/modules/AvogadroUse.cmake requires Eigen2. So it is not possible
 to build with Eigen3 only and the build fails. Is this some kind of
 intentional result or a bug?

 I'm attaching the build log.

It is a bug, Geoff submitted a patch to enable building with Eigen 3
for 1.1.1 (this is very new, and not well-tested - thanks for the
feedback). We can work on a fix for 1.1.2 (a few other things have
come up too), I will try and find some time to look into this further
unless Geoff gets to it first.

Marcus

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Re: [Avogadro-devel] Building Avogadro2 w/o MoleQueue on Arch Linux-64bit

[Marcus D. Hanwell]

On Sun, Dec 29, 2013 at 5:12 AM, Mark Lee m...@markelee.com wrote:
 Salutations!

 I have been trying to build Avogadro2 (to test it out) on my Arch Linux
 64 bit system. However, while building avogadrolibs-0.7.2; I get the
 following error from CMake:

snip

 Is there a way to disable the building of MoleQueue?

Not at this time, but that shouldn't be too hard to achieve. I will
try to make sure it can be done for the next release, I'm afraid this
one slipped through (and it only needs a tiny client library we could
consider simply bundling).

Marcus

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Re: [Avogadro-devel] Avogadro Low Resolution Icon in Arch Linux

[Marcus D. Hanwell]

On Mon, Dec 23, 2013 at 2:19 PM, Geoffrey Hutchison
geoff.hutchi...@gmail.com wrote:
 I can take a look at this, and will see if I can improve it. The report 
 doesn't reference what version you are referring to, but I presume 1.1.1?

 We have both a 512x512 icon and an SVG version, so this shouldn’t be too hard 
 to fix.

 https://github.com/cryos/avogadro/blob/master/avogadro/src/icons/avogadro.png
 https://raw.github.com/cryos/avogadro/master/avogadro/src/icons/avogadro.svg

 Or in the source tree, these are avogadro/src/icons/avogadro.*

 Does the .desktop file just need some patching? (Sorry, I’ve never used Arch.)

Yeah, I use Arch everyday for development so I don't mind patching this.

Marcus

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Re: [Avogadro-devel] Avogadro Low Resolution Icon in Arch Linux

[Marcus D. Hanwell]

On Mon, Dec 23, 2013 at 2:41 PM, Marcus D. Hanwell
marcus.hanw...@kitware.com wrote:
 On Mon, Dec 23, 2013 at 2:19 PM, Geoffrey Hutchison
 geoff.hutchi...@gmail.com wrote:
 I can take a look at this, and will see if I can improve it. The report 
 doesn't reference what version you are referring to, but I presume 1.1.1?

 We have both a 512x512 icon and an SVG version, so this shouldn’t be too 
 hard to fix.

 https://github.com/cryos/avogadro/blob/master/avogadro/src/icons/avogadro.png
 https://raw.github.com/cryos/avogadro/master/avogadro/src/icons/avogadro.svg

 Or in the source tree, these are avogadro/src/icons/avogadro.*

 Does the .desktop file just need some patching? (Sorry, I’ve never used 
 Arch.)

 Yeah, I use Arch everyday for development so I don't mind patching this.

Just to be clear, the .desktop file will of course affect all Linux
systems, but I don't think this will be an issue.

Marcus

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[Avogadro-devel] Avogadro 1.1.1 Released

[Marcus D. Hanwell]

We are very proud to announce the availability of Avogadro 1.1.1.

Avogadro 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 GNU GPLv2.

What does Avogadro do?
We've tried to make the best, most intuitive builder, including
common fragments, downloading directly from PDB or PubChem, and
peptide sequences
Innovative auto-optimize tool which allows you to continue to build
and modify, during molecular mechanics optimization
Interfaces to many common computational packages
Designed to help both educational users and advanced research
Plugins that allow Avogadro to be extended and customized
Well defined public API, library and Python bindings for development
Embedded Python interpreter
Translations available in 19+ languages

Download: https://sourceforge.net/projects/avogadro/files/avogadro/1.1.1

What's New? See the Release Notes:
http://avogadro.openmolecules.net/wiki/Avogadro_1.1.1

For more information: http://avogadro.openmolecules.net/wiki/

If you use Avogadro please check out the recently published Avogadro
paper, and consider citing it: http://www.jcheminf.com/content/4/1/17

This is a community project and we couldn't have made this release
without you. Many thanks to all the contributors to Avogadro including
those of you who submitted feedback, bug reports, and code. Particular
thanks go to all the translators.

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[Avogadro-devel] Avogadro 2 0.7.0 Released

[Marcus D. Hanwell]

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, please check out the recently
published Avogadro paper, and consider citing it:
http://www.jcheminf.com/content/4/1/17

This is a community project and we couldn't have made this release
without you. Many thanks to all the contributors to Avogadro including
those of you who submitted feedback, bug reports, and code. We
acknowledge that the development of Avogadro 2 has been funded by a US
Army SBIR with the Engineering Research Development Center under
contract (W912HZ-12-C-0005) at Kitware, Inc.

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Re: [Avogadro-devel] Eigen3 Support

[Marcus D. Hanwell]

Hi Geoff,

On Mon, Sep 30, 2013 at 8:17 PM, Geoffrey Hutchison geo...@pitt.edu wrote:
 I had a little time to fiddle this afternoon and I've push a patch to Gerrit 
 that allows building against Eigen3 using the support mode. This means that 
 Eigen3's API is not yet supported in Avogadro 1.1.x and that the ABI may 
 break.

The ABI does break, the Eigen vector classes changed some template
arguments for Vector3d defines for example, I hit this when porting
some of the QM code.

 I think this is a good thing -- it allows building against either Eigen 2 or 
 Eigen 3 (long requested). Considering Avogadro 1.x is something of an 
 evolutionary dead-end, I think there isn't really much motivation to migrate 
 all the code in the v1.x codebase. Such migration can occur as code is 
 migrated to 2.x.

 Thoughts?
 http://review.source.kitware.com/#/c/12868/

Most of the migration is relatively simple, I took a quick look and
the only change I would suggest is configuring the Eigen definition so
that users of the Avogadro API don't need to duplicate this define (or
would it work if they did not). Great to see it was so easy - I had
been meaning to take a look.

Marcus

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Re: [Avogadro-devel] Unable to configure OS X installation directory away from /Applications/Avogadro.app...

[Marcus D. Hanwell]

On Mon, Sep 2, 2013 at 1:33 AM, Christian Herbig c.her...@me.com wrote:
 I sincerely hope this is a question that can easily be answered, but I cannot 
 at all figure out how to change the final installation directory from 
 /Applications/Avogadro.app to /Applications/MacPorts/Avogadro.app.  I have 
 tried multiple permutations on -DCMAKE_INSTALL_PREFIX= , yet nothing seems to 
 change the final configuration from:

 set(Avogadro_INSTALL_PREFIX  /Applications/Avogadro.app/Contents)
 set(Avogadro_INCLUDE_DIRS/Applications/Avogadro.app/Contents/include)
 set(Avogadro_LIBRARY_DIRS/Applications/Avogadro.app/Contents/lib)
 set(Avogadro_LIB_SUFFIX  )
 set(Avogadro_PLUGIN_DIR  
 /Applications/Avogadro.app/Contents/lib/avogadro/1_1)
 set(Avogadro_BIN_DIRS“/Applications/Avogadro.app/Contents/bin)

 To be specific, I need to be able to do something like 
 -DCMAKE_INSTALL_PREFIX=${destroot}${applications_dir}

On the Mac we ended up hard wiring more than we perhaps should have to
make the default case work. I am not sure you can easily modify this
without modifying some of the CMake code, it is indeed a bug in the
way we wrote out CMakeLists.txt file. I have a lot of that figured out
now in newer build systems. I will see if I can find time to go back
and apply it to Avogadro 1, but I am not sure when I will have time.

Marcus

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[Avogadro-devel] CML, NWChem, FoX, Avogadro paper

[Marcus D. Hanwell]

Hi,

I wanted to point out our paper (part of the same special issue as the
Avogadro paper) was released recently. It discusses the use of CML
produced by NWChem using FoX and visualized in Avogadro.

www.jcheminf.com/content/5/1/25

We should hopefully see releases of NWChem soon that can output this
CML, and I will clean up the code and get it merged in soon too. This
has been part of an ongoing collaboration looking at how we can
improve the quality of the data coming out of computational codes, and
it is intended to be complimentary to log file parsing/other file
parsing we have been working on for years.

In other news, I just noticed that the Avogadro paper has hit 50
citations on Google Scholar already. Great to see so many from the
community citing it and using Avogadro.

Thanks,

Marcus

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Re: [Avogadro-devel] Packmol, Symmol and other Fortran through Webapps

[Marcus D. Hanwell]

On Fri, May 24, 2013 at 4:49 AM, Jens linuck...@gmail.com wrote:

 On 23 May 2013 18:15, Geoffrey Hutchison geo...@pitt.edu wrote:

 I've been silent on the lists, since I'm hard at work getting tenure (the
 package gets submitted in early August).

 But I had a brainstorm about some of the features we've discussed, like
 Packmol -- which is a Fortran code. While we can supply binaries and detect
 if the program is available at run-time, it might be nice to offer some of
 these programs as web applications as well.

 Right now, we offer integration with PubChem, the NIH resolver (also for
 compound naming) and a few other web services.

 But it'd be pretty easy to offer a web app that runs Packmol. A similar
 Fortran program which might be useful is symmol, which detects point group
 symmetry and can symmetrize molecules.

 To be clear, these programs are already available, and I'd suggest making
 the webapp interface layer available as open source (probably BSD-license).
 I'm just thinking that for many users and for development purposes, a webapp
 would be useful (i.e., no need to get a Fortran compiler for Windows or
 Mac).

 Thoughts?

 I think that sounds like a really good idea.

 I've always thought that it would be great to work towards a kind of
 eco-system of tools with Avogadro sitting in the middle and providing the
 interface to all of them and creating a really powerful modelling
 environment - something a bit like CCP4 have (http://www.ccp4.ac.uk/).

 There are so many helpful tools out there, but many aren't known about or
 difficult to integrate together. Avogadro could provide that glue and make
 them easy to use too.

 I don't know whether that would work best as a distributed software bundle,
 or as something that calls on webapps, but then there's no reason why a
 mixture of both wouldn't work.

One of the things we have been looking at is looser integration of
components using MoleQueue and separate processes, but more recently
we have been exploring easy ways to make and expose RESTful APIs that
allow you to query data sources or run external codes. At the core it
is just a simple RESTful API that returns results as JSON and one or
two other things. We have been experimenting with using Python as the
glue language on the server, and don't have anything worth exposing
yet but this might be one approach.

I totally agree on using a combination of the two, there are some new
developments in CMake for example that make it easier to use gfortran
from MinGW with Visual Studio for the C/C++ code.

Thanks,

Marcus

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Re: [Avogadro-devel] Avogadro 1.1.0 Released

[Marcus D. Hanwell]

On Fri, Apr 26, 2013 at 11:13 AM, Michael Banck mba...@debian.org wrote:
 Hi,

 On Wed, Sep 12, 2012 at 02:07:21PM -0400, Marcus D. Hanwell wrote:
 We are very proud to announce the availability of Avogadro 1.1.0.

 [...]

 Download: https://sourceforge.net/projects/avogadro/files/avogadro/1.1.0

 What's New? See the Release Notes:
 http://avogadro.openmolecules.net/wiki/Avogadro_1.1.0

 The release notes mention that this is a Beta release and that a 1.2.0
 release is forthcoming.  Is this still the case, or was this changed
 later on and 1.1.0 is a stable public release?

 If not, what is the timeline for a 1.2.0 release?

There were a lot of changes made in 1.1.0, and new stability issues
have cropped up since we made the release. I think we should make a
1.1.1 release addressing some of the stability issues if possible. Is
there a distro freeze date pressing?

Thanks,

Marcus

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

[Marcus D. Hanwell]

On Fri, Apr 12, 2013 at 9:29 AM, David Lonie david.lo...@kitware.com wrote:
 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 responsiveness was incredibly snappy.

 Great to hear the positive feedback! Out of curiousity, just how big
 were your molecules?

 Where's the place to log bug reports while it's still in the initial testing
 phase? I found one (see below) but it wasn't immediately obvious on the
 openchemistry website where the tracker was.

 We have a bug tracker up here:

 http://projects.openchemistry.org/

 I'll add a link on the openchemistry wiki and see about adding one to
 www.openchemistry.org.

The main site already has a link (Resources, Bug Tracker), we can
certainly get links on the wiki too. The Doxygen links there too, but
let's work on making it as obvious as possible.

 As for the bug:

 draw C atom, click Extensions - Open Babel - Add Hydrogens:

 Command-line output:

 OBProcess::executeObabel: Running
 /Volumes/Avogadro2-0.5.0-Darwin/Avogadro2.app/Contents/MacOS/obabel -icml
 -ocml -h
 /Volumes/Avogadro2-0.5.0-Darwin/Avogadro2.app/Contents/MacOS/obabel
 stderr:
  ==
 *** Open Babel Error  in RegisterOptionParam
   The number of parameters needed by option t in The LPMD file format.
 differs from an earlier registration.
 0 molecules converted
 
 Bad CML:  

 I noticed this odd behavior in obabel and brought it up on
 openbabel-devel a little while ago, see
 http://forums.openbabel.org/obabel-h-bug-while-adding-hydrogens-td4655976.html.
 This is a feature, not a bug from their perspective.

 We plan to implement our own add-hydrogens routine (and maybe even our
 own remove-hydrogens, if I can figure that out ;-) ). I've filed a
 bug for this here:

 http://projects.openchemistry.org/issues/169

There seem to be a few bugs on the Mac with obabel and CML too, so I
am afraid geometry optimization looks a little dicey. I think there
are some simple workarounds we can implement there to improve things
in the next release.

Thanks for the feedback Jens. I think ensuring anyone can have
Avogadro 1 and 2 installed should make it easier to try out the new
stuff without having to give up Avogadro 1.

Marcus

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[Avogadro-devel] First Avogadro 2 beta release

[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-devel] [Avogadro-Translations] Avogadro in Spanish for Windows

[Marcus D. Hanwell]

On Fri, Apr 5, 2013 at 2:47 PM, Louis Ricard
louis.ric...@polytechnique.edu wrote:
 Hi all,

 This is a recurrent problem for Windows users: Windows does not know i18n
 and, consequently, only english menus are available.
 Since the Windows version is not compiled with internationalization support,
 there are two solutions :
 1) compile the .po files from Launchpad: they will not correspond to those
 of the current Avogadro binaries, requires Qt deveopment
 tools installed;
 2) obtain the .qm files from a friend using a Mac or Linux (same version, 32
 or 64 bits) and install them under
 C:\Program Files\Avogadro\share\avogadro\i18n.

 If not other solution exists, this should be mentioned in the FAQS.

We should add this to the release notes, I used to make the copy when
making a Windows release but think I forgot the last few times. I will
try to do this for the next release, we never got the tools to work in
the build system on Windows correctly but I can always revisit that
too.

Thanks for reporting this, an FAQ entry would be reasonable but I will
try to improve the Windows i18n support in the next bug fix release.

Marcus

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Re: [Avogadro-devel] Contributor approval for 3-clause BSD relicensing (YOUR ACTION NEEDED)

[Marcus D. Hanwell]

On Mon, Mar 18, 2013 at 11:30 AM, Benoit Jacob jacob.benoi...@gmail.com wrote:
 Dear Avogadro developers,


 Yes, I agree to have all the code that I contributed to Avogadro
 relicensed to the 3-clause BSD license.

 Also, I would suggest moving to Eigen 3 if you haven't already: it is now
 MPL2-licenced, which is closer to the 3-clause BSD license than Eigen2's
 licensing options are.

Thanks, you may have recognized the relicensing email text which I
modeled on your emails ;-) Avogadro 2 is already using Eigen 3, and
there is possibly a patch to do most of this a contributor sent to me
recently - I need to take a look at it and assess the impact of it.

Thanks,

Marcus

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[Avogadro-devel] Avogadro relicensing agreement update

[Marcus D. Hanwell]

Hi,

Just a quick update from the replies I have received as far as
agreement to relicensing goes. Those who have replied positively (one
or two off-list, hopefully they will follow up with on list soon),

Marcus D. Hanwell
Casper Steinmann
David Lonie
Geoffrey Hutchison
Jens Thomas
Matthew Kennedy
Tim Vandermeersch
Eric Brown
Albert DeFusco
James Bunt
Jordan Mantha
Simon Ochsenreither
Gary Kedziora
Naomi Fox
Egon Willighagen

Those who have yet to reply,

Konstantin Tokarev
Donald Ephraim Curtis
Michael Banck
Jogvan Magnus Olsen
Benoit Jacob
Carsten Niehaus
Raimondas Galvelis
Ross Braithwaite
Shahzad Ali
Kristof Bal
Reinis Danne

Thanks to everyone who got back to me already, I will see if I can
follow up on a few of these in the next few days along with analyzing
the amount of code affected if some do not respond. As we get further
down the list there are less lines that were changed with the bottom
five all being less than 250 lines changed.

Marcus

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[Avogadro-devel] Contributor approval for 3-clause BSD relicensing (YOUR ACTION NEEDED)

[Marcus D. Hanwell]

Hi,

We have talked about this offline, and at times on the list. As many
of you already know we are working on a rewrite of Avogadro, and we
are preparing to make an initial alpha release. It features many great
new features, but does not yet have feature parity with Avogadro 1.x.
Avogadro 2 is a rewrite and re-architecture of Avogadro using a
simpler, more liberal 3-clause BSD license. A lot of the API has
changed, and we invite community participation. For some background to
the project please see,

http://wiki.openchemistry.org/
http://www.slideshare.net/cryos/the-open-chemistry-project

You can see the latest version make use of obabel command line tools
for file translation, geometry optimization, and other pieces using a
qprocess to manage execution. We are also looking at using this
approach to run Python and Java in a more loosely coupled form, and we
have ported most of the input generators to use a much simpler
scripting framework where the addition of scripts can add new
generators to the GUI using pure Python, or other languages.

To that end, we would like to know which of our Avogadro contributors
agree to relicensing their contributions under the 3-clause BSD
license, linked below,

http://opensource.org/licenses/BSD-3-Clause

If you contributed code to Avogadro, please reply to this email with
either one of the following statements (adapted from the Eigen
relicensing effort led by Benoit),

  Yes, I agree to have all the code that I contributed to Avogadro
relicensed to the 3-clause BSD license.

or

  No, I do not agree.

Anything other than the above Yes sentence will mean No. Without
your agreement we will make no attempt to port your contribution to
Avogadro 2's code base, we would also love input from our contributors
on Avogadro 2, and have made every attempt to address many of the
shortcomings we perceived in Avogadro.

Thanks,

Marcus

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Re: [Avogadro-devel] painter

[Marcus D. Hanwell]

On Fri, Mar 1, 2013 at 1:31 PM, Marc-André Dubois ma.dub...@me.com wrote:
 Hi everyone,
   I would like to draw a sphere in the molecule render area
 of avogadro. I simply tried to test this command:

  gl-painter()-drawSphere(center,13.0);

 where gl is my GLWidget, but I received: GLPainter not active. Is there
 something I don't understand? Thanks guys,

You must make these calls when the GL context is valid. The easiest
way is to write an Engine and do it in one of the virtual render calls
in the method. See the Van der Waals plugin for example. This ensures
the render call happens at the appropriate moment when the GL context
is current.

Marcus

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Re: [Avogadro-devel] Regarding request for suggestion.

[Marcus D. Hanwell]

On Sun, Feb 24, 2013 at 11:41 PM, Sujit Tangadpalliwar
sujit_tangadpalli...@persistent.co.in wrote:
 I am using your software
 Avogadro since a month as it having multiple functionality like
 visualization, molecule editor, optimization structure conversion etc. and
 it quite easy and user friendly. I want to use Avogadro in my project. I am
 trying to connect Avogadro with my Perl script but I am unable to find Perl
 module for this connection please guide me regarding my query.

 Hope for guidance to go my project smoothly in right direction.

I am not sure how you want to integrate Avogadro into a Perl script,
we have no Perl integration that I am aware of. You can call Avogadro
from the command line, if you want scripting then Python would be a
better way to go. We have wrapped the majority of our API in Python,
although most of the installers do not have the feature enabled by
default.

You would have to give us a little more detail on what you are trying
to accomplish to help any further.

Thanks,

Marcus

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Re: [Avogadro-devel] 300,000 Downloads

[Marcus D. Hanwell]

On Sun, Jan 27, 2013 at 1:33 PM, Geoffrey Hutchison geo...@pitt.edu wrote:
 I was pulling up statistics on Avogadro for an NSF proposal, and saw that we 
 finally broke the 300,000 download mark! In 2012, there were ~100,000 
 downloads alone.

 http://sourceforge.net/projects/avogadro/files/avogadro/stats/timeline?dates=2001-01-01+to+2013-01-26

 Incidentally, the usage is profoundly international. There are now 26 
 localizations with 50% coverage, including Vietnamese, Malay, and Indonesian.
 https://translations.launchpad.net/avogadro

That is awesome news, I saw we were getting close when I looked around
the new year. I just made a blog post and the Avogadro paper is also
the most viewed paper in the Journal of Cheminformatics over the last
year, and it is at number 10 all time I think.

http://blog.cryos.org/archives/262-Avogadro-Paper-Published-Open-Access.html

Showing 12 citations on Google Scholar too.

Marcus

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Re: [Avogadro-devel] Avogadro Paper Accesses

[Marcus D. Hanwell]

On Fri, Sep 14, 2012 at 10:35 AM, Geoffrey Hutchison geo...@pitt.eduwrote:

 I'll admit I've been very intrigued by the # of accesses statistic from J.
 Cheminf. I wish more journals showed this -- it's a very interesting way of
 measuring impact of particular articles.

 Thanks to Noel O'Boyle's recent blog post:

 http://baoilleach.blogspot.com/2012/09/plotting-accesses-on-axis-part-ii.html

 I've been able to finish up the graph of the first 30 days of the Avogadro
 paper (which is now #1 for the last 30 days and #19 for the last year). Not
 surprisingly, there was an exponential fall-off over the first few days,
 but we seem to be in the noisy long-tail now.

 Hi Geoff,

Thanks for collecting the numbers, I had started but missed too many days.
I noticed we had more than 3,000 accesses in the first 30 days too, but
didn't get the exact number - it is a shame they don't offer a details page
with more numbers.

Marcus
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[Avogadro-devel] Avogadro 1.1.0 Released

[Marcus D. Hanwell]

We are very proud to announce the availability of Avogadro 1.1.0.

Avogadro 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 GNU GPLv2.

What does Avogadro do?
* We've tried to make the best, most intuitive builder, including
common fragments, downloading directly from PDB or PubChem, and
peptide sequences
* Innovative auto-optimize tool which allows you to continue to
build and modify, during molecular mechanics optimization
* Interfaces to many common computational packages
* Designed to help both educational users and advanced research
* Plugins that allow Avogadro to be extended and customized
* Well defined public API, library and Python bindings for development
* Embedded Python interpreter
* Translations available in 19+ languages

Download: https://sourceforge.net/projects/avogadro/files/avogadro/1.1.0

What's New? See the Release Notes:
http://avogadro.openmolecules.net/wiki/Avogadro_1.1.0

For more information: http://avogadro.openmolecules.net/wiki/

If you use Avogadro please check out the recently published Avogadro
paper, and consider citing it: http://www.jcheminf.com/content/4/1/17

This is a community project and we couldn't have made this release
without you. Many thanks to all the contributors to Avogadro including
those of you who submitted feedback, bug reports, and code. Particular
thanks go to all the translators.

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Re: [Avogadro-devel] Upgrading SourceForge for Avogadro

[Marcus D. Hanwell]

On Wed, Sep 12, 2012 at 1:32 PM, Geoffrey Hutchison geo...@pitt.edu wrote:
 One thing we should consider with the release of 1.1.0 is to upgrade Avogadro 
 to the new SourceForge version:
 https://sourceforge.net/p/upgrade?search=avogadro

 I think the improved tracker would be great for handling many of the new bug 
 fixes, enhancements we're likely to get!

I am no fan of the current trackers, and so would be interested in
seeing how much better then new one is. I think we should switch, and
was tempted to do it. Do you want to flip the switch?

Marcus

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Re: [Avogadro-devel] Avogadro 1.1.0 tagging

[Marcus D. Hanwell]

On Tue, Sep 4, 2012 at 1:10 PM, Marcus D. Hanwell
marcus.hanw...@kitware.com wrote:
 On Tue, Sep 4, 2012 at 11:49 AM, Geoff Hutchison
 ge...@geoffhutchison.net wrote:
 I think we are more than ready to release once we have the Mac
 package. This is the first in the beta series to stabilize for a 1.2.0
 release. I would like to get some of the pending changes on Gerrit
 merged (and have a few things queued I would like to add) once we have
 this release out.

 I can spin a Mac package tomorrow -- unfortunately, due to the holiday, and 
 some prior commitments, I can't do that today.

 Thanks Marcus for all the hard work on finalizing the release. It will be 
 great to get it out there and show people what we've been working on!

 That sounds great, I figured with the holidays things might be hectic.
 I pushed the tag to the repository and the other files are all in
 staging on SourceForge (you should be able to see them and upload the
 Mac package).

Hi Geoff,

Did you get chance to create some Mac binaries? I would like to get an
announcement together in the next few days. I noticed that SourceForge
unveiled the staged binaries/tarballs (only holds them for three
days), and we are seeing quite a few downloads.

For those interested in trying out the latest Avogadro that is great,
nearly 300 downloads yesterday. I am inclined to leave the files
as-is, once the Mac binary is added I would like to add a news item
and update the main page etc.

Thanks,

Marcus

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