Avogadro-devel Digest, Vol 77, Issue 1

Development
1

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

On Tue, Mar 12, 2013 at 4:49 PM, <
avogadro-devel-request@lists.sourceforge.net> wrote:

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Today’s Topics:

  1. painter (Marc-Andr? Dubois)
  2. Re: painter (Marcus D. Hanwell)
  3. Eigen3 migration (Kirill Okhotnikov)
  4. Contributor approval for 3-clause BSD relicensing (YOUR
    ACTION NEEDED) (Marcus D. Hanwell)
  5. Re: Contributor approval for 3-clause BSD relicensing (YOUR
    ACTION NEEDED) (Marcus D. Hanwell)
  6. Re: Contributor approval for 3-clause BSD relicensing (YOUR
    ACTION NEEDED) (David Lonie)

Message: 1
Date: Fri, 01 Mar 2013 18:31:25 +0000 (GMT)
From: Marc-Andr? Dubois ma.dubois@me.com
Subject: [Avogadro-devel] painter
To: avogadro-devel@lists.sourceforge.net
Message-ID: a0397907-c880-4694-868e-b952d2d9825e@me.com
Content-Type: text/plain; charset=“utf-8”

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,

Marc
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Message: 2
Date: Fri, 1 Mar 2013 15:53:18 -0500
From: “Marcus D. Hanwell” mhanwell@gmail.com
Subject: Re: [Avogadro-devel] painter
To: Marc-Andr? Dubois ma.dubois@me.com
Cc: avogadro-devel@lists.sourceforge.net
Message-ID:
<
CAMkPkZWexpYx3efMYjnaXgqxFb_cWCY99vzerYuuhJvX11ThVg@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

On Fri, Mar 1, 2013 at 1:31 PM, Marc-Andr? Dubois ma.dubois@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

Message: 3
Date: Fri, 08 Mar 2013 12:57:54 +0100
From: Kirill Okhotnikov kirill.okhotnikov@gmail.com
Subject: [Avogadro-devel] Eigen3 migration
To: avogadro-devel@lists.sourceforge.net
Message-ID: 5139D242.50505@gmail.com
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Dear Avogadro developers,

I want to use Avogadro in my project to visualize molecules and crystal
structures. In my project, I’m using Eigen3 library, so I decide to get
into Avogadro code and change it to support Eigen3 API.

I did step-by-step migration, like described here.
http://eigen.tuxfamily.org/dox/Eigen2SupportModes.html and came to stage
EIGEN2_SUPPORT_STAGE40_FULL_EIGEN3_STRICTNESS, meaning that new code
should follow 100% Eigen3 API, but in old code still function
compatible with eigen2 exists (“eigen2_” prefix)

I have only one part of code, which is not working like before.
computeGeomInfo() in molecule.cpp

In Eigen3 library LeastSquares module was excluded, so I should write
the code for the fitting by myself. The investigation of the code showed
one problematic part.

void Molecule::computeGeomInfo() const
{
…
d->center.setZero();
… //some code not affecting d->center variable

 // compute radius and the farthest atom
 d->radius = std::numeric_limits<double>::min();
 foreach (Atom *atom, m_atomList) {
   double distanceToCenter = (*atom->pos() -

d->center).squaredNorm(); //!!! center is Zero
if(distanceToCenter > d->radius) {
d->radius = distanceToCenter;
d->farthestAtom = atom;
}
}
d->radius = sqrt(d->radius);

     ...... // Calculation of the center after

     // Calculate the center of the molecule too
     foreach (Atom *atom, m_atomList) {
       Vector3d *pos = &(*m_atomPos)[atom->id()];
       d->center += *pos;
       atomPositions[i++] = pos;
     }
     d->center /= static_cast<double>(nAtoms);

     ...

I just want to ask some questions.

  1. Are you interesting in the contribution (eigen2->eigen3).
  2. What should I do with geometry info procedure. Should I change the
    radius calculations.

Best regards,
Kirill.

Message: 4
Date: Tue, 12 Mar 2013 16:35:43 -0400
From: “Marcus D. Hanwell” mhanwell@gmail.com
Subject: [Avogadro-devel] Contributor approval for 3-clause BSD
relicensing (YOUR ACTION NEEDED)
To: Avogadro-devel Devel avogadro-devel@lists.sourceforge.net
Message-ID:
<
CAMkPkZWx9ce+c0rvZJoE15rvvSkqR60bj0DL2f+SQ+Lk1kd78g@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

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/
The Open Chemistry Project | PPT

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,

The 3-Clause BSD License – Open Source Initiative

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

Message: 5
Date: Tue, 12 Mar 2013 16:44:53 -0400
From: “Marcus D. Hanwell” mhanwell@gmail.com
Subject: Re: [Avogadro-devel] Contributor approval for 3-clause BSD
relicensing (YOUR ACTION NEEDED)
To: Avogadro-devel Devel avogadro-devel@lists.sourceforge.net
Message-ID:
<CAMkPkZUGLXB58Akf0H6Zbb02jjVWxnsd7=
hzLGXrbxPB7g5S9w@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

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

Thanks,

Marcus

On Tue, Mar 12, 2013 at 4:35 PM, Marcus D. Hanwell
mhanwell@gmail.com wrote:

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/
The Open Chemistry Project | PPT

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,

The 3-Clause BSD License – Open Source Initiative

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

Message: 6
Date: Tue, 12 Mar 2013 16:48:43 -0400
From: David Lonie david.lonie@kitware.com
Subject: Re: [Avogadro-devel] Contributor approval for 3-clause BSD
relicensing (YOUR ACTION NEEDED)
To: “Marcus D. Hanwell” mhanwell@gmail.com
Cc: Avogadro-devel Devel avogadro-devel@lists.sourceforge.net
Message-ID:
<CA+=
e1osdgeVDHS-4UiCfvThrWZ_VOfTVEkm3Z9oN32A5G3BChQ@mail.gmail.com>
Content-Type: text/plain; charset=“iso-8859-1”

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

(For the sake of clarity, I’ll point out that the XtalOpt extension code is
to remain GPLv2+ unless otherwise noted in the source files – my
relicensing permission extends only to code which I have directly
contributed to the Avogadro repository.).

Dave

On Tue, Mar 12, 2013 at 4:35 PM, Marcus D. Hanwell <
mhanwell@gmail.com> wrote:

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/
The Open Chemistry Project | PPT

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,

The 3-Clause BSD License – Open Source Initiative

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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Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
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End of Avogadro-devel Digest, Vol 77, Issue 1

–
Matthew Kennedy
matthew.kennedy.6@gmail.com
Ph. D. Candidate, Sherrill Group
Georgia Institute of Technology
404-376-0969