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, <
[email protected]> wrote:
> Send Avogadro-devel mailing list submissions to
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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 <[email protected]>
> Subject: [Avogadro-devel] painter
> To: [email protected]
> Message-ID: <[email protected]>
> 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
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 2
> Date: Fri, 1 Mar 2013 15:53:18 -0500
> From: "Marcus D. Hanwell" <[email protected]>
> Subject: Re: [Avogadro-devel] painter
> To: Marc-Andr? Dubois <[email protected]>
> Cc: [email protected]
> Message-ID:
> <
> camkpkzwexpyx3efmyjnaxgqxfb_cwcy99vzeryuuhjvx11t...@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Fri, Mar 1, 2013 at 1:31 PM, Marc-Andr? Dubois <[email protected]>
> 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 <[email protected]>
> Subject: [Avogadro-devel] Eigen3 migration
> To: [email protected]
> Message-ID: <[email protected]>
> 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" <[email protected]>
> Subject: [Avogadro-devel] Contributor approval for 3-clause BSD
> relicensing (YOUR ACTION NEEDED)
> To: Avogadro-devel Devel <[email protected]>
> Message-ID:
> <
> camkpkzwx9ce+c0rvzjoe15rvvskqr60bj0dl2f+sq+lk1kd...@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/
> 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
>
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 12 Mar 2013 16:44:53 -0400
> From: "Marcus D. Hanwell" <[email protected]>
> Subject: Re: [Avogadro-devel] Contributor approval for 3-clause BSD
> relicensing (YOUR ACTION NEEDED)
> To: Avogadro-devel Devel <[email protected]>
> Message-ID:
> <CAMkPkZUGLXB58Akf0H6Zbb02jjVWxnsd7=
> [email protected]>
> 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
> <[email protected]> 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/
> > 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
>
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 12 Mar 2013 16:48:43 -0400
> From: David Lonie <[email protected]>
> Subject: Re: [Avogadro-devel] Contributor approval for 3-clause BSD
> relicensing (YOUR ACTION NEEDED)
> To: "Marcus D. Hanwell" <[email protected]>
> Cc: Avogadro-devel Devel <[email protected]>
> Message-ID:
> <CA+=
> [email protected]>
> 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 <
> [email protected]> 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/
> > 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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> > Avogadro-devel mailing list
> > [email protected]
> > https://lists.sourceforge.net/lists/listinfo/avogadro-devel
> >
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> 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
[email protected]
Ph. D. Candidate, Sherrill Group
Georgia Institute of Technology
404-376-0969
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