Re: [Avogadro-devel] Google Summer of Code 2018 - GPU Accelerated Calculation of Molecular Surfaces and QM Data

[Geoffrey Hutchison]

Dear Tony,

Great to hear from you. Yes, I think it's important for the project to have 
some background in both programming and computational chemistry (e.g., knowing 
why you'd care about molecular surfaces, MOs, electron density, etc.)

Beyond that, if you're interested, I encourage you to write a draft and we'd be 
happy to provide some feedback.

I'd suggest you read the papers linked on the wiki and look at the application 
instructions:
http://wiki.openchemistry.org/Applying_to_GSoC 


I'd encourage you to consider a few concerns in the proposal. Right know, there 
are a few competing GPU techniques (e.g., OpenCL, Vulkan, CUDA, DirectX, 
Metal). What technology would provide the best cross-platform experience? How 
do you fall back to a multi-core CPU if the GPU isn't compatible? Are there 
ways of approximating some of the Gaussian integrals for visualization purposes 
(e.g. losing some accuracy but close enough for pixels)?

I would also encourage you to build Avogadro2 and consider submitting a small 
patch to GitHub as a way to get up-to-speed on the code.
http://wiki.openchemistry.org/Build

Hope that helps,
-Geoff

---
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web: https://hutchison.chem.pitt.edu/

> On Mar 8, 2018, at 10:52 AM, Yang, Tony  wrote:
> 
> Dear Geofrrey,
>  
> Greetings!
>  
> I am a final year chemistry student at Imperial College London, UK. After 
> learning some Python in my first two years of undergraduate study, I became 
> interested in programming, and self-taught some deeper programming knowledge. 
> I have been interested in GPU programming for a while now but only done some 
> superficial reading around it.
>  
> I did a computational chemistry summer project last year in Prof. Kendall 
> Houk’s lab. I used Gaussian for energy optimisation and calculations, and the 
> ability to visualise MOs does help chemists understanding interactions much 
> better.
>  
> Do you think I will be suitable for this GPU Accelerated Calculation of 
> Molecular Surfaces and QM Data project? If so, I will draft a proposal very 
> soon.
>  
> Best wishes,
> Tony
>  
> ·Name: Zeyu Tony Yang
> ·Email: zy2...@ic.ac.uk 
> ·Country & timezone: UK, GMT +0
> ·School Name & Study: Imperial College London, Chemistry, Year 4 
> (Final year)

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Re: [Avogadro-devel] [Google Summer Of Code 2016] Project Interest

[Geoffrey Hutchison]

Some level of chemistry would be extremely useful. The project you mention 
likely requires less chemistry knowledge, since embedding a Python scripting 
interpreter in the code requires more coding competence than chemistry 
background. However, a competitive proposal would likely require some example 
scripts useful to end-users.

I have mentioned to several students interested in the scripting bindings 
project that there are many approaches (e.g., Boost.Python, SIP / PyQt, SWIG, 
etc.) Some are collected here by the Cython project:
https://github.com/cython/cython/wiki/WrappingCorCpp

I think the most competitive proposals for this topic should take a simple demo 
program, ideally in Qt5 (like a Qt5 demo) and embed a Python scripting console 
using one of these techniques. The proposals should suggest some pro and cons 
for the different techniques and how you (the student doing the project) will 
evaluate the approaches.

Hope that helps,
-Geoff


> On Mar 9, 2016, at 1:37 AM, Allen Antony  wrote:
> 
> 
> Hey, 
> 
> My name is Allen Antony and I am a sophomore student from International 
> Institute Of Information Technology (IIIT) ,Hyderabad ,India. I am currently 
> pursuing Btech in Computer Science.
> 
> I was browsing through the Ideas list and found out that Scripting 
> Bindings(Avogadro 2) is something that I might be interested in.
> 
> 
> I have been coding in C++ ever since I was 15 and I love coding in it. Apart 
> from C++ I am proficient in other languages like Python ,Ruby , JavaScript ,C 
> , C# and Lua. Also I am very comfortable in OpenGL and have made few games 
> using it as part of academic projects (and also as a hobby). 
> 
> I am confused about the amount of knowledge in chemistry required for these 
> projects because apart from my schooling I have no experience in the field of 
> chemistry. But I hope my coding skills will more than compensate for my lack 
> of knowledge in chemistry.
>  
> Although Avogadro 2 is new to me ,I am always eager to learn. Please guide me 
> as to what my next move should be. I am itching to get my hands on some code 
> and hit the ground running right away !
> 
> Hoping to hear from you soon :)
> 
> Regards,
> Allen Antony

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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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Re: [Avogadro-devel] Google Summer of Code

[Karol Langner]

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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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] Google Summer of Code

[Geoffrey Hutchison]

 Personally, I'd like to see more interoperability between the
 open-source chemistry apps, including avogadro, openbabel and cclib

Indeed, I think one big push is for Avogadro v2 to use cclib to read QM file 
formats (e.g., MO coefficients, basis set, etc.) rather than implementing them 
all in C++.

As for Open Babel and cclib, I think some of that is simply a matter of not 
repeating the wheel - i.e., leaving QM-specific data in cclib, but certainly a 
lot more is important here.

I think these are good ideas. I’ll go create a wiki page somewhere to start 
storing some of them.

-Geoff

P.S. I don’t think it would be hard for Avogadro as a whole to get approved, 
since we’ve had 3 students working on Avogadro-related code in previous years. 
I do agree that an umbrella organization might be helpful.
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