cclib-devel Mailing List for cclib

Hi there!

I'm new to cclib, and enjoying it so far! It's a powerful tool. I wanted to
ask the community if you've worked on functions that would extract
particular distance, angle, or dihedral measurements (I need dihedrals for
my particular problem). I could read in the atomcoords and calculate them
myself, but I wanted to check if something else is available.

Regards,
Tyler

-- 
Tyler Josephson
PhD Chemical Engineering
Postdoctoral Research Associate, Siepmann Group
University of Minnesota, Twin Cities
651-269-1433 |  | LinkedIn <" rel="nofollow">https://www.linkedin.com/in/trjosephson/>

The timing is convenient for me, since I have a lot more free time. Aside
from the general 1.5.3 label, is there anything that should be prioritized?

On Wed, Mar 28, 2018 at 1:56 AM, Karol Langner <kar...@gm...>
wrote:

> Hi all,
>
> It's been a while since the last release again, and I want to get it out
> before GSOC starts. I've set the release to April 22 (just before
> announcing who the students are). The release might be off of that by a day
> or two, but I'd like to finalize it around that time.
>
> So, let's try to get as much in as we can for v1.5.3!
>
> Karol
>
> P. S. And, of course, I want to do another release right after GSOC ends,
> assuming there is a student.
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
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>
>

Nothing in particular comes to mind. We can try to narrow down what we
think is possible to do in 3 weeks, and move everything else to 1.5.4. We
should also take a look if it's time to go to v1.6. - typically this
happens if there is a new parser or major addition to methods or similar
thing.

On Fri, Mar 30, 2018 at 4:41 PM, Eric Berquist <er...@pi...> wrote:

> The timing is convenient for me, since I have a lot more free time. Aside
> from the general 1.5.3 label, is there anything that should be prioritized?
>
> On Wed, Mar 28, 2018 at 1:56 AM, Karol Langner <kar...@gm...>
> wrote:
>
>> Hi all,
>>
>> It's been a while since the last release again, and I want to get it out
>> before GSOC starts. I've set the release to April 22 (just before
>> announcing who the students are). The release might be off of that by a day
>> or two, but I'd like to finalize it around that time.
>>
>> So, let's try to get as much in as we can for v1.5.3!
>>
>> Karol
>>
>> P. S. And, of course, I want to do another release right after GSOC ends,
>> assuming there is a student.
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! https://na01.safelinks.protect
>> ion.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=
>> 01%7C01%7Cerb74%40pitt.edu%7C5cab2e4174ff4e05ea3f08d59470b58
>> 4%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=ynrjNxlL51L5o
>> u5%2BprRiTswTVAFhsl%2BZ0ZOMm935OQc%3D&reserved=0
>> _______________________________________________
>> cclib-devel mailing list
>> ccl...@li...
>> https://na01.safelinks.protection.outlook.com/?url=https%3A%
>> 2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fcclib-
>> devel&data=01%7C01%7Cerb74%40pitt.edu%7C5cab2e4174ff4e05e
>> a3f08d59470b584%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&
>> sdata=uwRN0SaLW%2FMfnVBJ32jEw01u8eMtqP7jiZ1c5oxxTx0%3D&reserved=0
>>
>>
>

Hello everyone!

I am a Chemical Engineering Student based in Argentina. I am Open Source enthusiast and I did programming in python for different research projects. I'm also working as a Teaching Assistant, teaching python to young Chemical Engineering Students.

I presented a project for the Google Summer of Code for about implementing AIM into cclib . (So fingers crossed). It's a shame that I didn't have the time to send the project o the list, so i could get your recommendations, however I got wonderful help from Karol Langer and Adam Tenderholt. So I hope that I would be able to do some development in cclib.


Best regards,

Agustin Ferrario

Hi all,

It's been a while since the last release again, and I want to get it out
before GSOC starts. I've set the release to April 22 (just before
announcing who the students are). The release might be off of that by a day
or two, but I'd like to finalize it around that time.

So, let's try to get as much in as we can for v1.5.3!

Karol

P. S. And, of course, I want to do another release right after GSOC ends,
assuming there is a student.

Hi Alok,

That's a nice first hack. Here are some questions you can consider.
1. How do you actually discover content online - I mean, we know NIST and
Pitt exist, a crawler should be able to also find new sources we did not
know about before.
2. Do you want to write a crawler for each repository out there (NIST,
Pitt, ...)?
3. When you rerun the crawler, do you need to go over the whole repo again?

Also, I'd encourage you to read through PEP8 (
https://www.python.org/dev/peps/pep-0008/) and try to apply it to the code
you write.

- Karol


On Tue, Mar 20, 2018 at 2:38 AM, Alok Kumar <alo...@gm...> wrote:

> *cclib project - Discovering computational chemistry content online*
>
> I was looking for databases to crawl logfiles and came across NIST database
> https://cccbdb.nist.gov/output.asp (edited)
> I wrote a crawler script in python to fetch the Gaussian input/output
> logfiles.
> https://github.com/DCoderGH/ccNIST-crawler
> [Use Python2]
> It not well documented yet but will add comments soon.
> Please have a look and share some feedback.
>
> I am not fully aware of the policies for crawling NIST databases.
> Also, do let me know about any open other databases which can be mined.
>
> -Alok
> `
>
> On Tue, Mar 6, 2018 at 10:53 PM, Karol Langner <kar...@gm...>
> wrote:
>
>> Hi Alok,
>>
>> No specific issue comes to mind at the moment, you can peruse the various
>> bugs we have filed at https://github.com/cclib/cclib/issues
>>
>> An idea for pre-project work: you could try to write a simplistic parser
>> and try to get it to crawl the github repository and find out test files.
>>
>> As far as the application is concerned, I would suggest putting a lot of
>> focus on what the project would achieve. For example, can you estimate the
>> number of logfiles out there you expect to find with the crawler?
>>
>>
>> On Tue, Mar 6, 2018 at 7:01 AM, Alok Kumar <alo...@gm...> wrote:
>>
>>> #cclib  #parser-crawler
>>>
>>> Hello. Had been busy with my mid-semester exams .
>>> Looked into various parser codes.
>>> I wanted to ask what should I start working upon - any specific issue in
>>> parser or building a crawler...
>>>
>>> Regards,
>>> Alok
>>>
>>> On Tue, Feb 20, 2018 at 9:38 PM, Karol Langner <kar...@gm...>
>>> wrote:
>>>
>>>> Done.
>>>>
>>>> On Tue, Feb 20, 2018 at 8:01 AM, ALOK KUMAR <alo...@gm...>
>>>> wrote:
>>>>
>>>>> I wanted to join the slack channel to follow the discussion .Can you
>>>>> please send Open Chemistry slack invite to my email
>>>>> alo...@gm...
>>>>>
>>>>> Regards,
>>>>> Alok
>>>>>
>>>>> On Tue, Feb 20, 2018 at 10:48 AM, Karol Langner <
>>>>> kar...@gm...> wrote:
>>>>>
>>>>>> Hi Alok,
>>>>>>
>>>>>> Good to hear from you. I don't think a deep understanding of
>>>>>> computational chemistry or web crawling is a prerequisite, but of course it
>>>>>> would be an advantage. You need to be familiar enough with these subjects
>>>>>> to be able to propose a project plan that would deliver results during the
>>>>>> summer. The only way we can judge this is your proposal and any
>>>>>> contributions you make before the application period.
>>>>>>
>>>>>> I would mention that this project is a little more research-y than
>>>>>> most others. You'll need to design a crawler/scraper that is appropriate
>>>>>> for this application, and figure what gaps need to be filled in in the
>>>>>> existing codebase.
>>>>>>
>>>>>> Let us know if you have any other questions
>>>>>>
>>>>>> - Karol
>>>>>>
>>>>>>
>>>>>> On Mon, Feb 19, 2018 at 1:09 PM, ALOK KUMAR <alo...@gm...>
>>>>>> wrote:
>>>>>>
>>>>>>> Hello everyone.
>>>>>>>     I am Alok , a second year undergraduate at Indian Institute of
>>>>>>> Technology Bombay , India. I have interest in computational chemistry and
>>>>>>> had taken up a course this semester in my college.
>>>>>>>
>>>>>>> Among the GSoC-2018 ideas I found projects under cclib quite
>>>>>>> interesting, particularly  ##Discovering computational chemistry content
>>>>>>> online##
>>>>>>>
>>>>>>> I am familiar with web scraping using BeautifulSoup and urllib in
>>>>>>> Python and had recently started looking into Scrapy as well.
>>>>>>>
>>>>>>> I wanted to know how much understanding / familiarity is expected
>>>>>>> for contributing to this project . Also,(if required) is deeper
>>>>>>> understanding of computational chemistry or advanced web crawling a
>>>>>>> prerequisite or can it be worked upon during the initial Coding phase of
>>>>>>> GSoC.
>>>>>>>
>>>>>>> Looking ahead to staying in touch with the Open Chemistry community.
>>>>>>>
>>>>>>> Regards,
>>>>>>>
>>>>>>> Alok Kumar
>>>>>>> alo...@gm...
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Openchemistry-developers mailing list
>>>>>>> Ope...@pu...
>>>>>>> https://public.kitware.com/mailman/listinfo/openchemistry-developers
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

That's right, forgot about that! (learned about it last year)

On Fri, Mar 16, 2018 at 6:04 AM, Adam Tenderholt <ate...@gm...>
wrote:

> It looks like MOLCAS is now (mostly?) open-source: https://gitlab.
> com/Molcas/OpenMolcas.
>
>
> On Fri, Mar 16, 2018 at 5:26 AM Kunal Sharma <ks0...@gm...> wrote:
>
>> Hello,
>>
>> I think it would be great if you can get in touch with the devs at
>> MOLCAS. Meanwhile I will look into the work Eric has done and get a first
>> draft for proposal up for review before the weekend.
>>
>> Thank you.
>>
>> Regards,
>> Kunal Sharma
>> _______________________________________________
>> Openchemistry-developers mailing list
>> Ope...@pu...
>> https://public.kitware.com/mailman/listinfo/openchemistry-developers
>>
>

It looks like MOLCAS is now (mostly?) open-source:
https://gitlab.com/Molcas/OpenMolcas.


On Fri, Mar 16, 2018 at 5:26 AM Kunal Sharma <ks0...@gm...> wrote:

> Hello,
>
> I think it would be great if you can get in touch with the devs at MOLCAS.
> Meanwhile I will look into the work Eric has done and get a first draft for
> proposal up for review before the weekend.
>
> Thank you.
>
> Regards,
> Kunal Sharma
> _______________________________________________
> Openchemistry-developers mailing list
> Ope...@pu...
> https://public.kitware.com/mailman/listinfo/openchemistry-developers
>

If we want to go after MOLCAS seriously, we could contact the devs there
and ask for an evaluation version or them to generate files with the most
recent version.

On Thu, Mar 15, 2018, 7:17 AM Eric Berquist <er...@pi...> wrote:

> Hi Kunal,
>
> I started work on the Molcas parser several years ago when I was trying to
> use Molcas for some of my work. Unfortunately, it looks like I deleted the
> branch but kept all the work and some initial inputs/outputs in a patch:
>
> https://git.io/vxLjf
>
> I think some basic things were working, so it might be a good starting
> point, at least for the calculations it contains.
>
> Eric
>
> On Thu, Mar 15, 2018 at 3:33 AM, Kunal Sharma <ks0...@gm...>
> wrote:
>
>>
>> This sender failed our fraud detection checks and may not be who they appear to be. Learn about
>> spoofing <" rel="nofollow">http://aka.ms/LearnAboutSpoofing>
>> Feedback <" rel="nofollow">http://aka.ms/SafetyTipsFeedback>
>> Hey Karol,
>>
>> Thanks for the reply. I understand and will make sure that I choose a
>> project which I am most confident in completing in this GSoC term.
>>
>> Additionally, I will make sure to select relevant softwares and show
>> proper time-line about the implementation of their parsers.
>>
>> Regarding https://github.com/cclib/cclib/issues/191
>> <," rel="nofollow">https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fcclib%2Fcclib%2Fissues%2F191&data=01%7C01%7Cerb74%40pitt.edu%7C43856b33cc2d4561e00608d58a470d23%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=5yfZpDNuTZkvHKFImuzH3oiFeea2ZTRsDykp5AxI7yo%3D&reserved=0>,
>> can someone please send me an output file for MOLCAS so that I may be able
>> to go through it and see how I would go about implementing its parser.
>>
>> Thanks a lot.
>>
>> Regards,
>> Kunal Sharma
>>
>>
>>
>>
>>
>> ‌
>>
>> On Wed, Mar 14, 2018 at 9:09 PM, Karol Langner <kar...@gm...>
>> wrote:
>>
>>> Hi Kunal,
>>>
>>> First of all, I need to say that bunching projects together will not
>>> necessarily increase your chances. We would much prefer to get one high
>>> quality project that will be finished comprehensively, than 2-3 projects
>>> with minimal implementations. I think there is enough room for a whole
>>> summer's worth of coding for all of these projects. So we might be
>>> concerned whether you can take on that much work.
>>>
>>> For new parsers, there are at least two active issues for cclib
>>> concerned with new parsers: https://github.com/cclib/cclib/issues/180
>>> <" rel="nofollow">https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fcclib%2Fcclib%2Fissues%2F180&data=01%7C01%7Cerb74%40pitt.edu%7C43856b33cc2d4561e00608d58a470d23%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=3yegMDS6hNmiFas1Si61Sj9goBhvrAyJye6eAgP9Yig%3D&reserved=0>
>>> and https://github.com/cclib/cclib/issues/191
>>> <." rel="nofollow">https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fcclib%2Fcclib%2Fissues%2F191&data=01%7C01%7Cerb74%40pitt.edu%7C43856b33cc2d4561e00608d58a470d23%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=5yfZpDNuTZkvHKFImuzH3oiFeea2ZTRsDykp5AxI7yo%3D&reserved=0>.
>>> Please also do you own research about what programs you think would be good
>>> to parse. A reasonable place to start would be, for example, the Wikipedia
>>> page listing computation chemistry programs. We'd be most interested,
>>> probably, in programs that support Hartree-Fock and post-HF methods:
>>> https://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_solid-state_physics_software
>>> <" rel="nofollow">https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FList_of_quantum_chemistry_and_solid-state_physics_software&data=01%7C01%7Cerb74%40pitt.edu%7C43856b33cc2d4561e00608d58a470d23%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=uqpUQFTWQM8%2BWdtGVc0ssixRJBgLRIbhiMvbFcNF98A%3D&reserved=0>
>>>
>>> HTH,
>>> Karol
>>>
>>>
>>> On Tue, Mar 13, 2018 at 8:26 PM, Kunal Sharma <ks0...@gm...>
>>> wrote:
>>>
>>>> Hello mentors,
>>>>
>>>> I have created a pull request for cclib issue #452 and have started to
>>>> work on my proposal for the following topics:
>>>> 1. Implement New Parsers
>>>> 2.Implement QC JSON schema in cclib
>>>> 3. Advanced Analysis of Quantum Chemistry data
>>>>
>>>>
>>>>
>>>> *I want to club 2 out of th 3 above mentioned topics as my project for
>>>> GSoC 2018. *
>>>>
>>>>
>>>> *I have the following queries I need your help with. *
>>>> 1. What new parsers are we looking at to implement?
>>>> 2. Can I club together two topics? I think working for about 35-40
>>>> hours a week will be give me enough time to implement two topics.
>>>> 3. What is the exact end goal for the QC JSON schema project?
>>>> 4. Along with the proposal what other work can I begin that will help
>>>> the chances of my proposal being selected?
>>>>
>>>> I have started work on my proposal and will get the first draft (for
>>>> you to look through) ready in a few days.
>>>>
>>>> Thank you.
>>>>
>>>> Yours truly,
>>>> Kunal Sharma
>>>>
>>>>
>>>> ‌
>>>>
>>>> _______________________________________________
>>>> Openchemistry-developers mailing list
>>>> Ope...@pu...
>>>> https://public.kitware.com/mailman/listinfo/openchemistry-developers
>>>> <" rel="nofollow">https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpublic.kitware.com%2Fmailman%2Flistinfo%2Fopenchemistry-developers&data=01%7C01%7Cerb74%40pitt.edu%7C43856b33cc2d4561e00608d58a470d23%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=pV5K%2B1eegTySkiqZMP140wxuCv9qAMroFYL5o9Tt0ug%3D&reserved=0>
>>>>
>>>>
>>>
>>
>> _______________________________________________
>> Openchemistry-developers mailing list
>> Ope...@pu...
>>
>> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpublic.kitware.com%2Fmailman%2Flistinfo%2Fopenchemistry-developers&data=01%7C01%7Cerb74%40pitt.edu%7C43856b33cc2d4561e00608d58a470d23%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=pV5K%2B1eegTySkiqZMP140wxuCv9qAMroFYL5o9Tt0ug%3D&reserved=0
>>
>>
>

Hi Kunal,

I started work on the Molcas parser several years ago when I was trying to
use Molcas for some of my work. Unfortunately, it looks like I deleted the
branch but kept all the work and some initial inputs/outputs in a patch:

https://git.io/vxLjf

I think some basic things were working, so it might be a good starting
point, at least for the calculations it contains.

Eric

On Thu, Mar 15, 2018 at 3:33 AM, Kunal Sharma <ks0...@gm...> wrote:

> This sender failed our fraud detection checks and may not
> be who they appear to be. Learn about spoofing
> <" rel="nofollow">http://aka.ms/LearnAboutSpoofing>
> Feedback <" rel="nofollow">http://aka.ms/SafetyTipsFeedback>
> Hey Karol,
>
> Thanks for the reply. I understand and will make sure that I choose a
> project which I am most confident in completing in this GSoC term.
>
> Additionally, I will make sure to select relevant softwares and show
> proper time-line about the implementation of their parsers.
>
> Regarding https://github.com/cclib/cclib/issues/191
> <," rel="nofollow">https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fcclib%2Fcclib%2Fissues%2F191&data=01%7C01%7Cerb74%40pitt.edu%7C43856b33cc2d4561e00608d58a470d23%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=5yfZpDNuTZkvHKFImuzH3oiFeea2ZTRsDykp5AxI7yo%3D&reserved=0>,
> can someone please send me an output file for MOLCAS so that I may be able
> to go through it and see how I would go about implementing its parser.
>
> Thanks a lot.
>
> Regards,
> Kunal Sharma
>
>
>
>
>
> ‌
>
> On Wed, Mar 14, 2018 at 9:09 PM, Karol Langner <kar...@gm...>
> wrote:
>
>> Hi Kunal,
>>
>> First of all, I need to say that bunching projects together will not
>> necessarily increase your chances. We would much prefer to get one high
>> quality project that will be finished comprehensively, than 2-3 projects
>> with minimal implementations. I think there is enough room for a whole
>> summer's worth of coding for all of these projects. So we might be
>> concerned whether you can take on that much work.
>>
>> For new parsers, there are at least two active issues for cclib concerned
>> with new parsers: https://github.com/cclib/cclib/issues/180
>> <" rel="nofollow">https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fcclib%2Fcclib%2Fissues%2F180&data=01%7C01%7Cerb74%40pitt.edu%7C43856b33cc2d4561e00608d58a470d23%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=3yegMDS6hNmiFas1Si61Sj9goBhvrAyJye6eAgP9Yig%3D&reserved=0>
>> and https://github.com/cclib/cclib/issues/191
>> <." rel="nofollow">https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fcclib%2Fcclib%2Fissues%2F191&data=01%7C01%7Cerb74%40pitt.edu%7C43856b33cc2d4561e00608d58a470d23%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=5yfZpDNuTZkvHKFImuzH3oiFeea2ZTRsDykp5AxI7yo%3D&reserved=0>.
>> Please also do you own research about what programs you think would be good
>> to parse. A reasonable place to start would be, for example, the Wikipedia
>> page listing computation chemistry programs. We'd be most interested,
>> probably, in programs that support Hartree-Fock and post-HF methods:
>> https://en.wikipedia.org/wiki/List_of_quantum_chemi
>> stry_and_solid-state_physics_software
>> <" rel="nofollow">https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FList_of_quantum_chemistry_and_solid-state_physics_software&data=01%7C01%7Cerb74%40pitt.edu%7C43856b33cc2d4561e00608d58a470d23%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=uqpUQFTWQM8%2BWdtGVc0ssixRJBgLRIbhiMvbFcNF98A%3D&reserved=0>
>>
>> HTH,
>> Karol
>>
>>
>> On Tue, Mar 13, 2018 at 8:26 PM, Kunal Sharma <ks0...@gm...>
>> wrote:
>>
>>> Hello mentors,
>>>
>>> I have created a pull request for cclib issue #452 and have started to
>>> work on my proposal for the following topics:
>>> 1. Implement New Parsers
>>> 2.Implement QC JSON schema in cclib
>>> 3. Advanced Analysis of Quantum Chemistry data
>>>
>>>
>>>
>>> *I want to club 2 out of th 3 above mentioned topics as my project for
>>> GSoC 2018. *
>>>
>>>
>>> *I have the following queries I need your help with. *
>>> 1. What new parsers are we looking at to implement?
>>> 2. Can I club together two topics? I think working for about 35-40 hours
>>> a week will be give me enough time to implement two topics.
>>> 3. What is the exact end goal for the QC JSON schema project?
>>> 4. Along with the proposal what other work can I begin that will help
>>> the chances of my proposal being selected?
>>>
>>> I have started work on my proposal and will get the first draft (for you
>>> to look through) ready in a few days.
>>>
>>> Thank you.
>>>
>>> Yours truly,
>>> Kunal Sharma
>>>
>>>
>>> ‌
>>>
>>> _______________________________________________
>>> Openchemistry-developers mailing list
>>> Ope...@pu...
>>> https://public.kitware.com/mailman/listinfo/openchemistry-developers
>>> <" rel="nofollow">https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpublic.kitware.com%2Fmailman%2Flistinfo%2Fopenchemistry-developers&data=01%7C01%7Cerb74%40pitt.edu%7C43856b33cc2d4561e00608d58a470d23%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=pV5K%2B1eegTySkiqZMP140wxuCv9qAMroFYL5o9Tt0ug%3D&reserved=0>
>>>
>>>
>>
>
> _______________________________________________
> Openchemistry-developers mailing list
> Ope...@pu...
> https://na01.safelinks.protection.outlook.com/?url=
> https%3A%2F%2Fpublic.kitware.com%2Fmailman%2Flistinfo%
> 2Fopenchemistry-developers&data=01%7C01%7Cerb74%40pitt.edu%
> 7C43856b33cc2d4561e00608d58a470d23%7C9ef9f489e0a04eeb87cc3a526112
> fd0d%7C1&sdata=pV5K%2B1eegTySkiqZMP140wxuCv9qAMroFYL5o9Tt0ug%3D&reserved=0
>
>

Hi Kunal,

First of all, I need to say that bunching projects together will not
necessarily increase your chances. We would much prefer to get one high
quality project that will be finished comprehensively, than 2-3 projects
with minimal implementations. I think there is enough room for a whole
summer's worth of coding for all of these projects. So we might be
concerned whether you can take on that much work.

For new parsers, there are at least two active issues for cclib concerned
with new parsers: https://github.com/cclib/cclib/issues/180 and
https://github.com/cclib/cclib/issues/191. Please also do you own research
about what programs you think would be good to parse. A reasonable place to
start would be, for example, the Wikipedia page listing computation
chemistry programs. We'd be most interested, probably, in programs that
support Hartree-Fock and post-HF methods:
https://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_solid-state_physics_software

HTH,
Karol


On Tue, Mar 13, 2018 at 8:26 PM, Kunal Sharma <ks0...@gm...> wrote:

> Hello mentors,
>
> I have created a pull request for cclib issue #452 and have started to
> work on my proposal for the following topics:
> 1. Implement New Parsers
> 2.Implement QC JSON schema in cclib
> 3. Advanced Analysis of Quantum Chemistry data
>
>
>
> *I want to club 2 out of th 3 above mentioned topics as my project for
> GSoC 2018.*
>
>
> *I have the following queries I need your help with.*
> 1. What new parsers are we looking at to implement?
> 2. Can I club together two topics? I think working for about 35-40 hours a
> week will be give me enough time to implement two topics.
> 3. What is the exact end goal for the QC JSON schema project?
> 4. Along with the proposal what other work can I begin that will help the
> chances of my proposal being selected?
>
> I have started work on my proposal and will get the first draft (for you
> to look through) ready in a few days.
>
> Thank you.
>
> Yours truly,
> Kunal Sharma
>
>
> ‌
>
> _______________________________________________
> Openchemistry-developers mailing list
> Ope...@pu...
> https://public.kitware.com/mailman/listinfo/openchemistry-developers
>
>

Hi Yue,

This is project is definitely about training an algo to extract data from
the text output files, not replacing the calculation method in programs.
There has been a bunch of work on the latter in the literature, and
although I am not averse to a project in that area it's not what I had in
mind. If you would like to propose a project that would predict molecular
properties or whatever, you're welcome to do that, but keep in mind it
should be a coding project, not a research-only thing.

If you would like to keep to the original intent for this project, then
it's like you said, using the text of the output file as input and the data
cclib extracts as output. In other words, can we train a model to extract
the data we want without writing a parser? As an example, we'd like to just
feed the logfile and get number of atoms, SCF energies, etc. To be honest,
I'm not sure what approach would be best or than anything would work well,
but the project is about exploring what can be done. We would expect you to
suggest several models and a procedure to evaluate them.

HTH,
Karol


On Fri, Mar 9, 2018 at 6:06 AM, Yue Wang <ywa...@jh...> wrote:

> Dear Karol,
>
>
> Thanks for your message and it helps a lot!
>
>
> I find cclib is really a huge project and I have some new questions about
> the machine learning part.
>
>
> First, the issues listed on Github are all about previous projects(i.e.,
> debug, maintainace). I've downloaded the cclib and read some of the
> python scripts. But I think  this kind of work needs great knowledge of
> target programs like ADF or ORCA. Thus, it might be difficult for me to
> solve them and I was wondering if you could list some machine learning
> tasks for student like me to work on.
>
>
> As you mentioned before, this machine learning project is brand new. So
> what's your expectation for it?(I've visited the GSOC website but the ideas
> list comes without details.) To be more specific, what's the predictor?
> and what's the target?  I think we cannot avoid reading the output files If
> we want to parse the logfiles. My plan is to set the numbers in the
> output files as predictor and the numbers in the parsed files as target.
> Furthermore, we can even use machine learning techniques to replace the
> calculation methods.
>
>
> Thanks again and I'm looking forward to hearing from you soon!
>
>
> Best,
>
> Yue
>
>
>
>
>
>
> ------------------------------
> *From:* Karol Langner <kar...@gm...>
> *Sent:* Sunday, February 25, 2018 9:49:02 AM
> *To:* Yue Wang
> *Cc:* openchemistry-developers public.kitware.com; cclib-dev List
> *Subject:* Re: Interested in Machine learning applied to parsing
> computational chemistry output
>
> Hi Yue,
>
> CC'ing relevant mailing lists.
>
> Nice to hear from you. To get started, I would recommend taking a look
> around the cclib repository (https://github.com/cclib/cclib) and docs (
> https://cclib.github.io/how_to_parse.html). The docs are not perfect, but
> give a reasonable overview (of course, please tell us what to improve). If
> you feel like digging into some contributions, feel free to send a pull
> request on GitHub or to peruse our current list of bugs and issues (
> https://github.com/cclib/cclib/issues).
> How to parse and write — cclib 1.5 documentation
> <" rel="nofollow">https://cclib.github.io/how_to_parse.html>
> cclib.github.io
> How to parse and write¶ The cclib package provides three scripts to parse
> and write data i.e. ccget, ccwrite, and cda. ccget is used to parse
> attribute data from ...
>
> GitHub - cclib/cclib: Parsers and algorithms for ...
> <" rel="nofollow">https://github.com/cclib/cclib>
> github.com
> cclib - Parsers and algorithms for computational chemistry logfiles
>
>
> As far as the ML project is concerned, it would somewhat more research-y
> than the other projects, simply because we haven't really tried to do this
> before. We would expect a student to independently survey what approaches
> would be reasonable, and define the metrics/assumption that can be applied.
>
> Hope that helps somewhat, don't hesitate to ask more questions.
>
> - Karol
>
>
> On Sat, Feb 24, 2018 at 4:48 AM, Yue Wang <ywa...@jh...> wrote:
>
> Hi Karol,
>
>
> I am a student at Johns Hopkins University and I am interested in your
> project idea: Machine learning applied to parsing computational chemistry
> output.
>
> I've experience with Python and Machine Learning and participated in
> Kaggle competition and UW's Data Science Incubator program. Also, I
> worked with Prof. Xiao Gu during my undergrad to do DFT calculation and
> participated in a project exploring alkali-resistant mechanism of a
> Hollandite deNOx catalyst, which was published on Environ. Sci. Technol in
> 2015.
>
> But I'm new to open source project and I do not know how to work with cclib
> to make some contribution. Could you give me some guide?
>
> Thanks!
>
> Best,
> Yue
>
>
>
>

Hi Tony,

Nice to hear from you. CC'ing two relevant mailing lists.

The ML project might be a bit of a stretch for you, unless you know you can
handle a lot of learning on the fly along with the coding. This particular
project is going to be research-y since we don't really know what will work
(if anything). We expect the student to suggest and explore possible
approaches that are worth trying in this area. So, I would say it's doable,
just depends on how much effort you're willing to put in. The application
needs to convince us there are enough options to try during the summer that
something useful could come out of it.

For the crawler project, the idea is to discover as many compchem logfiles
online as possible, and parse the data out of them. The proposal should at
a minimum cover data discovery, classifying documents as potential compchem
logfiles, and, well, parsing them finally. I think this project needs a
solid design of the process, since there will be challenges with scale. It
would be natural to connect this also with a system that provides access to
the search results, maybe some existing repository/database of compchem
results that already exists.

HTH
- Karol


On Thu, Mar 8, 2018 at 9:47 AM, Yang, Tony <zey...@im...>
wrote:

> Dear Karol,
>
>
>
> 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.
>
>
>
> Last summer, I did a computational organic chemistry research project in
> Prof. Kendall Houk’s lab in UCLA. During this project, I used Gaussian for
> geometry optimisations and energy calculations. And I remember the need for
> additional Python scripts to extract thermodynamic data from Gaussian’s
> output file. This was a tedious task to do and I really appreciate cclib’s
> effort in interpreting a range of computational chemistry softwares’ output.
>
>
>
> I am interested in the ‘Machine learning applied to parsing computational
> chemistry output’ project you proposed. But I only have minimum machine
> learning experience (I have tried Tensorflow’s MNIST tutorial). Would you
> say this project is still suitable for me to do?
>
>
>
> I am also interested in the ‘Discovering computational chemistry content
> online’ project. I think it’s very important that computational resources
> are not wasted to repeat already done calculations. Would you kindly give
> me a bit more details on the crawler in aid of my proposal?
>
>
>
> Hope to hear back from you soon!
>
>
>
> Best wishes,
>
> Tony
>
>
>
> ·        *Name:* Zeyu Tony Yang
>
> ·        *Email:* zy...@ic...
>
> ·        *Country & timezone:* UK, GMT +0
>
> ·        *School Name & Study:* Imperial College London, Chemistry, Year
> 4 (Final year)
>
>
>

Hi Mithlesh,

I think for this project the place to start is writing a crawler that would
find an index the logfile we keep in our repository for unit tests:
https://github.com/cclib/cclib/tree/master/data

Beyond that, I think that we would like to see an application that
describes a reasonable crawling process. This can become tricky due to the
scale of everything out there.

On Thu, Mar 8, 2018 at 4:41 AM, <mit...@ii...> wrote:

> Hello Sir,
> I would like to dive deep in Discovering computational chemistry content
> online.
> Sir where I can start? I mean discuss ideas. Please help Sir!
> Thanks Sir
> Mithlesh Kumar
> #copied from wiki.openchemistry.com ideas.
> Brief explanation: There are tens or hundreds of thousands of
> computational chemistry results available online - let's mine them!
>
> Expected results: Build a crawler that identifies and indexes
> computational chemistry content online, and provides the ability to
> extract data with cclib.
>
> Prerequisites: Experience with Python, and ideally familiarity with
> computational chemistry and web indexing.
>
>
>
>
>
> > Hello Mithlesh,
> >
> > There is still plenty of time to submit proposals - please follow the
> GSOC
> > timeline: https://developers.google.com/open-source/gsoc/timeline
> >
> > First of all, I would encourage you to look through the various ideas on
> > the OpenChemistry website:
> > http://wiki.openchemistry.org/GSoC_Ideas_2018#cclib_Project_Ideas, also
> > for
> > the other libraries, not only cclib. Try to find a project you think you
> > are a good fit for and would have fun doing.
> >
> > Best,
> > Karol
> >
> >
> > On Tue, Mar 6, 2018 at 1:04 PM, <mit...@ii...> wrote:
> >
> >> Hi Sir,
> >> I am currently pursuing B.Tech at Indian Institute of Technology
> >> Guwahati
> >> in Chemistry major. I have keen interest in Quantum Chemistry and
> >> Computational. I have already taken Computational Chemistry course in
> >> this
> >> semester . I have much experience with many programming languages
> >> especially Python,C/C++,Java. I love to contribute Open Chemistry
> >> (cclib)
> >> under your guidance. I know there is much less time to submit proposal.
> >> But I am quiet sure that I can do alot better.
> >> Thanks Sir for considering me
> >> Mithlesh Kumar
> >>
> >
>

Hello Mithlesh,

There is still plenty of time to submit proposals - please follow the GSOC
timeline: https://developers.google.com/open-source/gsoc/timeline

First of all, I would encourage you to look through the various ideas on
the OpenChemistry website:
http://wiki.openchemistry.org/GSoC_Ideas_2018#cclib_Project_Ideas, also for
the other libraries, not only cclib. Try to find a project you think you
are a good fit for and would have fun doing.

Best,
Karol


On Tue, Mar 6, 2018 at 1:04 PM, <mit...@ii...> wrote:

> Hi Sir,
> I am currently pursuing B.Tech at Indian Institute of Technology Guwahati
> in Chemistry major. I have keen interest in Quantum Chemistry and
> Computational. I have already taken Computational Chemistry course in this
> semester . I have much experience with many programming languages
> especially Python,C/C++,Java. I love to contribute Open Chemistry (cclib)
> under your guidance. I know there is much less time to submit proposal.
> But I am quiet sure that I can do alot better.
> Thanks Sir for considering me
> Mithlesh Kumar
>

Hi Rajat,

(CC'ing some relevant mailing lists)

For this project you'll want to brush up on Python, since cclib is written
in Python. Reasonable familiarity with computational chemistry is also
needed, since the project involves implementing analysis methods specific
to quantum chemistry.

- Karol


On Mon, Mar 5, 2018 at 11:05 PM, rajat bhushan <rjb...@gm...> wrote:

> hello sir! I am a b.tech 3rd year student from jaypee university india and
> i want to build the project named "    Advanced Analysis of Quantum
> Chemistry Data"
> sir it would be like a blessing for me if you guide me . i am left with
> about 20 days to submit the proposal for this  i am willing to dedicate
> myself towards learning anything required to build this project .i can put
> 10 -12 hours daily towards learning required skills and that will sum up
> with 200 hours approx.
> sir please tell me where should i put all these 200 hours .what are the
> skills do i need to learn to be  able to build this project .
> i know intermediate level c ,c++,java and matlab .and now learning python
> with data science ..
>
>
>

Hi Alok,

No specific issue comes to mind at the moment, you can peruse the various
bugs we have filed at https://github.com/cclib/cclib/issues

An idea for pre-project work: you could try to write a simplistic parser
and try to get it to crawl the github repository and find out test files.

As far as the application is concerned, I would suggest putting a lot of
focus on what the project would achieve. For example, can you estimate the
number of logfiles out there you expect to find with the crawler?


On Tue, Mar 6, 2018 at 7:01 AM, Alok Kumar <alo...@gm...> wrote:

> #cclib  #parser-crawler
>
> Hello. Had been busy with my mid-semester exams .
> Looked into various parser codes.
> I wanted to ask what should I start working upon - any specific issue in
> parser or building a crawler...
>
> Regards,
> Alok
>
> On Tue, Feb 20, 2018 at 9:38 PM, Karol Langner <kar...@gm...>
> wrote:
>
>> Done.
>>
>> On Tue, Feb 20, 2018 at 8:01 AM, ALOK KUMAR <alo...@gm...>
>> wrote:
>>
>>> I wanted to join the slack channel to follow the discussion .Can you
>>> please send Open Chemistry slack invite to my email
>>> alo...@gm...
>>>
>>> Regards,
>>> Alok
>>>
>>> On Tue, Feb 20, 2018 at 10:48 AM, Karol Langner <kar...@gm...
>>> > wrote:
>>>
>>>> Hi Alok,
>>>>
>>>> Good to hear from you. I don't think a deep understanding of
>>>> computational chemistry or web crawling is a prerequisite, but of course it
>>>> would be an advantage. You need to be familiar enough with these subjects
>>>> to be able to propose a project plan that would deliver results during the
>>>> summer. The only way we can judge this is your proposal and any
>>>> contributions you make before the application period.
>>>>
>>>> I would mention that this project is a little more research-y than most
>>>> others. You'll need to design a crawler/scraper that is appropriate for
>>>> this application, and figure what gaps need to be filled in in the existing
>>>> codebase.
>>>>
>>>> Let us know if you have any other questions
>>>>
>>>> - Karol
>>>>
>>>>
>>>> On Mon, Feb 19, 2018 at 1:09 PM, ALOK KUMAR <alo...@gm...>
>>>> wrote:
>>>>
>>>>> Hello everyone.
>>>>>     I am Alok , a second year undergraduate at Indian Institute of
>>>>> Technology Bombay , India. I have interest in computational chemistry and
>>>>> had taken up a course this semester in my college.
>>>>>
>>>>> Among the GSoC-2018 ideas I found projects under cclib quite
>>>>> interesting, particularly  ##Discovering computational chemistry content
>>>>> online##
>>>>>
>>>>> I am familiar with web scraping using BeautifulSoup and urllib in
>>>>> Python and had recently started looking into Scrapy as well.
>>>>>
>>>>> I wanted to know how much understanding / familiarity is expected for
>>>>> contributing to this project . Also,(if required) is deeper understanding
>>>>> of computational chemistry or advanced web crawling a prerequisite or can
>>>>> it be worked upon during the initial Coding phase of GSoC.
>>>>>
>>>>> Looking ahead to staying in touch with the Open Chemistry community.
>>>>>
>>>>> Regards,
>>>>>
>>>>> Alok Kumar
>>>>> alo...@gm...
>>>>>
>>>>> _______________________________________________
>>>>> Openchemistry-developers mailing list
>>>>> Ope...@pu...
>>>>> https://public.kitware.com/mailman/listinfo/openchemistry-developers
>>>>>
>>>>>
>>>>
>>>
>>
>