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From: Karol L. <kar...@gm...> - 2018-03-20 15:42:12
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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 >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > |
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From: Karol L. <kar...@gm...> - 2018-03-16 15:11:29
|
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 >> > |
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From: Adam T. <ate...@gm...> - 2018-03-16 13:04:39
|
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 > |
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From: Karol L. <kar...@gm...> - 2018-03-16 02:46:17
|
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 <http://aka.ms/LearnAboutSpoofing> >> Feedback <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 >> <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 >>> <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 >>> <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 >>> <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 >>>> <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 >> >> > |
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From: Eric B. <er...@pi...> - 2018-03-15 14:17:15
|
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 > <http://aka.ms/LearnAboutSpoofing> > Feedback <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 > <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 >> <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 >> <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 >> <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 >>> <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 > > |
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From: Karol L. <kar...@gm...> - 2018-03-14 15:40:05
|
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 > > |
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From: Karol L. <kar...@gm...> - 2018-03-11 06:14:24
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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 > <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 ... > <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 > > > > |
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From: Karol L. <kar...@gm...> - 2018-03-08 19:34:02
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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) > > > |
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From: Karol L. <kar...@gm...> - 2018-03-08 15:15:26
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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 > >> > > > |
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From: Karol L. <kar...@gm...> - 2018-03-07 15:39:17
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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 > |
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From: Karol L. <kar...@gm...> - 2018-03-06 17:36:50
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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 .. > > > |
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From: Karol L. <kar...@gm...> - 2018-03-06 17:24:08
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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 >>>>> >>>>> >>>> >>> >> > |
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From: Karol L. <kar...@gm...> - 2018-02-20 15:17:43
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Hi Pratik, I think these are very different projects, even though both are from cclib. For the advanced analysis project, the main goal is to implement existing methods, so pre-work might consist of exploring those various methods (ELF, AIM, DDEC, etc.) and mapping out what you think is doable during the summer. Some demo code for one method would go a long way there, I think. For the ML project, there will be a lot more exploration, since there's no "method" to implement yet and it's unclear what approach would work best. I expect much of the work, even during the summer, would be experimenting with various ML setups and understanding what actually makes sense for parsing. I think what we'd be looking for most in the application is how to evaluate an ML-based parser, as well as good overall strategy/plan since there's some danger here of not getting very far in uncharted territory. HTH, Karol On Tue, Feb 20, 2018 at 4:50 AM, Pratik Ranjan < pra...@gm...> wrote: > Sir, > I am interested in working on project ideas of CCLIB, which are Advanced > Analysis of Quantum Chemistry Data and Machine learning applied to parsing > computational chemistry output. As these project is related to the field of > my study.Can you help me out how to start working on these ideas? > > Regards > Pratik Ranjan. > > On 20-Feb-2018 11:20 AM, "Karol Langner" <kar...@gm...> wrote: > >> Hi Pratik, >> >> Please be more specific about which project you're interested in. >> >> - Karol >> >> On Mon, Feb 19, 2018 at 11:27 AM, Pratik Ranjan < >> pra...@gm...> wrote: >> >>> Hello everyone, >>> This is Pratik Ranjan, a third year student of IIT Guwahati. I am >>> pursuing B.Tech degree in Chemical Science and Technology which is based on >>> technical chemistry. During my semesters I have gone through the key >>> courses which involved Mathematics, Computer science and Chemistry. >>> Mathematics involved courses like advance calculus and vector algebra. I >>> did courses on Algorithm and Data structure in C. >>> In chemistry I have gone through the courses like Quantum chemistry, >>> Chemical kinetics, Spectrometry, Computational chemistry and Computational >>> physics. >>> In computational chemistry I did various programming assignments in >>> FORTRAN(95). The assignments were based on finding solutions of Schrodinger >>> equations, Hamiltonian operator, different energy level of the molecules, >>> did Molecular modeling – Determination of properties of molecules, >>> charge distribution, viewing the orbitals and vibrational spectra and >>> also did Fourier analysis. All these calculations involved complex matrix >>> calculations, like finding eigenvectors and eigenvalues of a matrix, >>> inversion of matrix etc.I used LAPACK for finding eigenvectors and >>> eigenvalues This course also involved calculation of kinetics of Ozone. In >>> computational Physics I did assignments in C++ which were based on >>> numerical analysis. In this course I learned numerical methods to solve >>> Differential equations, solving linear equations, Diagonalizing a N*N >>> dimensional matrix and finding eigenvalues and eigenvectors by using >>> similarity transformation. With the motivation from the above courses once >>> I tried to make an android app which can solve some Matrix calculations but >>> unfortunately I didn't succeeded due to lack of mentorship , but from there >>> I got some information about Machine learning that is if we involve machine >>> learnig in the app then it can read the question from image and give >>> solution to the problem, It may be impractical. But due to motivation from >>> the idea, now in present semester I am also doing Machine Learning course. >>> since, this project is related to my field of interest and my majoring >>> so I want to work in this project which will give me real experience of my >>> knowledge, but I am beginner to the open source and Openchemistry project >>> so if I get some help from the mentors,seniors and friends then it will be >>> very helpful for me. >>> Thank you. >>> >>> >>> >>> >>> _______________________________________________ >>> Openchemistry-developers mailing list >>> Ope...@pu... >>> https://public.kitware.com/mailman/listinfo/openchemistry-developers >>> >>> >> |
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From: Karol L. <kar...@gm...> - 2018-02-20 15:06:16
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Hi Somesh, Nice to hear from you. Which project is the "content enlisting project"? Do you mean the cclib web scraper? - Karol On Sun, Feb 18, 2018 at 2:09 AM, Somesh Mohapatra <pik...@gm...> wrote: > Dear Karol > > I have recently been accepted to MIT for PhD in Materials Science, and > looking forward to be a part of GSoC over the Summer of 2018. I have > earlier worked on Computational Materials Science and simulations for my > projects (Resume, attached), and then on Bioinformatics and Computational > Biology. > > I am looking forward to hone my coding skills and contribute to the > Computational Chemistry content enlisting project. I am open to > understanding other projects as well, if you see that based on my skillset, > I would be a better fit in another work. > > Looking forward to discuss more on the possibilities! > > Somesh Mohapatra > Graduate Student (Fall 18) > Department of Materials Science and Engineering > Massachusetts Institute of Technology > Contact - +91 7060 33 45 66 > E-Mail - pik...@gm... > Website - someshmohapatra.in > ᐧ > |
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From: Karol L. <kar...@gm...> - 2018-02-12 19:19:01
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Great to see OpenChemistry participating again. Like last year, cclib is part of it and we have a number of great project ideas for cclib ready for students! ---------- Forwarded message ---------- From: Geoff Hutchison <no...@ma...> Date: Mon, Feb 12, 2018 at 11:12 AM Subject: [Avogadro Discussion] [General Discussion] Avogadro Part of Google Summer of Code 2018 To: kar...@gm... ghutchis <https://discuss.avogadro.cc/u/ghutchis> February 12 As in the last 2 years, Avogadro is thrilled to be part of Google Summer of Code 2018 as part of Open Chemistry: https://summerofcode.withgoogle.com/organizations/6513013473935360/ We’re looking for some great students and great ideas… Some are listed here, but new ideas are also welcome (including from the community - i.e., *you*) http://wiki.openchemistry.org/GSoC_Ideas_2018 Got a good idea you’d like to see in Avogadro? ------------------------------ Visit Topic <https://discuss.avogadro.cc/t/avogadro-part-of-google-summer-of-code-2018/2622/1> or reply to this email to respond. To unsubscribe from these emails, click here <https://discuss.avogadro.cc/email/unsubscribe/9dad6296cea49a4bce9469e0dfab7eed39f52b7bc320fe1636dd7856979168d0> . |
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From: Trevor T. <u05...@ut...> - 2018-02-09 00:41:39
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Hi Dr. Tenderholt, Thank you for the kind e-mail! I really appreciate the advice and will definitely look into the MSDK and RDkit projects. Thanks again, Trevor On Tue, Feb 6, 2018 at 8:25 AM, Adam Tenderholt <ate...@gm...> wrote: > Hi Trevor, > > Your proposals sound like things that could be proposed to the MSDK and/or > RDkit projects, both of which are part of OpenChemistry. You should reach > out to those projects/mentors if you haven't done so already. > > Best regards, > > Adam > > > On Mon, Feb 5, 2018 at 2:46 PM Karol Langner <kar...@gm...> > wrote: > >> Hi Trevor, >> >> Good to hear from you. CC'ing two lists that will also be interested in >> this thread. >> >> 1. I'm sure there's interest in non-QM programs, the main question is >> whether cclib is the best vehicle for such parsers (cclib targets >> electronic structure data primarily). That's something to discuss, but even >> if that would be better suited for a new project, we could re-use some of >> the code between projects. Also, have you checked out if those formats are >> supported by Open Babel? If it's just structure, adding a parser for these >> formats to that project would be faster. >> >> 2. I think there's interest in biological assays, but again I'm not sure >> that fits into the scope of cclib. There are probably projects out there >> better suited for that. >> >> 3. Definitely, did you have any specific analyses in mind? Based on >> reactants, or something like reaction path calculations? >> >> Finally, I would point out you can propose a project of your own. Any of >> three things you mentioned would be well received by Open Chemistry, which >> is the umbrella project under cclib participates in GSOC. Check out the >> full list of ideas at http://wiki.openchemistry.org/GSoC_Ideas_2018 >> >> On Mon, Feb 5, 2018 at 2:31 PM, Trevor Tanner <u05...@ut...> wrote: >> >>> Dear Dr. Langner, >>> >>> As a huge cclib fan, I have been excited to read about its ideas for >>> this year's GSoC. I was just hoping to get some clarification on the >>> different projects. >>> >>> 1. For "implementing new parsers", would cclib have any interest in >>> supporting chemical data from non-QM computational chemistry programs? For >>> example, programs like SIRIUS 3 and MS-FINDER have separate schemes for >>> predicting potential structures from tandem mass spectrometry experiments. >>> Additionally, databases like Metacyc that contain computationally-predicted >>> metabolites from bacterial genomes store chemical structures in their own, >>> otherwise hard-to-access formats. >>> >>> 2. For "discovering computational chemistry content online", would there >>> be interest in biological assays and a lightweight machine learning >>> component? For example, many PubChem assays are simple binary >>> classifications that can be predicted using fast decision trees and >>> fingerprints. >>> >>> 3. For "advanced analysis of quantum chemistry data", would there be any >>> interest in basic analysis of simple chemical reactions? For example, it >>> could be useful to easily batch screen compounds with a pre-defined >>> reaction for their product favorability. >>> >>> Thank you for your time. I look forward to hearing back from you. >>> >>> Thanks again, >>> Trevor Tanner >>> (801) 742-5366 >>> >> >> _______________________________________________ >> Openchemistry-developers mailing list >> Ope...@pu... >> https://public.kitware.com/mailman/listinfo/openchemistry-developers >> > |
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From: Adam T. <ate...@gm...> - 2018-02-06 15:26:03
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Hi Trevor, Your proposals sound like things that could be proposed to the MSDK and/or RDkit projects, both of which are part of OpenChemistry. You should reach out to those projects/mentors if you haven't done so already. Best regards, Adam On Mon, Feb 5, 2018 at 2:46 PM Karol Langner <kar...@gm...> wrote: > Hi Trevor, > > Good to hear from you. CC'ing two lists that will also be interested in > this thread. > > 1. I'm sure there's interest in non-QM programs, the main question is > whether cclib is the best vehicle for such parsers (cclib targets > electronic structure data primarily). That's something to discuss, but even > if that would be better suited for a new project, we could re-use some of > the code between projects. Also, have you checked out if those formats are > supported by Open Babel? If it's just structure, adding a parser for these > formats to that project would be faster. > > 2. I think there's interest in biological assays, but again I'm not sure > that fits into the scope of cclib. There are probably projects out there > better suited for that. > > 3. Definitely, did you have any specific analyses in mind? Based on > reactants, or something like reaction path calculations? > > Finally, I would point out you can propose a project of your own. Any of > three things you mentioned would be well received by Open Chemistry, which > is the umbrella project under cclib participates in GSOC. Check out the > full list of ideas at http://wiki.openchemistry.org/GSoC_Ideas_2018 > > On Mon, Feb 5, 2018 at 2:31 PM, Trevor Tanner <u05...@ut...> wrote: > >> Dear Dr. Langner, >> >> As a huge cclib fan, I have been excited to read about its ideas for this >> year's GSoC. I was just hoping to get some clarification on the different >> projects. >> >> 1. For "implementing new parsers", would cclib have any interest in >> supporting chemical data from non-QM computational chemistry programs? For >> example, programs like SIRIUS 3 and MS-FINDER have separate schemes for >> predicting potential structures from tandem mass spectrometry experiments. >> Additionally, databases like Metacyc that contain computationally-predicted >> metabolites from bacterial genomes store chemical structures in their own, >> otherwise hard-to-access formats. >> >> 2. For "discovering computational chemistry content online", would there >> be interest in biological assays and a lightweight machine learning >> component? For example, many PubChem assays are simple binary >> classifications that can be predicted using fast decision trees and >> fingerprints. >> >> 3. For "advanced analysis of quantum chemistry data", would there be any >> interest in basic analysis of simple chemical reactions? For example, it >> could be useful to easily batch screen compounds with a pre-defined >> reaction for their product favorability. >> >> Thank you for your time. I look forward to hearing back from you. >> >> Thanks again, >> Trevor Tanner >> (801) 742-5366 >> > > _______________________________________________ > Openchemistry-developers mailing list > Ope...@pu... > https://public.kitware.com/mailman/listinfo/openchemistry-developers > |
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From: Karol L. <kar...@gm...> - 2018-02-05 22:46:31
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Hi Trevor, Good to hear from you. CC'ing two lists that will also be interested in this thread. 1. I'm sure there's interest in non-QM programs, the main question is whether cclib is the best vehicle for such parsers (cclib targets electronic structure data primarily). That's something to discuss, but even if that would be better suited for a new project, we could re-use some of the code between projects. Also, have you checked out if those formats are supported by Open Babel? If it's just structure, adding a parser for these formats to that project would be faster. 2. I think there's interest in biological assays, but again I'm not sure that fits into the scope of cclib. There are probably projects out there better suited for that. 3. Definitely, did you have any specific analyses in mind? Based on reactants, or something like reaction path calculations? Finally, I would point out you can propose a project of your own. Any of three things you mentioned would be well received by Open Chemistry, which is the umbrella project under cclib participates in GSOC. Check out the full list of ideas at http://wiki.openchemistry.org/GSoC_Ideas_2018 On Mon, Feb 5, 2018 at 2:31 PM, Trevor Tanner <u05...@ut...> wrote: > Dear Dr. Langner, > > As a huge cclib fan, I have been excited to read about its ideas for this > year's GSoC. I was just hoping to get some clarification on the different > projects. > > 1. For "implementing new parsers", would cclib have any interest in > supporting chemical data from non-QM computational chemistry programs? For > example, programs like SIRIUS 3 and MS-FINDER have separate schemes for > predicting potential structures from tandem mass spectrometry experiments. > Additionally, databases like Metacyc that contain computationally-predicted > metabolites from bacterial genomes store chemical structures in their own, > otherwise hard-to-access formats. > > 2. For "discovering computational chemistry content online", would there > be interest in biological assays and a lightweight machine learning > component? For example, many PubChem assays are simple binary > classifications that can be predicted using fast decision trees and > fingerprints. > > 3. For "advanced analysis of quantum chemistry data", would there be any > interest in basic analysis of simple chemical reactions? For example, it > could be useful to easily batch screen compounds with a pre-defined > reaction for their product favorability. > > Thank you for your time. I look forward to hearing back from you. > > Thanks again, > Trevor Tanner > (801) 742-5366 > |
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From: Karol L. <kar...@gm...> - 2018-01-18 16:18:06
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Hello, Like last year, cclib is working with Open Chemistry to apply for the Google Summer of Code 2018. If you're interested in participating or have some ideas for fun student projects, please let us know. |
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From: Eric B. <er...@pi...> - 2017-12-12 17:38:40
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Hello everyone, I think the workshop was relatively productive, even though there were only a few concrete products. Karol, it was good to finally meet in person. There is supposed to be a report eventually, but it hasn’t materialized yet. Current written results are located here <https://drive.google.com/drive/u/0/folders/0BwQDzp1VrB3veDdGRS1aTHI1d1E>. Here is a brief summary and my thoughts. - MolSSI has pledged to provide a definition of the schema via http://json-schema.org/, tools for validation, including a curl’able server, and tools for translation between AO normalization/ordering. - Like Chemical JSON, we are (at first) going with a “big” or “monolithic” layout. That means all atom coordinates are stored together, all basis set definitions are stored together, all atomic charges are together, etc. The opposite would be to have each atom carry its own coordinates, charge, basis functions, etc. This is something like a procedural/imperative vs. object-oriented structure, though accessing attributes only changes from frame.xyz[4] to frame.atoms[4].xyz and so on. - Like Chemical JSON, I think we also agreed on completely flat arrays. I am unsure if we’re doing C or Fortran ordering or what the precedent is. I suspect CJSON is row-major. It should *not* be on a per-attribute basis. - There is an open question about how to store data for multiple geometries. Should each geometry carry its own coordinates and MO coefficients, or should those be up a level with an additional pre-index, like how we do it? Also no idea how compressed/binary data will work. - There will be different levels of adherence to the spec. The bare minimum we should adhere to, and a concrete goal, is the “Molden” level, meaning we can read and write everything that the Molden format can handle. - There are going to be vendor-specific extensions, allowing arbitrary keys to be added to the schema, similar to how we are going to redo attributes to hold arbitrary program-specific properties. We had a few discussions about provenance, the storage of which will map to metadata. See here <https://docs.google.com/document/d/11-Q9UpcgCOf_ssKlyKLzhNf8C7g-QCnzElP8hMvwG7g/edit#heading=h.exa5ufsjljlk> for an example from Geoff and myself. - The path forward is not super clear, and there has been little activity in the schema repository. Bob Hanson pledged a sort of living implementation for the community to discuss, which is already available. I had also agreed to do the same thing. My cclib-related questions and proposal: - Is our Molden writer feature-complete? Along with all the CJSON already done, it will make a great starting template. If it isn’t, we should finish that first. As an aside, I have bits of a Molden reader and reorganizer somewhere… - We have a request in 451 <https://github.com/cclib/cclib/issues/451> to add more things to metadata. There is currently no overlap with what Bob has added to Jmol. I propose we just start adding things to metadata within some reasonable structure. It looks like provenance and input-related things will go entirely in metadata? We could discuss it in the issue thread, since we have an actual user. Eric On Mon, Nov 20, 2017 at 5:55 PM, Karol Langner <kar...@gm...> wrote: > Yes, looking forward to being there! > > On Fri, Nov 17, 2017 at 8:02 AM, Eric Berquist <er...@pi...> wrote: > >> Based on the schedule and working group outlines, I think we will learn a >> lot more by the time the workshop is done, and I'll write up with a >> detailed report for us. Right now, I think the most we can ask for is a >> well-defined schema with good documentation, which would be more useful to >> us than monetary support. >> >> I can't think of any other input right now specifically for MolSSI. We're >> all reasonably responsive for communication, in case they require something >> from us. Since we've been discussing it recently with external pushes to >> add more attributes and metadata, we should set a target date for releasing >> v2.0. I think it should be either when we have an initial implementation of >> the MolSSI spec, or the end of spring 2018, whichever comes first. That >> means we should set a date for v1.5.3, maybe by the end of December. >> >> Karol, I noticed your name as part of some working groups. Are you >> actually attending in-person at all? >> >> Eric >> >> On Sun, Oct 15, 2017 at 3:59 AM, Karol Langner <kar...@gm...> >> wrote: >> >>> I think this is a valuable initiative, please push it forward as much as >>> possible! Is there any specific input or decision from us (cclib as a >>> whole) that you would like on this topic? >>> >>> On Fri, Oct 13, 2017 at 10:41 AM, Eric Berquist <er...@pi...> wrote: >>> >>>> Hi everyone, >>>> >>>> I've been invited to attend the a MolSSI workshop on quantum chemistry >>>> schema at LBNL on 11/30 and 12/1; I've attached a PDF of the solicitation. >>>> Here is Daniel Smith's email to me: >>>> >>>> >>>>> During a MolSSI Interoperability Workshop this year, one topic that >>>>> came up was an interoperable schema between various quantum chemistry >>>>> programs so that users and developers could have a unified interface to >>>>> move data in and out of these very large programs as opposed to processing >>>>> ASCII files and building custom inputs. To this end, we have been tweaking >>>>> a base schema and talking to the creators of the many different schema >>>>> already out there in the hope of unifying these diverse groups. We hope to >>>>> pull in approximately 30 quantum chemistry developers from a broad set of >>>>> backgrounds and programs to make this a reality. >>>>> >>>>> The current version and primary discussion of the schema can be found >>>>> on GitHub here: https://github.com/MolSSI/QC_JSON_Schema >>>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FMolSSI%2FQC_JSON_Schema&data=01%7C01%7Cerb74%40pitt.edu%7C473d47bc11b145effed008d513a2aad8%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=ZBuo3wngMsab4aiLzsjJJeCUFjHm07l75Ca8SkTmI8M%3D&reserved=0> >>>>> >>>>> We would encourage your entire community to discuss the schema in its >>>>> current form in order to spur more discussion and tune the overall scope of >>>>> the schema on the GitHub page, otherwise feel free to email me back >>>>> personally if you have any questions. For the workshop participant, we are >>>>> looking for one developer that would represent your community to help >>>>> finalize the schema and decide on future governance and communication plans. >>>>> >>>> >>>> As of right now, I am not representing cclib since we should come to >>>> some census decision about our path. I do feel it gives us more exposure, >>>> which is good, and would push development a bit, which could be a pro or a >>>> con. We are well-positioned to implement (now or soon) all of their >>>> requirements (https://github.com/MolSSI/QC_ >>>> JSON_Schema/blob/master/Requirements.md >>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FMolSSI%2FQC_JSON_Schema%2Fblob%2Fmaster%2FRequirements.md&data=01%7C01%7Cerb74%40pitt.edu%7C473d47bc11b145effed008d513a2aad8%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=oUhxcu3jVdKYVu3lfNgzLX04P%2FSM7Vi%2Bw%2FUW95wF3b0%3D&reserved=0>), >>>> especially for QM packages that will certainly not support the schema >>>> directly. A substantial amount of work was already done by Sanjeed during >>>> GSoC last year as part of CJSON, which itself is being unified. Our >>>> transition to more modular attributes, which we've already started >>>> discussing, can only make this easier. >>>> >>>> Their repository is just a few Markdown files and is worth reading. As >>>> far as what our obligation would be, I think it would be to implement their >>>> spec, with their development assistance if need be. Implicit in my >>>> invitation to the workshop is that I'd do most of the heavy lifting. In >>>> particular, since large data (MO coefficients, densities, response vectors, >>>> ...) will need to be stored, we will probably need an HDF5 interface that >>>> can be optional, similar to how our other bridges are already optional. One >>>> question is whether or not there will be a fallback non-binary >>>> representation for these fields. >>>> >>>> Please let me know your thoughts/questions/suggestions/concerns. >>>> >>>> Eric >>>> >>>> ------------------------------------------------------------ >>>> ------------------ >>>> Check out the vibrant tech community on one of the world's most >>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=01%7C01%7Cerb74%40pitt.edu%7C473d47bc11b145effed008d513a2aad8%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=VwbxblmY2NxxxgcAxGzkfsnfjsyiQdtJdQxCIpcthjg%3D&reserved=0> >>>> _______________________________________________ >>>> cclib-devel mailing list >>>> ccl...@li... >>>> https://lists.sourceforge.net/lists/listinfo/cclib-devel >>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fcclib-devel&data=01%7C01%7Cerb74%40pitt.edu%7C473d47bc11b145effed008d513a2aad8%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=7omT%2FSuUEMSVkxNVXIiHsmvF75t%2FezyeLz8sM15idFk%3D&reserved=0> >>>> >>>> >>> >> > |
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From: Karol L. <kar...@gm...> - 2017-11-20 22:55:12
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Yes, looking forward to being there! On Fri, Nov 17, 2017 at 8:02 AM, Eric Berquist <er...@pi...> wrote: > Based on the schedule and working group outlines, I think we will learn a > lot more by the time the workshop is done, and I'll write up with a > detailed report for us. Right now, I think the most we can ask for is a > well-defined schema with good documentation, which would be more useful to > us than monetary support. > > I can't think of any other input right now specifically for MolSSI. We're > all reasonably responsive for communication, in case they require something > from us. Since we've been discussing it recently with external pushes to > add more attributes and metadata, we should set a target date for releasing > v2.0. I think it should be either when we have an initial implementation of > the MolSSI spec, or the end of spring 2018, whichever comes first. That > means we should set a date for v1.5.3, maybe by the end of December. > > Karol, I noticed your name as part of some working groups. Are you > actually attending in-person at all? > > Eric > > On Sun, Oct 15, 2017 at 3:59 AM, Karol Langner <kar...@gm...> > wrote: > >> I think this is a valuable initiative, please push it forward as much as >> possible! Is there any specific input or decision from us (cclib as a >> whole) that you would like on this topic? >> >> On Fri, Oct 13, 2017 at 10:41 AM, Eric Berquist <er...@pi...> wrote: >> >>> Hi everyone, >>> >>> I've been invited to attend the a MolSSI workshop on quantum chemistry >>> schema at LBNL on 11/30 and 12/1; I've attached a PDF of the solicitation. >>> Here is Daniel Smith's email to me: >>> >>> >>>> During a MolSSI Interoperability Workshop this year, one topic that >>>> came up was an interoperable schema between various quantum chemistry >>>> programs so that users and developers could have a unified interface to >>>> move data in and out of these very large programs as opposed to processing >>>> ASCII files and building custom inputs. To this end, we have been tweaking >>>> a base schema and talking to the creators of the many different schema >>>> already out there in the hope of unifying these diverse groups. We hope to >>>> pull in approximately 30 quantum chemistry developers from a broad set of >>>> backgrounds and programs to make this a reality. >>>> >>>> The current version and primary discussion of the schema can be found >>>> on GitHub here: https://github.com/MolSSI/QC_JSON_Schema >>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FMolSSI%2FQC_JSON_Schema&data=01%7C01%7Cerb74%40pitt.edu%7C473d47bc11b145effed008d513a2aad8%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=ZBuo3wngMsab4aiLzsjJJeCUFjHm07l75Ca8SkTmI8M%3D&reserved=0> >>>> >>>> We would encourage your entire community to discuss the schema in its >>>> current form in order to spur more discussion and tune the overall scope of >>>> the schema on the GitHub page, otherwise feel free to email me back >>>> personally if you have any questions. For the workshop participant, we are >>>> looking for one developer that would represent your community to help >>>> finalize the schema and decide on future governance and communication plans. >>>> >>> >>> As of right now, I am not representing cclib since we should come to >>> some census decision about our path. I do feel it gives us more exposure, >>> which is good, and would push development a bit, which could be a pro or a >>> con. We are well-positioned to implement (now or soon) all of their >>> requirements (https://github.com/MolSSI/QC_ >>> JSON_Schema/blob/master/Requirements.md >>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FMolSSI%2FQC_JSON_Schema%2Fblob%2Fmaster%2FRequirements.md&data=01%7C01%7Cerb74%40pitt.edu%7C473d47bc11b145effed008d513a2aad8%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=oUhxcu3jVdKYVu3lfNgzLX04P%2FSM7Vi%2Bw%2FUW95wF3b0%3D&reserved=0>), >>> especially for QM packages that will certainly not support the schema >>> directly. A substantial amount of work was already done by Sanjeed during >>> GSoC last year as part of CJSON, which itself is being unified. Our >>> transition to more modular attributes, which we've already started >>> discussing, can only make this easier. >>> >>> Their repository is just a few Markdown files and is worth reading. As >>> far as what our obligation would be, I think it would be to implement their >>> spec, with their development assistance if need be. Implicit in my >>> invitation to the workshop is that I'd do most of the heavy lifting. In >>> particular, since large data (MO coefficients, densities, response vectors, >>> ...) will need to be stored, we will probably need an HDF5 interface that >>> can be optional, similar to how our other bridges are already optional. One >>> question is whether or not there will be a fallback non-binary >>> representation for these fields. >>> >>> Please let me know your thoughts/questions/suggestions/concerns. >>> >>> Eric >>> >>> ------------------------------------------------------------ >>> ------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=01%7C01%7Cerb74%40pitt.edu%7C473d47bc11b145effed008d513a2aad8%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=VwbxblmY2NxxxgcAxGzkfsnfjsyiQdtJdQxCIpcthjg%3D&reserved=0> >>> _______________________________________________ >>> cclib-devel mailing list >>> ccl...@li... >>> https://lists.sourceforge.net/lists/listinfo/cclib-devel >>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fcclib-devel&data=01%7C01%7Cerb74%40pitt.edu%7C473d47bc11b145effed008d513a2aad8%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=7omT%2FSuUEMSVkxNVXIiHsmvF75t%2FezyeLz8sM15idFk%3D&reserved=0> >>> >>> >> > |
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From: Eric B. <er...@pi...> - 2017-11-17 16:02:57
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Based on the schedule and working group outlines, I think we will learn a lot more by the time the workshop is done, and I'll write up with a detailed report for us. Right now, I think the most we can ask for is a well-defined schema with good documentation, which would be more useful to us than monetary support. I can't think of any other input right now specifically for MolSSI. We're all reasonably responsive for communication, in case they require something from us. Since we've been discussing it recently with external pushes to add more attributes and metadata, we should set a target date for releasing v2.0. I think it should be either when we have an initial implementation of the MolSSI spec, or the end of spring 2018, whichever comes first. That means we should set a date for v1.5.3, maybe by the end of December. Karol, I noticed your name as part of some working groups. Are you actually attending in-person at all? Eric On Sun, Oct 15, 2017 at 3:59 AM, Karol Langner <kar...@gm...> wrote: > I think this is a valuable initiative, please push it forward as much as > possible! Is there any specific input or decision from us (cclib as a > whole) that you would like on this topic? > > On Fri, Oct 13, 2017 at 10:41 AM, Eric Berquist <er...@pi...> wrote: > >> Hi everyone, >> >> I've been invited to attend the a MolSSI workshop on quantum chemistry >> schema at LBNL on 11/30 and 12/1; I've attached a PDF of the solicitation. >> Here is Daniel Smith's email to me: >> >> >>> During a MolSSI Interoperability Workshop this year, one topic that came >>> up was an interoperable schema between various quantum chemistry programs >>> so that users and developers could have a unified interface to move data in >>> and out of these very large programs as opposed to processing ASCII files >>> and building custom inputs. To this end, we have been tweaking a base >>> schema and talking to the creators of the many different schema already out >>> there in the hope of unifying these diverse groups. We hope to pull in >>> approximately 30 quantum chemistry developers from a broad set of >>> backgrounds and programs to make this a reality. >>> >>> The current version and primary discussion of the schema can be found on >>> GitHub here: https://github.com/MolSSI/QC_JSON_Schema >>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FMolSSI%2FQC_JSON_Schema&data=01%7C01%7Cerb74%40pitt.edu%7C473d47bc11b145effed008d513a2aad8%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=ZBuo3wngMsab4aiLzsjJJeCUFjHm07l75Ca8SkTmI8M%3D&reserved=0> >>> >>> We would encourage your entire community to discuss the schema in its >>> current form in order to spur more discussion and tune the overall scope of >>> the schema on the GitHub page, otherwise feel free to email me back >>> personally if you have any questions. For the workshop participant, we are >>> looking for one developer that would represent your community to help >>> finalize the schema and decide on future governance and communication plans. >>> >> >> As of right now, I am not representing cclib since we should come to some >> census decision about our path. I do feel it gives us more exposure, which >> is good, and would push development a bit, which could be a pro or a con. >> We are well-positioned to implement (now or soon) all of their requirements >> (https://github.com/MolSSI/QC_JSON_Schema/blob/master/Requirements.md >> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FMolSSI%2FQC_JSON_Schema%2Fblob%2Fmaster%2FRequirements.md&data=01%7C01%7Cerb74%40pitt.edu%7C473d47bc11b145effed008d513a2aad8%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=oUhxcu3jVdKYVu3lfNgzLX04P%2FSM7Vi%2Bw%2FUW95wF3b0%3D&reserved=0>), >> especially for QM packages that will certainly not support the schema >> directly. A substantial amount of work was already done by Sanjeed during >> GSoC last year as part of CJSON, which itself is being unified. Our >> transition to more modular attributes, which we've already started >> discussing, can only make this easier. >> >> Their repository is just a few Markdown files and is worth reading. As >> far as what our obligation would be, I think it would be to implement their >> spec, with their development assistance if need be. Implicit in my >> invitation to the workshop is that I'd do most of the heavy lifting. In >> particular, since large data (MO coefficients, densities, response vectors, >> ...) will need to be stored, we will probably need an HDF5 interface that >> can be optional, similar to how our other bridges are already optional. One >> question is whether or not there will be a fallback non-binary >> representation for these fields. >> >> Please let me know your thoughts/questions/suggestions/concerns. >> >> Eric >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=01%7C01%7Cerb74%40pitt.edu%7C473d47bc11b145effed008d513a2aad8%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=VwbxblmY2NxxxgcAxGzkfsnfjsyiQdtJdQxCIpcthjg%3D&reserved=0> >> _______________________________________________ >> cclib-devel mailing list >> ccl...@li... >> https://lists.sourceforge.net/lists/listinfo/cclib-devel >> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fcclib-devel&data=01%7C01%7Cerb74%40pitt.edu%7C473d47bc11b145effed008d513a2aad8%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=7omT%2FSuUEMSVkxNVXIiHsmvF75t%2FezyeLz8sM15idFk%3D&reserved=0> >> >> > |
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From: Noel O'B. <bao...@gm...> - 2017-10-15 10:28:45
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Yes - sounds great. And I see Geoff Hutchison is involved too. - Noel On 15 October 2017 at 08:59, Karol Langner <kar...@gm...> wrote: > I think this is a valuable initiative, please push it forward as much as > possible! Is there any specific input or decision from us (cclib as a > whole) that you would like on this topic? > > On Fri, Oct 13, 2017 at 10:41 AM, Eric Berquist <er...@pi...> wrote: > >> Hi everyone, >> >> I've been invited to attend the a MolSSI workshop on quantum chemistry >> schema at LBNL on 11/30 and 12/1; I've attached a PDF of the solicitation. >> Here is Daniel Smith's email to me: >> >> >>> During a MolSSI Interoperability Workshop this year, one topic that came >>> up was an interoperable schema between various quantum chemistry programs >>> so that users and developers could have a unified interface to move data in >>> and out of these very large programs as opposed to processing ASCII files >>> and building custom inputs. To this end, we have been tweaking a base >>> schema and talking to the creators of the many different schema already out >>> there in the hope of unifying these diverse groups. We hope to pull in >>> approximately 30 quantum chemistry developers from a broad set of >>> backgrounds and programs to make this a reality. >>> >>> The current version and primary discussion of the schema can be found on >>> GitHub here: https://github.com/MolSSI/QC_JSON_Schema >>> >>> We would encourage your entire community to discuss the schema in its >>> current form in order to spur more discussion and tune the overall scope of >>> the schema on the GitHub page, otherwise feel free to email me back >>> personally if you have any questions. For the workshop participant, we are >>> looking for one developer that would represent your community to help >>> finalize the schema and decide on future governance and communication plans. >>> >> >> As of right now, I am not representing cclib since we should come to some >> census decision about our path. I do feel it gives us more exposure, which >> is good, and would push development a bit, which could be a pro or a con. >> We are well-positioned to implement (now or soon) all of their requirements >> (https://github.com/MolSSI/QC_JSON_Schema/blob/master/Requirements.md), >> especially for QM packages that will certainly not support the schema >> directly. A substantial amount of work was already done by Sanjeed during >> GSoC last year as part of CJSON, which itself is being unified. Our >> transition to more modular attributes, which we've already started >> discussing, can only make this easier. >> >> Their repository is just a few Markdown files and is worth reading. As >> far as what our obligation would be, I think it would be to implement their >> spec, with their development assistance if need be. Implicit in my >> invitation to the workshop is that I'd do most of the heavy lifting. In >> particular, since large data (MO coefficients, densities, response vectors, >> ...) will need to be stored, we will probably need an HDF5 interface that >> can be optional, similar to how our other bridges are already optional. One >> question is whether or not there will be a fallback non-binary >> representation for these fields. >> >> Please let me know your thoughts/questions/suggestions/concerns. >> >> Eric >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> cclib-devel mailing list >> ccl...@li... >> https://lists.sourceforge.net/lists/listinfo/cclib-devel >> >> > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > cclib-devel mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-devel > > |
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From: Karol L. <kar...@gm...> - 2017-10-15 07:59:37
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I think this is a valuable initiative, please push it forward as much as possible! Is there any specific input or decision from us (cclib as a whole) that you would like on this topic? On Fri, Oct 13, 2017 at 10:41 AM, Eric Berquist <er...@pi...> wrote: > Hi everyone, > > I've been invited to attend the a MolSSI workshop on quantum chemistry > schema at LBNL on 11/30 and 12/1; I've attached a PDF of the solicitation. > Here is Daniel Smith's email to me: > > >> During a MolSSI Interoperability Workshop this year, one topic that came >> up was an interoperable schema between various quantum chemistry programs >> so that users and developers could have a unified interface to move data in >> and out of these very large programs as opposed to processing ASCII files >> and building custom inputs. To this end, we have been tweaking a base >> schema and talking to the creators of the many different schema already out >> there in the hope of unifying these diverse groups. We hope to pull in >> approximately 30 quantum chemistry developers from a broad set of >> backgrounds and programs to make this a reality. >> >> The current version and primary discussion of the schema can be found on >> GitHub here: https://github.com/MolSSI/QC_JSON_Schema >> >> We would encourage your entire community to discuss the schema in its >> current form in order to spur more discussion and tune the overall scope of >> the schema on the GitHub page, otherwise feel free to email me back >> personally if you have any questions. For the workshop participant, we are >> looking for one developer that would represent your community to help >> finalize the schema and decide on future governance and communication plans. >> > > As of right now, I am not representing cclib since we should come to some > census decision about our path. I do feel it gives us more exposure, which > is good, and would push development a bit, which could be a pro or a con. > We are well-positioned to implement (now or soon) all of their requirements > (https://github.com/MolSSI/QC_JSON_Schema/blob/master/Requirements.md), > especially for QM packages that will certainly not support the schema > directly. A substantial amount of work was already done by Sanjeed during > GSoC last year as part of CJSON, which itself is being unified. Our > transition to more modular attributes, which we've already started > discussing, can only make this easier. > > Their repository is just a few Markdown files and is worth reading. As far > as what our obligation would be, I think it would be to implement their > spec, with their development assistance if need be. Implicit in my > invitation to the workshop is that I'd do most of the heavy lifting. In > particular, since large data (MO coefficients, densities, response vectors, > ...) will need to be stored, we will probably need an HDF5 interface that > can be optional, similar to how our other bridges are already optional. One > question is whether or not there will be a fallback non-binary > representation for these fields. > > Please let me know your thoughts/questions/suggestions/concerns. > > Eric > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > cclib-devel mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-devel > > |
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From: Eric B. <er...@pi...> - 2017-10-13 17:41:48
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Hi everyone, I've been invited to attend the a MolSSI workshop on quantum chemistry schema at LBNL on 11/30 and 12/1; I've attached a PDF of the solicitation. Here is Daniel Smith's email to me: > During a MolSSI Interoperability Workshop this year, one topic that came > up was an interoperable schema between various quantum chemistry programs > so that users and developers could have a unified interface to move data in > and out of these very large programs as opposed to processing ASCII files > and building custom inputs. To this end, we have been tweaking a base > schema and talking to the creators of the many different schema already out > there in the hope of unifying these diverse groups. We hope to pull in > approximately 30 quantum chemistry developers from a broad set of > backgrounds and programs to make this a reality. > > The current version and primary discussion of the schema can be found on > GitHub here: https://github.com/MolSSI/QC_JSON_Schema > > We would encourage your entire community to discuss the schema in its > current form in order to spur more discussion and tune the overall scope of > the schema on the GitHub page, otherwise feel free to email me back > personally if you have any questions. For the workshop participant, we are > looking for one developer that would represent your community to help > finalize the schema and decide on future governance and communication plans. > As of right now, I am not representing cclib since we should come to some census decision about our path. I do feel it gives us more exposure, which is good, and would push development a bit, which could be a pro or a con. We are well-positioned to implement (now or soon) all of their requirements (https://github.com/MolSSI/QC_JSON_Schema/blob/master/Requirements.md), especially for QM packages that will certainly not support the schema directly. A substantial amount of work was already done by Sanjeed during GSoC last year as part of CJSON, which itself is being unified. Our transition to more modular attributes, which we've already started discussing, can only make this easier. Their repository is just a few Markdown files and is worth reading. As far as what our obligation would be, I think it would be to implement their spec, with their development assistance if need be. Implicit in my invitation to the workshop is that I'd do most of the heavy lifting. In particular, since large data (MO coefficients, densities, response vectors, ...) will need to be stored, we will probably need an HDF5 interface that can be optional, similar to how our other bridges are already optional. One question is whether or not there will be a fallback non-binary representation for these fields. Please let me know your thoughts/questions/suggestions/concerns. Eric |
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