cclib-devel — Developer's mailing list

[cclib-devel] Release 1.7!

[Karol L. <kar...@gm...>]

Hello everyone,

It's my pleasure to let you know that we recently released v1.7 of cclib.
The main change for this release (not the minor version change) is letting
go of Python2 support.

You can find the release and all details at:
https://github.com/cclib/cclib/releases/tag/v1.7

Best regards,
cclib developers

[cclib-devel] v1.7 and dropping Python2 support

[Karol L. <kar...@gm...>]

Hello everyone,

We had a dev meeting recently and decided that we will accelerate our
sunsetting of support for Python2. We're going to drop Python2 in the
coming days in master, and plan to release v1.7 in about two weeks. This
will let us clean up the codebase and make future development easier.

If anyone has concerns about dropping Python2, please reach out to us.

Thank you,
cclib dev team

[cclib-devel] cclib-v1.6.4 is now out!

[Karol L. <kar...@gm...>]

Hello everyone,

I recently finalized the v1.6.4 release. Here are the links:
GitHub: https://github.com/cclib/cclib/releases/tag/v1.6.4
PyPI: https://pypi.org/project/cclib
Conda: https://anaconda.org/conda-forge/cclib

Thanks for all the work!

Karol

[cclib-devel] cclib-v1.6.3 is now published!

[Karol L. <kar...@gm...>]

Hello everyone,

I just finalized the v1.6.3 release:
https://github.com/cclib/cclib/releases/tag/v1.6.3. The new version is now
also available in pypi <https://pypi.org/project/cclib/> and conda
<https://anaconda.org/conda-forge/cclib>.

Thanks for all the work, and I think we'll do another release after the
summer when Minsik's GSOC project is finished.

Karol

Re: [cclib-devel] Inquiry about cclib's GSoC projects

[Karol L. <kar...@gm...>]

Hi Hussein,

Great to hear from you, and sorry for the delay. My advice would be to
consider each of the projects and decide on one that seems most interesting
and impactful for you and clear in terms of what you think should be done.
You are also free to suggest a different project, if you have something
else in mind.

In ca
se you haven't noticed, we do have a list of cclib issues that might be
appropriate for "beginners":
https://github.com/cclib/cclib/issues?q=is%3Aopen+is%3Aissue+label%3Abeginner

+cclib-dev List <ccl...@li...> in case someone else
wants to chime in

Let us know if you any questions,
Karol

On Sun, Feb 23, 2020 at 2:16 PM Hussein Faara <hfa...@my...>
wrote:

> Hi Dr. Langner,
>
>
>
> I hope you’re doing great. As a fan of open-source projects, I was reading
> on proposed chemistry projects for this year’s GSoC when I came across the
> cclib’s project descriptions. As someone who’s familiar with computational
> chemistry and its potential in helping science fast-track most
> time-consuming tasks, I want to contribute to any of such projects in any
> way I can. I’m particularly interested in the web crawler project but
> understanding that either of the projects would extend the functionality of
> cclib makes me eager to work on any of them.
>
>
>
>        I know you’re very busy, but I was wondering if I could possibly
> start communication with you about reasonable benchmarks etc. for the
> project, since I’m confident the experience will be very rewarding to both
> myself and anyone who uses cclib. Thank you for your time, and I look
> forward to hearing from you.
>
>
>
>
>
> Regards,
>
> Hussein
>

Re: [cclib-devel] Queries on Advanced Analysis of Quantum Chemistry Data in GSoC-20

[Karol L. <kar...@gm...>]

Hi Jishnu,

+Geoffrey Hutchison <geo...@gm...> who is the other potential
mentor on this project

It's great to hear from you. It sounds like you have a reasonable
background for this project. The selection process is based mostly on your
application and any evidence we have of programming ability. For the
latter, it's useful to take a look at the cclib codebase and perhaps try to
tackle one of the outstanding issues we have labeled for beginners:
https://github.com/cclib/cclib/issues?q=is%3Aopen+is%3Aissue+label%3Abeginner

Also +cclib-dev List <ccl...@li...> if other want to
chime in.

Hope that helps,
Karol

On Mon, Mar 2, 2020 at 9:11 AM Jishnu Biswas <jis...@ii...>
wrote:

> Hey,
> I am a second year undergraduate of Chemical Engineering Department of
> Indian Institute of Technology, Kharagpur(IIT-Kharagpur). I have read the
> project idea 'Advanced Analysis of Quantum Chemistry Data' under cclib
> projects of Open Chemistry. I am very much interested to contribute in the
> topics of additional calculation method of quantum chemistry and also in
> Electron localisation function. I have a decent knowledge in C, C++, python
> , MATLAB programming language and also very must familiar with linear
> algebra stuffs and techniques required to solve any linear and non-linear
> system of equations and differential equations(ODE and PDES) using
> numerical procedures with detail stability and convergence analysis. I am
> doing coursework on these topics. Currently I am accomplishing a project on
> Soft-Glassy Rheological Modelling(Paper by Prof. Peter Sollich) in MATLAB
> and python with numerical solution techniques. Can you please tell me what
> the stuffs I have to do now in order to get selected in your project work
> and can contribute in the same?
>
> Thanking you in anticipation.
>
> Regards,
> Jishnu Biswas
> Dept. of Chemical Engineering
> Indian Institute of Technology-Kharagpur
> Kharagpur, West Bengal, India
>

Re: [cclib-devel] GSoC 2020 Project

[Karol L. <kar...@gm...>]

Hi Varun,

Sorry again for the delay. Adding +cclib-dev List
<ccl...@li...> in case others want to chime in

You're right, the idea for the project is set up a system/pipeline to
discover and harvest computational results online. I think the problem
statement is quite clear, if terse. We do expect prospective students to be
self-starters and already somewhat familiar or at least able to become
reasonably familiar with the computational chemistry landscape online.
Perhaps consider following up on the following:
- continue perusing our codebase and docs, just as you've been doing
- you can try to tackle on of the issues for cclib marked for beginners
<https://github.com/cclib/cclib/issues?q=is%3Aopen+is%3Aissue+label%3Abeginner>
- try to start writing an application for your idea
- consider sources - what repositories of computational chemistry results
already exist online?
- consider prior art - has anybody already done something similar?

Hope that helps,
Karol


On Wed, Feb 26, 2020 at 12:26 PM Karol Langner <kar...@gm...>
wrote:

> Hello Varun,
>
> Thank you for you email, and sorry for the delay. I have been travelling
> the last few days and am behind on my email. I will get back to you soon.
>
> - Karol
>
> On Wed, Feb 26, 2020 at 9:17 AM Varun Balasaheb Bankar <
> f20...@go...> wrote:
>
>> Dear Karol,
>>
>> I had mailed you regarding the project "Discovering Computational
>> Chemistry Content Online" for GSoC 2020 but did not hear back from you. I
>> am sending this mail to check if you are could share some information
>> regarding the project as very little information was given in the
>> description of the project. Meanwhile, I have started reading the
>> documentation of cclib at http://cclib.github.io and trying to
>> understand the codebase. Waiting to hear from you regarding if you have any
>> problem statement as such for me to work upon to showcase my ability for
>> working on this project. From the description of the project, I understood
>> that the project is mainly about discovering content from the web and then
>> using cclib to parse the information from them.
>>
>> Hope to hear from you soon.
>>
>> Thank you.
>>
>> Regards,
>> Varun Bankar
>>
>

Re: [cclib-devel] GSoC 2019 - Project Discussion

[Karol L. <kar...@gm...>]

Hi Bhavay,

Here are my opinionated responses to your questions. Please treat them with
a grain of salt :) Also CC'ing two mailing list in case others would like
to chime in.

1) I think of this project as an "infrastructure component". That means
that it would result in code that others could use to more easily build a
service that searches the content. But maybe it is feasible and even more
reasonable to set up a whole server in the summer, as a prototype. I'm not
sure about this and would love to hear your thoughts. But I do see those
two things as rather separate. I think the main issue pinning down the
scope of the crawling and what content should be indexed. Note that there
are things like Chemspider out there, so it's worthwhile to see the
functionality those currently provide.

2) It's hard to call out one specific problem this is meant to solve. I see
this as more of a systematic gap in the comp chem sphere. Let's say I'm
researching how nitrogen behaves close to metal surfaces.... I can search
the web, literature, structural databases. But people must have done
thousands of computations already for nitrogen and metals... there's
currently no way to get that list and build on top of it. That really
should be the starting point. And that would be pretty cool to have. Now, I
don't think we can index all past computations, since people haven't
generally been uploading their raw outputs along side scientific articles.
But something like this could help nudge people in that direction. There's
also a whole universe of possibilities if we had a publicly available
database of computational results at our disposable, like re-using orbitals
and other properties, learning on top of results, etc.

3) As a field I would say computational chemistry is VERY mature. It's been
around for decades and the main methods are well studied and entrenched. A
lot of current work happens around the edge cases and adds minor
improvements to existing numerical methods. Of course, there are some
really interesting new things going on, but most research of the type "run
program X wiht method Y on system Z". Most people treat comp chem programs
as black boxes, which is why treating their raw results as research outputs
makes a lot of sense.

4) The main constraint is the GSOC timeline, so you need to think about how
to structure work in a way that fits in to the space of a summer.

I don't have specific questions for you, but I would encourage you to also
look at other projects and how they relate to this one. For example, the
project around producing QCJSON output is really interesting. If you think
about how to make search results in this project available, you'll quickly
come to the conclusion that it should be some kind of common format or data
structure. This is exactly what QCJSON is trying to achieve. Of course, we
could just provide the Python API internal to cclib, but it makes a lot of
sense to rely on something self-contained.

Hope that helps a little,
Karol

On Thu, Mar 21, 2019 at 12:12 PM Bhavay Aggarwal <bha...@ii...>
wrote:

> Hi,
>
> I got a bit confused after reading the wiki but I think I understand now.I
> thought we would be calculating using cclib so that's gone. I think
> building the crawler first is necessary before we can think of any
> additional functionalities and for the time being, I can only think of web
> integration which also requires the completion of the major task first. I
> was wanted to ask some other questions related to the project which would
> be helpful with the proposal.
> 1) How does this project help OpenChem and its users?
> 2) Similar to the above but are there any problems we are trying to solve
> with this?
> 3) I was not very familiar with computational chemistry so as a filed is
> it still in its beginning stages to its major audience?
> 4) Since currently there is only a single project to work on do I need a
> rigid timeline?
>
> If there are any questions you would like me to answer, I would be more
> than happy to do so,
>
> Thanks
>
>>

Re: [cclib-devel] Inquiry regarding GSOC 2019

[Karol L. <kar...@gm...>]

Hi Rtain,

We get this question a lot, so I added the "beginner" label to a bunch of
issues that could be good targets for a beginning contributor to cclib:
https://github.com/cclib/cclib/labels/beginner

CC'ing the dev list to raise visibility.

HTH,
Karol

On Tue, Mar 19, 2019 at 10:43 AM Ratin Kumar <rat...@gm...>
wrote:

> My name is Ratin Kumar, CS undergrad at National Institute of Technology
> India. I was interested in your Project: Discovering computational
> chemistry content online. I understand there is a vast amount of knowledge
> available on the internet and it could be interpreted and harnessed. I
> really enjoy web scraping and parsing. I had previously made a website
> which would crawl websites and search for ebooks available for download.
>
> If you could provide me with any task, to test my skills or provide more
> information about the project I would love to extend the discussion and
> make some demos to show my understanding of the subject and how helpful I
> could be to the project.
>
> Regards,
>   Ratin
>

Re: [cclib-devel] GSoC 2019

[Karol L. <kar...@gm...>]

Oh, so https://github.com/cclib/cclib/issues/610.

I was thinking more of a snapshot of current citing literature... you can
download the list and format it with some script into markdown. Then
repeating it next year won't be so much work. I don't think we need the
hassle of any dynamic or crawling system.

Maybe even just linking to a list of citation in Google Scholar would be
sufficient for now.

- Karol

On Fri, Mar 15, 2019 at 12:56 PM Bhavay Aggarwal <bha...@ii...>
wrote:

> Hi,
> We were discussing ways to solve the issue regarding expanding the
> literature citing/using cclib.
>
> On Fri, Mar 15, 2019 at 9:07 PM Karol Langner <kar...@gm...>
> wrote:
>
>> Sorry for the late reply. What discussion thread was this from? There's
>> no context in this email.
>>
>> On Fri, Mar 8, 2019 at 1:47 AM Bhavay Aggarwal <bha...@ii...>
>> wrote:
>>
>>> The only other alternative I can think of is to manually document them.
>>> If there are any other method you would like this to be implemented by
>>> please let me know. I will continue to work on ways to do this.
>>>
>>>>

Re: [cclib-devel] Regarding machine learning to complement cclib

[Karol L. <kar...@gm...>]

Hi Aditya,

Sorry for the late reply. Yes, we took out the ML project, since it seems
both too research-y and probably too advanced for a GSOC project. I still
think it's worth exploring, but maybe just as a hobby someday.

As far as training a model to estimate electronic structure properties,
which is what your describing, there have already been many studies done in
this area, although most aim to produce the electronic structure directly
and not properties based on other properties as you suggest. The latter
presumes you already get the electronic structure from somewhere else.

In any case, I don't think (anymore) that these are good projects for GSOC.
If you'd like to go in this direction with a software project in GSOC,
consider looking at DeepChem's project ideas (also part of OpenChemistry).

Hope that helps,
Karol

On Mon, Mar 4, 2019 at 11:20 PM Aditya Kamath <adt...@gm...> wrote:

> Dear Karol,
> I have gone through the features and functions of cclib. I had been trying
> to look into your idea of using machine learning for parsing data. However,
> this seems very ambitious as it would involve NLP as well as complex deep
> neural networks. I have noticed that you have changed your project idea
> towards mining data.
>
> I still believe we can use machine learning to compliment cclib. An Idea I
> have is to try to search for relations between the parsed data. As
> cclib deals with different software outputs, it has access to a large
> amount of data like electronic transition energies, molecular orbital
> energies, vibrational frequencies etc for different kind of molecular
> systems.
>
> Usually, a computational chemist would have to model the molecule and
> setup numerical calculations to solve for the energies and vibrational
> frequencies etc. I suspect a Neural Network is smart enough to directly
> predict these states given the essential information about the molecular
> system- which is also extracted by cclib.
>
> In essence,
> http://cclib.sourceforge.net/wiki/index.php/Development_parsed_data
> we split the list in the table into parameters and results. The model will
> then train using the extracted data and can predict results for a new set
> of parameter data without having any computation done for the new cases.
>
> Please let me know if this is something you might be interested in. I will
> be happy to explain this idea further.
>
> Bests,
> Aditya
> ᐧ
>
> On Wed, Feb 6, 2019 at 2:02 AM Karol Langner <kar...@gm...>
> wrote:
>
>> Hi guys,
>>
>> I think Tyler is spot on here, generally. Which is why we haven't really
>> explored this path and converted cclib to a machine learned model.
>>
>> While output files are typically structured and somewhat organized, as a
>> developer of cclib parsers I would qualify that statement significantly...
>> maybe it's fair to say they are
>> usually-well-organized-but-with-many-caveats-and-subtle-changes-over-time-which-require-much-debugging-and-testing-to-get-consistent
>> :)
>>
>> Really, the purpose of this project would be to see how far ML can get
>> you in extracting chemical facts. It would definitely need to leverage the
>> strong prior knowledge we have about the data we want to parse, and use it
>> to enforce invariants/constraints. The goal, however, is not to estimate
>> the values, but extract them from the logfile and classify them as
>> attributes. If the model extracts the wrong data, then it is still exact,
>> but just classified wrong. This is something a human might also do, and
>> I've seen students do before (oops, wrong orbital!). There has been some
>> work along those lines in the past for extraction, although not in this
>> particular domain. And it's not clear that this sort of model is easily
>> achievable. But then again, maybe it is, I haven't tried. On the flip side,
>> if it is possible, then we wouldn't have to write this complicated parsing
>> code, just teach the model and tune it for a specific new program or output
>> type.
>>
>> Anyway, it is true that if you're interested in standard ML methods and
>> chemistry, there are much more "hot" topics out there.
>>
>> - Karol
>>
>>
>> On Tue, Feb 5, 2019 at 12:14 PM Tyler Josephson <jos...@um...> wrote:
>>
>>> Hi Aditya,
>>>
>>> While I think ML is exciting and promising for learning potential energy
>>> surfaces or efficiently interpolating/extrapolating properties of materials
>>> and molecules within a particular domain, I don't see it's value for
>>> parsing electronic structure output files.
>>> Because output files from simulation are quite well-organized, values
>>> can be extracted by simply following the logic of the output file and
>>> reading the relevant text into memory. Not only are the values *exact* this
>>> way, rather than estimates, it likely requires fewer operations for the
>>> computer to perform than a DL approach; parsing is quite cheap as far as
>>> computational tasks are concerned.
>>>
>>> DL might also be able to find interesting correlations and patterns in
>>> the data that humans tend to miss; using the whole simulation output, not
>>> the just values we assume to be important, may lead to new insights.
>>>
>>> Best,
>>> Tyler
>>>
>>> On Tue, Feb 5, 2019 at 9:59 AM Karol Langner <kar...@gm...>
>>> wrote:
>>>
>>>> Well, the parsers are not organized by method or whatnot... there's a
>>>> base class with a parse method (
>>>> https://github.com/cclib/cclib/blob/master/cclib/parser/logfileparser.py#L281)
>>>> and the various parsers inherit from that and implement and extract method
>>>> which is called by the parse method (for NWChem, for example:
>>>> https://github.com/cclib/cclib/blob/master/cclib/parser/nwchemparser.py#L42).
>>>> So there's no function really that would be replaced. It's the whole
>>>> parsing that would be imitated by the machine learned thing. Of course, one
>>>> could as a first step try to learn to parse rather easy things like number
>>>> of atoms and charge.
>>>>
>>>> HTH,
>>>> Karol
>>>>
>>>> On Tue, Feb 5, 2019 at 3:32 AM Aditya Kamath <adt...@gm...>
>>>> wrote:
>>>>
>>>>> Hi Karol,
>>>>> Thank you for responding to my message. In that case, the problem
>>>>> becomes information extraction. I think it is possible using Deep Learning.
>>>>> Can you tell me some examples of cclib parsing functions you feel can be
>>>>> replaced with ML?
>>>>> Best Regards,
>>>>> Aditya
>>>>>
>>>>> On Wed, Jan 30, 2019 at 1:12 AM Karol Langner <kar...@gm...>
>>>>> wrote:
>>>>>
>>>>>> Hi Aditya,
>>>>>>
>>>>>> My intention with the idea was solely data extraction from log files,
>>>>>> so parsing. But if you see other applications of ML within the scope of
>>>>>> cclib, we're definitely interested. Please note other projects under the
>>>>>> OpenChemistry umbrella also have ML ideas, and many of those are more
>>>>>> straightforward. Here, with parsing, things will be much more researchy.
>>>>>>
>>>>>>
>>>>>> HTH,
>>>>>> Karol
>>>>>>
>>>>>> On Tue, Jan 29, 2019, 2:13 AM Aditya Kamath <adt...@gm...>
>>>>>> wrote:
>>>>>>
>>>>>>> Dear Karol,
>>>>>>> I am Aditya, I read your GSoC project Idea to possibly implement
>>>>>>> machine learning to compete with cclib as an efficient data parser. From
>>>>>>> what I understand, you wish to train a machine learning model to handle and
>>>>>>> convert data between various software outputs.
>>>>>>>
>>>>>>> I suggest that the role of machine learning is not to handle or
>>>>>>> parse data but rather to analyze it. cclib can benefit from backend trained
>>>>>>> ML models to do tasks like classify file data, identify and extract
>>>>>>> information from files. It can also perform very accurate regression and
>>>>>>> emulate complex function maps which could benefit any calculation methods
>>>>>>> used by cclib.
>>>>>>>
>>>>>>> We can use algorithms like CRF's to label and identify data in data
>>>>>>> files or use neural networks or any other regression methods to compliment
>>>>>>> calculations.
>>>>>>>
>>>>>>> I am a final year student, looking for a prospective GSoC project to
>>>>>>> work with. I have previously worked with a research group implementing
>>>>>>> machine learning for ODE solvers to compete with Gaussian software
>>>>>>> calculations, ab initio calculations. I would be happy to discuss further
>>>>>>> on how we can work with cclib functionalities. I look forward to hearing
>>>>>>> from you.
>>>>>>>
>>>>>>> Best Wishes,
>>>>>>> Aditya Kamath
>>>>>>>
>>>>>> _______________________________________________
>>>> cclib-devel mailing list
>>>> ccl...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>>>>
>>>
>>>
>>> --
>>> Tyler Josephson
>>> PhD Chemical Engineering
>>> Postdoctoral Research Associate, Siepmann Group
>>> University of Minnesota, Twin Cities
>>> 651-269-1433 |  | LinkedIn <https://www.linkedin.com/in/trjosephson/>
>>>
>>

Re: [cclib-devel] Regarding GSOC project

[Karol L. <kar...@gm...>]

Hi Jay,

Sorry for the late reply and thanks for your interest. The ideas page lists
project ideas, the actual tasks will depend on how you decide to implement
the project. I would recommend getting a sense of which project you're most
interested in, and trying to figure out what you need to do to move it
along. I don't quite understand what you mean by "branch" in the last
sentence - as far as GitHub is concerned, we usually merge all new changes
into the master branch.

Hope that helps,
Karol

On Fri, Mar 8, 2019 at 8:33 PM Jay dev Jha <jay...@gm...> wrote:

> Respected Sir,
> Myself Jay Dev Jha , Indian Institute of Information Technology, Manipur,
> India , Computer Science and Engineering Department, eagers to work with
> this organization.
> I went through the ideas list and wants to work under your supervision as
> I am familiar with python and Chemistry is an area of my interest since 6th
> standard.
> I had used so many computational chemistry software such as Atomistix
> Toolkit,Brian QC,DFTB+,Exabyte.io,GPAW,HORTON etc.
> I went through the ideas page but couldn't get clarified about the actual
> task and moreover which specific branch this project is going to deal with.
> So please guide me so as to proceed further.
> Thanking you
> With Regards
> JayDev
>

Re: [cclib-devel] Google Summer of Code 2019

[Karol L. <kar...@gm...>]

Hello Utkarsh,

Sorry for the late reply. As far as GSOC is concerned, I think at this
point you should focus on the application. Keep in mind that the timeline
is limited to the summer. So, for example:
1. Which methods do you think are feasible to finish during the summer? All
three? A subset? If it's tough to say, does it make sense to set a stretch
target?
2. For these methods, what are the key ingredients, and which aspects do
you think will be problematic to implement?
3. Will the implementation live within cclib, or be based on it and live
separately?
4. Are there any significant performance bottlenecks? Do you have ideas
about how to handle these?

Hopefully that helps somewhat.

Best,
Karol

On Thu, Mar 14, 2019 at 7:57 AM Utkarsh <utk...@re...>
wrote:

> Dear Hutchison and Langner,
>
> I am still looking forward to hear from you.
> Thanking you in anticipation.
>
> Regards,
> Utkarsh
>
> ----- Original Message -----
> From: "Utkarsh" <utk...@re...>
> To: "geoffh" <ge...@pi...>, "karol langner" <kar...@gm...>
> Sent: Saturday, March 9, 2019 8:21:15 PM
> Subject: Google Summer of Code 2019
>
> Dear Hutchison and Langner,
>
> My name is Utkarsh. I’m a third-year student currently enrolled in a dual
> degree programme: B-Tech in Computer Science and MS by Research in
> Computational Natural Sciences, at International Institute of Information
> Technology, Hyderabad.
> I'm a science enthusiast with a vigorous passion for algorithms and logic.
> I've had a past experience of working on quantum chemistry as part of my
> both coursework and research projects. I've also used python intensively
> for scientific computing. It is for these reasons I'm hoping to choose the
> project - "Advanced Analysis of Quantum Chemistry Data", mentored by you.
> As a beginner, I've had a thorough read on the following research papers:
> ": https://arxiv.org/abs/1512.08270", "
> https://www.ias.ac.in/article/fulltext/jcsc/128/10/1527-1536", and "
> https://doi.org/10.1016/S1380-7323(07)80006-9".
> If given a chance, I'll surely be thrilled to work with both of you on
> this as my GSoC-2019 summer project. So, I would request you to guide me
> through with the next required steps.
>
> Regards,
> Utkarsh
>

Re: [cclib-devel] GSoC - Regarding the Project: Support for QCSchema JSON output

[Karol L. <kar...@gm...>]

Hi Bhuvan,

Thanks for the interest. I would encourage you to go over the following
pages thoroughly, if you haven't already:
http://wiki.openchemistry.org/Applying_to_GSoC
https://github.com/cclib/cclib/issues/643

If you have, I would then recommend digging into the cclib code, especially
the io modules, and then trying to grok the actual QSchema repository (
https://github.com/MolSSI/QCSchema). I think spending some time between
those two repositories will give you a good idea about how to approach this
project.

Hope this helps, and let us know if you have any other questions,
Karol

On Tue, Mar 12, 2019 at 3:38 PM Bhuvan Singla <bhu...@gm...>
wrote:

> Hello Eric and Karol,
>
> I am an undergraduate student at the Indian Institute of Technology (IIT),
> Kanpur. I am interested in working on the project 'Support for QCSchema
> JSON output'. I have experience in Python. Also, I have good basic
> knowledge of the concepts of physics and chemistry. I request you to please
> guide me through this project and get started. I will really like to
> contribute to it.
>
> I have also attached my resume for your reference.
>
> Regards,
> *Bhuvan Singla*
> Undergraduate Student
> Indian Institute of Technology, Kanpur
>

Re: [cclib-devel] [Openchemistry-developers] GSoC'19 Introduction and Interest

[Karol L. <kar...@gm...>]

Hi Rounak,

Great to hear from you. CC'ing another mailing list (cclib-devel) you might
be interested in.

- Karol

On Sun, Mar 10, 2019 at 10:20 AM Berquist, Eric John <er...@pi...> wrote:

> Hello Rounak,
>
> Here is an invitation link to the Open Chemistry Slack:
> http://bit.ly/ocGSOC19
>
> Most of what you need to know is outlined on our how-to page (
> http://wiki.openchemistry.org/Applying_to_GSoC). You can also take a look
> at our current issues (https://github.com/cclib/cclib/issues) and pull
> requests to see what we've been working on. Ideally, we'd like to see if
> you can contribute something to the project before the proposal, even if
> it's small.
>
> Eric
>
> On Fri, Mar 8, 2019 at 2:22 AM Rounak Agarwal <rou...@gm...>
> wrote:
>
>> Hello,
>>
>> I am Rounak Agarwal, a third year CSE undergraduate at IIIT Jabalpur,
>> India. I am looking to contribute to *cclib* under* Open Chemistry* as
>> part of GSoC'19. I went through the ideas listed at
>> http://wiki.openchemistry.org/GSoC_Ideas_2019#cclib_Project_Ideas
>> <https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwiki.openchemistry.org%2FGSoC_Ideas_2019%23cclib_Project_Ideas&data=02%7C01%7Cerb74%40pitt.edu%7C2859938bfb214b84d04c08d6a396ca5d%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C636876265385727292&sdata=H%2Fl0DsISMGfnQleUUdWGJp8dtykZ9EtrvaqDMisASow%3D&reserved=0>
>>
>> I am interested in the idea *Support for QCSchema JSON output*
>>
>> I am familiar with Git and Github having contributed to Open Source
>> projects before. My Github profile: https://github.com/agarwalrounak
>> <https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fagarwalrounak&data=02%7C01%7Cerb74%40pitt.edu%7C2859938bfb214b84d04c08d6a396ca5d%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C636876265385727292&sdata=HblSIGYJW9xmwlaCfCcJzmJEYA8lEUDkpOd8xHuvh0Q%3D&reserved=0>
>>
>> You can read more about my previous Open Source contributions here:
>> https://medium.com/@agarwalrounak
>> <https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmedium.com%2F%40agarwalrounak&data=02%7C01%7Cerb74%40pitt.edu%7C2859938bfb214b84d04c08d6a396ca5d%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C636876265385737297&sdata=lWwK2eT5BpCGs%2FQUYZMtm8IexVz0NuGxJwpjAfMPVKo%3D&reserved=0>
>>
>> I also have a lot of experience with Python as most of the projects I
>> have worked on involved Python. Furthermore, I have dealt with JSON before
>> as I have created an application where I had to parse the JSON output
>> returned by the API for useful information. The same project can be found
>> here: https://github.com/agarwalrounak/Codigo_Maestro
>> <https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fagarwalrounak%2FCodigo_Maestro&data=02%7C01%7Cerb74%40pitt.edu%7C2859938bfb214b84d04c08d6a396ca5d%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C636876265385737297&sdata=kyWzrpFdwe7cLveM1S7LOG2J2dCkGgEGB6PcBR5Cxb4%3D&reserved=0>
>>
>> Also, I have some experience with physics and chemistry since I had
>> science as my major in class 12.
>> To discuss further on the idea, I request an invitation to the slack
>> channel https://openchemistry.slack.com/
>> <https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fopenchemistry.slack.com%2F&data=02%7C01%7Cerb74%40pitt.edu%7C2859938bfb214b84d04c08d6a396ca5d%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C636876265385747306&sdata=0khL8DEXG9znzhcfLG%2FxEoAS%2BwRNCJwfAbasLUZj41c%3D&reserved=0>
>>
>> Also, I would like to know how I can move ahead with the idea so that I
>> can prepare a proposal.
>>
>> Looking forward to a lot of fruitful discussion on the idea.
>>
>> Regards,
>>
>> Rounak Agarwal
>> _______________________________________________
>> Openchemistry-developers mailing list
>> Ope...@pu...
>>
>> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpublic.kitware.com%2Fmailman%2Flistinfo%2Fopenchemistry-developers&amp;data=02%7C01%7Cerb74%40pitt.edu%7C2859938bfb214b84d04c08d6a396ca5d%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C636876265385757311&amp;sdata=DSHZib4AGSU%2Frcuq8qFC2Jsq6NEw9fDOkwAeBNUHM5k%3D&amp;reserved=0
>>
> _______________________________________________
> Openchemistry-developers mailing list
> Ope...@pu...
> https://public.kitware.com/mailman/listinfo/openchemistry-developers
>

Re: [cclib-devel] Regarding Google Summer of Code GSoC-2019

[Karol L. <kar...@gm...>]

Hi Jishnu,

Eric gave an excellent intro. I'm just CC'ing some mailing lists you might
be interested in following.

- Karol

On Sun, Mar 10, 2019 at 10:31 AM Eric Berquist <eri...@gm...>
wrote:

> Hello Jishnu,
>
> If you're interested, here is an invitation link to the Open Chemistry
> Slack: http://bit.ly/ocGSOC19
>
> It's great that you have a lot of experience running quantum chemistry
> software; it should give you intuition for how different parts of quantum
> chemical output will map to a JSON representation. Most of what you need to
> know is outlined on our how-to page (
> http://wiki.openchemistry.org/Applying_to_GSoC). You can also take a look
> at our current issues (https://github.com/cclib/cclib/issues) and pull
> requests to see what we've been working on. Ideally, we'd like to see if
> you can contribute something to the project before the proposal, even if
> it's small and unrelated to the proposal.
>
> One of the issues is for QCSchema integration, so take a look at that and
> the MolSSI repo to start building ideas.
>
> Eric
>
> On Fri, Mar 8, 2019 at 8:56 AM JISHNU V <jis...@gm...> wrote:
>
>> Dear Sir,
>>
>> I'm Jishnu V, a final year Masters student working in Computational
>> Chemistry at National Institute of Science Education and Research (NISER) ,
>> Department of Atomic Energy, India. I'm writing this with regards to Open
>> Chemistry organization's project idea for Google Summer of Code titled " *Support
>> for QCSchema JSON output* "
>>
>> I have experience with python and C++ and has been familiar with
>> computational chemistry software such as GAMESS, Gaussian16, NWchem,
>> Molpro, Molden, Avogadro, Firefly, Venus etc as I'm using them everyday as
>> a part of my Masters Project since past two years. I'm working in Molecular
>> Reaction Dynamics lab at NISER and so i'm familiar with Quantum Mechanics,
>> electronic structure calculations and computational chemistry packages
>> which are the essential parts of these software, and also I'm a part of
>> coding club at NISER. Adding all this I'm naturally interested in working
>> on this project.
>>
>> I request you to brief me with next steps to apply for this project, I
>> look forward to hear back from you.
>>
>> Sincerely,
>> JISHNU V
>> Int.MSc, NISER, Bhubaneswar
>> Ph:+91-9078694585
>>
>

Re: [cclib-devel] GSoC 2019

[Karol L. <kar...@gm...>]

I'm not sure that writing a bibliographic parser and indexer is something
we want to sign up for. There are already many out there.

On Thu, Mar 7, 2019 at 11:48 AM Bhavay Aggarwal <bha...@ii...>
wrote:

> Wouldnt it is easier to search for cclib citations and the corresponding
> literature and then be mentioned in the docs if we wish to and that's why i
> was thinking of a web crawler.
>
> On Fri, Mar 8, 2019 at 12:44 AM Karol Langner <kar...@gm...>
> wrote:
>
>> Well, I'm not entirely sure what needs to be done, but the end state for
>> #612 would be to have the documentation (at least the part with data nodes)
>> in the code itself, instead of in separate files.
>>
>> Why are you thinking about building a web crawler?
>>
>> On Thu, Mar 7, 2019 at 9:54 AM Bhavay Aggarwal <bha...@ii...>
>> wrote:
>>
>>> Hi, I tried to solve the issue (
>>> https://github.com/cclib/cclib/issues/612) and but I cannot fully
>>> understand what really needs to be done. Also, for expanding the literature
>>> using cclib (https://github.com/cclib/cclib/issues/610), I am thinking
>>> of building a web crawler which I will start working on and tell you the
>>> results later.
>>>
>>> Thanks
>>>
>>> On Fri, Mar 1, 2019 at 1:25 AM Karol Langner <kar...@gm...>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> Thanks for your interest, Adam's suggestions are good. I invited you to
>>>> the OpenChemistry slack, although using your @gmail address which you used
>>>> in a previous email.
>>>>
>>>> Best,
>>>> Karol
>>>>
>>>> On Thu, Feb 28, 2019 at 6:04 AM Adam Tenderholt <ate...@gm...>
>>>> wrote:
>>>>
>>>>> Hi Bhavay,
>>>>>
>>>>> Thanks for your interest, and apologies for not getting back to you
>>>>> sooner. You should take a look at our open issues (
>>>>> https://github.com/cclib/cclib/issues) and see if there is anything
>>>>> you can tackle. We also have (outdated) guidelines for applying with
>>>>> OpenChemistry, so look those over:
>>>>> http://wiki.openchemistry.org/Applying_to_GSoC.
>>>>>
>>>>> Best regards,
>>>>>
>>>>> Adam
>>>>>
>>>>>
>>>>> On Tue, Feb 26, 2019 at 7:16 PM Bhavay Aggarwal <
>>>>> bha...@ii...> wrote:
>>>>>
>>>>>> Hello,
>>>>>> I am a first-year undergraduate Computer Science student at
>>>>>> Indraprastha Institute of Information Technology, Delhi (IIIT-D), India and
>>>>>> am interested in gaining some work experience this summer. I know that
>>>>>> there is no certainty that your team will again be selected for GSoC this
>>>>>> year but I have been an avid chemistry fan since high school and this seems
>>>>>> to be a very exciting organization to be contributing for and also to get a
>>>>>> headstart on a project I could be working on.
>>>>>>
>>>>>> About my technical skills, I have experience in Python, C++, HTML,
>>>>>> CSS and Javascript. Also, I have worked on an assignment in which I was
>>>>>> required to handle JSON data so I am interested in the cclib project ideas
>>>>>> specifically the project "Discovering computational chemistry content
>>>>>> online" or "Implement new parsers". I really like some of the others too
>>>>>> but for now, I don't want to take too much on my hands and instead try to
>>>>>> put in all my effort into a single project first.
>>>>>>
>>>>>> It would be really helpful if you could guide me on how I should
>>>>>> start working on these projects and what all I should start studying in
>>>>>> order to be capable in doing these.Also I cannot enter the slack discussion
>>>>>> page without an invitation from the administrator and any help regarding
>>>>>> this would be appreciated.
>>>>>>
>>>>>> Thank You
>>>>>>
>>>>>> Bhavay Aggarwal
>>>>>> bha...@ii...
>>>>>>
>>>>>

Re: [cclib-devel] Discovering computational chemistry content online and mentor

[Karol L. <kar...@gm...>]

Hi Yibo,

There's definitely the possibility!

I think there are indeed a lot of things in this area that could sidetrack
you, rabbit holes like exposing the data to the whole world, organizing it
and using it in smart ways. Defining the scope is really your job and one
of the main things you need to think about for the application. You need to
now what your strengths are and how much you can do in 12 weeks. I would
encourage you to be as narrow as possible, and detailed within the scope
you think is realistic.

Hope that helps,
Karol

On Thu, Mar 7, 2019 at 11:22 AM Zhang, Yibo <yz...@wi...> wrote:

> Hello koral,
>
> Cool, that make sense.
>
> So, I want to know what's the next step. I guess we need to store them
> into database( I have some experience with mongodb in javascript). And then
> what kind of application can it be used? Maybe transfer them into a small
> chemistry structure search engine or maybe can be used to some machine
> learning materials or the project stops there as it’s just 12 weeks
> projects. Yeah, I know It's kind of overthinking, but I want to know the
> scope of this project.
>
> Also I can write a proposal, which you can give me some suggestions based
> on, if you think I have some some possibility to join this project.
>
> Thanks,
> Yibo
> On Mar 6, 2019, 22:54 -0500, Karol Langner <kar...@gm...>,
> wrote:
>
> Hi Yibo,
>
> Great to hear from you. You've covered a lot of ground there, so let me
> respond to your questions in points:
> 1. You understood correctly, cclib will not parse "papers", it's sole
> purpose is to parse the output of comp chem programs like NWChem.
> 2. There are projects specifically trying to extract data from papers,
> this project is not meant to address that at all.
> 3. There are various places/sources of comp chem logfiles oneline,
> including supplementary information uploaded with papers and bulk
> repositories.
> 4. I am not doing anything at the moment like this project, but it seems
> like a natural extension of what cclib does.
>
> Hopefully that answers your questions. LMK if there's something else.
>
> - Karol
>
> On Wed, Mar 6, 2019 at 2:42 PM Zhang, Yibo <yz...@wi...>
> wrote:
>
>> Hello Karol,
>>
>>
>> I’m Yibo Zhang, a first year PHD student majoring in computational
>> chemistry at University of New Hampshire. I found your project(Discovering
>> computational chemistry content online) under GSoC Ideas 2019, it’s really
>> cool. There’s several reasons why this project attracts me a lot. The first
>> one is that I need to do a machine learning project about a chemical
>> sensor, so collecting a big data is a kind of precursor. Another reason is
>> that crawler always interest me especially combined with chemistry. I've
>> learned how to crawl a web and extract some interesting information and
>> I’m a fan of RSS(kind of crawler). Also learning more good tools like cclib
>> is helpful, because in my group we use another software to handle data,
>> which is not super handy for me.
>>
>>
>> However, I have a question about your project. As I have read through the
>> cclib’s description and learned how to use it, I found it can read the
>> output file like Nwchem, which I work with. However, if we want the crawler
>> to grab information from any published paper, it can not be processed by
>> cclib directly. What I think is we need to use Regex to extract some useful
>> information then store them into database, which is unrelated to cclib.
>> Another possible way is that some published paper may contain the output
>> file, then we only grab that kind of paper then handle them with cclib.
>> However, as fas as I know, not too much paper contains the output file if
>> there’s any. My final guess could be that there’s some websites storing a
>> lot of computational model, then we can grab them and put them into cclib.
>>
>>
>> Please give me a hint as I’m really curious about what you are going to
>> do.
>>
>> Thanks,
>> Yibo
>>
>

Re: [cclib-devel] GSoC 2019

[Karol L. <kar...@gm...>]

Well, I'm not entirely sure what needs to be done, but the end state for
#612 would be to have the documentation (at least the part with data nodes)
in the code itself, instead of in separate files.

Why are you thinking about building a web crawler?

On Thu, Mar 7, 2019 at 9:54 AM Bhavay Aggarwal <bha...@ii...>
wrote:

> Hi, I tried to solve the issue (https://github.com/cclib/cclib/issues/612)
> and but I cannot fully understand what really needs to be done. Also, for
> expanding the literature using cclib (
> https://github.com/cclib/cclib/issues/610), I am thinking of building a
> web crawler which I will start working on and tell you the results later.
>
> Thanks
>
> On Fri, Mar 1, 2019 at 1:25 AM Karol Langner <kar...@gm...>
> wrote:
>
>> Hi,
>>
>> Thanks for your interest, Adam's suggestions are good. I invited you to
>> the OpenChemistry slack, although using your @gmail address which you used
>> in a previous email.
>>
>> Best,
>> Karol
>>
>> On Thu, Feb 28, 2019 at 6:04 AM Adam Tenderholt <ate...@gm...>
>> wrote:
>>
>>> Hi Bhavay,
>>>
>>> Thanks for your interest, and apologies for not getting back to you
>>> sooner. You should take a look at our open issues (
>>> https://github.com/cclib/cclib/issues) and see if there is anything you
>>> can tackle. We also have (outdated) guidelines for applying with
>>> OpenChemistry, so look those over:
>>> http://wiki.openchemistry.org/Applying_to_GSoC.
>>>
>>> Best regards,
>>>
>>> Adam
>>>
>>>
>>> On Tue, Feb 26, 2019 at 7:16 PM Bhavay Aggarwal <bha...@ii...>
>>> wrote:
>>>
>>>> Hello,
>>>> I am a first-year undergraduate Computer Science student at
>>>> Indraprastha Institute of Information Technology, Delhi (IIIT-D), India and
>>>> am interested in gaining some work experience this summer. I know that
>>>> there is no certainty that your team will again be selected for GSoC this
>>>> year but I have been an avid chemistry fan since high school and this seems
>>>> to be a very exciting organization to be contributing for and also to get a
>>>> headstart on a project I could be working on.
>>>>
>>>> About my technical skills, I have experience in Python, C++, HTML, CSS
>>>> and Javascript. Also, I have worked on an assignment in which I was
>>>> required to handle JSON data so I am interested in the cclib project ideas
>>>> specifically the project "Discovering computational chemistry content
>>>> online" or "Implement new parsers". I really like some of the others too
>>>> but for now, I don't want to take too much on my hands and instead try to
>>>> put in all my effort into a single project first.
>>>>
>>>> It would be really helpful if you could guide me on how I should start
>>>> working on these projects and what all I should start studying in order to
>>>> be capable in doing these.Also I cannot enter the slack discussion page
>>>> without an invitation from the administrator and any help regarding this
>>>> would be appreciated.
>>>>
>>>> Thank You
>>>>
>>>> Bhavay Aggarwal
>>>> bha...@ii...
>>>>
>>>

Re: [cclib-devel] [Openchemistry-developers] Regarding Slack Channel and GSoC'19

[Karol L. <kar...@gm...>]

Hi Amartya,

I just sent the invite.

For the project, at this point I would recommend thinking about the basics,
such as:
1. Which methods exactly do you think are most important to implement? How
many do you think are reasonable to cover in a summer?
2. Review those methods, and let us know if there's anything you don't
understand... any tough equations, or things you anticipate problems with
in the implementation?
3. Where do you think this will live? Would the code go into the cclib
repository, or something built on top of it?

One of the things we really look at is intro work and any contributions,
however small, since that's a good indicator or the quality of code you
will contribute during the summer. Take a look at our current issues in
cclib, maybe take a stab at one of them. Try to work with the code, read
through it a little bit.

Another thought for you (and others applying): cclib has been around for a
long time as far as OOS projects go (>10 years), so there are a lot of
warts and legacy bits in there. Sometimes those stand in the way of new
ideas and projects - consider if and how this would affect your project.

Hope that helps a little,
Karol

On Thu, Mar 7, 2019 at 9:04 AM Amartya Prusty <apr...@gm...> wrote:

> Dear Karol,
> I am Amartya Kumar Prusty, a 3rd year undergraduate student at IIT Kanpur,
> India and I am interested in learning and contributing to your
> organization. I have a strong interest in programming and more specifically
> in algorithms. I am also pursuing a minors in Quantum Mechanics and have
> experience in Molecular Dynamics and Density Functional Theory.
> I am interested in the project "Advanced Analysis of Quantum Chemistry
> Data" and I would like to know more and work on this with the help you and
> the co-mentors available.
> Therefore, I request you for a slack invite for the same so that I can
> start working on it at the earliest.
> Yours sincerely,
> Amartya Kumar Prusty,
> B.Tech., Indian Institute of Technology Kanpur,
> Contact : apr...@gm...
> _______________________________________________
> Openchemistry-developers mailing list
> Ope...@pu...
> https://public.kitware.com/mailman/listinfo/openchemistry-developers
>

Re: [cclib-devel] Mentorship for GSOC Project

[Karol L. <kar...@gm...>]

Hi Kumar,

Well, typically the first phase consists of scoping out the project. I
would recommend pondering the following questions first:
1. What exactly are the types of content we're talking about here?
2. Where can we find it?
3. What would be a reasonable approach to search for it?
4. Can we do a little intro work to estimate the amount of content really
out there?
5. What would be the tangible result of the project? Would it be code, or
rather a working service/process?

One of the most important factors we consider other than the application
itself is any contributions, however minor, to the codebase. These are
excellent signals for us, indicating what we can expect from your
contributions during summer.

I hope that helps,
Karol

On Wed, Mar 6, 2019 at 10:10 PM kumar saurabh <b1...@ii...> wrote:

> Hi Karol,
>
> Thanks for pointing it out.I have gone through all the ideas and those two
> interests me a lot.
>
> Apparently,i would like to contribute to project of discovering chemistry
> online.
>
> Please help where to start and specific areas you would like to focus.
>
> Thanks.
>
> Regards,
> Kumar Saurabh
>
> On Thu, 7 Mar, 2019, 11:21 AM Karol Langner <kar...@gm...
> wrote:
>
>> Hi Kumar,
>>
>> The title you mentioned ("Implementing new parsers and discovering
>> computational chemistry content online") is actually two projects on our
>> ideas page. Are you specifically thinking about one?
>>
>> I'd recommend you also go through the page with general instructions:
>> http://wiki.openchemistry.org/Applying_to_GSoC
>>
>> Best,
>> Karol
>>
>> On Tue, Mar 5, 2019 at 10:57 AM kumar saurabh <b1...@ii...>
>> wrote:
>>
>>> Hi ,
>>>
>>> I, Kumar Saurabh, a final year student at IIIT Bhubaneswar, majoring in
>>> Computer Science and engineering. Being passionate about product
>>> development, I find developing application development exciting.q  A
>>> background in engineering has allowed me to develop an in-depth, analytical
>>> approach and strengthen my critical thinking ability;
>>>
>>> I have written this email to seek mentorship for GSOC project .I
>>> thoroughly gone through the projects.*Implementing new parsers and
>>> discovering computational chemistry content online *interests me lot.I
>>> am quite proficient in Python and done quite amount of projects in creating
>>> parsers and web crawler.I am quite comfortable in API development . Could
>>> you help me with some basic initial information,so that i can get some
>>> head-start .Once i get acquainted with the existing workflow,I will present
>>> you a Proof of Concept ,so that we can be on same page.
>>>
>>> Also i am very much interested in participating with you guys this years
>>> GSoC but i seek in first knowing more about Open Chemistry and begin
>>> contributions. Any help would be greatly appreciated mentors.
>>>
>>>  I look forward hearing from you.
>>>
>>> Thank you.
>>>
>>> Kind regards,
>>>
>>> --
>>> Kumar Saurabh
>>> Dept. of Computer Science & Engineering
>>> BTech | Class of 2019
>>> IIIT Bhubaneswar
>>> LinkedIn <http://linkedin.com/in/kumar-saurabh-451625113>
>>>
>>

Re: [cclib-devel] Discovering computational chemistry content online and mentor

[Karol L. <kar...@gm...>]

Hi Yibo,

Great to hear from you. You've covered a lot of ground there, so let me
respond to your questions in points:
1. You understood correctly, cclib will not parse "papers", it's sole
purpose is to parse the output of comp chem programs like NWChem.
2. There are projects specifically trying to extract data from papers, this
project is not meant to address that at all.
3. There are various places/sources of comp chem logfiles oneline,
including supplementary information uploaded with papers and bulk
repositories.
4. I am not doing anything at the moment like this project, but it seems
like a natural extension of what cclib does.

Hopefully that answers your questions. LMK if there's something else.

- Karol

On Wed, Mar 6, 2019 at 2:42 PM Zhang, Yibo <yz...@wi...> wrote:

> Hello Karol,
>
>
> I’m Yibo Zhang, a first year PHD student majoring in computational
> chemistry at University of New Hampshire. I found your project(Discovering
> computational chemistry content online) under GSoC Ideas 2019, it’s really
> cool. There’s several reasons why this project attracts me a lot. The first
> one is that I need to do a machine learning project about a chemical
> sensor, so collecting a big data is a kind of precursor. Another reason is
> that crawler always interest me especially combined with chemistry. I've
> learned how to crawl a web and extract some interesting information and
> I’m a fan of RSS(kind of crawler). Also learning more good tools like cclib
> is helpful, because in my group we use another software to handle data,
> which is not super handy for me.
>
>
> However, I have a question about your project. As I have read through the
> cclib’s description and learned how to use it, I found it can read the
> output file like Nwchem, which I work with. However, if we want the crawler
> to grab information from any published paper, it can not be processed by
> cclib directly. What I think is we need to use Regex to extract some useful
> information then store them into database, which is unrelated to cclib.
> Another possible way is that some published paper may contain the output
> file, then we only grab that kind of paper then handle them with cclib.
> However, as fas as I know, not too much paper contains the output file if
> there’s any. My final guess could be that there’s some websites storing a
> lot of computational model, then we can grab them and put them into cclib.
>
>
> Please give me a hint as I’m really curious about what you are going to
> do.
>
> Thanks,
> Yibo
>

Re: [cclib-devel] GSOC 19 - Advanced Analysis of Quantum Chemistry Data

[Karol L. <kar...@gm...>]

Hi Vignesh,

Thanks for the interest. There is some overlap between the code base on
this project idea, namely we have some methods implemented already. I don't
think we have any issues currently enumerating the methods mentioned in the
project idea - feel free to create an issue!

I invited you to the OpenChemistry slack workspace.

Also, are you aware that DeepChem is also participating in GSOC this year
as part of OpenChemistry? Be sure to check out their ideas (
http://wiki.openchemistry.org/GSoC_Ideas_2019#DeepChem_Project_Ideas),
perhaps they are more to your liking. That being said, of course I'm not
discouraging you from looking into cclib, just raising awareness to make
sure you find what's most interesting for you :)

Best,
Karol

On Thu, Feb 28, 2019 at 4:20 PM Vignesh Ram Somnath <
vso...@st...> wrote:

> Hi Karol,
>
> My name is Vignesh and I'm a Master student in Computational Biology at
> ETH Zurich. I was applying to the Google Summer of Code and was looking at
> projects under Open Chemistry, and was interested in the project *Advanced
> Analysis of Quantum Chemistry data. *
>
> My open source experience so far has been with DepeChem and you can find a
> list of my contributions at:
> https://github.com/deepchem/deepchem/pulls?q=is%3Apr+is%3Aclosed+author%3AVIGS25
>
> I wanted to get started with gaining some familiarity either with the
> quantum chemistry details of the project / the codebase for cclib.
>
> One doubt I had was how much overlap exists between the project idea and
> the current codebase. If a fair amount does, which issues should I start
> solving first, since I couldn't find issues marked for beginners.
>
> Regards,
> Vignesh Ram Somnath
> First Year Master's student
> Computational Biology and Bioinformatics
> ETH Zürich, Switzerland
>

Re: [cclib-devel] Regarding getting started with GSoC 2019 (Open Chemistry Project)

[Karol L. <kar...@gm...>]

Also invited you to the OpenChemstry slack workspace.

On Sat, Mar 2, 2019 at 6:17 PM Karol Langner <kar...@gm...>
wrote:

> Thanks for your interest. You should take a look at the cclib code and our
> open issues (https://github.com/cclib/cclib/issues), and see if there is
> anything you can tackle. We also have (a bit outdated) guidelines for
> applying with OpenChemistry, so look those over:
> http://wiki.openchemistry.org/Applying_to_GSoC.
>
> On Fri, Mar 1, 2019 at 10:52 AM srijan verma <sri...@gm...>
> wrote:
>
>> Respected Sir,
>>
>> Hope your week is going well!
>>
>> I'm Srijan Verma, 3rd yr undergraduate (Bachelor's in Pharmacy) student
>> from BITS Pilani, India.
>> Reaching out to you to explore an opportunity to contribute to the
>> following area listed at GSoC 2019(cclib project ideas) :
>>
>>    - Discovering computational chemistry content online
>>
>> I believe my skill sets (Python, making web crawlers) converge well with
>> the given above problem.
>> I have done a couple of projects centered around Machine Learning, python
>> coding, and extracting data from online resources using python.
>>
>> Please let me know how I can start contributing, and what I need to do
>> next.
>> Also attached below is my CV for your kind perusal.
>>
>> Looking forward to work and learn from you!
>>
>> Thanking you
>> Srijan Verma
>>
>> Penultimate Year
>>
>> Bachelor’s (Hons.) in Pharmacy
>>
>>
>>
>> *Birla Institute of Technology and Science Pilani*
>>
>> *Vidya Vihar, Pilani*
>> *Rajasthan - 333031, India*
>> ᐧ
>>
>

Re: [cclib-devel] Regarding getting started with GSoC 2019 (Open Chemistry Project)

[Karol L. <kar...@gm...>]

Thanks for your interest. You should take a look at the cclib code and our
open issues (https://github.com/cclib/cclib/issues), and see if there is
anything you can tackle. We also have (a bit outdated) guidelines for
applying with OpenChemistry, so look those over:
http://wiki.openchemistry.org/Applying_to_GSoC.

On Fri, Mar 1, 2019 at 10:52 AM srijan verma <sri...@gm...>
wrote:

> Respected Sir,
>
> Hope your week is going well!
>
> I'm Srijan Verma, 3rd yr undergraduate (Bachelor's in Pharmacy) student
> from BITS Pilani, India.
> Reaching out to you to explore an opportunity to contribute to the
> following area listed at GSoC 2019(cclib project ideas) :
>
>    - Discovering computational chemistry content online
>
> I believe my skill sets (Python, making web crawlers) converge well with
> the given above problem.
> I have done a couple of projects centered around Machine Learning, python
> coding, and extracting data from online resources using python.
>
> Please let me know how I can start contributing, and what I need to do
> next.
> Also attached below is my CV for your kind perusal.
>
> Looking forward to work and learn from you!
>
> Thanking you
> Srijan Verma
>
> Penultimate Year
>
> Bachelor’s (Hons.) in Pharmacy
>
>
>
> *Birla Institute of Technology and Science Pilani*
>
> *Vidya Vihar, Pilani*
> *Rajasthan - 333031, India*
> ᐧ
>