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From: Karol L. <kar...@gm...> - 2017-09-05 16:43:49
|
---------- Forwarded message ----------
From: Otero Calvi <ao...@is...>
Date: Tue, Sep 5, 2017 at 7:55 AM
Subject: about cclib v1.5.2, HOMO/LUMO orbitals and the use of ECP
To: Karol Langner <kar...@gm...>
Hello Karol
I have some comments about cclib v1.5.2.
Normally I use pseudopotentials (ECP) in my calculations with transition
metal in GAMESS, at this point I have some comments.
1. When cclib obtain the HOMO, the value that cclib shows correspond with
an incorrect HOMO. Other programs like Gabedit or Molden shows the correct
HOMO. cclib obtain the core electrons but not use this information to
update the HOMO.
2. In this version of cclib, the inclusion of molden and wfx format to
export, have this problem, when you compare the Molden file generated by
Molden and by cclib have differences, and of course, wfx format too.
I have made a few modification of the gamessparser code to extract
HOMO/LUMO orbitals that correct this problem and is valid to restricted and
unrestricted wavefunction.
I'm not a developer, I send to you this code attached at this mail, if you
consider that it is OK, you can replace this in the original gamessparser
file. Whit this solution the molden format is exported correctly. In the
case of wfx format I think that other corrections are needed. You can use
CdtetraM1B3LYP.log in the regression list of cclib to check the code and
other output of GAMESS that not use ECP.
Best regards,
Alexis
|
|
From: Karol L. <kar...@gm...> - 2017-09-01 09:30:51
|
Hello, Earlier today I released cclib v1.5.2, which includes two new writers (Molden and WFX) and other Google Summer of Code work by Sagar Gaur. Congrats! There are also some new attributes and various bug fixes in this release. Please see the release history on github ( https://github.com/cclib/cclib/releases/tag/v1.5.2) for details. I moved most pending changes to v1.5.3, but it looks like this might be released sometime soon if we wrap up more things. I think there is some energy now to try harder to finish up existing PRs, and close or finalize existing issues. Let's try to follow up. There are also some topics we're discussing for a future backwards incompatible 2.x release. Stay tuned! - Karol |
|
From: Eric B. <er...@pi...> - 2017-08-28 20:39:09
|
Great! I will catch up on everything tonight. On Mon, Aug 28, 2017 at 12:54 PM, Karol Langner <kar...@gm...> wrote: > So I'm going to go forward with this. Opened issue to track: > https://github.com/cclib/cclib-data/issues/72 > <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fcclib%2Fcclib-data%2Fissues%2F72&data=01%7C01%7Cerb74%40pitt.edu%7Cdf52b2290577470a954808d4ee3581c7%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=sJs%2FOB0bGbINuT%2BeXwY05ll53P%2FGVyBPvkJDcoH905s%3D&reserved=0> > > On Mon, Aug 14, 2017 at 9:59 AM, Karol Langner <kar...@gm...> > wrote: > >> I've been thinking about moving the regression test code back to the main >> 'cclib' repository. We moved it over to cclib-data to make the repos more >> independent, but ultimately I think it wasn't worth it. Here are some >> reasons: >> 1. There is a still dependence between cclib and cclib-data, which the >> move was supposed to solve, so it didn't really solve anything. Namely, we >> still need to submit a bug fix before the regression test code goes in. >> 2. I think having the test code along with the fix is better value than >> having the test alongside the data. >> >> Let me know if you have any reservation, otherwise I'll prepare the move >> for v1.5.2. I'd like to prepare the new release as GSOC comes to a close so >> that it includes all of Sagar's work during the summer. >> > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! https://na01.safelinks. > protection.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=01%7C01% > 7Cerb74%40pitt.edu%7Cdf52b2290577470a954808d4ee3581c7% > 7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata= > vaMBgluT3QYtS2qAodC44P4qBcYU2jEyXoOKqtiqUos%3D&reserved=0 > _______________________________________________ > cclib-devel mailing list > ccl...@li... > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists. > sourceforge.net%2Flists%2Flistinfo%2Fcclib-devel&data= > 01%7C01%7Cerb74%40pitt.edu%7Cdf52b2290577470a954808d4ee3581c7% > 7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata= > LWkoFaH1ZLVQ2TQ3dsxh219xHBvk03ypehjy7nqpJHg%3D&reserved=0 > > |
|
From: Karol L. <kar...@gm...> - 2017-08-28 16:54:52
|
So I'm going to go forward with this. Opened issue to track: https://github.com/cclib/cclib-data/issues/72 On Mon, Aug 14, 2017 at 9:59 AM, Karol Langner <kar...@gm...> wrote: > I've been thinking about moving the regression test code back to the main > 'cclib' repository. We moved it over to cclib-data to make the repos more > independent, but ultimately I think it wasn't worth it. Here are some > reasons: > 1. There is a still dependence between cclib and cclib-data, which the > move was supposed to solve, so it didn't really solve anything. Namely, we > still need to submit a bug fix before the regression test code goes in. > 2. I think having the test code along with the fix is better value than > having the test alongside the data. > > Let me know if you have any reservation, otherwise I'll prepare the move > for v1.5.2. I'd like to prepare the new release as GSOC comes to a close so > that it includes all of Sagar's work during the summer. > |
|
From: Karol L. <kar...@gm...> - 2017-08-14 16:59:20
|
I've been thinking about moving the regression test code back to the main 'cclib' repository. We moved it over to cclib-data to make the repos more independent, but ultimately I think it wasn't worth it. Here are some reasons: 1. There is a still dependence between cclib and cclib-data, which the move was supposed to solve, so it didn't really solve anything. Namely, we still need to submit a bug fix before the regression test code goes in. 2. I think having the test code along with the fix is better value than having the test alongside the data. Let me know if you have any reservation, otherwise I'll prepare the move for v1.5.2. I'd like to prepare the new release as GSOC comes to a close so that it includes all of Sagar's work during the summer. |
|
From: Karol L. <kar...@gm...> - 2017-08-14 02:59:26
|
It actually bothers me quite a bit, but I haven't had the energy to follow up on everything. To be fair, some of the long standing PRs have resulted in merging code in. But I agree, we should review all open PRs and and decide what to do. If there are PRs we'd like to hold off for some reason, we can mark them with a 1.6 or 2.x milestone. On Sun, Aug 13, 2017 at 1:34 PM, Eric Berquist <er...@pi...> wrote: > Hello everyone, > > I noticed a week ago that when Jan Jensen tweeted out a link to cclib's > GitHub page, someone responded: > > yikes! PRs over a year old! >> > > https://twitter.com/ifndef_define/status/894490849521930240 > > While this doesn't bother me too much, I think that we should make a > decision about all outstanding PRs for both main repositories before 1.5.2 > is released. Does everyone else agree? > > 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 > > |
|
From: Eric B. <er...@pi...> - 2017-08-13 23:50:40
|
Hello everyone, I noticed a week ago that when Jan Jensen tweeted out a link to cclib's GitHub page, someone responded: yikes! PRs over a year old! > https://twitter.com/ifndef_define/status/894490849521930240 While this doesn't bother me too much, I think that we should make a decision about all outstanding PRs for both main repositories before 1.5.2 is released. Does everyone else agree? Eric |
|
From: Karol L. <kar...@gm...> - 2017-05-15 07:11:09
|
Hi everyone, I just released cclib v1.5.1, which includes two new attributes and other minor changes and fixes. Thanks for all the hard work that went into this. It's been another few months, and this is a good way to have a clean start for GSOC 2017 (looking forward to Sagar's work over the summer). I moved a lot of the pending issues to v1.5.2, which I'd like to release during the summer if there are enough changes. Best, Karol |
|
From: Noel O'B. <bao...@gm...> - 2017-05-11 07:41:35
|
Hi Nitish, Welcome and best of luck. Hope you enjoy your project, and I look forward to seeing your progress. - Noel O'Boyle On 8 May 2017 at 14:06, Nitish Garg <nit...@gm...> wrote: > Hi everyone, > > I am working on the project "Computational Chemistry Web repository" during > GSoC 2017. > This project will require using cclib, 3Dmol.js, OpenBabel (and probably > RDKit in extension of this project) and thus, it suits to introduce this > project to the various mailing lists. > > This project is completely new and I would love to receive ideas from the > community on additional functionalities that can be added to this project. > Also, the official name of this project is yet to be fixed. I had suggested > 'CCviewer'. Let us discuss an appropriate name for the project. > > Project abstract: > cclib is used to parse calculation results from various chemistry software > log files. This project will be a flask-based framework making use of cclib > to parse a collection of such log files, store the parsed data in a database > and enable searching & filtering of these data records via a REST API. The > web front-end will be based on this API. Also, a chemistry software log file > can be uploaded on the webpage which will be parsed with cclib to show the > results. > Thus, this project will provide a web GUI for cclib, add searching > capability and also make use of 3Dmol.js to visualize the molecule in > browser (when file is uploaded as well as in search results). > > I had started with the simple functionality of showing parsed results from > uploaded file. The current code can be seen at : > https://github.com/nitish6174/cclib-web. > I hope to migrate the code to a new repository under OpenChemistry's github. > > Thanks, > Nitish Garg > B.Tech undergraduate, IIT Guwahati > GitHub : https://github.com/nitish6174 > Website : http://nitish6174.com/ > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > OpenBabel-Devel mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > |
|
From: Nitish G. <nit...@gm...> - 2017-05-08 13:07:20
|
Hi everyone, I am working on the project "Computational Chemistry Web repository <https://summerofcode.withgoogle.com/organizations/6519372857212928/#6682363720368128>" during GSoC 2017. This project will require using cclib, 3Dmol.js, OpenBabel (and probably RDKit in extension of this project) and thus, it suits to introduce this project to the various mailing lists. This project is completely new and I would love to receive ideas from the community on additional functionalities that can be added to this project. Also, the official name of this project is yet to be fixed. I had suggested 'CCviewer'. Let us discuss an appropriate name for the project. Project abstract: cclib is used to parse calculation results from various chemistry software log files. This project will be a flask-based framework making use of cclib to parse a collection of such log files, store the parsed data in a database and enable searching & filtering of these data records via a REST API. The web front-end will be based on this API. Also, a chemistry software log file can be uploaded on the webpage which will be parsed with cclib to show the results. Thus, this project will provide a web GUI for cclib, add searching capability and also make use of 3Dmol.js to visualize the molecule in browser (when file is uploaded as well as in search results). I had started with the simple functionality of showing parsed results from uploaded file. The current code can be seen at : https://github.com/nitish6174/cclib-web. I hope to migrate the code to a new repository under OpenChemistry's github. Thanks, Nitish Garg B.Tech undergraduate, IIT Guwahati GitHub : https://github.com/nitish6174 Website : http://nitish6174.com/ |
|
From: Eric B. <er...@pi...> - 2017-05-06 19:37:12
|
Sounds good to me. On Fri, May 5, 2017 at 8:01 PM, Karol Langner <kar...@gm...> wrote: > Hi guys, > > Since GSOC is starting, I think it'd be good to put out a baseline release > very soon. I was thinking about rolling out 1.5.1 as is, perhaps just with > Noel's issue fixed (https://github.com/cclib/cclib/issues/369 > <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fcclib%2Fcclib%2Fissues%2F369&data=01%7C01%7Cerb74%40pitt.edu%7C9ed88d981f4c4453165008d49413144c%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=JQ5LIxT8D1U73gbYPqTiP1s0lO6ueQ%2BPyQULWwXd8RM%3D&reserved=0>). > We can deal with the other issues for the next release. > > That do you think? > Karol > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! https://na01.safelinks. > protection.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=01%7C01% > 7Cerb74%40pitt.edu%7C9ed88d981f4c4453165008d49413144c% > 7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=es8trU04K4Y8VeLw%2B% > 2B4fxHGtOGBNEr%2BRk%2BYxmjXDkUI%3D&reserved=0 > _______________________________________________ > cclib-devel mailing list > ccl...@li... > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists. > sourceforge.net%2Flists%2Flistinfo%2Fcclib-devel&data= > 01%7C01%7Cerb74%40pitt.edu%7C9ed88d981f4c4453165008d49413144c% > 7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata= > S75MHrRf79fFZA9GGxoIDSmFtXRqOsNdtaXIniwfZ3Q%3D&reserved=0 > > |
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From: Karol L. <kar...@gm...> - 2017-05-06 00:01:40
|
Hi guys, Since GSOC is starting, I think it'd be good to put out a baseline release very soon. I was thinking about rolling out 1.5.1 as is, perhaps just with Noel's issue fixed (https://github.com/cclib/cclib/issues/369). We can deal with the other issues for the next release. That do you think? Karol |
|
From: Karol L. <kar...@gm...> - 2017-04-29 07:10:47
|
Well, if you can change it on your end that would be great. Perhaps we could agree for the future that the "cclib" namespace will not change? We can create aliases there that will be updated in case code moves around again. For ccopen: https://github.com/cclib/cclib/pull/366 On Fri, Apr 28, 2017 at 10:10 AM, Noel O'Boyle <bao...@gm...> wrote: > No worries, though if I'm using the API wrongly, then it's something I > should fix at my end. Maybe I should read the docs now :-) > > On 28 April 2017 at 16:22, Karol Langner <kar...@gm...> wrote: > > Hey Noel, > > > > We now have both reading and writing in cclib.io. > > > > I'm the perpetrator, and wasn't aware something depended on this. We > should > > do a better job of documenting the public API... > > > > Looking back, the move was made last year to avoid a circular import, > when > > writing some new writers IIRC. I'm sure we can figure out a way around > this. > > > > Could you file an issue for this? > > > > - Karol > > > > > > On Fri, Apr 28, 2017 at 5:30 AM, Noel O'Boyle <bao...@gm...> > wrote: > >> > >> Hi there, > >> > >> I might be a bit out of the loop, but is there any chance of moving > >> ccopen back to where it was with the parsers? This is a breaking API > >> change (affects GaussSum for example), and also, it seems > >> unneccessary. This might be a simplification but everything in io is > >> for writing, everything in parsers is for reading (unless I've missed > >> something). > >> > >> I can workaround myself, as I bundle cclib with the Windows GaussSum, > >> but the Linux distros versions use the system one so ideally the cclib > >> library version should be bumped to 2.0. > >> > >> Regards, > >> - Noel > >> > >> > >> ------------------------------------------------------------ > ------------------ > >> 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 > > > > > |
|
From: Noel O'B. <bao...@gm...> - 2017-04-28 17:10:32
|
No worries, though if I'm using the API wrongly, then it's something I should fix at my end. Maybe I should read the docs now :-) On 28 April 2017 at 16:22, Karol Langner <kar...@gm...> wrote: > Hey Noel, > > We now have both reading and writing in cclib.io. > > I'm the perpetrator, and wasn't aware something depended on this. We should > do a better job of documenting the public API... > > Looking back, the move was made last year to avoid a circular import, when > writing some new writers IIRC. I'm sure we can figure out a way around this. > > Could you file an issue for this? > > - Karol > > > On Fri, Apr 28, 2017 at 5:30 AM, Noel O'Boyle <bao...@gm...> wrote: >> >> Hi there, >> >> I might be a bit out of the loop, but is there any chance of moving >> ccopen back to where it was with the parsers? This is a breaking API >> change (affects GaussSum for example), and also, it seems >> unneccessary. This might be a simplification but everything in io is >> for writing, everything in parsers is for reading (unless I've missed >> something). >> >> I can workaround myself, as I bundle cclib with the Windows GaussSum, >> but the Linux distros versions use the system one so ideally the cclib >> library version should be bumped to 2.0. >> >> Regards, >> - Noel >> >> >> ------------------------------------------------------------------------------ >> 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...> - 2017-04-28 15:22:50
|
Hey Noel, We now have both reading and writing in cclib.io. I'm the perpetrator, and wasn't aware something depended on this. We should do a better job of documenting the public API... Looking back, the move was made last year to avoid a circular import, when writing some new writers IIRC. I'm sure we can figure out a way around this. Could you file an issue for this? - Karol On Fri, Apr 28, 2017 at 5:30 AM, Noel O'Boyle <bao...@gm...> wrote: > Hi there, > > I might be a bit out of the loop, but is there any chance of moving > ccopen back to where it was with the parsers? This is a breaking API > change (affects GaussSum for example), and also, it seems > unneccessary. This might be a simplification but everything in io is > for writing, everything in parsers is for reading (unless I've missed > something). > > I can workaround myself, as I bundle cclib with the Windows GaussSum, > but the Linux distros versions use the system one so ideally the cclib > library version should be bumped to 2.0. > > Regards, > - Noel > > ------------------------------------------------------------ > ------------------ > 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: Adam T. <ate...@gm...> - 2017-04-28 13:39:33
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Hi Nitish, What version does apt-get install? My guess that an older version before the cclib.io module was created. I did notice that cclib 1.5 is in pip ( https://pypi.python.org/pypi/cclib/1.5.post1), although it didn't actually work for me in a virtual env. So I think you have three options right now: 1) Figure out how to package up the current version of cclib into a deb, and use COPY to put it onto your Docker image for install via dpkg -i (?). I'm sure the deb maintainers would also appreciate an update to cclib. 2) Install cclib into your source tree and use COPY to put it into your docker image. 3) Use the older version from apt-get, but then do something like: try from cclib.io import ccopen except: from cclib.parser import ccopen Best regards, Adam On Fri, Apr 28, 2017 at 3:00 AM Nitish Garg <nit...@gm...> wrote: > Hi all, > > When dockerizing my application, I was initially installing cclib using > apt-get. But then, *import cclib.io <http://cclib.io>* was failing > (although *import cclib.parser* works fine). Things work fine when I > setup cclib from source itself. > So I want to confirm if cclib.io is not included in the apt-get package. > Also, is there any other way I can install complete cclib in docker image > without keeping the source code? I believe it is not pip installable > currently. > > Regards > Nitish Garg > > On Thu, Apr 13, 2017 at 4:59 AM, Nitish Garg <nit...@gm...> > wrote: > >> Hi all, >> >> This mail is in continuation to the discussion over my GSOC proposal for >> the "Computational Chemistry Web Repository" project. >> (The groundwork for this project can be found at : >> https://github.com/nitish6174/cclib-web) >> >> Please note the issue in MOPAC parser as mentioned at bottom of mail. >> >> The schema looks like a good start. Where are you getting the IUPAC >>> names? If you haven't found an online resource or library that >>> automatically determines them, I don't know how often they'd be used. Out >>> of the hundreds of calculations I've ever run, I never figured out the >>> IUPAC name for any. >> >> >> I am focusing on detecting the InChI (or InChIKey) of the molecule as >> from that, a lot of information can be found about that molecule (Using >> PubChemPy to get compund from InChI/InChIKey >> <http://pubchempy.readthedocs.io/en/latest/api.html#pubchempy.get_compounds> >> ). >> As many log files may not contain enough data to generate InChI, we can >> resort to manual input of InChI or common name for molecule (Using >> PubChemPy to find compund from common name >> <http://pubchempy.readthedocs.io/en/latest/api.html#pubchempy.get_compounds> >> ). >> The found PubChemPy compund can be used to get IUPAC name and other >> details. Anyway, won't talk much about IUPAC from now on as its not >> important. Also, I guess showing molecule specific properties is not that >> important for this project. >> >> I think you should assume that any attribute may potentially be different >>> for each log file. For your 'atommasses' example, one could be interested >>> in frequency calculations (IR or Raman) that are part of a study using >>> isotopic shifts (e.g. 1H -> 2H or 16O -> 18O) so there could be two >>> calculations that are essentially identical except for atommasses (and the >>> corresponding changes to the vib* attributes). >> >> >> Yes, I believe almost all the result fields might differ with each log >> file. Actually instead of 'atommasses', I should have taken atom numbers as >> example that if I have 10 log files for H2O, atom numbers should be stored >> just once and not 10 times. Will fix that. >> >> We'd appreciate if you could let us know which files are having problems, >>> especially if they are from the cclib or cclib-data repos. Make sure you're >>> using an up-to-date version of cclib, and if so, please create an Issue for >>> cclib. >> >> >> The ccread() function failed on these 2 files : "MOPAC/h2o-force.out" and >> "regression/Gaussian/Gaussian09/coeffs.log" >> This is because MOPAC parser has a typo `line.split[2]` in line 194. >> Also, `math` module is missing. >> I had fixed these in my fork and was about to submit a PR but saw that >> this issue is already opened (#346) but not yet resolved (the referenced PR >> (#347) on that issue has a Travis build fail). I have made a PR #365 which >> might fix this issue but if #347 can be corrected, my PR will be redundant. >> I hope the "coeffs.log" was meant for run_regressions test and not to be >> parsed. >> >> Regards >> Nitish Garg >> GitHub : https://github.com/nitish6174 >> >> > |
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From: Noel O'B. <bao...@gm...> - 2017-04-28 12:30:40
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Hi there, I might be a bit out of the loop, but is there any chance of moving ccopen back to where it was with the parsers? This is a breaking API change (affects GaussSum for example), and also, it seems unneccessary. This might be a simplification but everything in io is for writing, everything in parsers is for reading (unless I've missed something). I can workaround myself, as I bundle cclib with the Windows GaussSum, but the Linux distros versions use the system one so ideally the cclib library version should be bumped to 2.0. Regards, - Noel |
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From: Karol L. <kar...@gm...> - 2017-02-12 17:28:15
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Hi Chinmay, Good to hear from you. Please be aware that at this stage we do not know whether OpenChemistry will get selected this year - they will published the accepted organizations on Feb 27. If you would like to contribute to cclib regardless, please feel free to take up and existing issue (https://github.com/cclib/cclib/issues) and hack away! There are also other interesting libraries in OpenChemistry you might interested in. - Karol +relevant mailing lists On Sun, Feb 12, 2017 at 8:35 AM, Chinmay Pandhare <100...@gm... > wrote: > Sir, > I am Chinmay Pandhare, from BITS Pilani University, India. > I am interested in doing my GSoC 2017 project in your organization, Open > Chemistry, > as a part of the cclib projects, "Refractor Parsers" and "Write new > Parsers". > > I am a Python Programmer with particular interests in ML, Scraping and > Data Analysis. > > As an example, I parsed data of all Organizations which participated in > GSoC from 2009 to 2016 and all their projects in Python, to find out the > ones which I would be interested in, and would be able to do. > > Please guide me on how to proceed. > > -- > *Chinmay Pandhare* > > *Contact: 9829533001, 7718823969* > > *100...@gm... <100...@gm...>* > > *GitHub: http://github.com/ccpandhare <http://github.com/ccpandhare>* > > *▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄* > > *BITS Pilani* (Pilani Campus) > > Rajasthan - 333 031, INDIA > |
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From: Karol L. <kar...@gm...> - 2017-02-12 16:15:20
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Well, we actually have an issue where we discussed refactoring the parsers: https://github.com/cclib/cclib/issues/335 with some ideas about refactoring. My personal preference is to discuss more and put some effort into design before starting to code, because it will take some time to refactor everything. Of course, you're welcome to refactor as much as you want in a clone. We also have a minor release that is overdue. Feel free to jump into any of the issues for that: https://github.com/cclib/cclib/milestone/10 On Sun, Feb 5, 2017 at 8:38 PM, Utkarsh <ban...@gm...> wrote: > The code makes sense to me. I can certainly try. Where would you like me > to start? > > > > Karol Langner <kar...@gm...> wrote: > > Well, in that case do you have an idea about how to refactor our parsers? > > On Sun, Feb 5, 2017 at 11:43 AM, Utkarsh Bansal <ban...@gm...> > wrote: > >> No, I don't have any background in computational chemistry. Interested in >> Python. >> >> Regards, >> Utkarsh >> >> On Mon, Feb 6, 2017 at 1:10 AM, Karol Langner <kar...@gm...> >> wrote: >> >>> Hi Utkarsh, >>> >>> Welcome. Do you have prior computational chemistry background, or are >>> you just interested in Python? >>> >>> Karol >>> >>> >>> On Sun, Feb 5, 2017 at 8:52 AM, Utkarsh Bansal <ban...@gm... >>> > wrote: >>> >>>> Hello everyone, >>>> >>>> I am Utkarsh Bansal, an undergraduate student currently pursuing my >>>> bachelor’s degree in Computer Science and Engineering. I’d like to >>>> contribute to cclib, in particular help with refactoring parsers. I have >>>> been working with Python with over 2.5 years, so I’m quite comfortable with >>>> it. Could someone help me in getting started? >>>> >>>> Regards, >>>> Utkarsh >>>> ------------------------------------------------------------ >>>> ------------------ >>>> 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: Utkarsh <ban...@gm...> - 2017-02-06 04:39:07
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The code makes sense to me. I can certainly try. Where would you like me to start? Karol Langner <kar...@gm...> wrote: >Well, in that case do you have an idea about how to refactor our parsers? > >On Sun, Feb 5, 2017 at 11:43 AM, Utkarsh Bansal <ban...@gm...> >wrote: > >> No, I don't have any background in computational chemistry. Interested in >> Python. >> >> Regards, >> Utkarsh >> >> On Mon, Feb 6, 2017 at 1:10 AM, Karol Langner <kar...@gm...> >> wrote: >> >>> Hi Utkarsh, >>> >>> Welcome. Do you have prior computational chemistry background, or are you >>> just interested in Python? >>> >>> Karol >>> >>> >>> On Sun, Feb 5, 2017 at 8:52 AM, Utkarsh Bansal <ban...@gm...> >>> wrote: >>> >>>> Hello everyone, >>>> >>>> I am Utkarsh Bansal, an undergraduate student currently pursuing my >>>> bachelor’s degree in Computer Science and Engineering. I’d like to >>>> contribute to cclib, in particular help with refactoring parsers. I have >>>> been working with Python with over 2.5 years, so I’m quite comfortable with >>>> it. Could someone help me in getting started? >>>> >>>> Regards, >>>> Utkarsh >>>> ------------------------------------------------------------ >>>> ------------------ >>>> 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...> - 2017-02-05 21:54:10
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Well, in that case do you have an idea about how to refactor our parsers? On Sun, Feb 5, 2017 at 11:43 AM, Utkarsh Bansal <ban...@gm...> wrote: > No, I don't have any background in computational chemistry. Interested in > Python. > > Regards, > Utkarsh > > On Mon, Feb 6, 2017 at 1:10 AM, Karol Langner <kar...@gm...> > wrote: > >> Hi Utkarsh, >> >> Welcome. Do you have prior computational chemistry background, or are you >> just interested in Python? >> >> Karol >> >> >> On Sun, Feb 5, 2017 at 8:52 AM, Utkarsh Bansal <ban...@gm...> >> wrote: >> >>> Hello everyone, >>> >>> I am Utkarsh Bansal, an undergraduate student currently pursuing my >>> bachelor’s degree in Computer Science and Engineering. I’d like to >>> contribute to cclib, in particular help with refactoring parsers. I have >>> been working with Python with over 2.5 years, so I’m quite comfortable with >>> it. Could someone help me in getting started? >>> >>> Regards, >>> Utkarsh >>> ------------------------------------------------------------ >>> ------------------ >>> 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: Utkarsh B. <ban...@gm...> - 2017-02-05 19:43:58
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No, I don't have any background in computational chemistry. Interested in Python. Regards, Utkarsh On Mon, Feb 6, 2017 at 1:10 AM, Karol Langner <kar...@gm...> wrote: > Hi Utkarsh, > > Welcome. Do you have prior computational chemistry background, or are you > just interested in Python? > > Karol > > > On Sun, Feb 5, 2017 at 8:52 AM, Utkarsh Bansal <ban...@gm...> > wrote: > >> Hello everyone, >> >> I am Utkarsh Bansal, an undergraduate student currently pursuing my >> bachelor’s degree in Computer Science and Engineering. I’d like to >> contribute to cclib, in particular help with refactoring parsers. I have >> been working with Python with over 2.5 years, so I’m quite comfortable with >> it. Could someone help me in getting started? >> >> Regards, >> Utkarsh >> ------------------------------------------------------------ >> ------------------ >> 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...> - 2017-02-05 19:40:47
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Hi Utkarsh, Welcome. Do you have prior computational chemistry background, or are you just interested in Python? Karol On Sun, Feb 5, 2017 at 8:52 AM, Utkarsh Bansal <ban...@gm...> wrote: > Hello everyone, > > I am Utkarsh Bansal, an undergraduate student currently pursuing my > bachelor’s degree in Computer Science and Engineering. I’d like to > contribute to cclib, in particular help with refactoring parsers. I have > been working with Python with over 2.5 years, so I’m quite comfortable with > it. Could someone help me in getting started? > > Regards, > Utkarsh > ------------------------------------------------------------ > ------------------ > 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: Utkarsh B. <ban...@gm...> - 2017-02-05 16:53:06
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Hello everyone, I am Utkarsh Bansal, an undergraduate student currently pursuing my bachelor’s degree in Computer Science and Engineering. I’d like to contribute to cclib, in particular help with refactoring parsers. I have been working with Python with over 2.5 years, so I’m quite comfortable with it. Could someone help me in getting started? Regards, Utkarsh |
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From: Karol L. <kar...@gm...> - 2017-01-04 15:36:23
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Happy New year! Kudos and it has been great to see more people contribute to cclib over the years. Getting a decennial article out there has come up and it's one of the things I'll push in 2017. On Wed, Jan 4, 2017 at 1:47 AM, Noel O'Boyle <bao...@gm...> wrote: > What a nice email to start the year. I'm glad cclib has helped you and > I'm equally glad you have contributed so much to cclib. > > Regards, > - Noel > > On 2 January 2017 at 22:40, Eric Berquist <er...@pi...> wrote: > > Hi all, > > > > After over 1.5 years of work, I have 2 papers where I used cclib, > > appropriately cited, to parse probably over 100,000 Q-Chem calculations > for > > vibrational frequencies: > > > > http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b09489 > > > > http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b09509 > > > > I had to write custom parsers for ALMO-EDA and SAPT. I'm not sure if > those > > are general-interest methods, but "fragment" support is something I would > > like to revisit this year. I'm also planning on adding support for the > new > > polarizability, NMR, and EPR methods I'm adding to Q-Chem, which means we > > have a few new attributes to discuss :) > > > > So, thank you for letting me be a contributor to my first open source > > project, hopefully with many more to come. > > > > 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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