cclib-devel Mailing List for cclib

Hi Karol,

I have submitted the first pull request for writing a CSX file from DALTON.
Once it has been merged into master, I'll submit more for other packages.

Another thing is that we might want to update the information on the
website http://cclib.github.io/. I don't know who is responsible for the
maintenance of the website, but I am more than happy to help the update.

Thank you!

Bing



On Tue, Mar 15, 2016 at 5:32 PM, Karol Langner <kar...@gm...>
wrote:

> Sounds good.
>
> On Tue, Mar 15, 2016 at 1:39 PM, Bing Wang <bwa...@gm...> wrote:
>
>> Hi Karol,
>>
>> I have created a fork from cclib. My plan is to submit a pull request for
>> each package. I think only the first pull request is relatively big,
>> because I have to add the CSX stuff. The rest ones should be small. Is it
>> OK?
>>
>> Thank you!
>>
>> Bing
>>
>>
>> On Tue, Mar 15, 2016 at 2:23 AM, Karol Langner <kar...@gm...>
>> wrote:
>>
>>> Hi,
>>>
>>> I roughly looked through your commits and they looks reasonable.
>>> However, please split out your contributions and create pull requests for
>>> specific fixes/improvements.
>>>
>>> Also, if you want to contribute changes to our repository you'll need to
>>> create a real fork.
>>>
>>> Karol
>>>
>>>
>>> On Thu, Mar 10, 2016 at 12:55 PM, Bing Wang <bwa...@gm...> wrote:
>>>
>>>> Hi Karol,
>>>>
>>>> Did you look at my version of cclib, which could generate a CSX file
>>>> and publish it on our portal? Any comments and suggestions are welcome. Is
>>>> it OK for me to submit my contributions on the cclib github?
>>>>
>>>> In the mean time, I have add the NMR parsing for Gauessian and
>>>> vibrational analysis and NMR parsing for Dalton.
>>>>
>>>> Thank you!
>>>>
>>>> Bing
>>>>
>>>>
>>>>
>>>> On Mon, Feb 15, 2016 at 8:51 PM, Karol Langner <kar...@gm...
>>>> > wrote:
>>>>
>>>>> I glanced quickly and it looks good. I will take a detailed dive next
>>>>> week when I get back home (or someone beats me to it).
>>>>> On Feb 15, 2016 7:31 AM, "Bing Wang" <bwa...@gm...> wrote:
>>>>>
>>>>>> Hi Karol and other cclib developers,
>>>>>>
>>>>>> Sorry about the delayed response. I have been working on the cclib
>>>>>> and csx integration. Here is the list I added into cclib:
>>>>>>
>>>>>> 1. The cclib is able to write out the csx file using ccwrite.
>>>>>> 2. I added the NMR parsing into Gamess, NWChem, QChem modules.
>>>>>> (Gaussian is coming).
>>>>>> 3. I added the vibrational analysis parsing into NWChem.
>>>>>> 4. Many other minor fixes.
>>>>>>
>>>>>> You could check out my codes at https://github.com/chemsem/cclib
>>>>>>
>>>>>> If you think everything is fine, I could check my codes into the main
>>>>>> repository of cclib.
>>>>>>
>>>>>> Once the csx file generated, you could publish it on our portal
>>>>>> demo386.chemsem.com (registration first). The uploading instruction
>>>>>> is the following:
>>>>>>
>>>>>> 1. click "Add publication" button, and a basic information page pops
>>>>>> up.
>>>>>> 2. fill out those basic information (title, abstract, category, etc.)
>>>>>> 3. click "save changes" button, and a "Data sets" tab appears.
>>>>>> 4. click "Browse" button, select the csx file you want to upload in
>>>>>> your local machine.
>>>>>> 5. select "Add CSX/CML file" option in the dropdown box.
>>>>>> 6. click "Upload file".
>>>>>>
>>>>>> Even better, at step 4, you could directly select the output file
>>>>>> from quantum chemistry, and at step 5, select "Add Output file". You could
>>>>>> do this because our portal uses my version of cclib to parse the output
>>>>>> file.
>>>>>>
>>>>>> If you have any questions and comments, please let me know!
>>>>>>
>>>>>> Bing
>>>>>>
>>>>>>
>>>>>> On Tue, Dec 1, 2015 at 2:03 AM, Karol Langner <
>>>>>> kar...@gm...> wrote:
>>>>>>
>>>>>>> Hi Bing,
>>>>>>>
>>>>>>> Of course, this would be a welcomed addition to cclib. The goal of
>>>>>>> this library is to facilitate interchange between computational chemistry
>>>>>>> formats and enable new methods on that basis. So what you are proposing
>>>>>>> fits this exactly. Please feel free to contribute code, preferably by
>>>>>>> submitting a pull request on github.
>>>>>>>
>>>>>>> Let us know if you have any questions.
>>>>>>>
>>>>>>> Karol
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Fri, Nov 13, 2015 at 8:17 AM, Bing Wang <bwa...@gm...>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Dear cclib developers.
>>>>>>>>
>>>>>>>> My name is Bing Wang, a programmer at Chemical Semantics, Inc. (
>>>>>>>> www.chemicalsemantics.com). Our company is trying to apply the
>>>>>>>> semantic web into computational chemistry data. We have developed our XML
>>>>>>>> format, which is called CSX, for containing the computational chemistry
>>>>>>>> data. The cclib fits our needs very well. I am wondering if we could
>>>>>>>> contribute our code into cclib so that cclib users could generate the CSX
>>>>>>>> file and upload into our portal.
>>>>>>>>
>>>>>>>> Thank you!
>>>>>>>>
>>>>>>>> Bing
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> cclib-devel mailing list
>>>>>>>> ccl...@li...
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>
>>>
>>
>

Reposting here in case there is a student among cclib users and
contributors that might be interested.

---------- Forwarded message ----------
From: Geoffrey Hutchison <ge...@pi...>
Date: Tue, Mar 1, 2016 at 7:56 AM
Subject: [BlueObelisk-discuss] Google Summer of Code
To: BlueObelisk-Discuss <blu...@li...>



OpenChemistry has been accepted into the Google Summer of Code for 2016 -
including Open Babel, Avogadro, cclib and 3DMol.js
https://summerofcode.withgoogle.com/organizations/6290185763422208/
http://wiki.openchemistry.org/GSoC_Ideas_2016

If you are a student and interested in doing open chemistry software
development this summer (or know of someone who is), we're definitely
interested in good proposal ideas.

Looking forward to a summer of great science!

Cheers,
-Geoff
------------------------------------------------------------------------------
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Hi Bert,

Cross-posting to cclib-dev. That is something we are definitely eager to
build into cclib.

Karol

On Tue, Mar 1, 2016 at 10:21 AM, Wibe de Jong <wad...@lb...> wrote:

> Just look dat cclib. Marcus and I worked on parsing everything in an
> NWChem output via a Python script, and putting the data in a Chemical JSON
> format for NWChem. I probably should contribute some of this here. Also
> have a Fortran90 Chemical JSON writer that allows QC codes to write out
> directly to Chemical JSON. Looking to build a C++ analogue as both will
> cover most codes.
>
> Bert
>
> On Tue, Mar 1, 2016 at 7:56 AM, Geoffrey Hutchison <ge...@pi...>
> wrote:
>
>>
>> OpenChemistry has been accepted into the Google Summer of Code for 2016 -
>> including Open Babel, Avogadro, cclib and 3DMol.js
>> https://summerofcode.withgoogle.com/organizations/6290185763422208/
>> http://wiki.openchemistry.org/GSoC_Ideas_2016
>>
>> If you are a student and interested in doing open chemistry software
>> development this summer (or know of someone who is), we're definitely
>> interested in good proposal ideas.
>>
>> Looking forward to a summer of great science!
>>
>> Cheers,
>> -Geoff
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>> _______________________________________________
>> Blueobelisk-discuss mailing list
>> Blu...@li...
>> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>>
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> _______________________________________________
> Blueobelisk-discuss mailing list
> Blu...@li...
> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>
>