cclib-devel — Developer's mailing list

[cclib-devel] v1.4.1 deadline

[Eric B. <er...@pi...>]

Hi all,

There is a chance that I will miss the 1.4.1 deadline on 7/23 again; I have
two weeks left for my summer internship in San Francisco and I'm not sure
how busy I'll be in the remaining time, and the internet can be spotty
where I'm staying.

Of the remaining items here (https://github.com/cclib/cclib/milestone/9),
are there any that are especially high priority?

Eric

[cclib-devel] Fwd: [cclib/cclib] Added suport for Gaussian BOMD trajectories (1 trajectory per file) (#283)

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

Seems like a new "time" attribute is coming. Any thoughts about this?

---------- Forwarded message ----------
From: Ramon Crehuet <not...@gi...>
Date: Tue, Jun 21, 2016 at 12:05 PM
Subject: [cclib/cclib] Added suport for Gaussian BOMD trajectories (1
trajectory per file) (#283)
To: cclib/cclib <cc...@no...>


This also adds the attribute time to the parsed data.
Only energies, times and geometries are parsed, not orbitals.
The main cclib version failed because the integration step sometimes
rejects a step and re-calculates, but cclib parsed all of them, creating
too many geometries and energies (that did not agree with the number of
steps).
Currently it onyl works with files containing a single trajectory. Only
tested with DFT runs.
------------------------------
You can view, comment on, or merge this pull request online at:

  https://github.com/cclib/cclib/pull/283
Commit Summary

   - Added suport for Gaussian BOMD trajectories (1 trajectory per file)

File Changes

   - *M* src/cclib/parser/gaussianparser.py
   <https://github.com/cclib/cclib/pull/283/files#diff-0> (80)

Patch Links:

   - https://github.com/cclib/cclib/pull/283.patch
   - https://github.com/cclib/cclib/pull/283.diff

—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
<https://github.com/cclib/cclib/pull/283>, or mute the thread
<https://github.com/notifications/unsubscribe/AAtZEnWbzUF2Dye4JQRy_oFQvXGyPnUmks5qN7d3gaJpZM4I6kB0>
.

Re: [cclib-devel] [cclib-users] gamessparser

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

File will go in with https://github.com/cclib/cclib-data/pull/33 and the
fix with https://github.com/cclib/cclib/pull/277.

On Sat, May 14, 2016 at 1:12 AM, Karol Langner <kar...@gm...>
wrote:

> Oh, it won't go through, probably because it's a zip archive. I'll just
> add it to cclib-data straight away.
>
> On Sat, May 14, 2016 at 1:10 AM, Karol Langner <kar...@gm...>
> wrote:
>
>> Will forward Alexis's file in a moment as well.
>>
>> ---------- Forwarded message ----------
>> From: Alexis Otero Calvi <ao...@is...>
>> Date: Wed, May 11, 2016 at 7:14 AM
>> Subject: Re: [cclib-users] gamessparser
>> To: Karol Langner <kar...@gm...>
>>
>>
>> Hi Karol
>> Ok, you can use.
>>
>> Alexis
>>
>> ------------------------------
>> *De: *"Karol Langner" <kar...@gm...>
>> *Para: *"Alexis Otero Calvi" <ao...@is...>
>> *Enviados: *Miércoles, 11 de Mayo 2016 3:47:30
>>
>> *Asunto: *Re: [cclib-users] gamessparser
>>
>> Hi Alexis,
>>
>> I have a fix ready for this. Are you OK with releasing this logfile to
>> the Public Domain so that we can use it as a regression test for future
>> versions?
>>
>> Best,
>> Karol
>>
>>
>> On Mon, May 9, 2016 at 6:20 AM, Alexis Otero Calvi <ao...@is...>
>> wrote:
>>
>>> Hi Karol
>>> output file of Cd complexes.
>>>
>>> Alexis
>>>
>>>
>>> ------------------------------
>>> *De: *"Karol Langner" <kar...@gm...>
>>> *Para: *"Alexis Otero Calvi" <ao...@is...>
>>> *CC: *ccl...@li...
>>> *Enviados: *Viernes, 6 de Mayo 2016 15:36:13
>>> *Asunto: *Re: [cclib-users] gamessparser
>>>
>>>
>>> Hi Alexis,
>>>
>>> Could you provide us with an example output file that causes this error?
>>>
>>> Karol
>>>
>>> On Fri, May 6, 2016 at 9:55 AM, Alexis Otero Calvi <ao...@is...>
>>> wrote:
>>>
>>>> Hi all
>>>>
>>>> I tried to use cclib to extract information of Gamess log files, but
>>>> have met with the following
>>>>
>>>> Traceback (most recent call last):
>>>>   File "/usr/local/bin/ccget", line 180, in <module>
>>>>     ccget()
>>>>   File "/usr/local/bin/ccget", line 153, in ccget
>>>>     data = ccread(filename, **kwargs)
>>>>   File "/usr/local/lib/python2.7/dist-packages/cclib/parser/ccio.py",
>>>> line 107, in ccread
>>>>     return log.parse()
>>>>   File
>>>> "/usr/local/lib/python2.7/dist-packages/cclib/parser/logfileparser.py",
>>>> line 309, in parse
>>>>     self.extract(inputfile, line)
>>>>   File
>>>> "/usr/local/lib/python2.7/dist-packages/cclib/parser/gamessparser.py", line
>>>> 968, in extract
>>>>     self.mocoeffs[0][base+j, i] = float(coeffs[j * 11:(j + 1) * 11])
>>>> ValueError: could not convert string to float: B
>>>>
>>>> How I can solve it?
>>>>
>>>> cclib version 1.4
>>>>
>>>>
>>>> Instituto Superior Minero Metalúrgico de Moa Dr. Antonio Núñez Jiménez
>>>> 40 años al servicio de la docencia, la investigación y la innovación
>>>> tecnológica
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Find and fix application performance issues faster with Applications
>>>> Manager
>>>> Applications Manager provides deep performance insights into multiple
>>>> tiers of
>>>> your business applications. It resolves application problems quickly and
>>>> reduces your MTTR. Get your free trial!
>>>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>>>> _______________________________________________
>>>> cclib-users mailing list
>>>> ccl...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>>
>>>
>>>
>>>
>>> Instituto Superior Minero Metalúrgico de Moa Dr. Antonio Núñez Jiménez.
>>> 40 años al servicio de la docencia, la investigación y la innovación
>>> tecnológica.
>>> ------------------------------
>>> www.ismm.edu.cu
>>>
>>
>>
>>
>> Instituto Superior Minero Metalúrgico de Moa Dr. Antonio Núñez Jiménez.
>> 40 años al servicio de la docencia, la investigación y la innovación
>> tecnológica.
>> ------------------------------
>> www.ismm.edu.cu
>>
>>
>

Re: [cclib-devel] [cclib-users] gamessparser

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

Oh, it won't go through, probably because it's a zip archive. I'll just add
it to cclib-data straight away.

On Sat, May 14, 2016 at 1:10 AM, Karol Langner <kar...@gm...>
wrote:

> Will forward Alexis's file in a moment as well.
>
> ---------- Forwarded message ----------
> From: Alexis Otero Calvi <ao...@is...>
> Date: Wed, May 11, 2016 at 7:14 AM
> Subject: Re: [cclib-users] gamessparser
> To: Karol Langner <kar...@gm...>
>
>
> Hi Karol
> Ok, you can use.
>
> Alexis
>
> ------------------------------
> *De: *"Karol Langner" <kar...@gm...>
> *Para: *"Alexis Otero Calvi" <ao...@is...>
> *Enviados: *Miércoles, 11 de Mayo 2016 3:47:30
>
> *Asunto: *Re: [cclib-users] gamessparser
>
> Hi Alexis,
>
> I have a fix ready for this. Are you OK with releasing this logfile to the
> Public Domain so that we can use it as a regression test for future
> versions?
>
> Best,
> Karol
>
>
> On Mon, May 9, 2016 at 6:20 AM, Alexis Otero Calvi <ao...@is...>
> wrote:
>
>> Hi Karol
>> output file of Cd complexes.
>>
>> Alexis
>>
>>
>> ------------------------------
>> *De: *"Karol Langner" <kar...@gm...>
>> *Para: *"Alexis Otero Calvi" <ao...@is...>
>> *CC: *ccl...@li...
>> *Enviados: *Viernes, 6 de Mayo 2016 15:36:13
>> *Asunto: *Re: [cclib-users] gamessparser
>>
>>
>> Hi Alexis,
>>
>> Could you provide us with an example output file that causes this error?
>>
>> Karol
>>
>> On Fri, May 6, 2016 at 9:55 AM, Alexis Otero Calvi <ao...@is...>
>> wrote:
>>
>>> Hi all
>>>
>>> I tried to use cclib to extract information of Gamess log files, but
>>> have met with the following
>>>
>>> Traceback (most recent call last):
>>>   File "/usr/local/bin/ccget", line 180, in <module>
>>>     ccget()
>>>   File "/usr/local/bin/ccget", line 153, in ccget
>>>     data = ccread(filename, **kwargs)
>>>   File "/usr/local/lib/python2.7/dist-packages/cclib/parser/ccio.py",
>>> line 107, in ccread
>>>     return log.parse()
>>>   File
>>> "/usr/local/lib/python2.7/dist-packages/cclib/parser/logfileparser.py",
>>> line 309, in parse
>>>     self.extract(inputfile, line)
>>>   File
>>> "/usr/local/lib/python2.7/dist-packages/cclib/parser/gamessparser.py", line
>>> 968, in extract
>>>     self.mocoeffs[0][base+j, i] = float(coeffs[j * 11:(j + 1) * 11])
>>> ValueError: could not convert string to float: B
>>>
>>> How I can solve it?
>>>
>>> cclib version 1.4
>>>
>>>
>>> Instituto Superior Minero Metalúrgico de Moa Dr. Antonio Núñez Jiménez
>>> 40 años al servicio de la docencia, la investigación y la innovación
>>> tecnológica
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Find and fix application performance issues faster with Applications
>>> Manager
>>> Applications Manager provides deep performance insights into multiple
>>> tiers of
>>> your business applications. It resolves application problems quickly and
>>> reduces your MTTR. Get your free trial!
>>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>>> _______________________________________________
>>> cclib-users mailing list
>>> ccl...@li...
>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>
>>
>>
>>
>> Instituto Superior Minero Metalúrgico de Moa Dr. Antonio Núñez Jiménez.
>> 40 años al servicio de la docencia, la investigación y la innovación
>> tecnológica.
>> ------------------------------
>> www.ismm.edu.cu
>>
>
>
>
> Instituto Superior Minero Metalúrgico de Moa Dr. Antonio Núñez Jiménez.
> 40 años al servicio de la docencia, la investigación y la innovación
> tecnológica.
> ------------------------------
> www.ismm.edu.cu
>
>

[cclib-devel] Fwd: [cclib-users] gamessparser

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

Will forward Alexis's file in a moment as well.

---------- Forwarded message ----------
From: Alexis Otero Calvi <ao...@is...>
Date: Wed, May 11, 2016 at 7:14 AM
Subject: Re: [cclib-users] gamessparser
To: Karol Langner <kar...@gm...>


Hi Karol
Ok, you can use.

Alexis

------------------------------
*De: *"Karol Langner" <kar...@gm...>
*Para: *"Alexis Otero Calvi" <ao...@is...>
*Enviados: *Miércoles, 11 de Mayo 2016 3:47:30

*Asunto: *Re: [cclib-users] gamessparser

Hi Alexis,

I have a fix ready for this. Are you OK with releasing this logfile to the
Public Domain so that we can use it as a regression test for future
versions?

Best,
Karol


On Mon, May 9, 2016 at 6:20 AM, Alexis Otero Calvi <ao...@is...>
wrote:

> Hi Karol
> output file of Cd complexes.
>
> Alexis
>
>
> ------------------------------
> *De: *"Karol Langner" <kar...@gm...>
> *Para: *"Alexis Otero Calvi" <ao...@is...>
> *CC: *ccl...@li...
> *Enviados: *Viernes, 6 de Mayo 2016 15:36:13
> *Asunto: *Re: [cclib-users] gamessparser
>
>
> Hi Alexis,
>
> Could you provide us with an example output file that causes this error?
>
> Karol
>
> On Fri, May 6, 2016 at 9:55 AM, Alexis Otero Calvi <ao...@is...>
> wrote:
>
>> Hi all
>>
>> I tried to use cclib to extract information of Gamess log files, but have
>> met with the following
>>
>> Traceback (most recent call last):
>>   File "/usr/local/bin/ccget", line 180, in <module>
>>     ccget()
>>   File "/usr/local/bin/ccget", line 153, in ccget
>>     data = ccread(filename, **kwargs)
>>   File "/usr/local/lib/python2.7/dist-packages/cclib/parser/ccio.py",
>> line 107, in ccread
>>     return log.parse()
>>   File
>> "/usr/local/lib/python2.7/dist-packages/cclib/parser/logfileparser.py",
>> line 309, in parse
>>     self.extract(inputfile, line)
>>   File
>> "/usr/local/lib/python2.7/dist-packages/cclib/parser/gamessparser.py", line
>> 968, in extract
>>     self.mocoeffs[0][base+j, i] = float(coeffs[j * 11:(j + 1) * 11])
>> ValueError: could not convert string to float: B
>>
>> How I can solve it?
>>
>> cclib version 1.4
>>
>>
>> Instituto Superior Minero Metalúrgico de Moa Dr. Antonio Núñez Jiménez
>> 40 años al servicio de la docencia, la investigación y la innovación
>> tecnológica
>>
>>
>> ------------------------------------------------------------------------------
>> Find and fix application performance issues faster with Applications
>> Manager
>> Applications Manager provides deep performance insights into multiple
>> tiers of
>> your business applications. It resolves application problems quickly and
>> reduces your MTTR. Get your free trial!
>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>
>
>
> Instituto Superior Minero Metalúrgico de Moa Dr. Antonio Núñez Jiménez.
> 40 años al servicio de la docencia, la investigación y la innovación
> tecnológica.
> ------------------------------
> www.ismm.edu.cu
>



Instituto Superior Minero Metalúrgico de Moa Dr. Antonio Núñez Jiménez. 40
años al servicio de la docencia, la investigación y la innovación
tecnológica.
------------------------------
www.ismm.edu.cu

[cclib-devel] cclib v1.4 released

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

Hello cclib users and devs,

On behalf of the cclib development team, we are pleased to announce the
release of cclib 1.4, which is now available for download from
http://cclib.github.io. This is a major update to version 1.3.1 that
includes new parsers and attributes, as well as many bug fixes and small
improvements.

cclib is an open source library, written in Python, for parsing and
interpreting the results of computational chemistry packages. It currently
parses output files from ADF, DALTON, Firefly, GAMESS (US), GAMESS-UK,
Gaussian, Jaguar, Molpro, NWChem, ORCA, Psi and QChem.

Among other data, cclib extracts:
    * coordinates and energies
    * information about geometry optimization
    * atomic orbital information
    * molecular orbital information
    * information on vibrational modes
    * the results of a TD-DFT calculation
    * charges and mutlipole moments
(For a complete list see http://cclib.github.io/data.html).

cclib also provides some calculation methods for interpreting the
electronic properties of molecules using analyses such as:
    * Mulliken and Lowdin population analyses
    * Overlap population analysis
    * Calculation of Mayer's bond orders.
(For a complete list see http://cclib.github.io/methods.html).

For information on how to use cclib, see
    http://cclib.github.io/tutorial.html

If you need help, find a bug, want new features or have any questions,
please send an email to our mailing list:
    https://lists.sourceforge.net/lists/listinfo/cclib-users

If your published work uses cclib, please support its development by citing
the following article:
    N. M. O'Boyle, A. L. Tenderholt, K. M. Langner, cclib: a library for
package-independent computational chemistry algorithms, J. Comp. Chem. 29
(5), 839-845 (2008)
You can also specifically reference this version of cclib as:
    Eric Berquist, Karol M. Langner, Noel M. O'Boyle, and Adam L.
Tenderholt. Release of cclib version 1.4. 2016.
http://dx.doi.org/10.5281/zenodo.50324

Regards,
The cclib development team

———

Summary of changes since cclib 1.3.1:
    * New parser: cclib can now parse DALTON files
    * New parser: cclib can now parse ORCA files
    * New attribute optstatus for status during geometry optimizations and
scans
    * Improvements to the unit test and regression suites
    * Support for Python 3.5
    * Many bugfixes and patches thanks to Sagar Gaur, mwykes, Martin Peeks
and others

Re: [cclib-devel] Fwd: [Avogadro-devel] Google Summer of Code 2016

[Sanjeed S. <san...@gm...>]

Thank you for the introduction Karol, I am ecstatic that my project
proposal was selected.

Let me introduce myself to the group.:
My name is Sanjeed Schamnad, I am a final year undergraduate student
majoring in Chemistry and Computer Science at Birla Institute of Technology
and Science - Pilani, India. For the majority of my undergraduate studies,
my areas of interest were in the DFT study of selenium containing
compounds.

As part of project proposal, I plan to incorporate the cclib package with
Avogadro-2 by means of the Chemical JSON format. I shall be asking for help
here when the need arises :)

On Sat, Apr 23, 2016 at 2:31 AM, Karol Langner <kar...@gm...>
wrote:

> Reposting from Avogadro-devel...
>
> cclib is part of OpenChemistry, and Sanjeed's project to tighten
> integration with Avogadro was one of the three selected. Specifically, he
> will be working on transport between cclib and Avogadro using CJSON.
> Congrats!
>
> ---------- Forwarded message ----------
> From: Geoffrey Hutchison <ge...@pi...>
> Date: Fri, Apr 22, 2016 at 12:24 PM
> Subject: [Avogadro-devel] Google Summer of Code 2016
> To: Avogadro-devel Devel <avo...@li...>
>
>
> Avogadro and Open Chemistry are part of Google Summer of Code 2016. I
> would like to congratulate Reinis, Patrick, and Sanjeed for 3 excellent
> project proposals:
>
> https://summerofcode.withgoogle.com/organizations/6290185763422208/
>
> * Reinis Danne - Python scripting support for Avogadro 2
> * Patrick Avery - Materials science advances for Avogadro 2
> * Sanjeed Schamnad - Integration of cclib using Chemical JSON
>
> I think I speak for everyone that we’re excited to see more progress on
> Avogadro 2 this summer - and hopefully the first official release of
> Avogadro 2.0 this fall.
>
> -Geoff
>
> ------------------------------------------------------------------------------
> Find and fix application performance issues faster with Applications
> Manager
> Applications Manager provides deep performance insights into multiple
> tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial!
> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
> _______________________________________________
> Avogadro-devel mailing list
> Avo...@li...
> https://lists.sourceforge.net/lists/listinfo/avogadro-devel
>
>
>
> ------------------------------------------------------------------------------
> Find and fix application performance issues faster with Applications
> Manager
> Applications Manager provides deep performance insights into multiple
> tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial!
> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
> _______________________________________________
> cclib-devel mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>
>


-- 
*Sanjeed Schamnad*
2011-2016
M.Sc.(Hons.) Chemistry
B.E. (Hons.) Computer Science


*Birla Institute of Technology & Science,* Pilani
Pilani Campus, Rajasthan 333 031, INDIA

[cclib-devel] Fwd: [Avogadro-devel] Google Summer of Code 2016

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

Reposting from Avogadro-devel...

cclib is part of OpenChemistry, and Sanjeed's project to tighten
integration with Avogadro was one of the three selected. Specifically, he
will be working on transport between cclib and Avogadro using CJSON.
Congrats!

---------- Forwarded message ----------
From: Geoffrey Hutchison <ge...@pi...>
Date: Fri, Apr 22, 2016 at 12:24 PM
Subject: [Avogadro-devel] Google Summer of Code 2016
To: Avogadro-devel Devel <avo...@li...>


Avogadro and Open Chemistry are part of Google Summer of Code 2016. I would
like to congratulate Reinis, Patrick, and Sanjeed for 3 excellent project
proposals:

https://summerofcode.withgoogle.com/organizations/6290185763422208/

* Reinis Danne - Python scripting support for Avogadro 2
* Patrick Avery - Materials science advances for Avogadro 2
* Sanjeed Schamnad - Integration of cclib using Chemical JSON

I think I speak for everyone that we’re excited to see more progress on
Avogadro 2 this summer - and hopefully the first official release of
Avogadro 2.0 this fall.

-Geoff
------------------------------------------------------------------------------
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers
of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
_______________________________________________
Avogadro-devel mailing list
Avo...@li...
https://lists.sourceforge.net/lists/listinfo/avogadro-devel

Re: [cclib-devel] cclib.github.io Examples

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

Hello Sanjeed,

I saw your PR and will take a look at it soon. Sorry for not getting to it
earlier.

Karol

On Sat, Apr 9, 2016 at 10:44 PM, Sanjeed Schamnad <san...@gm...>
wrote:

> Dear cclib developers,
>
> My name is Sanjeed Schamnad,  I am a final year student at BITS-Pilani,
> Pilani campus, India. I am currently interning with Amazon-Bangalore.
>
> I've been utilizing cclib for the past 1 month and have written an
> examples section for the cclib Documentation. I have written a few examples
> of utilizing ccget and ccwrite using a Benzeneselenol.out (G09) file which
> I used during my graduate Thesis. I have submitted a pull request here
> <https://github.com/cclib/cclib.github.io/pull/14>. I have also updated
> the parent thread <https://github.com/cclib/cclib.github.io/issues/6> with
> an update.
>
> It would be helpful if you could take a look at the request and suggest
> any changes that I might have to do.
>
> Presently I am working on a few examples where the script is used in
> larger python programs. Will submit another pull request once that is
> complete.
>
> --
> *Sanjeed Schamnad*
> 2011-2016
> M.Sc.(Hons.) Chemistry
> B.E. (Hons.) Computer Science
>
>
> *Birla Institute of Technology & Science,* Pilani
> Pilani Campus, Rajasthan 333 031, INDIA
>
>
> ------------------------------------------------------------------------------
> Find and fix application performance issues faster with Applications
> Manager
> Applications Manager provides deep performance insights into multiple
> tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
> gampad/clk?id=1444514301&iu=/ca-pub-7940484522588532
> _______________________________________________
> cclib-devel mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>
>

[cclib-devel] cclib.github.io Examples

[Sanjeed S. <san...@gm...>]

Dear cclib developers,

My name is Sanjeed Schamnad,  I am a final year student at BITS-Pilani,
Pilani campus, India. I am currently interning with Amazon-Bangalore.

I've been utilizing cclib for the past 1 month and have written an examples
section for the cclib Documentation. I have written a few examples of
utilizing ccget and ccwrite using a Benzeneselenol.out (G09) file which I
used during my graduate Thesis. I have submitted a pull request here
<https://github.com/cclib/cclib.github.io/pull/14>. I have also
updated the parent
thread <https://github.com/cclib/cclib.github.io/issues/6> with an update.

It would be helpful if you could take a look at the request and suggest any
changes that I might have to do.

Presently I am working on a few examples where the script is used in larger
python programs. Will submit another pull request once that is complete.

-- 
*Sanjeed Schamnad*
2011-2016
M.Sc.(Hons.) Chemistry
B.E. (Hons.) Computer Science


*Birla Institute of Technology & Science,* Pilani
Pilani Campus, Rajasthan 333 031, INDIA

Re: [cclib-devel] cclib and csx

[Bing W. <bwa...@gm...>]

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
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>
>>>
>>
>

[cclib-devel] Fwd: [BlueObelisk-discuss] Google Summer of Code

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

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
------------------------------------------------------------------------------
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

Re: [cclib-devel] [BlueObelisk-discuss] Google Summer of Code

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

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
>
>

Re: [cclib-devel] cclib and csx

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

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
>>>
>>>
>>
>

Re: [cclib-devel] cclib and csx

[Bing W. <bwa...@gm...>]

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
>>
>>
>

[cclib-devel] Created DOI for v1.3.2 and updated release

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

FYI

I uploaded v1.3.2 to Zenodo and updated the release with the DOI
(10.5281/zenodo.44552).

Zenodo record: https://zenodo.org/record/44552

Best,
Karol

Re: [cclib-devel] cclib and csx

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

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
>
>

[cclib-devel] cclib and csx

[Bing W. <bwa...@gm...>]

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] Fwd: [cclib-users] About gamessparser in cclib

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

Permission from Alexis...

---------- Forwarded message ----------
From: Otero Calvi <ao...@is...>
Date: Thu, Sep 10, 2015 at 8:03 AM
Subject: Re: [cclib-users] About gamessparser in cclib
To: Karol Langner <kar...@gm...>


Hi karol
Yes, you can use in the regressions test.

Alexis


------------------------------
*De: *"Karol Langner" <kar...@gm...>
*Para: *"Otero Calvi" <ao...@is...>
*Enviados: *Miércoles, 9 de Septiembre 2015 16:05:34

*Asunto: *Re: [cclib-users] About gamessparser in cclib

Hi Alexis,

You don't need to send it anywhere - it's just that we'd like to use your
file in our regressions suite (https://github.com/cclib/cclib-data) so that
the bug stays fixed. But it would be best if your give us permission,
explicitely :)

Best,
Karol


On Wed, Sep 9, 2015 at 12:44 PM, Otero Calvi <ao...@is...> wrote:

> Karol
> Thanks, I will download the master...I think that is not necessary send
> the test file to the Public Domain, because this is a simple optimization
> of the water molecule to show you the error....the zero value that I obtain
> was a mistake too of my knowlege of python, I fixe the problem and all is
> ok.
>
> Alexis
>
> ------------------------------
> *De: *"Karol Langner" <kar...@gm...>
> *Para: *"Otero Calvi" <ao...@is...>,
> ccl...@li..., "Adam Tenderholt" <
> ate...@gm...>
> *Enviados: *Miércoles, 9 de Septiembre 2015 15:27:12
>
> *Asunto: *Re: [cclib-users] About gamessparser in cclib
>
> Alexis,
>
> The fix is now in the master branch on our github repository and will go
> into the next relase (probably at the end of September).
>
> Please let us know if you are releasing the test files you sent us into
> the Public Domain.
>
> Best,
> Karol
>
> On Sat, Sep 5, 2015 at 10:34 PM, Karol Langner <kar...@gm...>
> wrote:
>
>> Hi Alexis,
>>
>> Thanks for the files. Are you placing these in the Public Domain? Please
>> let us know explicitly, in which case we can use it as a regression test.
>>
>> Changing the typo fixes the problem for me:
>> ~$ ccget mocoeffs h2o.log
>> Attempting to read h2o.log
>> mocoeffs:
>> [array([[-0.994216, -0.025847,  0.      ,  0.      , -0.004164,  0.005584,
>>          0.005584],
>>        [-0.233765,  0.844446,  0.      ,  0.      ,  0.122842,  0.155595,
>>          0.155595],
>> (...)
>> which are the values from the MOLECULAR ORBITALS block. I'm not sure why
>> you were getting zeros.
>>
>> Anyway, I should be able to get a fix into github within a few days.
>>
>> Best,
>> Karol
>>
>>
>> On Tue, Sep 1, 2015 at 11:00 AM, Otero Calvi <ao...@is...> wrote:
>>
>>> Karol
>>> Any file of gamess or firefly whenever you try to extract information
>>> concerning the molecular orbitals section shows the related to eigenvector
>>> section.
>>> I send 3 files, h2o.log (firefly result), Orbitales.py (code to extract
>>> molecular orbital information) and orbitales.out (information obtained with
>>> Orbitales.py that correspond with the values of eigenvector and not with
>>> the molecular orbital of the optimized structure)
>>>
>>> Thanks
>>>    Alexis
>>>
>>>
>>> ------------------------------
>>> *De: *"Karol Langner" <kar...@gm...>
>>> *Para: *"Otero Calvi" <ao...@is...>
>>> *CC: *"Adam Tenderholt" <ate...@gm...>,
>>> ccl...@li...
>>> *Enviados: *Martes, 1 de Septiembre 2015 11:55:17
>>> *Asunto: *Re: [cclib-users] About gamessparser in cclib
>>>
>>>
>>> Hi Alexis,
>>>
>>> Thanks for reporting this! It would be great if you could supply us with
>>> an example output file exhibiting this problem. Is that possible?
>>>
>>> Best,
>>> Karol
>>>
>>> On Tue, Sep 1, 2015 at 6:48 AM, Otero Calvi <ao...@is...> wrote:
>>>
>>>> Hi,
>>>>
>>>> I found an error in gamessparser, trying to extract the molecular
>>>> orbital coefficients. In line 844 where says
>>>> if line.find ("EIGENVECTORS") == 10 or line.find ("MOLECULAR OBRITALS")
>>>> == 10:
>>>> must be
>>>> if line.find ("EIGENVECTORS") == 10 or line.find ("MOLECULAR ORBITALS")
>>>> == 10:
>>>>
>>>> The error is in O B R I T A L S where should be O R B I T A L S ... I
>>>> modified the code and wrote ORBITALS but does not work, when I try to find
>>>> the coefficients is not possible, that is for example, mocoeffs is always
>>>> zero.
>>>>
>>>> Thanks,
>>>>   Alexis
>>>>
>>>> Participe en la VIII Conferencia Internacional de Aprovechamiento de
>>>> Recursos Minerales CINAREM-2015 En Moa, del 17 al 19 de noviembre de 2015
>>>> http://www.ismm.edu.cu
>>>> Email:ci...@is...
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> _______________________________________________
>>>> cclib-users mailing list
>>>> ccl...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>>
>>>
>>>
>>>
>>>
>>> Participe en la VIII Conferencia Internacional de Aprovechamiento de
>>> Recursos Minerales CINAREM-2015 En Moa
>>>
>>> Del 17 al 19 de noviembre de 2015
>>> *www.ismm.edu.cu* <http://www.ismm.edu.cu>
>>>
>>> Email:ci...@is...
>>>
>>>
>>
>
>
>
> Participe en la VIII Conferencia Internacional de Aprovechamiento de
> Recursos Minerales CINAREM-2015 En Moa
>
> Del 17 al 19 de noviembre de 2015
> *www.ismm.edu.cu* <http://www.ismm.edu.cu>
>
> Email:ci...@is...
>
>



Participe en la VIII Conferencia Internacional de Aprovechamiento de
Recursos Minerales CINAREM-2015 En Moa

Del 17 al 19 de noviembre de 2015
*www.ismm.edu.cu* <http://www.ismm.edu.cu>

Email:ci...@is...

Re: [cclib-devel] Fwd: [Debichem-devel] cclib 1.3.1-1 MIGRATED to testing

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

Very nice. I should also have an increasing amount of time for cclib in the
coming weeks/months.

On Thu, Sep 10, 2015 at 12:45 PM, Eric Berquist <er...@pi...> wrote:

> Yes, I was hoping to update a lot of the written documentation, since
> information about the newest parsers is a bit sparse.
>
> I've also been working on a set of IPython/Jupyter notebooks for the
> undergrads I mentor that show how to use Python for quantum chemistry. The
> start of an incomplete one on cclib is here:
>
>
> https://github.com/berquist/ipython_notebooks_for_qc/blob/master/notebooks/Using%20cclib.ipynb
>
> On Thu, Sep 10, 2015 at 2:23 AM, Karol Langner <kar...@gm...>
> wrote:
>
>> That is great! Perhaps we could update the tutorial on cclib.github.io
>> to reflect that.
>>
>> On Wed, Sep 9, 2015 at 12:21 PM, Eric Berquist <er...@pi...> wrote:
>>
>>> On a related note, a few months ago I made cclib packages for Arch
>>> Linux, since that's what I develop on:
>>>
>>> https://aur.archlinux.org/packages/?O=0&K=cclib
>>>
>>> On Tue, Sep 8, 2015 at 10:34 PM, Karol Langner <kar...@gm...>
>>> wrote:
>>>
>>>> FYI 1.3.1 is now in Debian testing.
>>>>
>>>> ---------- Forwarded message ----------
>>>> From: Debian testing watch <no...@re...>
>>>> Date: Fri, Sep 4, 2015 at 9:39 AM
>>>> Subject: [Debichem-devel] cclib 1.3.1-1 MIGRATED to testing
>>>> To: cc...@pa...
>>>>
>>>>
>>>> FYI: The status of the cclib source package
>>>> in Debian's testing distribution has changed.
>>>>
>>>>   Previous version: 1.1-1
>>>>   Current version:  1.3.1-1
>>>>
>>>> --
>>>> This email is automatically generated once a day.  As the installation
>>>> of
>>>> new packages into testing happens multiple times a day you will receive
>>>> later changes on the next day.
>>>> See https://release.debian.org/testing-watch/ for more information.
>>>>
>>>> _______________________________________________
>>>> Debichem-devel mailing list
>>>> Deb...@li...
>>>> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debichem-devel
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
>>>> Get real-time metrics from all of your servers, apps and tools
>>>> in one place.
>>>> SourceForge users - Click here to start your Free Trial of Datadog now!
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140
>>>> _______________________________________________
>>>> cclib-devel mailing list
>>>> ccl...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>>>>
>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
>>> Get real-time metrics from all of your servers, apps and tools
>>> in one place.
>>> SourceForge users - Click here to start your Free Trial of Datadog now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140
>>> _______________________________________________
>>> cclib-devel mailing list
>>> ccl...@li...
>>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>>>
>>>
>>
>

Re: [cclib-devel] Fwd: [Debichem-devel] cclib 1.3.1-1 MIGRATED to testing

[Eric B. <er...@pi...>]

Yes, I was hoping to update a lot of the written documentation, since
information about the newest parsers is a bit sparse.

I've also been working on a set of IPython/Jupyter notebooks for the
undergrads I mentor that show how to use Python for quantum chemistry. The
start of an incomplete one on cclib is here:

https://github.com/berquist/ipython_notebooks_for_qc/blob/master/notebooks/Using%20cclib.ipynb

On Thu, Sep 10, 2015 at 2:23 AM, Karol Langner <kar...@gm...>
wrote:

> That is great! Perhaps we could update the tutorial on cclib.github.io to
> reflect that.
>
> On Wed, Sep 9, 2015 at 12:21 PM, Eric Berquist <er...@pi...> wrote:
>
>> On a related note, a few months ago I made cclib packages for Arch Linux,
>> since that's what I develop on:
>>
>> https://aur.archlinux.org/packages/?O=0&K=cclib
>>
>> On Tue, Sep 8, 2015 at 10:34 PM, Karol Langner <kar...@gm...>
>> wrote:
>>
>>> FYI 1.3.1 is now in Debian testing.
>>>
>>> ---------- Forwarded message ----------
>>> From: Debian testing watch <no...@re...>
>>> Date: Fri, Sep 4, 2015 at 9:39 AM
>>> Subject: [Debichem-devel] cclib 1.3.1-1 MIGRATED to testing
>>> To: cc...@pa...
>>>
>>>
>>> FYI: The status of the cclib source package
>>> in Debian's testing distribution has changed.
>>>
>>>   Previous version: 1.1-1
>>>   Current version:  1.3.1-1
>>>
>>> --
>>> This email is automatically generated once a day.  As the installation of
>>> new packages into testing happens multiple times a day you will receive
>>> later changes on the next day.
>>> See https://release.debian.org/testing-watch/ for more information.
>>>
>>> _______________________________________________
>>> Debichem-devel mailing list
>>> Deb...@li...
>>> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debichem-devel
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
>>> Get real-time metrics from all of your servers, apps and tools
>>> in one place.
>>> SourceForge users - Click here to start your Free Trial of Datadog now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140
>>> _______________________________________________
>>> cclib-devel mailing list
>>> ccl...@li...
>>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
>> Get real-time metrics from all of your servers, apps and tools
>> in one place.
>> SourceForge users - Click here to start your Free Trial of Datadog now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140
>> _______________________________________________
>> cclib-devel mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>>
>>
>

[cclib-devel] cclib used to win Nobel prize

[Noel O'B. <bao...@gm...>]

So I just noticed that Roald Hoffmann is an ace Python programmer, or
else possibly his co-author Martin Rahm, and is all over cclib:

http://pubs.acs.org/doi/abs/10.1021/jacs.5b05600

Maybe one of us should get in touch and see can we integrate this.

- Noel

Re: [cclib-devel] Fwd: [Debichem-devel] cclib 1.3.1-1 MIGRATED to testing

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

That is great! Perhaps we could update the tutorial on cclib.github.io to
reflect that.

On Wed, Sep 9, 2015 at 12:21 PM, Eric Berquist <er...@pi...> wrote:

> On a related note, a few months ago I made cclib packages for Arch Linux,
> since that's what I develop on:
>
> https://aur.archlinux.org/packages/?O=0&K=cclib
>
> On Tue, Sep 8, 2015 at 10:34 PM, Karol Langner <kar...@gm...>
> wrote:
>
>> FYI 1.3.1 is now in Debian testing.
>>
>> ---------- Forwarded message ----------
>> From: Debian testing watch <no...@re...>
>> Date: Fri, Sep 4, 2015 at 9:39 AM
>> Subject: [Debichem-devel] cclib 1.3.1-1 MIGRATED to testing
>> To: cc...@pa...
>>
>>
>> FYI: The status of the cclib source package
>> in Debian's testing distribution has changed.
>>
>>   Previous version: 1.1-1
>>   Current version:  1.3.1-1
>>
>> --
>> This email is automatically generated once a day.  As the installation of
>> new packages into testing happens multiple times a day you will receive
>> later changes on the next day.
>> See https://release.debian.org/testing-watch/ for more information.
>>
>> _______________________________________________
>> Debichem-devel mailing list
>> Deb...@li...
>> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debichem-devel
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
>> Get real-time metrics from all of your servers, apps and tools
>> in one place.
>> SourceForge users - Click here to start your Free Trial of Datadog now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140
>> _______________________________________________
>> cclib-devel mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>>
>>
>
>
> ------------------------------------------------------------------------------
> Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
> Get real-time metrics from all of your servers, apps and tools
> in one place.
> SourceForge users - Click here to start your Free Trial of Datadog now!
> http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140
> _______________________________________________
> cclib-devel mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>
>

Re: [cclib-devel] Fwd: [Debichem-devel] cclib 1.3.1-1 MIGRATED to testing

[Eric B. <er...@pi...>]

On a related note, a few months ago I made cclib packages for Arch Linux,
since that's what I develop on:

https://aur.archlinux.org/packages/?O=0&K=cclib

On Tue, Sep 8, 2015 at 10:34 PM, Karol Langner <kar...@gm...>
wrote:

> FYI 1.3.1 is now in Debian testing.
>
> ---------- Forwarded message ----------
> From: Debian testing watch <no...@re...>
> Date: Fri, Sep 4, 2015 at 9:39 AM
> Subject: [Debichem-devel] cclib 1.3.1-1 MIGRATED to testing
> To: cc...@pa...
>
>
> FYI: The status of the cclib source package
> in Debian's testing distribution has changed.
>
>   Previous version: 1.1-1
>   Current version:  1.3.1-1
>
> --
> This email is automatically generated once a day.  As the installation of
> new packages into testing happens multiple times a day you will receive
> later changes on the next day.
> See https://release.debian.org/testing-watch/ for more information.
>
> _______________________________________________
> Debichem-devel mailing list
> Deb...@li...
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debichem-devel
>
>
>
> ------------------------------------------------------------------------------
> Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
> Get real-time metrics from all of your servers, apps and tools
> in one place.
> SourceForge users - Click here to start your Free Trial of Datadog now!
> http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140
> _______________________________________________
> cclib-devel mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>
>

[cclib-devel] Fwd: [Debichem-devel] cclib 1.3.1-1 MIGRATED to testing

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

FYI 1.3.1 is now in Debian testing.

---------- Forwarded message ----------
From: Debian testing watch <no...@re...>
Date: Fri, Sep 4, 2015 at 9:39 AM
Subject: [Debichem-devel] cclib 1.3.1-1 MIGRATED to testing
To: cc...@pa...


FYI: The status of the cclib source package
in Debian's testing distribution has changed.

  Previous version: 1.1-1
  Current version:  1.3.1-1

--
This email is automatically generated once a day.  As the installation of
new packages into testing happens multiple times a day you will receive
later changes on the next day.
See https://release.debian.org/testing-watch/ for more information.

_______________________________________________
Debichem-devel mailing list
Deb...@li...
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debichem-devel