cclib-devel — Developer's mailing list

Re: [cclib-devel] Recent publications

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

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
>

Re: [cclib-devel] Recent publications

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

Congratulations Eric :)

On Tue, Jan 3, 2017 at 4:10 AM, 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
>
>


-- 
*Sanjeed Schamnad*
Amazon Development Centre
Bangalore, India

[cclib-devel] Recent publications

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

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

Re: [cclib-devel] [cclib/cclib.github.io] Updates for v1.5 (#20)

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

Merged - new content is now live.

Thanks again.

On Wed, Dec 7, 2016 at 11:20 PM, Karol Langner <kar...@gm...>
wrote:

>
> I updated the docs here: https://github.com/cclib/cclib.github.io/pull/22
>
> If no one comments on the pull request soon, I'm going to merge it
> tomorrow so that the docs are up to date.
>
> - Karol
>
> ---------- Forwarded message ----------
> From: Michael Banck <not...@gi...>
> Date: Thu, Nov 24, 2016 at 1:35 AM
> Subject: Re: [cclib/cclib.github.io] Updates for v1.5 (#20)
> To: "cclib/cclib.github.io" <ccl...@no...>
> Cc: "Karol M. Langner" <kar...@gm...>, Author <
> au...@no...>
>
>
> 1.5 has long since happened, and apart from the above, the webpage still
> mentions 1.4 as latest version all over the place.
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/cclib/cclib.github.io/issues/20#issuecomment-262730857>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AAtZElZBT9RGQ3PE442pXP5Pq8rFQhzcks5rBVpigaJpZM4JpIzV>
> .
>
>

[cclib-devel] Fwd: [cclib/cclib.github.io] Updates for v1.5 (#20)

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

I updated the docs here: https://github.com/cclib/cclib.github.io/pull/22

If no one comments on the pull request soon, I'm going to merge it tomorrow
so that the docs are up to date.

- Karol

---------- Forwarded message ----------
From: Michael Banck <not...@gi...>
Date: Thu, Nov 24, 2016 at 1:35 AM
Subject: Re: [cclib/cclib.github.io] Updates for v1.5 (#20)
To: "cclib/cclib.github.io" <ccl...@no...>
Cc: "Karol M. Langner" <kar...@gm...>, Author <
au...@no...>


1.5 has long since happened, and apart from the above, the webpage still
mentions 1.4 as latest version all over the place.

—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<https://github.com/cclib/cclib.github.io/issues/20#issuecomment-262730857>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AAtZElZBT9RGQ3PE442pXP5Pq8rFQhzcks5rBVpigaJpZM4JpIzV>
.

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Re: [cclib-devel] Fwd: Are you frustrated??

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

Thanks! I have no objection or preference either, don't know if one is
better. So let's stay at SF for now...

On Sun, Dec 4, 2016 at 3:12 AM, Noel O'Boyle <bao...@gm...> wrote:

> Done. Will send admin password offlist. I'm amazed we've gone this long
> without a filter as new members are not moderated.
>
> Re moving to google groups, I feel that the mailing lists are the only
> good thing about SF. My feeling is that GG is the same or worse, but no
> real objection.
>
>
>
>
> On 4 Dec 2016 3:50 a.m., "Karol Langner" <kar...@gm...> wrote:
>
> Hi Noel,
>
> Could you enable spam filtering for the cclib* mailing lists (per
> https://sourceforge.net/p/forge/documentation/Mailing%20List
> s/#filtering-spam-from-your-list), or transfer ownership to Adam or
> myself?
>
> In the longer term, would anyone be opposed to moving the mailing lists
> off of Sourceforge? I don't know if Google Groups is a good alternative -
> any auggestions?
>
> Thanks,
> Karol
>
> ---------- Forwarded message ----------
> From: Oana Afloarei <sup...@er...>
> Date: Sat, Dec 3, 2016 at 5:13 AM
> Subject: [cclib-devel] Are you frustrated??
> To: ccl...@li...
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> ------------------
> 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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Re: [cclib-devel] Fwd: Are you frustrated??

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

Done. Will send admin password offlist. I'm amazed we've gone this long
without a filter as new members are not moderated.

Re moving to google groups, I feel that the mailing lists are the only good
thing about SF. My feeling is that GG is the same or worse, but no real
objection.




On 4 Dec 2016 3:50 a.m., "Karol Langner" <kar...@gm...> wrote:

Hi Noel,

Could you enable spam filtering for the cclib* mailing lists (per
https://sourceforge.net/p/forge/documentation/Mailing%
20Lists/#filtering-spam-from-your-list), or transfer ownership to Adam or
myself?

In the longer term, would anyone be opposed to moving the mailing lists off
of Sourceforge? I don't know if Google Groups is a good alternative - any
auggestions?

Thanks,
Karol

---------- Forwarded message ----------
From: Oana Afloarei <sup...@er...>
Date: Sat, Dec 3, 2016 at 5:13 AM
Subject: [cclib-devel] Are you frustrated??
To: ccl...@li...


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_______________________________________________
cclib-devel mailing list
ccl...@li...
https://lists.sourceforge.net/lists/listinfo/cclib-devel

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[cclib-devel] Fwd: Are you frustrated??

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

Hi Noel,

Could you enable spam filtering for the cclib* mailing lists (per
https://sourceforge.net/p/forge/documentation/Mailing%20Lists/#filtering-spam-from-your-list),
or transfer ownership to Adam or myself?

In the longer term, would anyone be opposed to moving the mailing lists off
of Sourceforge? I don't know if Google Groups is a good alternative - any
auggestions?

Thanks,
Karol

---------- Forwarded message ----------
From: Oana Afloarei <sup...@er...>
Date: Sat, Dec 3, 2016 at 5:13 AM
Subject: [cclib-devel] Are you frustrated??
To: ccl...@li...


Are you frustrated with all the garbage programs
that promise you results and deliver crushed dreams?

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------------------------------------------------------------
------------------
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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Re: [cclib-devel] Molden format input parser

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

Hi Mirko,

The short answer is: we don't handle the spherical/Cartesian distinction.
There are some ideas to do this to some extend or detect which is the case,
but we haven't acted on it yet.

Your plan sounds fine. Please let us know if you need any help from the
cclib side.

- Karol


On Fri, Oct 28, 2016 at 4:19 AM, Mirko Scholz <sc...@ch...>
wrote:

> Hello Karol.
>
> One thing that is not entirely clear to me.  How do you handle
> spherical/Cartesian
> basis functions?  The unit tests seem to specify which program packet uses
> spherical functions.  PyQante only uses Cartesians.
>
> I am still working to fully understand cclib.method.volume.electrondensity
> so
> I would wait with the pull request until I've actually generated density
> from the MOLDEN files.  Ok?
>
> Mirko
>

Re: [cclib-devel] Molden format input parser

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

Hi Mirko,

Looks practically ready for merging. Are you going to create a pull request?

- Karol

On Thu, Oct 27, 2016 at 12:43 AM, Mirko Scholz <sc...@ch...>
wrote:

> Hello,
>
> I've started to implement reading Molden formatted [1] input files.
> Finished is to read in the molecular orbital description (Atoms,
> GTO, MO sections).
>
> If you are interested the branch is on GitHub [2].
>
> Regards
>
> Mirko
>
> [1] http://www.cmbi.ru.nl/molden/molden_format.html
>
> [2] https://github.com/srtlg/cclib/tree/development-parse-molden
>
>
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[cclib-devel] Molden format input parser

[Mirko S. <sc...@ch...>]

Hello,

I've started to implement reading Molden formatted [1] input files.
Finished is to read in the molecular orbital description (Atoms,
GTO, MO sections).

If you are interested the branch is on GitHub [2].

Regards

Mirko

[1] http://www.cmbi.ru.nl/molden/molden_format.html

[2] https://github.com/srtlg/cclib/tree/development-parse-molden

[cclib-devel] Release v1.5

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

Hello everyone,

I just released cclib v1.5, which includes CJSON read/write functionality
(yay GSOC!), a new parser for MOPAC and various minor features and bug
fixes. Please see the changelog
<https://github.com/cclib/cclib/blob/master/CHANGELOG> for details.

There are a number of things to follow up on and add to this release, so I
anticipate v1.5.1 sometime later this year. If you have time to spare,
please take a look at the dozens of issues waiting to be resolved on GitHub
<https://github.com/cclib/cclib/issues> and dig in.

The core dev team has also grown with this release - welcome Geoff
Hutchison (known as @ghutchis <https://github.com/ghutchis> on GitHub).
Geoff will probably be most active in the area of integrating cclib with
Avogadro.

Best,
Karol

[cclib-devel] Release v1.4.1

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

Hi everyone,

I just released cclib v1.4.1, which includes a number of fixes and some
preliminary features for v1.5.

I don't think there's enough time to release v1.4.2 so I've simply pushed
back all remaining issues to v1.5. I set the release date for August 14th,
which is right before GSOC end this year. Ideally, we'd get all of
Sanjeed's CJSON contributions in that release, as well as the planned CSX
writer support.

Best,
Karol

Re: [cclib-devel] v1.4.1 deadline

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

No problem, we can just move some issues to the next release. I would not
want to delay again - if I can get the main things done (CSX mostly) I
planned for 1.4.1.

On Sat, Jul 16, 2016 at 2:01 PM, Eric Berquist <er...@pi...> wrote:

> 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
>
>
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