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[cclib-devel] Fwd: New release of cclib (1.6.1) on PyPI

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

---------- Forwarded message ---------
From: Libraries <not...@li...>
Date: Thu, Feb 14, 2019 at 1:11 PM
Subject: New release of cclib (1.6.1) on PyPI
To: <kar...@gm...>


Hi langner

I detected that version 1.6.1 <https://libraries.io/pypi/cclib/1.6.1> of
cclib <https://libraries.io/pypi/cclib> was released on PyPI at February
14, 2019 21:09

Check out all the details here: https://libraries.io/pypi/cclib/1.6.1

>From your friendly neighborhood robot, Libby.
------------------------------

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[cclib-devel] Version 1.6.1 is out!

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

Hi all,

I just finished up the v1.6.1 release:
https://github.com/cclib/cclib/releases/tag/v1.6.1

I also uploaded to PyPI, and I noticed it has been picked up by conda-forge
(https://github.com/conda-forge/cclib-feedstock/pull/1). So that's that.
Let me know if I missed something in the release process.

Thanks for all the work. And on to v1.6.2!

- Karol

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

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

Hi guys,

I think Tyler is spot on here, generally. Which is why we haven't really
explored this path and converted cclib to a machine learned model.

While output files are typically structured and somewhat organized, as a
developer of cclib parsers I would qualify that statement significantly...
maybe it's fair to say they are
usually-well-organized-but-with-many-caveats-and-subtle-changes-over-time-which-require-much-debugging-and-testing-to-get-consistent
:)

Really, the purpose of this project would be to see how far ML can get you
in extracting chemical facts. It would definitely need to leverage the
strong prior knowledge we have about the data we want to parse, and use it
to enforce invariants/constraints. The goal, however, is not to estimate
the values, but extract them from the logfile and classify them as
attributes. If the model extracts the wrong data, then it is still exact,
but just classified wrong. This is something a human might also do, and
I've seen students do before (oops, wrong orbital!). There has been some
work along those lines in the past for extraction, although not in this
particular domain. And it's not clear that this sort of model is easily
achievable. But then again, maybe it is, I haven't tried. On the flip side,
if it is possible, then we wouldn't have to write this complicated parsing
code, just teach the model and tune it for a specific new program or output
type.

Anyway, it is true that if you're interested in standard ML methods and
chemistry, there are much more "hot" topics out there.

- Karol


On Tue, Feb 5, 2019 at 12:14 PM Tyler Josephson <jos...@um...> wrote:

> Hi Aditya,
>
> While I think ML is exciting and promising for learning potential energy
> surfaces or efficiently interpolating/extrapolating properties of materials
> and molecules within a particular domain, I don't see it's value for
> parsing electronic structure output files.
> Because output files from simulation are quite well-organized, values can
> be extracted by simply following the logic of the output file and reading
> the relevant text into memory. Not only are the values *exact* this way,
> rather than estimates, it likely requires fewer operations for the computer
> to perform than a DL approach; parsing is quite cheap as far as
> computational tasks are concerned.
>
> DL might also be able to find interesting correlations and patterns in the
> data that humans tend to miss; using the whole simulation output, not the
> just values we assume to be important, may lead to new insights.
>
> Best,
> Tyler
>
> On Tue, Feb 5, 2019 at 9:59 AM Karol Langner <kar...@gm...>
> wrote:
>
>> Well, the parsers are not organized by method or whatnot... there's a
>> base class with a parse method (
>> https://github.com/cclib/cclib/blob/master/cclib/parser/logfileparser.py#L281)
>> and the various parsers inherit from that and implement and extract method
>> which is called by the parse method (for NWChem, for example:
>> https://github.com/cclib/cclib/blob/master/cclib/parser/nwchemparser.py#L42).
>> So there's no function really that would be replaced. It's the whole
>> parsing that would be imitated by the machine learned thing. Of course, one
>> could as a first step try to learn to parse rather easy things like number
>> of atoms and charge.
>>
>> HTH,
>> Karol
>>
>> On Tue, Feb 5, 2019 at 3:32 AM Aditya Kamath <adt...@gm...>
>> wrote:
>>
>>> Hi Karol,
>>> Thank you for responding to my message. In that case, the problem
>>> becomes information extraction. I think it is possible using Deep Learning.
>>> Can you tell me some examples of cclib parsing functions you feel can be
>>> replaced with ML?
>>> Best Regards,
>>> Aditya
>>>
>>> On Wed, Jan 30, 2019 at 1:12 AM Karol Langner <kar...@gm...>
>>> wrote:
>>>
>>>> Hi Aditya,
>>>>
>>>> My intention with the idea was solely data extraction from log files,
>>>> so parsing. But if you see other applications of ML within the scope of
>>>> cclib, we're definitely interested. Please note other projects under the
>>>> OpenChemistry umbrella also have ML ideas, and many of those are more
>>>> straightforward. Here, with parsing, things will be much more researchy.
>>>>
>>>>
>>>> HTH,
>>>> Karol
>>>>
>>>> On Tue, Jan 29, 2019, 2:13 AM Aditya Kamath <adt...@gm...>
>>>> wrote:
>>>>
>>>>> Dear Karol,
>>>>> I am Aditya, I read your GSoC project Idea to possibly implement
>>>>> machine learning to compete with cclib as an efficient data parser. From
>>>>> what I understand, you wish to train a machine learning model to handle and
>>>>> convert data between various software outputs.
>>>>>
>>>>> I suggest that the role of machine learning is not to handle or parse
>>>>> data but rather to analyze it. cclib can benefit from backend trained ML
>>>>> models to do tasks like classify file data, identify and extract
>>>>> information from files. It can also perform very accurate regression and
>>>>> emulate complex function maps which could benefit any calculation methods
>>>>> used by cclib.
>>>>>
>>>>> We can use algorithms like CRF's to label and identify data in data
>>>>> files or use neural networks or any other regression methods to compliment
>>>>> calculations.
>>>>>
>>>>> I am a final year student, looking for a prospective GSoC project to
>>>>> work with. I have previously worked with a research group implementing
>>>>> machine learning for ODE solvers to compete with Gaussian software
>>>>> calculations, ab initio calculations. I would be happy to discuss further
>>>>> on how we can work with cclib functionalities. I look forward to hearing
>>>>> from you.
>>>>>
>>>>> Best Wishes,
>>>>> Aditya Kamath
>>>>>
>>>> _______________________________________________
>> cclib-devel mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>>
>
>
> --
> Tyler Josephson
> PhD Chemical Engineering
> Postdoctoral Research Associate, Siepmann Group
> University of Minnesota, Twin Cities
> 651-269-1433 |  | LinkedIn <https://www.linkedin.com/in/trjosephson/>
>

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

[Tyler J. <jos...@um...>]

Hi Aditya,

While I think ML is exciting and promising for learning potential energy
surfaces or efficiently interpolating/extrapolating properties of materials
and molecules within a particular domain, I don't see it's value for
parsing electronic structure output files.
Because output files from simulation are quite well-organized, values can
be extracted by simply following the logic of the output file and reading
the relevant text into memory. Not only are the values *exact* this way,
rather than estimates, it likely requires fewer operations for the computer
to perform than a DL approach; parsing is quite cheap as far as
computational tasks are concerned.

DL might also be able to find interesting correlations and patterns in the
data that humans tend to miss; using the whole simulation output, not the
just values we assume to be important, may lead to new insights.

Best,
Tyler

On Tue, Feb 5, 2019 at 9:59 AM Karol Langner <kar...@gm...>
wrote:

> Well, the parsers are not organized by method or whatnot... there's a base
> class with a parse method (
> https://github.com/cclib/cclib/blob/master/cclib/parser/logfileparser.py#L281)
> and the various parsers inherit from that and implement and extract method
> which is called by the parse method (for NWChem, for example:
> https://github.com/cclib/cclib/blob/master/cclib/parser/nwchemparser.py#L42).
> So there's no function really that would be replaced. It's the whole
> parsing that would be imitated by the machine learned thing. Of course, one
> could as a first step try to learn to parse rather easy things like number
> of atoms and charge.
>
> HTH,
> Karol
>
> On Tue, Feb 5, 2019 at 3:32 AM Aditya Kamath <adt...@gm...> wrote:
>
>> Hi Karol,
>> Thank you for responding to my message. In that case, the problem becomes
>> information extraction. I think it is possible using Deep Learning. Can you
>> tell me some examples of cclib parsing functions you feel can be replaced
>> with ML?
>> Best Regards,
>> Aditya
>>
>> On Wed, Jan 30, 2019 at 1:12 AM Karol Langner <kar...@gm...>
>> wrote:
>>
>>> Hi Aditya,
>>>
>>> My intention with the idea was solely data extraction from log files, so
>>> parsing. But if you see other applications of ML within the scope of cclib,
>>> we're definitely interested. Please note other projects under the
>>> OpenChemistry umbrella also have ML ideas, and many of those are more
>>> straightforward. Here, with parsing, things will be much more researchy.
>>>
>>>
>>> HTH,
>>> Karol
>>>
>>> On Tue, Jan 29, 2019, 2:13 AM Aditya Kamath <adt...@gm...>
>>> wrote:
>>>
>>>> Dear Karol,
>>>> I am Aditya, I read your GSoC project Idea to possibly implement
>>>> machine learning to compete with cclib as an efficient data parser. From
>>>> what I understand, you wish to train a machine learning model to handle and
>>>> convert data between various software outputs.
>>>>
>>>> I suggest that the role of machine learning is not to handle or parse
>>>> data but rather to analyze it. cclib can benefit from backend trained ML
>>>> models to do tasks like classify file data, identify and extract
>>>> information from files. It can also perform very accurate regression and
>>>> emulate complex function maps which could benefit any calculation methods
>>>> used by cclib.
>>>>
>>>> We can use algorithms like CRF's to label and identify data in data
>>>> files or use neural networks or any other regression methods to compliment
>>>> calculations.
>>>>
>>>> I am a final year student, looking for a prospective GSoC project to
>>>> work with. I have previously worked with a research group implementing
>>>> machine learning for ODE solvers to compete with Gaussian software
>>>> calculations, ab initio calculations. I would be happy to discuss further
>>>> on how we can work with cclib functionalities. I look forward to hearing
>>>> from you.
>>>>
>>>> Best Wishes,
>>>> Aditya Kamath
>>>>
>>> _______________________________________________
> cclib-devel mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>


-- 
Tyler Josephson
PhD Chemical Engineering
Postdoctoral Research Associate, Siepmann Group
University of Minnesota, Twin Cities
651-269-1433 |  | LinkedIn <https://www.linkedin.com/in/trjosephson/>

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

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

Well, the parsers are not organized by method or whatnot... there's a base
class with a parse method (
https://github.com/cclib/cclib/blob/master/cclib/parser/logfileparser.py#L281)
and the various parsers inherit from that and implement and extract method
which is called by the parse method (for NWChem, for example:
https://github.com/cclib/cclib/blob/master/cclib/parser/nwchemparser.py#L42).
So there's no function really that would be replaced. It's the whole
parsing that would be imitated by the machine learned thing. Of course, one
could as a first step try to learn to parse rather easy things like number
of atoms and charge.

HTH,
Karol

On Tue, Feb 5, 2019 at 3:32 AM Aditya Kamath <adt...@gm...> wrote:

> Hi Karol,
> Thank you for responding to my message. In that case, the problem becomes
> information extraction. I think it is possible using Deep Learning. Can you
> tell me some examples of cclib parsing functions you feel can be replaced
> with ML?
> Best Regards,
> Aditya
>
> On Wed, Jan 30, 2019 at 1:12 AM Karol Langner <kar...@gm...>
> wrote:
>
>> Hi Aditya,
>>
>> My intention with the idea was solely data extraction from log files, so
>> parsing. But if you see other applications of ML within the scope of cclib,
>> we're definitely interested. Please note other projects under the
>> OpenChemistry umbrella also have ML ideas, and many of those are more
>> straightforward. Here, with parsing, things will be much more researchy.
>>
>>
>> HTH,
>> Karol
>>
>> On Tue, Jan 29, 2019, 2:13 AM Aditya Kamath <adt...@gm...> wrote:
>>
>>> Dear Karol,
>>> I am Aditya, I read your GSoC project Idea to possibly implement machine
>>> learning to compete with cclib as an efficient data parser. From what I
>>> understand, you wish to train a machine learning model to handle and
>>> convert data between various software outputs.
>>>
>>> I suggest that the role of machine learning is not to handle or parse
>>> data but rather to analyze it. cclib can benefit from backend trained ML
>>> models to do tasks like classify file data, identify and extract
>>> information from files. It can also perform very accurate regression and
>>> emulate complex function maps which could benefit any calculation methods
>>> used by cclib.
>>>
>>> We can use algorithms like CRF's to label and identify data in data
>>> files or use neural networks or any other regression methods to compliment
>>> calculations.
>>>
>>> I am a final year student, looking for a prospective GSoC project to
>>> work with. I have previously worked with a research group implementing
>>> machine learning for ODE solvers to compete with Gaussian software
>>> calculations, ab initio calculations. I would be happy to discuss further
>>> on how we can work with cclib functionalities. I look forward to hearing
>>> from you.
>>>
>>> Best Wishes,
>>> Aditya Kamath
>>>
>>

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

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

Hi Aditya,

My intention with the idea was solely data extraction from log files, so
parsing. But if you see other applications of ML within the scope of cclib,
we're definitely interested. Please note other projects under the
OpenChemistry umbrella also have ML ideas, and many of those are more
straightforward. Here, with parsing, things will be much more researchy.


HTH,
Karol

On Tue, Jan 29, 2019, 2:13 AM Aditya Kamath <adt...@gm...> wrote:

> Dear Karol,
> I am Aditya, I read your GSoC project Idea to possibly implement machine
> learning to compete with cclib as an efficient data parser. From what I
> understand, you wish to train a machine learning model to handle and
> convert data between various software outputs.
>
> I suggest that the role of machine learning is not to handle or parse data
> but rather to analyze it. cclib can benefit from backend trained ML models
> to do tasks like classify file data, identify and extract information from
> files. It can also perform very accurate regression and emulate complex
> function maps which could benefit any calculation methods used by cclib.
>
> We can use algorithms like CRF's to label and identify data in data files
> or use neural networks or any other regression methods to compliment
> calculations.
>
> I am a final year student, looking for a prospective GSoC project to work
> with. I have previously worked with a research group implementing machine
> learning for ODE solvers to compete with Gaussian software calculations, ab
> initio calculations. I would be happy to discuss further on how we can work
> with cclib functionalities. I look forward to hearing from you.
>
> Best Wishes,
> Aditya Kamath
>

[cclib-devel] Towards v1.6.1

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

Hi everyone,

I'd like to do the next release at the end of this month, or early in
February. To that end, I've created a v1.6.2 milestone (
https://github.com/cclib/cclib/milestone/15) and will start moving stuff
there from the v1.6.1 milestone (https://github.com/cclib/cclib/milestone/14)
if they don't seem imminent.

- Karol

[cclib-devel] Closing GSOC2018 project

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

Hi,

I'm going to close the GSOC2018 project in a few days:
https://github.com/orgs/cclib/projects/1

I cleaned up all the hanging PRs. There's only some notes left by Eric,
which I'm not sure are actionable right now. Eric, if they are, could you
please create issues for them, since that's the main way we've been
tracking work?

I don't think the project thingy worked that well during the summer,
really. Still, it was good to try.

- Karol

[cclib-devel] Version 1.6 is released!

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

Hello cclibers,

I just completed the v1.6 release on GitHub and PyPI. This is a minor
version increment (previous was v1.5.3), because we have some new parsers...

Speaking of which, this version includes most of the GSOC 2018 work done by
Kunal over the summer. We had a great time working with him, and I think he
was quite productive. As a result, cclib now has some degree of support for
both Molcas and Turbomole. Thanks Kunal!

Summary of changes since last version:
 - New parser: cclib can now parse Molcas files (Kunal Sharma)
 - New parser: cclib can now parse Turbomole files (Christopher Rowley,
Kunal Sharma)
 - New script: ccframe writes data table files from logfiles (Felipe
Schneider)
 - Support time attribute and BOMD output in Gaussian, NWChem, ORCA and
QChem
 - Support package version in metadata for most parsers
 - Many other minor improvements and bug fixes from Jonathon Vandezande,
Jaime Rodríguez-Guerra and others

I would also add that we now have documentation that automatically builds
and updates after each commit (and sources are alongside the code), thanks
to Eric Berquist's work. This is a very positive change in my mind, and I
hope the docs will continue improving in quality.

As always, the main place to coordinate future work is GitHub:
https://github.com/cclib/cclib

Best,
Karol

Re: [cclib-devel] Fwd: [cclib/cclib] Molcas: Added files for Molcas CCSD calculations (#572)

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

Thanks for that additional context, I was not aware of it. I though it was
a strict subset that will continue to lag behind the closed version. Makes
me happy to see the closed version not being developed further.

On Sat, Jul 28, 2018 at 9:39 PM, Eric Berquist <er...@pi...> wrote:

> You should think of it in a way similar to GAMESS in terms of naming:
>
> GAMESS/
>     basicFirefly8.0/
>     basicGAMESS-US2014/
>     basicGAMESS-US2017/
>
> Molcas/
>     basicMolcas7.0/
>     basicMolcas8.0/
>     basicOpenMolcas18.0/
>     basicOpenMolcas19.0/
>
> though for GAMESS, Firefly has diverged considerably, and OpenMolcas is
> just another version of the same program. The non-free version of Molcas
> will not be developed further. The reason there may be missing "features",
> which are thing we'd never parse anyway, are that they couldn't get
> everyone to relicense their code under the GPL.
>
> On Sat, Jul 28, 2018 at 2:04 AM, Karol Langner <kar...@gm...>
> wrote:
>
> Just to continue this topic of the Molcas directories... I commetned on
>> #571 but I suppose it's not good form to continue discussion on a closed PR
>> :)
>>
>> Functionality may be limited, but if the open version is a strict subset
>> of the full version then in my mind they should share the unit test
>> logfiles. In other words, if someone were to contribute files from the full
>> version, I don't see the value of having separate Molcas/basicMolcas* d
>> irectories.
>>
>> ---------- Forwarded message ----------
>> From: Eric Berquist <not...@gi...>
>> Date: Fri, Jul 27, 2018 at 3:56 PM
>> Subject: Re: [cclib/cclib] Molcas: Added files for Molcas CCSD
>> calculations (#572)
>> To: cclib/cclib <cc...@no...>
>> Cc: "Karol M. Langner" <kar...@gm...>, Mention <
>> me...@no...>
>>
>>
>> Merged #572
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fcclib%2Fcclib%2Fpull%2F572&data=01%7C01%7Cerb74%40pitt.edu%7Ca035838c1cd04646593308d5f4665647%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=XeZllfbxU%2BtUXaR6gjrsVIIaVuIkERMi%2FhmGQXPul4s%3D&reserved=0>
>> .
>>
>> —
>> You are receiving this because you were mentioned.
>> Reply to this email directly, view it on GitHub
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fcclib%2Fcclib%2Fpull%2F572%23event-1757335116&data=01%7C01%7Cerb74%40pitt.edu%7Ca035838c1cd04646593308d5f4665647%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=Zq84ztDvj6Kd4P5EThkPLtx%2F%2FGQmlXLsVReim9CbXlY%3D&reserved=0>,
>> or mute the thread
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAAtZEu5ei_LsdHHZzPlo0OEuATtqdTpJks5uKxwJgaJpZM4Vh5gb&data=01%7C01%7Cerb74%40pitt.edu%7Ca035838c1cd04646593308d5f4665647%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=6V2Iyj%2F3GjPIpkiVcxlkBx1Va5kP%2BjWnVmRmsnDkh8Y%3D&reserved=0>
>> .
>>
>>
>> ------------------------------------------------------------
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Re: [cclib-devel] Fwd: [cclib/cclib] Molcas: Added files for Molcas CCSD calculations (#572)

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

You should think of it in a way similar to GAMESS in terms of naming:

GAMESS/
    basicFirefly8.0/
    basicGAMESS-US2014/
    basicGAMESS-US2017/

Molcas/
    basicMolcas7.0/
    basicMolcas8.0/
    basicOpenMolcas18.0/
    basicOpenMolcas19.0/

though for GAMESS, Firefly has diverged considerably, and OpenMolcas is
just another version of the same program. The non-free version of Molcas
will not be developed further. The reason there may be missing "features",
which are thing we'd never parse anyway, are that they couldn't get
everyone to relicense their code under the GPL.

On Sat, Jul 28, 2018 at 2:04 AM, Karol Langner <kar...@gm...>
wrote:

Just to continue this topic of the Molcas directories... I commetned on
> #571 but I suppose it's not good form to continue discussion on a closed PR
> :)
>
> Functionality may be limited, but if the open version is a strict subset
> of the full version then in my mind they should share the unit test
> logfiles. In other words, if someone were to contribute files from the full
> version, I don't see the value of having separate Molcas/basicMolcas* d
> irectories.
>
> ---------- Forwarded message ----------
> From: Eric Berquist <not...@gi...>
> Date: Fri, Jul 27, 2018 at 3:56 PM
> Subject: Re: [cclib/cclib] Molcas: Added files for Molcas CCSD
> calculations (#572)
> To: cclib/cclib <cc...@no...>
> Cc: "Karol M. Langner" <kar...@gm...>, Mention <
> me...@no...>
>
>
> Merged #572
> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fcclib%2Fcclib%2Fpull%2F572&data=01%7C01%7Cerb74%40pitt.edu%7Ca035838c1cd04646593308d5f4665647%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=XeZllfbxU%2BtUXaR6gjrsVIIaVuIkERMi%2FhmGQXPul4s%3D&reserved=0>
> .
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fcclib%2Fcclib%2Fpull%2F572%23event-1757335116&data=01%7C01%7Cerb74%40pitt.edu%7Ca035838c1cd04646593308d5f4665647%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=Zq84ztDvj6Kd4P5EThkPLtx%2F%2FGQmlXLsVReim9CbXlY%3D&reserved=0>,
> or mute the thread
> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAAtZEu5ei_LsdHHZzPlo0OEuATtqdTpJks5uKxwJgaJpZM4Vh5gb&data=01%7C01%7Cerb74%40pitt.edu%7Ca035838c1cd04646593308d5f4665647%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=6V2Iyj%2F3GjPIpkiVcxlkBx1Va5kP%2BjWnVmRmsnDkh8Y%3D&reserved=0>
> .
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! https://na01.safelinks.
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>
>

[cclib-devel] Fwd: [cclib/cclib] Molcas: Added files for Molcas CCSD calculations (#572)

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

Just to continue this topic of the Molcas directories... I commetned on
#571 but I suppose it's not good form to continue discussion on a closed PR
:)

Functionality may be limited, but if the open version is a strict subset of
the full version then in my mind they should share the unit test logfiles.
In other words, if someone were to contribute files from the full version,
I don't see the value of having separate Molcas/basicMolcas* directories.

---------- Forwarded message ----------
From: Eric Berquist <not...@gi...>
Date: Fri, Jul 27, 2018 at 3:56 PM
Subject: Re: [cclib/cclib] Molcas: Added files for Molcas CCSD calculations
(#572)
To: cclib/cclib <cc...@no...>
Cc: "Karol M. Langner" <kar...@gm...>, Mention <
me...@no...>


Merged #572 <https://github.com/cclib/cclib/pull/572>.

—
You are receiving this because you were mentioned.
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.

[cclib-devel] Version 1.5.3 just release

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

Hi all,

I just published v1.5.3 in GitHub, merged it into master and uploaded to
PyPI. We'll now be working to fix as many additional things for v1.5.4 and
get that out before GSOC 2018 starts in May.

Best,
Karol

Re: [cclib-devel] Distance, Angle, Dihedral

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

I've made an issue to track this: https://github.com/cclib/cclib/issues/489

On Tue, Apr 3, 2018 at 3:17 AM, Karol Langner <kar...@gm...>
wrote:

> Hi guys,
>
> This is a good idea - let's create a GitHub issue for it lest we forget
> about it. This has come up in the past when we talked about having
> Z-matrices. I guess that would be the next step.
>
> Regarding the coordinate-to-angle calculations - they'll be so fast for
> 99% of the cases that it's not worthwhile to think about calculating things
> on-the-fly.
>
> - Karol
>
>
> On Mon, Apr 2, 2018 at 3:44 PM, Eric Berquist <er...@pi...> wrote:
>
>> Hi Tyler,
>>
>> I know you didn't ask this, but regarding the different implementations,
>> I'll implement them and try them out. In general, I think that assuming
>> performance doesn't vary too wildly, we're more interested in
>> implementations that are close to the original intent (the equations),
>> thought the "fast" one seems reasonable. A better timing test would compare
>> both small molecules and very large ones, like MOFs or proteins, using
>> `timeit`.
>>
>> > should one calculate all bonds, angles, dihedrals automatically, or
>> should the code simply return specific bonds/angles/dihedrals that are
>> requested by the user (or both)?
>>
>> What I propose is a new method (see https://github.com/cclib/cclib
>> /tree/master/src/cclib/method
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fcclib%2Fcclib%2Ftree%2Fmaster%2Fsrc%2Fcclib%2Fmethod&data=01%7C01%7Cerb74%40pitt.edu%7Cc7e776a577974aa5c75e08d59932ebeb%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=0jscbsSZPM18PtDpSaGf6nSX26m%2BOAsvSYOwn3RGrz4%3D&reserved=0>)
>> that would take a `ccdata` instance and calculate all possible distances,
>> angles, and torsions. In general, when we parse, we don't compute derived
>> data; the only things we compute are quantities for attributes _if_ they
>> can be computed from other attributes. The need for this is rare (see
>> trickery for `coreelectrons` in Q-Chem). Once the `ccdata` is passed to the
>> method, it is probably fine to precompute all values rather than
>> on-the-fly, but this is not as important as keeping the calculation
>> separate from the parsing. Eventually we could do both.
>>
>> See if you can write a method that would basically look like the
>> `Molecule` but is initialized from a `ccdata` instance.
>>
>> Eric
>>
>> On Mon, Apr 2, 2018 at 10:10 AM, Tyler Josephson <jos...@um...>
>> wrote:
>>
>>> Thanks, Eric, this is helpful!
>>>
>>> I did find a useful and simple implementation of dihedrals in Python on
>>> this page: https://stackoverflow.com/questions/20305272/dihedral-
>>> torsion-angle-from-four-points-in-cartesian-coordinates-in-python
>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstackoverflow.com%2Fquestions%2F20305272%2Fdihedral-torsion-angle-from-four-points-in-cartesian-coordinates-in-python&data=01%7C01%7Cerb74%40pitt.edu%7C0cb5cf0f698b4584176e08d598a3a50c%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=LRIupf4KL2vU2HJH0SuJpkEdUie0rUOiSgEGq61VZv0%3D&reserved=0>
>>> I especially like Praexolitic's careful evaluation of the different
>>> equations in order to select the fastest one.
>>>
>>> For my current application, I added this in a rather ad-hoc manner to a
>>> copy of the ccget script, calling it from within an if statement to be
>>> executed when attr == 'atomcoords' . So I have what I need for now. I would
>>> be interested in helping add this to cclib in a more formal way. After
>>> seeing your code, I realize the community should probably have a discussion
>>> about what this should entail and how it should be organized - should one
>>> calculate all bonds, angles, dihedrals automatically, or should the code
>>> simply return specific bonds/angles/dihedrals that are requested by the
>>> user (or both)?
>>>
>>> What would you recommend? I'm rather new to collaborative code
>>> development.
>>>
>>> Regards,
>>> Tyler
>>>
>>>
>>>
>>> On Sun, Apr 1, 2018 at 10:09 PM, Eric Berquist <er...@pi...> wrote:
>>>
>>>> Hi Tyler,
>>>>
>>>> Nothing is present right now in the package to do that, though it may
>>>> be a useful method in the future.
>>>>
>>>> For reference, if you're looking for the expressions, I've coded up
>>>> distances, torsions, and angles in the past from this project:
>>>> https://github.com/CrawfordGroup/ProgrammingProject
>>>> s/tree/master/Project%2301
>>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FCrawfordGroup%2FProgrammingProjects%2Ftree%2Fmaster%2FProject%252301&data=01%7C01%7Cerb74%40pitt.edu%7C0cb5cf0f698b4584176e08d598a3a50c%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=RVJgFfkFGATY7cQmozjV8zYWZuCOa2KWhxYBE5l3uC8%3D&reserved=0>
>>>>
>>>> Some of it is available (https://github.com/berquist/p
>>>> rogramming_party/blob/master/eric/molecule.py
>>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fberquist%2Fprogramming_party%2Fblob%2Fmaster%2Feric%2Fmolecule.py&data=01%7C01%7Cerb74%40pitt.edu%7C0cb5cf0f698b4584176e08d598a3a50c%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=rHZe4h49qc4HM3Tow2VMDdfHYm9hWxlLEBr58Kk5zL4%3D&reserved=0>),
>>>> though the torsions aren't present for some reason. I can find them if
>>>> you're interested.
>>>>
>>>> Eric
>>>>
>>>> On Sat, Mar 31, 2018 at 7:14 AM, Tyler Josephson <jos...@um...>
>>>> wrote:
>>>>
>>>>> Hi there!
>>>>>
>>>>> I'm new to cclib, and enjoying it so far! It's a powerful tool. I
>>>>> wanted to ask the community if you've worked on functions that would
>>>>> extract particular distance, angle, or dihedral measurements (I need
>>>>> dihedrals for my particular problem). I could read in the atomcoords and
>>>>> calculate them myself, but I wanted to check if something else is available.
>>>>>
>>>>> Regards,
>>>>> Tyler
>>>>>
>>>>> --
>>>>> Tyler Josephson
>>>>> PhD Chemical Engineering
>>>>> Postdoctoral Research Associate, Siepmann Group
>>>>> University of Minnesota, Twin Cities
>>>>> 651-269-1433 |  | LinkedIn
>>>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linkedin.com%2Fin%2Ftrjosephson%2F&data=01%7C01%7Cerb74%40pitt.edu%7C99323476a9ec40b3fa1d08d596fb6271%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=bqoJnaPbbc1W%2BSq81RrBgbARpQHFmXsemHI2Sbi9eiY%3D&reserved=0>
>>>>>
>>>>> ------------------------------------------------------------
>>>>> ------------------
>>>>> Check out the vibrant tech community on one of the world's most
>>>>> engaging tech sites, Slashdot.org! https://na01.safelinks.protect
>>>>> ion.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=0
>>>>> 1%7C01%7Cerb74%40pitt.edu%7C99323476a9ec40b3fa1d08d596fb6271
>>>>> %7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=9ijts%2FUMc6h6
>>>>> 5RYv2EYB3lVuEHgIjuFVLInwZ3z1SKI%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%7C99323476a9ec40b3fa1d08d596
>>>>> fb6271%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=vtaWqxXd
>>>>> aJ13NDCnSkApw%2FCihxRwbWBxJK9fDfK%2FpeY%3D&reserved=0
>>>>>
>>>>>
>>>>
>>>
>>>
>>> --
>>> Tyler Josephson
>>> PhD Chemical Engineering
>>> Postdoctoral Research Associate, Siepmann Group
>>> University of Minnesota, Twin Cities
>>> 651-269-1433 |  | LinkedIn
>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linkedin.com%2Fin%2Ftrjosephson%2F&data=01%7C01%7Cerb74%40pitt.edu%7C0cb5cf0f698b4584176e08d598a3a50c%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=qV%2BEiuoXrqlCNf9K8scXONaMiRvip5fImikj%2BYFdalc%3D&reserved=0>
>>>
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=01%7C01%7Cerb74%40pitt.edu%7Cc7e776a577974aa5c75e08d59932ebeb%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=PqD9nmeVymmkU2RsxQ%2BQsaYd%2BGi7rg4zECHuDRvgMcA%3D&reserved=0>
>> _______________________________________________
>> cclib-devel mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fcclib-devel&data=01%7C01%7Cerb74%40pitt.edu%7Cc7e776a577974aa5c75e08d59932ebeb%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=9CvlgA4PZCkSvuIusHvwYL3LsxOxgoHLsLhYEdeICtk%3D&reserved=0>
>>
>>
>

Re: [cclib-devel] Upcoming v1.5.3

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

I have noticed that Q-Chem 5.1 is very broken, but it won't be released
until May, so it's not worth rushing that.

On Wed, Apr 4, 2018 at 10:33 AM, Karol Langner <kar...@gm...>
wrote:

> I think it's a good idea to accelerate v1.5.3 and get it out in the next
> 2-3 days. We can do another release before GSOC starts in May, if there are
> any interesting changes/fixes.
>
> On Fri, Mar 30, 2018 at 5:20 PM, Karol Langner <kar...@gm...>
> wrote:
>
>> Nothing in particular comes to mind. We can try to narrow down what we
>> think is possible to do in 3 weeks, and move everything else to 1.5.4. We
>> should also take a look if it's time to go to v1.6. - typically this
>> happens if there is a new parser or major addition to methods or similar
>> thing.
>>
>> On Fri, Mar 30, 2018 at 4:41 PM, Eric Berquist <er...@pi...> wrote:
>>
>>> The timing is convenient for me, since I have a lot more free time.
>>> Aside from the general 1.5.3 label, is there anything that should be
>>> prioritized?
>>>
>>> On Wed, Mar 28, 2018 at 1:56 AM, Karol Langner <kar...@gm...>
>>> wrote:
>>>
>>>> Hi all,
>>>>
>>>> It's been a while since the last release again, and I want to get it
>>>> out before GSOC starts. I've set the release to April 22 (just before
>>>> announcing who the students are). The release might be off of that by a day
>>>> or two, but I'd like to finalize it around that time.
>>>>
>>>> So, let's try to get as much in as we can for v1.5.3!
>>>>
>>>> Karol
>>>>
>>>> P. S. And, of course, I want to do another release right after GSOC
>>>> ends, assuming there is a student.
>>>>
>>>> ------------------------------------------------------------
>>>> ------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! https://na01.safelinks.protect
>>>> ion.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=0
>>>> 1%7C01%7Cerb74%40pitt.edu%7C5cab2e4174ff4e05ea3f08d59470b584
>>>> %7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=ynrjNxlL51L5ou
>>>> 5%2BprRiTswTVAFhsl%2BZ0ZOMm935OQc%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%7C5cab2e4174ff4e05ea3f08d594
>>>> 70b584%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=uwRN0SaL
>>>> W%2FMfnVBJ32jEw01u8eMtqP7jiZ1c5oxxTx0%3D&reserved=0
>>>>
>>>>
>>>
>>
>

Re: [cclib-devel] Upcoming v1.5.3

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

I think it's a good idea to accelerate v1.5.3 and get it out in the next
2-3 days. We can do another release before GSOC starts in May, if there are
any interesting changes/fixes.

On Fri, Mar 30, 2018 at 5:20 PM, Karol Langner <kar...@gm...>
wrote:

> Nothing in particular comes to mind. We can try to narrow down what we
> think is possible to do in 3 weeks, and move everything else to 1.5.4. We
> should also take a look if it's time to go to v1.6. - typically this
> happens if there is a new parser or major addition to methods or similar
> thing.
>
> On Fri, Mar 30, 2018 at 4:41 PM, Eric Berquist <er...@pi...> wrote:
>
>> The timing is convenient for me, since I have a lot more free time. Aside
>> from the general 1.5.3 label, is there anything that should be prioritized?
>>
>> On Wed, Mar 28, 2018 at 1:56 AM, Karol Langner <kar...@gm...>
>> wrote:
>>
>>> Hi all,
>>>
>>> It's been a while since the last release again, and I want to get it out
>>> before GSOC starts. I've set the release to April 22 (just before
>>> announcing who the students are). The release might be off of that by a day
>>> or two, but I'd like to finalize it around that time.
>>>
>>> So, let's try to get as much in as we can for v1.5.3!
>>>
>>> Karol
>>>
>>> P. S. And, of course, I want to do another release right after GSOC
>>> ends, assuming there is a student.
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! https://na01.safelinks.protect
>>> ion.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=0
>>> 1%7C01%7Cerb74%40pitt.edu%7C5cab2e4174ff4e05ea3f08d59470b584
>>> %7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=ynrjNxlL51L5ou
>>> 5%2BprRiTswTVAFhsl%2BZ0ZOMm935OQc%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%7C5cab2e4174ff4e05ea3f08d5
>>> 9470b584%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=
>>> uwRN0SaLW%2FMfnVBJ32jEw01u8eMtqP7jiZ1c5oxxTx0%3D&reserved=0
>>>
>>>
>>
>

Re: [cclib-devel] Distance, Angle, Dihedral

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

Hi guys,

This is a good idea - let's create a GitHub issue for it lest we forget
about it. This has come up in the past when we talked about having
Z-matrices. I guess that would be the next step.

Regarding the coordinate-to-angle calculations - they'll be so fast for 99%
of the cases that it's not worthwhile to think about calculating things
on-the-fly.

- Karol


On Mon, Apr 2, 2018 at 3:44 PM, Eric Berquist <er...@pi...> wrote:

> Hi Tyler,
>
> I know you didn't ask this, but regarding the different implementations,
> I'll implement them and try them out. In general, I think that assuming
> performance doesn't vary too wildly, we're more interested in
> implementations that are close to the original intent (the equations),
> thought the "fast" one seems reasonable. A better timing test would compare
> both small molecules and very large ones, like MOFs or proteins, using
> `timeit`.
>
> > should one calculate all bonds, angles, dihedrals automatically, or
> should the code simply return specific bonds/angles/dihedrals that are
> requested by the user (or both)?
>
> What I propose is a new method (see https://github.com/cclib/
> cclib/tree/master/src/cclib/method) that would take a `ccdata` instance
> and calculate all possible distances, angles, and torsions. In general,
> when we parse, we don't compute derived data; the only things we compute
> are quantities for attributes _if_ they can be computed from other
> attributes. The need for this is rare (see trickery for `coreelectrons` in
> Q-Chem). Once the `ccdata` is passed to the method, it is probably fine to
> precompute all values rather than on-the-fly, but this is not as important
> as keeping the calculation separate from the parsing. Eventually we could
> do both.
>
> See if you can write a method that would basically look like the
> `Molecule` but is initialized from a `ccdata` instance.
>
> Eric
>
> On Mon, Apr 2, 2018 at 10:10 AM, Tyler Josephson <jos...@um...> wrote:
>
>> Thanks, Eric, this is helpful!
>>
>> I did find a useful and simple implementation of dihedrals in Python on
>> this page: https://stackoverflow.com/questions/20305272/dihedral-
>> torsion-angle-from-four-points-in-cartesian-coordinates-in-python
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstackoverflow.com%2Fquestions%2F20305272%2Fdihedral-torsion-angle-from-four-points-in-cartesian-coordinates-in-python&data=01%7C01%7Cerb74%40pitt.edu%7C0cb5cf0f698b4584176e08d598a3a50c%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=LRIupf4KL2vU2HJH0SuJpkEdUie0rUOiSgEGq61VZv0%3D&reserved=0>
>> I especially like Praexolitic's careful evaluation of the different
>> equations in order to select the fastest one.
>>
>> For my current application, I added this in a rather ad-hoc manner to a
>> copy of the ccget script, calling it from within an if statement to be
>> executed when attr == 'atomcoords' . So I have what I need for now. I would
>> be interested in helping add this to cclib in a more formal way. After
>> seeing your code, I realize the community should probably have a discussion
>> about what this should entail and how it should be organized - should one
>> calculate all bonds, angles, dihedrals automatically, or should the code
>> simply return specific bonds/angles/dihedrals that are requested by the
>> user (or both)?
>>
>> What would you recommend? I'm rather new to collaborative code
>> development.
>>
>> Regards,
>> Tyler
>>
>>
>>
>> On Sun, Apr 1, 2018 at 10:09 PM, Eric Berquist <er...@pi...> wrote:
>>
>>> Hi Tyler,
>>>
>>> Nothing is present right now in the package to do that, though it may be
>>> a useful method in the future.
>>>
>>> For reference, if you're looking for the expressions, I've coded up
>>> distances, torsions, and angles in the past from this project:
>>> https://github.com/CrawfordGroup/ProgrammingProject
>>> s/tree/master/Project%2301
>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FCrawfordGroup%2FProgrammingProjects%2Ftree%2Fmaster%2FProject%252301&data=01%7C01%7Cerb74%40pitt.edu%7C0cb5cf0f698b4584176e08d598a3a50c%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=RVJgFfkFGATY7cQmozjV8zYWZuCOa2KWhxYBE5l3uC8%3D&reserved=0>
>>>
>>> Some of it is available (https://github.com/berquist/p
>>> rogramming_party/blob/master/eric/molecule.py
>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fberquist%2Fprogramming_party%2Fblob%2Fmaster%2Feric%2Fmolecule.py&data=01%7C01%7Cerb74%40pitt.edu%7C0cb5cf0f698b4584176e08d598a3a50c%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=rHZe4h49qc4HM3Tow2VMDdfHYm9hWxlLEBr58Kk5zL4%3D&reserved=0>),
>>> though the torsions aren't present for some reason. I can find them if
>>> you're interested.
>>>
>>> Eric
>>>
>>> On Sat, Mar 31, 2018 at 7:14 AM, Tyler Josephson <jos...@um...>
>>> wrote:
>>>
>>>> Hi there!
>>>>
>>>> I'm new to cclib, and enjoying it so far! It's a powerful tool. I
>>>> wanted to ask the community if you've worked on functions that would
>>>> extract particular distance, angle, or dihedral measurements (I need
>>>> dihedrals for my particular problem). I could read in the atomcoords and
>>>> calculate them myself, but I wanted to check if something else is available.
>>>>
>>>> Regards,
>>>> Tyler
>>>>
>>>> --
>>>> Tyler Josephson
>>>> PhD Chemical Engineering
>>>> Postdoctoral Research Associate, Siepmann Group
>>>> University of Minnesota, Twin Cities
>>>> 651-269-1433 |  | LinkedIn
>>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linkedin.com%2Fin%2Ftrjosephson%2F&data=01%7C01%7Cerb74%40pitt.edu%7C99323476a9ec40b3fa1d08d596fb6271%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=bqoJnaPbbc1W%2BSq81RrBgbARpQHFmXsemHI2Sbi9eiY%3D&reserved=0>
>>>>
>>>> ------------------------------------------------------------
>>>> ------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! https://na01.safelinks.protect
>>>> ion.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=0
>>>> 1%7C01%7Cerb74%40pitt.edu%7C99323476a9ec40b3fa1d08d596fb6271
>>>> %7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=9ijts%2FUMc6h6
>>>> 5RYv2EYB3lVuEHgIjuFVLInwZ3z1SKI%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%7C99323476a9ec40b3fa1d08d596
>>>> fb6271%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=vtaWqxXd
>>>> aJ13NDCnSkApw%2FCihxRwbWBxJK9fDfK%2FpeY%3D&reserved=0
>>>>
>>>>
>>>
>>
>>
>> --
>> Tyler Josephson
>> PhD Chemical Engineering
>> Postdoctoral Research Associate, Siepmann Group
>> University of Minnesota, Twin Cities
>> 651-269-1433 |  | LinkedIn
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linkedin.com%2Fin%2Ftrjosephson%2F&data=01%7C01%7Cerb74%40pitt.edu%7C0cb5cf0f698b4584176e08d598a3a50c%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=qV%2BEiuoXrqlCNf9K8scXONaMiRvip5fImikj%2BYFdalc%3D&reserved=0>
>>
>
>
> ------------------------------------------------------------
> ------------------
> 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] Distance, Angle, Dihedral

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

Hi Tyler,

I know you didn't ask this, but regarding the different implementations,
I'll implement them and try them out. In general, I think that assuming
performance doesn't vary too wildly, we're more interested in
implementations that are close to the original intent (the equations),
thought the "fast" one seems reasonable. A better timing test would compare
both small molecules and very large ones, like MOFs or proteins, using
`timeit`.

> should one calculate all bonds, angles, dihedrals automatically, or
should the code simply return specific bonds/angles/dihedrals that are
requested by the user (or both)?

What I propose is a new method (see
https://github.com/cclib/cclib/tree/master/src/cclib/method) that would
take a `ccdata` instance and calculate all possible distances, angles, and
torsions. In general, when we parse, we don't compute derived data; the
only things we compute are quantities for attributes _if_ they can be
computed from other attributes. The need for this is rare (see trickery for
`coreelectrons` in Q-Chem). Once the `ccdata` is passed to the method, it
is probably fine to precompute all values rather than on-the-fly, but this
is not as important as keeping the calculation separate from the parsing.
Eventually we could do both.

See if you can write a method that would basically look like the `Molecule`
but is initialized from a `ccdata` instance.

Eric

On Mon, Apr 2, 2018 at 10:10 AM, Tyler Josephson <jos...@um...> wrote:

> Thanks, Eric, this is helpful!
>
> I did find a useful and simple implementation of dihedrals in Python on
> this page: https://stackoverflow.com/questions/20305272/dihedral-
> torsion-angle-from-four-points-in-cartesian-coordinates-in-python
> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstackoverflow.com%2Fquestions%2F20305272%2Fdihedral-torsion-angle-from-four-points-in-cartesian-coordinates-in-python&data=01%7C01%7Cerb74%40pitt.edu%7C0cb5cf0f698b4584176e08d598a3a50c%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=LRIupf4KL2vU2HJH0SuJpkEdUie0rUOiSgEGq61VZv0%3D&reserved=0>
> I especially like Praexolitic's careful evaluation of the different
> equations in order to select the fastest one.
>
> For my current application, I added this in a rather ad-hoc manner to a
> copy of the ccget script, calling it from within an if statement to be
> executed when attr == 'atomcoords' . So I have what I need for now. I would
> be interested in helping add this to cclib in a more formal way. After
> seeing your code, I realize the community should probably have a discussion
> about what this should entail and how it should be organized - should one
> calculate all bonds, angles, dihedrals automatically, or should the code
> simply return specific bonds/angles/dihedrals that are requested by the
> user (or both)?
>
> What would you recommend? I'm rather new to collaborative code development.
>
> Regards,
> Tyler
>
>
>
> On Sun, Apr 1, 2018 at 10:09 PM, Eric Berquist <er...@pi...> wrote:
>
>> Hi Tyler,
>>
>> Nothing is present right now in the package to do that, though it may be
>> a useful method in the future.
>>
>> For reference, if you're looking for the expressions, I've coded up
>> distances, torsions, and angles in the past from this project:
>> https://github.com/CrawfordGroup/ProgrammingProject
>> s/tree/master/Project%2301
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FCrawfordGroup%2FProgrammingProjects%2Ftree%2Fmaster%2FProject%252301&data=01%7C01%7Cerb74%40pitt.edu%7C0cb5cf0f698b4584176e08d598a3a50c%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=RVJgFfkFGATY7cQmozjV8zYWZuCOa2KWhxYBE5l3uC8%3D&reserved=0>
>>
>> Some of it is available (https://github.com/berquist/p
>> rogramming_party/blob/master/eric/molecule.py
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fberquist%2Fprogramming_party%2Fblob%2Fmaster%2Feric%2Fmolecule.py&data=01%7C01%7Cerb74%40pitt.edu%7C0cb5cf0f698b4584176e08d598a3a50c%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=rHZe4h49qc4HM3Tow2VMDdfHYm9hWxlLEBr58Kk5zL4%3D&reserved=0>),
>> though the torsions aren't present for some reason. I can find them if
>> you're interested.
>>
>> Eric
>>
>> On Sat, Mar 31, 2018 at 7:14 AM, Tyler Josephson <jos...@um...>
>> wrote:
>>
>>> Hi there!
>>>
>>> I'm new to cclib, and enjoying it so far! It's a powerful tool. I wanted
>>> to ask the community if you've worked on functions that would extract
>>> particular distance, angle, or dihedral measurements (I need dihedrals for
>>> my particular problem). I could read in the atomcoords and calculate them
>>> myself, but I wanted to check if something else is available.
>>>
>>> Regards,
>>> Tyler
>>>
>>> --
>>> Tyler Josephson
>>> PhD Chemical Engineering
>>> Postdoctoral Research Associate, Siepmann Group
>>> University of Minnesota, Twin Cities
>>> 651-269-1433 |  | LinkedIn
>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linkedin.com%2Fin%2Ftrjosephson%2F&data=01%7C01%7Cerb74%40pitt.edu%7C99323476a9ec40b3fa1d08d596fb6271%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=bqoJnaPbbc1W%2BSq81RrBgbARpQHFmXsemHI2Sbi9eiY%3D&reserved=0>
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! https://na01.safelinks.protect
>>> ion.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=0
>>> 1%7C01%7Cerb74%40pitt.edu%7C99323476a9ec40b3fa1d08d596fb6271
>>> %7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=9ijts%2FUMc6h6
>>> 5RYv2EYB3lVuEHgIjuFVLInwZ3z1SKI%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%7C99323476a9ec40b3fa1d08d5
>>> 96fb6271%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=
>>> vtaWqxXdaJ13NDCnSkApw%2FCihxRwbWBxJK9fDfK%2FpeY%3D&reserved=0
>>>
>>>
>>
>
>
> --
> Tyler Josephson
> PhD Chemical Engineering
> Postdoctoral Research Associate, Siepmann Group
> University of Minnesota, Twin Cities
> 651-269-1433 |  | LinkedIn
> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linkedin.com%2Fin%2Ftrjosephson%2F&data=01%7C01%7Cerb74%40pitt.edu%7C0cb5cf0f698b4584176e08d598a3a50c%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=qV%2BEiuoXrqlCNf9K8scXONaMiRvip5fImikj%2BYFdalc%3D&reserved=0>
>

Re: [cclib-devel] Distance, Angle, Dihedral

[Tyler J. <jos...@um...>]

Thanks, Eric, this is helpful!

I did find a useful and simple implementation of dihedrals in Python on
this page: https://stackoverflow.com/questions/20305272/
dihedral-torsion-angle-from-four-points-in-cartesian-coordinates-in-python
I especially like Praexolitic's careful evaluation of the different
equations in order to select the fastest one.

For my current application, I added this in a rather ad-hoc manner to a
copy of the ccget script, calling it from within an if statement to be
executed when attr == 'atomcoords' . So I have what I need for now. I would
be interested in helping add this to cclib in a more formal way. After
seeing your code, I realize the community should probably have a discussion
about what this should entail and how it should be organized - should one
calculate all bonds, angles, dihedrals automatically, or should the code
simply return specific bonds/angles/dihedrals that are requested by the
user (or both)?

What would you recommend? I'm rather new to collaborative code development.

Regards,
Tyler



On Sun, Apr 1, 2018 at 10:09 PM, Eric Berquist <er...@pi...> wrote:

> Hi Tyler,
>
> Nothing is present right now in the package to do that, though it may be a
> useful method in the future.
>
> For reference, if you're looking for the expressions, I've coded up
> distances, torsions, and angles in the past from this project:
> https://github.com/CrawfordGroup/ProgrammingProjects/tree/
> master/Project%2301
>
> Some of it is available (https://github.com/berquist/
> programming_party/blob/master/eric/molecule.py), though the torsions
> aren't present for some reason. I can find them if you're interested.
>
> Eric
>
> On Sat, Mar 31, 2018 at 7:14 AM, Tyler Josephson <jos...@um...> wrote:
>
>> Hi there!
>>
>> I'm new to cclib, and enjoying it so far! It's a powerful tool. I wanted
>> to ask the community if you've worked on functions that would extract
>> particular distance, angle, or dihedral measurements (I need dihedrals for
>> my particular problem). I could read in the atomcoords and calculate them
>> myself, but I wanted to check if something else is available.
>>
>> Regards,
>> Tyler
>>
>> --
>> Tyler Josephson
>> PhD Chemical Engineering
>> Postdoctoral Research Associate, Siepmann Group
>> University of Minnesota, Twin Cities
>> 651-269-1433 |  | LinkedIn
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linkedin.com%2Fin%2Ftrjosephson%2F&data=01%7C01%7Cerb74%40pitt.edu%7C99323476a9ec40b3fa1d08d596fb6271%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=bqoJnaPbbc1W%2BSq81RrBgbARpQHFmXsemHI2Sbi9eiY%3D&reserved=0>
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! https://na01.safelinks.protect
>> ion.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=
>> 01%7C01%7Cerb74%40pitt.edu%7C99323476a9ec40b3fa1d08d596fb627
>> 1%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=9ijts%2FUMc6h
>> 65RYv2EYB3lVuEHgIjuFVLInwZ3z1SKI%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%7C99323476a9ec40b3f
>> a1d08d596fb6271%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&
>> sdata=vtaWqxXdaJ13NDCnSkApw%2FCihxRwbWBxJK9fDfK%2FpeY%3D&reserved=0
>>
>>
>


-- 
Tyler Josephson
PhD Chemical Engineering
Postdoctoral Research Associate, Siepmann Group
University of Minnesota, Twin Cities
651-269-1433 |  | LinkedIn <https://www.linkedin.com/in/trjosephson/>

Re: [cclib-devel] Distance, Angle, Dihedral

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

Hi Tyler,

Nothing is present right now in the package to do that, though it may be a
useful method in the future.

For reference, if you're looking for the expressions, I've coded up
distances, torsions, and angles in the past from this project:
https://github.com/CrawfordGroup/ProgrammingProjects/tree/master/Project%2301

Some of it is available (
https://github.com/berquist/programming_party/blob/master/eric/molecule.py),
though the torsions aren't present for some reason. I can find them if
you're interested.

Eric

On Sat, Mar 31, 2018 at 7:14 AM, Tyler Josephson <jos...@um...> wrote:

> Hi there!
>
> I'm new to cclib, and enjoying it so far! It's a powerful tool. I wanted
> to ask the community if you've worked on functions that would extract
> particular distance, angle, or dihedral measurements (I need dihedrals for
> my particular problem). I could read in the atomcoords and calculate them
> myself, but I wanted to check if something else is available.
>
> Regards,
> Tyler
>
> --
> Tyler Josephson
> PhD Chemical Engineering
> Postdoctoral Research Associate, Siepmann Group
> University of Minnesota, Twin Cities
> 651-269-1433 |  | LinkedIn
> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linkedin.com%2Fin%2Ftrjosephson%2F&data=01%7C01%7Cerb74%40pitt.edu%7C99323476a9ec40b3fa1d08d596fb6271%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=bqoJnaPbbc1W%2BSq81RrBgbARpQHFmXsemHI2Sbi9eiY%3D&reserved=0>
>
> ------------------------------------------------------------
> ------------------
> 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%7C99323476a9ec40b3fa1d08d596fb6271%
> 7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=9ijts%
> 2FUMc6h65RYv2EYB3lVuEHgIjuFVLInwZ3z1SKI%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%7C99323476a9ec40b3fa1d08d596fb6271%
> 7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=vtaWqxXdaJ13NDCnSkApw%
> 2FCihxRwbWBxJK9fDfK%2FpeY%3D&reserved=0
>
>

[cclib-devel] Distance, Angle, Dihedral

[Tyler J. <jos...@um...>]

Hi there!

I'm new to cclib, and enjoying it so far! It's a powerful tool. I wanted to
ask the community if you've worked on functions that would extract
particular distance, angle, or dihedral measurements (I need dihedrals for
my particular problem). I could read in the atomcoords and calculate them
myself, but I wanted to check if something else is available.

Regards,
Tyler

-- 
Tyler Josephson
PhD Chemical Engineering
Postdoctoral Research Associate, Siepmann Group
University of Minnesota, Twin Cities
651-269-1433 |  | LinkedIn <https://www.linkedin.com/in/trjosephson/>

Re: [cclib-devel] Upcoming v1.5.3

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

The timing is convenient for me, since I have a lot more free time. Aside
from the general 1.5.3 label, is there anything that should be prioritized?

On Wed, Mar 28, 2018 at 1:56 AM, Karol Langner <kar...@gm...>
wrote:

> Hi all,
>
> It's been a while since the last release again, and I want to get it out
> before GSOC starts. I've set the release to April 22 (just before
> announcing who the students are). The release might be off of that by a day
> or two, but I'd like to finalize it around that time.
>
> So, let's try to get as much in as we can for v1.5.3!
>
> Karol
>
> P. S. And, of course, I want to do another release right after GSOC ends,
> assuming there is a student.
>
> ------------------------------------------------------------
> ------------------
> 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%7C5cab2e4174ff4e05ea3f08d59470b584%
> 7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=ynrjNxlL51L5ou5%
> 2BprRiTswTVAFhsl%2BZ0ZOMm935OQc%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%7C5cab2e4174ff4e05ea3f08d59470b584%
> 7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=uwRN0SaLW%
> 2FMfnVBJ32jEw01u8eMtqP7jiZ1c5oxxTx0%3D&reserved=0
>
>

Re: [cclib-devel] Upcoming v1.5.3

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

Nothing in particular comes to mind. We can try to narrow down what we
think is possible to do in 3 weeks, and move everything else to 1.5.4. We
should also take a look if it's time to go to v1.6. - typically this
happens if there is a new parser or major addition to methods or similar
thing.

On Fri, Mar 30, 2018 at 4:41 PM, Eric Berquist <er...@pi...> wrote:

> The timing is convenient for me, since I have a lot more free time. Aside
> from the general 1.5.3 label, is there anything that should be prioritized?
>
> On Wed, Mar 28, 2018 at 1:56 AM, Karol Langner <kar...@gm...>
> wrote:
>
>> Hi all,
>>
>> It's been a while since the last release again, and I want to get it out
>> before GSOC starts. I've set the release to April 22 (just before
>> announcing who the students are). The release might be off of that by a day
>> or two, but I'd like to finalize it around that time.
>>
>> So, let's try to get as much in as we can for v1.5.3!
>>
>> Karol
>>
>> P. S. And, of course, I want to do another release right after GSOC ends,
>> assuming there is a student.
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! https://na01.safelinks.protect
>> ion.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=
>> 01%7C01%7Cerb74%40pitt.edu%7C5cab2e4174ff4e05ea3f08d59470b58
>> 4%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=ynrjNxlL51L5o
>> u5%2BprRiTswTVAFhsl%2BZ0ZOMm935OQc%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%7C5cab2e4174ff4e05e
>> a3f08d59470b584%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&
>> sdata=uwRN0SaLW%2FMfnVBJ32jEw01u8eMtqP7jiZ1c5oxxTx0%3D&reserved=0
>>
>>
>

[cclib-devel] Hello World!

[Agustin F. <agu...@ho...>]

Hello everyone!

I am a Chemical Engineering Student based in Argentina. I am Open Source enthusiast and I did programming in python for different research projects. I'm also working as a Teaching Assistant, teaching python to young Chemical Engineering Students.

I presented a project for the Google Summer of Code for about implementing AIM into cclib . (So fingers crossed). It's a shame that I didn't have the time to send the project o the list, so i could get your recommendations, however I got wonderful help from Karol Langer and Adam Tenderholt. So I hope that I would be able to do some development in cclib.


Best regards,

Agustin Ferrario

[cclib-devel] Upcoming v1.5.3

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

Hi all,

It's been a while since the last release again, and I want to get it out
before GSOC starts. I've set the release to April 22 (just before
announcing who the students are). The release might be off of that by a day
or two, but I'd like to finalize it around that time.

So, let's try to get as much in as we can for v1.5.3!

Karol

P. S. And, of course, I want to do another release right after GSOC ends,
assuming there is a student.