[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...
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
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>>>> 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...