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From: Mikolaj F. <mik...@gm...> - 2012-10-04 16:51:25
Attachments:
job.out.gz
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Dear cclib users, cclib makes a really great job of calculating atomic properties, for example atomic charges or spin densities. However, I was wondering whether those properties could also be extracted from existing output files, since they are calculated by default by most of the quantum chemical programs. For cclib to perform a population analysis, the output file should contain an overlap matrix and eigenvectors and it considerably grows in size. But the values I want to calculate are already in the file and it would make more sense to simply extract them from there. I am particularly interested in extracting/parsing Mulliken atomic charges and spin densities from ORCA output files. Is there a chance for such a feature to be implemented in cclib in the nearest future? I enclose a sample file. Cheers, mfx |
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From: Karol M. L. <kar...@gm...> - 2012-10-05 16:50:55
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Mikolaj, Are making this sample file public domain? If so, we can then include in our test suite. Thanks, Karol On Oct 04 2012, Mikolaj Feliks wrote: > > Dear cclib users, > > cclib makes a really great job of calculating atomic properties, for > example atomic charges or spin densities. > > However, I was wondering whether those properties could also be > extracted from existing output files, since they are calculated by > default by most of the quantum chemical programs. For cclib to > perform a population analysis, the output file should contain an > overlap matrix and eigenvectors and it considerably grows in size. > But the values I want to calculate are already in the file and it > would make more sense to simply extract them from there. > > I am particularly interested in extracting/parsing Mulliken atomic > charges and spin densities from ORCA output files. Is there a chance > for such a feature to be implemented in cclib in the nearest future? > I enclose a sample file. > > Cheers, mfx > > ------------------------------------------------------------------------------ > Don't let slow site performance ruin your business. Deploy New Relic APM > Deploy New Relic app performance management and know exactly > what is happening inside your Ruby, Python, PHP, Java, and .NET app > Try New Relic at no cost today and get our sweet Data Nerd shirt too! > http://p.sf.net/sfu/newrelic-dev2dev > _______________________________________________ > cclib-users mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-users -- written by Karol M. Langner Fri Oct 5 18:49:22 CEST 2012 |
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From: Mikolaj F. <mik...@gm...> - 2012-10-05 16:55:44
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Hi Karol, I see no problem making this file public. Go ahead! Cheers, mfx On 10/05/12 18:50, Karol M. Langner wrote: > Mikolaj, > > Are making this sample file public domain? If so, we can then include in > our test suite. > > Thanks, > Karol > > On Oct 04 2012, Mikolaj Feliks wrote: >> >> Dear cclib users, >> >> cclib makes a really great job of calculating atomic properties, for >> example atomic charges or spin densities. >> >> However, I was wondering whether those properties could also be >> extracted from existing output files, since they are calculated by >> default by most of the quantum chemical programs. For cclib to >> perform a population analysis, the output file should contain an >> overlap matrix and eigenvectors and it considerably grows in size. >> But the values I want to calculate are already in the file and it >> would make more sense to simply extract them from there. >> >> I am particularly interested in extracting/parsing Mulliken atomic >> charges and spin densities from ORCA output files. Is there a chance >> for such a feature to be implemented in cclib in the nearest future? >> I enclose a sample file. >> >> Cheers, mfx >> > > >> ------------------------------------------------------------------------------ >> Don't let slow site performance ruin your business. Deploy New Relic APM >> Deploy New Relic app performance management and know exactly >> what is happening inside your Ruby, Python, PHP, Java, and .NET app >> Try New Relic at no cost today and get our sweet Data Nerd shirt too! >> http://p.sf.net/sfu/newrelic-dev2dev > >> _______________________________________________ >> cclib-users mailing list >> ccl...@li... >> https://lists.sourceforge.net/lists/listinfo/cclib-users > > |
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From: Karol M. L. <kar...@gm...> - 2012-10-05 17:23:21
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Hi, OK, thanks! This is perhaps a good thing to add, since it is not always trivial to recalculate a population analysis for methods other than RHF, and the overlaps/coefficients are sometimes simply not there. As far as the implementation is concerned, there is a problem. Namely, aotmic partial charges and spin densities are arbitrary, that is, they can be defined in many varieties -- Mulliken, Loewden, etc. We can't assume that the parsed charge/spin densities are any one of these. So, Noel, Adam... what do you think? We can't have na attribute for every type of population analysis parsed. I see two options: 1) use a dictionary, with keys like 'Mulliken', 'Loewdin' 2) use a list of tuples consisting of a string and an array of charges Any other ideas? - Karol On Oct 05 2012, Mikolaj Feliks wrote: > > Hi Karol, > > I see no problem making this file public. Go ahead! > > Cheers, mfx > > > On 10/05/12 18:50, Karol M. Langner wrote: > > Mikolaj, > > > > Are making this sample file public domain? If so, we can then include in > > our test suite. > > > > Thanks, > > Karol > > > > On Oct 04 2012, Mikolaj Feliks wrote: > >> > >> Dear cclib users, > >> > >> cclib makes a really great job of calculating atomic properties, for > >> example atomic charges or spin densities. > >> > >> However, I was wondering whether those properties could also be > >> extracted from existing output files, since they are calculated by > >> default by most of the quantum chemical programs. For cclib to > >> perform a population analysis, the output file should contain an > >> overlap matrix and eigenvectors and it considerably grows in size. > >> But the values I want to calculate are already in the file and it > >> would make more sense to simply extract them from there. > >> > >> I am particularly interested in extracting/parsing Mulliken atomic > >> charges and spin densities from ORCA output files. Is there a chance > >> for such a feature to be implemented in cclib in the nearest future? > >> I enclose a sample file. > >> > >> Cheers, mfx > >> > > > > > >> ------------------------------------------------------------------------------ > >> Don't let slow site performance ruin your business. Deploy New Relic APM > >> Deploy New Relic app performance management and know exactly > >> what is happening inside your Ruby, Python, PHP, Java, and .NET app > >> Try New Relic at no cost today and get our sweet Data Nerd shirt too! > >> http://p.sf.net/sfu/newrelic-dev2dev > > > >> _______________________________________________ > >> cclib-users mailing list > >> ccl...@li... > >> https://lists.sourceforge.net/lists/listinfo/cclib-users > > > > > > ------------------------------------------------------------------------------ > Don't let slow site performance ruin your business. Deploy New Relic APM > Deploy New Relic app performance management and know exactly > what is happening inside your Ruby, Python, PHP, Java, and .NET app > Try New Relic at no cost today and get our sweet Data Nerd shirt too! > http://p.sf.net/sfu/newrelic-dev2dev > _______________________________________________ > cclib-users mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-users -- written by Karol M. Langner Fri Oct 5 19:17:52 CEST 2012 |
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From: Karol M. L. <kar...@gm...> - 2012-10-06 18:31:25
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Mikolaj,
The current development code should parse this information correctly for
ORCA, and present it in a dictionary with Mulliken and Lowdin values.
For example:
$ ccget atomcharges atomspins job.out.gz
Attempting to parse job.out.gz
atomcharges:
{'lowdin':
array([ 0.109834, -0.48075 , 0.144867, 0.219485, -0.045542, -0.111878,
0.113258, 0.152248, -0.500877, 0.412007, -0.043762, 0.127572,
-0.528491, 0.383448, -0.114098, 0.10012 , 0.121108, -0.437476,
0.378927]),
'mulliken':
array([ 0.126447, -0.613018, 0.189146, 0.320041, -0.068218, -0.009025,
...
atomspins:
{'lowdin': array([ 2.48200000e-03, -4.93200000e-03, 1.46740000e-02,
... you get the idea ...
Cheers,
Karol
On Oct 04 2012, Mikolaj Feliks wrote:
>
> Dear cclib users,
>
> cclib makes a really great job of calculating atomic properties, for
> example atomic charges or spin densities.
>
> However, I was wondering whether those properties could also be
> extracted from existing output files, since they are calculated by
> default by most of the quantum chemical programs. For cclib to
> perform a population analysis, the output file should contain an
> overlap matrix and eigenvectors and it considerably grows in size.
> But the values I want to calculate are already in the file and it
> would make more sense to simply extract them from there.
>
> I am particularly interested in extracting/parsing Mulliken atomic
> charges and spin densities from ORCA output files. Is there a chance
> for such a feature to be implemented in cclib in the nearest future?
> I enclose a sample file.
>
> Cheers, mfx
>
> ------------------------------------------------------------------------------
> Don't let slow site performance ruin your business. Deploy New Relic APM
> Deploy New Relic app performance management and know exactly
> what is happening inside your Ruby, Python, PHP, Java, and .NET app
> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
> http://p.sf.net/sfu/newrelic-dev2dev
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
--
written by Karol M. Langner
Sat Oct 6 20:25:47 CEST 2012
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From: Mikolaj F. <mik...@gm...> - 2012-10-26 14:47:37
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Hi Karol,
it works - thanks a lot!!
All the best,
mfx
On 10/06/2012 08:31 PM, Karol M. Langner wrote:
> Mikolaj,
>
> The current development code should parse this information correctly for
> ORCA, and present it in a dictionary with Mulliken and Lowdin values.
>
> For example:
> $ ccget atomcharges atomspins job.out.gz
> Attempting to parse job.out.gz
> atomcharges:
> {'lowdin':
> array([ 0.109834, -0.48075 , 0.144867, 0.219485, -0.045542, -0.111878,
> 0.113258, 0.152248, -0.500877, 0.412007, -0.043762, 0.127572,
> -0.528491, 0.383448, -0.114098, 0.10012 , 0.121108, -0.437476,
> 0.378927]),
> 'mulliken':
> array([ 0.126447, -0.613018, 0.189146, 0.320041, -0.068218, -0.009025,
> ...
> atomspins:
> {'lowdin': array([ 2.48200000e-03, -4.93200000e-03, 1.46740000e-02,
> ... you get the idea ...
>
> Cheers,
> Karol
>
> On Oct 04 2012, Mikolaj Feliks wrote:
>>
>> Dear cclib users,
>>
>> cclib makes a really great job of calculating atomic properties, for
>> example atomic charges or spin densities.
>>
>> However, I was wondering whether those properties could also be
>> extracted from existing output files, since they are calculated by
>> default by most of the quantum chemical programs. For cclib to
>> perform a population analysis, the output file should contain an
>> overlap matrix and eigenvectors and it considerably grows in size.
>> But the values I want to calculate are already in the file and it
>> would make more sense to simply extract them from there.
>>
>> I am particularly interested in extracting/parsing Mulliken atomic
>> charges and spin densities from ORCA output files. Is there a chance
>> for such a feature to be implemented in cclib in the nearest future?
>> I enclose a sample file.
>>
>> Cheers, mfx
>>
>
>
>> ------------------------------------------------------------------------------
>> Don't let slow site performance ruin your business. Deploy New Relic APM
>> Deploy New Relic app performance management and know exactly
>> what is happening inside your Ruby, Python, PHP, Java, and .NET app
>> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
>> http://p.sf.net/sfu/newrelic-dev2dev
>
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>
|
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