cclib-users — Help and support for cclib users

[cclib-users] parsing US-GAMESS open-shell species failed

[Martin R. <mar...@gm...>]

Hi,

I think I brought this up earlier, and that it was concluded a bug. Has it
been fixed, and if so will it be included in the next version?

    print data.moenergies[1]

IndexError: list index out of range


Thanks,

Martin

Re: [cclib-users] orbital occupation numbers

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

Axel,

Thanks for the files. Can I use them in our publicly available test suite? In other
words, do you release these files into the Public Domain? Also, if you have the Molpro
file with the long list of coefficients, that would be helpful, too.

We are about to release cclib v1.3, and this certainly won't make it there. But I have
already written some code which will go into the dev version:
https://github.com/cclib/cclib/pull/148

Thanks,
Karol

On Oct 27 2014, Axel Schild wrote:
> Karol,
> 
> I could give you more Gaussian or GamessUS files, but they don't give
> anything new compared to the files in
> https://github.com/cclib/cclib/tree/master/data
> 
> Attached please find two Molpro logfiles and a psi3 logfile. We don't have
> other file formats because we don't use the respective programs (but we
> thought about using cclib to load these file formats for users that do use
> them).
> 
> Cheers
> Axel
> 
> PS: I removed the long list of CI coefficients of the Molpro output for
> CH2O.
> 
> On Fri, Oct 24, 2014 at 3:35 PM, Karol Langner <kar...@gm...>
> wrote:
> 
> > Axel,
> >
> > Would you be wlling to help by providing logfiles for programs that you
> > would like parse this for?
> >
> > Karol
> >
> > On Fri, Oct 24, 2014 at 2:42 AM, Axel Schild <axe...@go...>
> > wrote:
> >
> >> Hi Karol,
> >>
> >> thank you! I just compared to my test files and yes, those are the
> >> numbers that we want.
> >>
> >> I will follow the progress on the development version to see when we can
> >> use cclib for orbkit.
> >>
> >> Cheers
> >> Axel
> >>
> >> On Thu, Oct 23, 2014 at 6:38 PM, Karol Langner <kar...@gm...>
> >> wrote:
> >>
> >>> I created an issue for this:
> >>> https://github.com/cclib/cclib/issues/143
> >>>
> >>>
> >>> On Thu, Oct 23, 2014 at 12:31 PM, Karol Langner <kar...@gm...
> >>> > wrote:
> >>>
> >>>> Axel,
> >>>>
> >>>> The terminology seems to be a little tricky. To be specific, the NO
> >>>> coefficients that we currently parse (for Gaussian) are those that define
> >>>> the natural orbital as an eigenvector of the diagonalized density matrix.
> >>>>
> >>>> Here is an example of the output from out unit tests:
> >>>>
> >>>> https://github.com/cclib/cclib/blob/master/data/Gaussian/basicGaussian09/water_cis.log#L578
> >>>>
> >>>> The eigenvalues printed there, I think, are the occupoation numbers you
> >>>> need (the population in each orbital), although in that particular case
> >>>> some are negative (maybe because the basis set is so small?). Anyway, we
> >>>> don't parse them, but we could of course, if that will be useful for you.
> >>>>
> >>>> Cheers,
> >>>> Karol
> >>>>
> >>>> P.S. A new release of cclib (1.3) is coming out soon. Which version are
> >>>> you using? In any case, this will not make it into 1.3, so you will need to
> >>>> use the dev version from github.
> >>>>
> >>>>
> >>>> On Thu, Oct 23, 2014 at 12:07 PM, Axel Schild <
> >>>> axe...@go...> wrote:
> >>>>
> >>>>> Hi Karol,
> >>>>>
> >>>>> I suppose that NO coefficients and orbital occupation numbers are the
> >>>>> same, i.e. they should be the diagonals of the diagonalized density
> >>>>> matrix.For single-determinant methods they are 2 (or 1) and for
> >>>>> multi-determinant methods they have some value between 0 and 2 (or 1).
> >>>>>
> >>>>> At least I cannot think of any other meaning of "NO coefficients", but
> >>>>> I never heard that term so far.
> >>>>>
> >>>>> Thanks, I hope that this feature is available soon as it would be
> >>>>> pretty nice to use cclib!
> >>>>>
> >>>>> Cheers
> >>>>> Axel
> >>>>>
> >>>>> On Thu, Oct 23, 2014 at 2:18 PM, Karol Langner <
> >>>>> kar...@gm...> wrote:
> >>>>>
> >>>>>> Hi Axel,
> >>>>>>
> >>>>>> The attribute nocoeffs parses NO coefficients, and only for Gaussian
> >>>>>> at the moment, I believe. It could be easily extended to other programs,
> >>>>>> assuming our test logfiles contain the data.
> >>>>>>
> >>>>>> If I understand correctly, occupation numbers can be calculated from
> >>>>>> the NO coefficients. Is that correct?
> >>>>>>
> >>>>>> Cheers,
> >>>>>> Karol
> >>>>>>
> >>>>>>
> >>>>>> On Thu, Oct 23, 2014 at 3:40 AM, Axel Schild <
> >>>>>> axe...@go...> wrote:
> >>>>>>
> >>>>>>> Hi,
> >>>>>>>
> >>>>>>> I'm one of the developers of orbkit (
> >>>>>>> http://sourceforge.net/projects/orbkit). So far, we are using our
> >>>>>>> own Molden, GAMESS US, Gaussian log-file/fchk-file, and WFN-file parser,
> >>>>>>> but we thought about (also) using cclib to be able to read all the file
> >>>>>>> formats that you support.
> >>>>>>>
> >>>>>>> However, we need orbital occupation numbers (like those of MCSCF
> >>>>>>> orbitals or of natural orbitals).
> >>>>>>>
> >>>>>>> Is this the data that is stored in the variable <nocoeffs> in the
> >>>>>>> development version? If so, will it be available for any other than the
> >>>>>>> GAMESS and Gaussian parsers anytime soon? If not, is this feature planned
> >>>>>>> to be included?
> >>>>>>>
> >>>>>>> Cheers
> >>>>>>> Axel
> >>>>>>>
> >>>>>>>
> >>>>>>> ------------------------------------------------------------------------------
> >>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> cclib-users mailing list
> >>>>>>> ccl...@li...
> >>>>>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>
> >>>>
> >>>
> >>
> >

-- 
written by Karol M. Langner
Wed Oct 29 10:46:23 EDT 2014

Re: [cclib-users] orbital occupation numbers

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

Axel,

Would you be wlling to help by providing logfiles for programs that you
would like parse this for?

Karol

On Fri, Oct 24, 2014 at 2:42 AM, Axel Schild <axe...@go...>
wrote:

> Hi Karol,
>
> thank you! I just compared to my test files and yes, those are the numbers
> that we want.
>
> I will follow the progress on the development version to see when we can
> use cclib for orbkit.
>
> Cheers
> Axel
>
> On Thu, Oct 23, 2014 at 6:38 PM, Karol Langner <kar...@gm...>
> wrote:
>
>> I created an issue for this:
>> https://github.com/cclib/cclib/issues/143
>>
>>
>> On Thu, Oct 23, 2014 at 12:31 PM, Karol Langner <kar...@gm...>
>> wrote:
>>
>>> Axel,
>>>
>>> The terminology seems to be a little tricky. To be specific, the NO
>>> coefficients that we currently parse (for Gaussian) are those that define
>>> the natural orbital as an eigenvector of the diagonalized density matrix.
>>>
>>> Here is an example of the output from out unit tests:
>>>
>>> https://github.com/cclib/cclib/blob/master/data/Gaussian/basicGaussian09/water_cis.log#L578
>>>
>>> The eigenvalues printed there, I think, are the occupoation numbers you
>>> need (the population in each orbital), although in that particular case
>>> some are negative (maybe because the basis set is so small?). Anyway, we
>>> don't parse them, but we could of course, if that will be useful for you.
>>>
>>> Cheers,
>>> Karol
>>>
>>> P.S. A new release of cclib (1.3) is coming out soon. Which version are
>>> you using? In any case, this will not make it into 1.3, so you will need to
>>> use the dev version from github.
>>>
>>>
>>> On Thu, Oct 23, 2014 at 12:07 PM, Axel Schild <
>>> axe...@go...> wrote:
>>>
>>>> Hi Karol,
>>>>
>>>> I suppose that NO coefficients and orbital occupation numbers are the
>>>> same, i.e. they should be the diagonals of the diagonalized density
>>>> matrix.For single-determinant methods they are 2 (or 1) and for
>>>> multi-determinant methods they have some value between 0 and 2 (or 1).
>>>>
>>>> At least I cannot think of any other meaning of "NO coefficients", but
>>>> I never heard that term so far.
>>>>
>>>> Thanks, I hope that this feature is available soon as it would be
>>>> pretty nice to use cclib!
>>>>
>>>> Cheers
>>>> Axel
>>>>
>>>> On Thu, Oct 23, 2014 at 2:18 PM, Karol Langner <kar...@gm...
>>>> > wrote:
>>>>
>>>>> Hi Axel,
>>>>>
>>>>> The attribute nocoeffs parses NO coefficients, and only for Gaussian
>>>>> at the moment, I believe. It could be easily extended to other programs,
>>>>> assuming our test logfiles contain the data.
>>>>>
>>>>> If I understand correctly, occupation numbers can be calculated from
>>>>> the NO coefficients. Is that correct?
>>>>>
>>>>> Cheers,
>>>>> Karol
>>>>>
>>>>>
>>>>> On Thu, Oct 23, 2014 at 3:40 AM, Axel Schild <
>>>>> axe...@go...> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I'm one of the developers of orbkit (
>>>>>> http://sourceforge.net/projects/orbkit). So far, we are using our
>>>>>> own Molden, GAMESS US, Gaussian log-file/fchk-file, and WFN-file parser,
>>>>>> but we thought about (also) using cclib to be able to read all the file
>>>>>> formats that you support.
>>>>>>
>>>>>> However, we need orbital occupation numbers (like those of MCSCF
>>>>>> orbitals or of natural orbitals).
>>>>>>
>>>>>> Is this the data that is stored in the variable <nocoeffs> in the
>>>>>> development version? If so, will it be available for any other than the
>>>>>> GAMESS and Gaussian parsers anytime soon? If not, is this feature planned
>>>>>> to be included?
>>>>>>
>>>>>> Cheers
>>>>>> Axel
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>>
>>>>>> _______________________________________________
>>>>>> cclib-users mailing list
>>>>>> ccl...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

Re: [cclib-users] orbital occupation numbers

[Axel S. <axe...@go...>]

Hi Karol,

thank you! I just compared to my test files and yes, those are the numbers
that we want.

I will follow the progress on the development version to see when we can
use cclib for orbkit.

Cheers
Axel

On Thu, Oct 23, 2014 at 6:38 PM, Karol Langner <kar...@gm...>
wrote:

> I created an issue for this:
> https://github.com/cclib/cclib/issues/143
>
>
> On Thu, Oct 23, 2014 at 12:31 PM, Karol Langner <kar...@gm...>
> wrote:
>
>> Axel,
>>
>> The terminology seems to be a little tricky. To be specific, the NO
>> coefficients that we currently parse (for Gaussian) are those that define
>> the natural orbital as an eigenvector of the diagonalized density matrix.
>>
>> Here is an example of the output from out unit tests:
>>
>> https://github.com/cclib/cclib/blob/master/data/Gaussian/basicGaussian09/water_cis.log#L578
>>
>> The eigenvalues printed there, I think, are the occupoation numbers you
>> need (the population in each orbital), although in that particular case
>> some are negative (maybe because the basis set is so small?). Anyway, we
>> don't parse them, but we could of course, if that will be useful for you.
>>
>> Cheers,
>> Karol
>>
>> P.S. A new release of cclib (1.3) is coming out soon. Which version are
>> you using? In any case, this will not make it into 1.3, so you will need to
>> use the dev version from github.
>>
>>
>> On Thu, Oct 23, 2014 at 12:07 PM, Axel Schild <axe...@go...
>> > wrote:
>>
>>> Hi Karol,
>>>
>>> I suppose that NO coefficients and orbital occupation numbers are the
>>> same, i.e. they should be the diagonals of the diagonalized density
>>> matrix.For single-determinant methods they are 2 (or 1) and for
>>> multi-determinant methods they have some value between 0 and 2 (or 1).
>>>
>>> At least I cannot think of any other meaning of "NO coefficients", but I
>>> never heard that term so far.
>>>
>>> Thanks, I hope that this feature is available soon as it would be pretty
>>> nice to use cclib!
>>>
>>> Cheers
>>> Axel
>>>
>>> On Thu, Oct 23, 2014 at 2:18 PM, Karol Langner <kar...@gm...>
>>> wrote:
>>>
>>>> Hi Axel,
>>>>
>>>> The attribute nocoeffs parses NO coefficients, and only for Gaussian at
>>>> the moment, I believe. It could be easily extended to other programs,
>>>> assuming our test logfiles contain the data.
>>>>
>>>> If I understand correctly, occupation numbers can be calculated from
>>>> the NO coefficients. Is that correct?
>>>>
>>>> Cheers,
>>>> Karol
>>>>
>>>>
>>>> On Thu, Oct 23, 2014 at 3:40 AM, Axel Schild <
>>>> axe...@go...> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I'm one of the developers of orbkit (
>>>>> http://sourceforge.net/projects/orbkit). So far, we are using our own
>>>>> Molden, GAMESS US, Gaussian log-file/fchk-file, and WFN-file parser, but we
>>>>> thought about (also) using cclib to be able to read all the file formats
>>>>> that you support.
>>>>>
>>>>> However, we need orbital occupation numbers (like those of MCSCF
>>>>> orbitals or of natural orbitals).
>>>>>
>>>>> Is this the data that is stored in the variable <nocoeffs> in the
>>>>> development version? If so, will it be available for any other than the
>>>>> GAMESS and Gaussian parsers anytime soon? If not, is this feature planned
>>>>> to be included?
>>>>>
>>>>> Cheers
>>>>> Axel
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>>
>>>>> _______________________________________________
>>>>> cclib-users mailing list
>>>>> ccl...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>>>
>>>>>
>>>>
>>>
>>
>

Re: [cclib-users] orbital occupation numbers

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

I created an issue for this:
https://github.com/cclib/cclib/issues/143

On Thu, Oct 23, 2014 at 12:31 PM, Karol Langner <kar...@gm...>
wrote:

> Axel,
>
> The terminology seems to be a little tricky. To be specific, the NO
> coefficients that we currently parse (for Gaussian) are those that define
> the natural orbital as an eigenvector of the diagonalized density matrix.
>
> Here is an example of the output from out unit tests:
>
> https://github.com/cclib/cclib/blob/master/data/Gaussian/basicGaussian09/water_cis.log#L578
>
> The eigenvalues printed there, I think, are the occupoation numbers you
> need (the population in each orbital), although in that particular case
> some are negative (maybe because the basis set is so small?). Anyway, we
> don't parse them, but we could of course, if that will be useful for you.
>
> Cheers,
> Karol
>
> P.S. A new release of cclib (1.3) is coming out soon. Which version are
> you using? In any case, this will not make it into 1.3, so you will need to
> use the dev version from github.
>
>
> On Thu, Oct 23, 2014 at 12:07 PM, Axel Schild <axe...@go...>
> wrote:
>
>> Hi Karol,
>>
>> I suppose that NO coefficients and orbital occupation numbers are the
>> same, i.e. they should be the diagonals of the diagonalized density
>> matrix.For single-determinant methods they are 2 (or 1) and for
>> multi-determinant methods they have some value between 0 and 2 (or 1).
>>
>> At least I cannot think of any other meaning of "NO coefficients", but I
>> never heard that term so far.
>>
>> Thanks, I hope that this feature is available soon as it would be pretty
>> nice to use cclib!
>>
>> Cheers
>> Axel
>>
>> On Thu, Oct 23, 2014 at 2:18 PM, Karol Langner <kar...@gm...>
>> wrote:
>>
>>> Hi Axel,
>>>
>>> The attribute nocoeffs parses NO coefficients, and only for Gaussian at
>>> the moment, I believe. It could be easily extended to other programs,
>>> assuming our test logfiles contain the data.
>>>
>>> If I understand correctly, occupation numbers can be calculated from the
>>> NO coefficients. Is that correct?
>>>
>>> Cheers,
>>> Karol
>>>
>>>
>>> On Thu, Oct 23, 2014 at 3:40 AM, Axel Schild <axe...@go...
>>> > wrote:
>>>
>>>> Hi,
>>>>
>>>> I'm one of the developers of orbkit (
>>>> http://sourceforge.net/projects/orbkit). So far, we are using our own
>>>> Molden, GAMESS US, Gaussian log-file/fchk-file, and WFN-file parser, but we
>>>> thought about (also) using cclib to be able to read all the file formats
>>>> that you support.
>>>>
>>>> However, we need orbital occupation numbers (like those of MCSCF
>>>> orbitals or of natural orbitals).
>>>>
>>>> Is this the data that is stored in the variable <nocoeffs> in the
>>>> development version? If so, will it be available for any other than the
>>>> GAMESS and Gaussian parsers anytime soon? If not, is this feature planned
>>>> to be included?
>>>>
>>>> Cheers
>>>> Axel
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>>
>>>> _______________________________________________
>>>> cclib-users mailing list
>>>> ccl...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>>
>>>>
>>>
>>
>

Re: [cclib-users] orbital occupation numbers

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

Axel,

The terminology seems to be a little tricky. To be specific, the NO
coefficients that we currently parse (for Gaussian) are those that define
the natural orbital as an eigenvector of the diagonalized density matrix.

Here is an example of the output from out unit tests:
https://github.com/cclib/cclib/blob/master/data/Gaussian/basicGaussian09/water_cis.log#L578

The eigenvalues printed there, I think, are the occupoation numbers you
need (the population in each orbital), although in that particular case
some are negative (maybe because the basis set is so small?). Anyway, we
don't parse them, but we could of course, if that will be useful for you.

Cheers,
Karol

P.S. A new release of cclib (1.3) is coming out soon. Which version are you
using? In any case, this will not make it into 1.3, so you will need to use
the dev version from github.


On Thu, Oct 23, 2014 at 12:07 PM, Axel Schild <axe...@go...>
wrote:

> Hi Karol,
>
> I suppose that NO coefficients and orbital occupation numbers are the
> same, i.e. they should be the diagonals of the diagonalized density
> matrix.For single-determinant methods they are 2 (or 1) and for
> multi-determinant methods they have some value between 0 and 2 (or 1).
>
> At least I cannot think of any other meaning of "NO coefficients", but I
> never heard that term so far.
>
> Thanks, I hope that this feature is available soon as it would be pretty
> nice to use cclib!
>
> Cheers
> Axel
>
> On Thu, Oct 23, 2014 at 2:18 PM, Karol Langner <kar...@gm...>
> wrote:
>
>> Hi Axel,
>>
>> The attribute nocoeffs parses NO coefficients, and only for Gaussian at
>> the moment, I believe. It could be easily extended to other programs,
>> assuming our test logfiles contain the data.
>>
>> If I understand correctly, occupation numbers can be calculated from the
>> NO coefficients. Is that correct?
>>
>> Cheers,
>> Karol
>>
>>
>> On Thu, Oct 23, 2014 at 3:40 AM, Axel Schild <axe...@go...>
>> wrote:
>>
>>> Hi,
>>>
>>> I'm one of the developers of orbkit (
>>> http://sourceforge.net/projects/orbkit). So far, we are using our own
>>> Molden, GAMESS US, Gaussian log-file/fchk-file, and WFN-file parser, but we
>>> thought about (also) using cclib to be able to read all the file formats
>>> that you support.
>>>
>>> However, we need orbital occupation numbers (like those of MCSCF
>>> orbitals or of natural orbitals).
>>>
>>> Is this the data that is stored in the variable <nocoeffs> in the
>>> development version? If so, will it be available for any other than the
>>> GAMESS and Gaussian parsers anytime soon? If not, is this feature planned
>>> to be included?
>>>
>>> Cheers
>>> Axel
>>>
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> cclib-users mailing list
>>> ccl...@li...
>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>
>>>
>>
>

[cclib-users] orbital occupation numbers

[Axel S. <axe...@go...>]

Hi,

I'm one of the developers of orbkit (http://sourceforge.net/projects/orbkit).
So far, we are using our own Molden, GAMESS US, Gaussian
log-file/fchk-file, and WFN-file parser, but we thought about (also) using
cclib to be able to read all the file formats that you support.

However, we need orbital occupation numbers (like those of MCSCF orbitals
or of natural orbitals).

Is this the data that is stored in the variable <nocoeffs> in the
development version? If so, will it be available for any other than the
GAMESS and Gaussian parsers anytime soon? If not, is this feature planned
to be included?

Cheers
Axel

Re: [cclib-users] Can cclib extract nuclear repulsion energy?

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

It seems that the number of digits in our internal unit convertor was
causing these discrepancies. I've updated that and added a new method,
called Nuclear, which does the calculation in pull request 142 (
https://github.com/cclib/cclib/pull/142), which will probably show up in
master soon.

On Tue, Oct 21, 2014 at 11:41 AM, Martin Rahm <mar...@gm...> wrote:

> Yes, when I check this on AsH3, the Gaussian output provides
> 35.6243303658:
> the script gives:
> 35.6245283504
> and so the difference is:
> 0.0001979846 Hartree
>
>
> On Tue, Oct 21, 2014 at 10:25 AM, Karol Langner <kar...@gm...>
> wrote:
>
>> OK, However, I don't understand something about the precision, which
>> should be something like N*(N-1) times the precision of the coordinates,
>> right? However, for the QChem file cited in the example I get 8.88705387953
>> as opposed to 8.8870062630 hartrees. The difference 0.00005 is much more
>> than I would expect.
>>
>> Could you do a similar comparison for you example?
>>
>> - Karol
>>
>>
>> On Mon, Oct 20, 2014 at 11:14 PM, Martin Rahm <mar...@gm...>
>> wrote:
>>
>>> My bad, it was reading the first structure of several..
>>>
>>>
>>>
>>>
>>>
>>> On Mon, Oct 20, 2014 at 11:05 PM, Martin Rahm <mar...@gm...>
>>> wrote:
>>>
>>>> I double checked it on AsH3, where the gaussian output reads 35.1700177407,
>>>> the script produces 35.1702110106, hence a difference of 0.12
>>>> kcal/mol. I suspect there might not be way around this, save to read the
>>>> file directly...
>>>>
>>>> Cheers,
>>>> Martin
>>>>
>>>> On Mon, Oct 20, 2014 at 10:56 PM, Martin Rahm <mar...@gm...>
>>>> wrote:
>>>>
>>>>> Works like charm, thanks a bunch for the quick reply. And yes, why not
>>>>> include it as a method, saves code space!
>>>>>
>>>>> Cheers,
>>>>> Martin
>>>>>
>>>>> On Mon, Oct 20, 2014 at 10:49 PM, Karol Langner <
>>>>> kar...@gm...> wrote:
>>>>>
>>>>>> I wrote up a gist showing how the NRE can be calculated:
>>>>>> https://gist.github.com/langner/ac912b36122c367c5ab4
>>>>>>
>>>>>> If you run that, it should print around 8.88 hartress, which is also
>>>>>> the value in that output file:
>>>>>>
>>>>>> https://github.com/cclib/cclib/blob/master/data/QChem/basicQChem4.2/water_mp4sdq.out#L97
>>>>>>
>>>>>> Perhaps including it as a method with cclib would be a good solution?
>>>>>>
>>>>>> Cheers,
>>>>>> Karol
>>>>>>
>>>>>>
>>>>>> On Mon, Oct 20, 2014 at 10:29 PM, Karol Langner <
>>>>>> kar...@gm...> wrote:
>>>>>>
>>>>>>> Hi Martin,
>>>>>>>
>>>>>>> That is not parsed currently. It could be included, but if I'm not
>>>>>>> mistaken it's very straightforward to calculate it based on parsed
>>>>>>> coordinates and nuclear charges, right?
>>>>>>>
>>>>>>> Karol
>>>>>>>
>>>>>>> On Mon, Oct 20, 2014 at 9:37 PM, Martin Rahm <mar...@gm...>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> This is a very simple thing, but one I'm not sure cclib can do.
>>>>>>>> Have I simply missed it, or could it be included?
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Martin
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> Comprehensive Server Monitoring with Site24x7.
>>>>>>>> Monitor 10 servers for $9/Month.
>>>>>>>> Get alerted through email, SMS, voice calls or mobile push
>>>>>>>> notifications.
>>>>>>>> Take corrective actions from your mobile device.
>>>>>>>> http://p.sf.net/sfu/Zoho
>>>>>>>> _______________________________________________
>>>>>>>> cclib-users mailing list
>>>>>>>> ccl...@li...
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

Re: [cclib-users] Can cclib extract nuclear repulsion energy?

[Martin R. <mar...@gm...>]

Yes, when I check this on AsH3, the Gaussian output provides
35.6243303658:
the script gives:
35.6245283504
and so the difference is:
0.0001979846 Hartree


On Tue, Oct 21, 2014 at 10:25 AM, Karol Langner <kar...@gm...>
wrote:

> OK, However, I don't understand something about the precision, which
> should be something like N*(N-1) times the precision of the coordinates,
> right? However, for the QChem file cited in the example I get 8.88705387953
> as opposed to 8.8870062630 hartrees. The difference 0.00005 is much more
> than I would expect.
>
> Could you do a similar comparison for you example?
>
> - Karol
>
>
> On Mon, Oct 20, 2014 at 11:14 PM, Martin Rahm <mar...@gm...>
> wrote:
>
>> My bad, it was reading the first structure of several..
>>
>>
>>
>>
>>
>> On Mon, Oct 20, 2014 at 11:05 PM, Martin Rahm <mar...@gm...>
>> wrote:
>>
>>> I double checked it on AsH3, where the gaussian output reads 35.1700177407,
>>> the script produces 35.1702110106, hence a difference of 0.12 kcal/mol.
>>> I suspect there might not be way around this, save to read the file
>>> directly...
>>>
>>> Cheers,
>>> Martin
>>>
>>> On Mon, Oct 20, 2014 at 10:56 PM, Martin Rahm <mar...@gm...>
>>> wrote:
>>>
>>>> Works like charm, thanks a bunch for the quick reply. And yes, why not
>>>> include it as a method, saves code space!
>>>>
>>>> Cheers,
>>>> Martin
>>>>
>>>> On Mon, Oct 20, 2014 at 10:49 PM, Karol Langner <
>>>> kar...@gm...> wrote:
>>>>
>>>>> I wrote up a gist showing how the NRE can be calculated:
>>>>> https://gist.github.com/langner/ac912b36122c367c5ab4
>>>>>
>>>>> If you run that, it should print around 8.88 hartress, which is also
>>>>> the value in that output file:
>>>>>
>>>>> https://github.com/cclib/cclib/blob/master/data/QChem/basicQChem4.2/water_mp4sdq.out#L97
>>>>>
>>>>> Perhaps including it as a method with cclib would be a good solution?
>>>>>
>>>>> Cheers,
>>>>> Karol
>>>>>
>>>>>
>>>>> On Mon, Oct 20, 2014 at 10:29 PM, Karol Langner <
>>>>> kar...@gm...> wrote:
>>>>>
>>>>>> Hi Martin,
>>>>>>
>>>>>> That is not parsed currently. It could be included, but if I'm not
>>>>>> mistaken it's very straightforward to calculate it based on parsed
>>>>>> coordinates and nuclear charges, right?
>>>>>>
>>>>>> Karol
>>>>>>
>>>>>> On Mon, Oct 20, 2014 at 9:37 PM, Martin Rahm <mar...@gm...>
>>>>>> wrote:
>>>>>>
>>>>>>> This is a very simple thing, but one I'm not sure cclib can do. Have
>>>>>>> I simply missed it, or could it be included?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Martin
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> Comprehensive Server Monitoring with Site24x7.
>>>>>>> Monitor 10 servers for $9/Month.
>>>>>>> Get alerted through email, SMS, voice calls or mobile push
>>>>>>> notifications.
>>>>>>> Take corrective actions from your mobile device.
>>>>>>> http://p.sf.net/sfu/Zoho
>>>>>>> _______________________________________________
>>>>>>> cclib-users mailing list
>>>>>>> ccl...@li...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

Re: [cclib-users] Can cclib extract nuclear repulsion energy?

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

OK, However, I don't understand something about the precision, which should
be something like N*(N-1) times the precision of the coordinates, right?
However, for the QChem file cited in the example I get 8.88705387953 as
opposed to 8.8870062630 hartrees. The difference 0.00005 is much more than
I would expect.

Could you do a similar comparison for you example?

- Karol

On Mon, Oct 20, 2014 at 11:14 PM, Martin Rahm <mar...@gm...> wrote:

> My bad, it was reading the first structure of several..
>
>
>
>
>
> On Mon, Oct 20, 2014 at 11:05 PM, Martin Rahm <mar...@gm...>
> wrote:
>
>> I double checked it on AsH3, where the gaussian output reads 35.1700177407,
>> the script produces 35.1702110106, hence a difference of 0.12 kcal/mol.
>> I suspect there might not be way around this, save to read the file
>> directly...
>>
>> Cheers,
>> Martin
>>
>> On Mon, Oct 20, 2014 at 10:56 PM, Martin Rahm <mar...@gm...>
>> wrote:
>>
>>> Works like charm, thanks a bunch for the quick reply. And yes, why not
>>> include it as a method, saves code space!
>>>
>>> Cheers,
>>> Martin
>>>
>>> On Mon, Oct 20, 2014 at 10:49 PM, Karol Langner <kar...@gm...
>>> > wrote:
>>>
>>>> I wrote up a gist showing how the NRE can be calculated:
>>>> https://gist.github.com/langner/ac912b36122c367c5ab4
>>>>
>>>> If you run that, it should print around 8.88 hartress, which is also
>>>> the value in that output file:
>>>>
>>>> https://github.com/cclib/cclib/blob/master/data/QChem/basicQChem4.2/water_mp4sdq.out#L97
>>>>
>>>> Perhaps including it as a method with cclib would be a good solution?
>>>>
>>>> Cheers,
>>>> Karol
>>>>
>>>>
>>>> On Mon, Oct 20, 2014 at 10:29 PM, Karol Langner <
>>>> kar...@gm...> wrote:
>>>>
>>>>> Hi Martin,
>>>>>
>>>>> That is not parsed currently. It could be included, but if I'm not
>>>>> mistaken it's very straightforward to calculate it based on parsed
>>>>> coordinates and nuclear charges, right?
>>>>>
>>>>> Karol
>>>>>
>>>>> On Mon, Oct 20, 2014 at 9:37 PM, Martin Rahm <mar...@gm...>
>>>>> wrote:
>>>>>
>>>>>> This is a very simple thing, but one I'm not sure cclib can do. Have
>>>>>> I simply missed it, or could it be included?
>>>>>>
>>>>>> Thanks,
>>>>>> Martin
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Comprehensive Server Monitoring with Site24x7.
>>>>>> Monitor 10 servers for $9/Month.
>>>>>> Get alerted through email, SMS, voice calls or mobile push
>>>>>> notifications.
>>>>>> Take corrective actions from your mobile device.
>>>>>> http://p.sf.net/sfu/Zoho
>>>>>> _______________________________________________
>>>>>> cclib-users mailing list
>>>>>> ccl...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

Re: [cclib-users] Can cclib extract nuclear repulsion energy?

[Martin R. <mar...@gm...>]

I double checked it on AsH3, where the gaussian output reads 35.1700177407,
the script produces 35.1702110106, hence a difference of 0.12 kcal/mol. I
suspect there might not be way around this, save to read the file
directly...

Cheers,
Martin

On Mon, Oct 20, 2014 at 10:56 PM, Martin Rahm <mar...@gm...> wrote:

> Works like charm, thanks a bunch for the quick reply. And yes, why not
> include it as a method, saves code space!
>
> Cheers,
> Martin
>
> On Mon, Oct 20, 2014 at 10:49 PM, Karol Langner <kar...@gm...>
> wrote:
>
>> I wrote up a gist showing how the NRE can be calculated:
>> https://gist.github.com/langner/ac912b36122c367c5ab4
>>
>> If you run that, it should print around 8.88 hartress, which is also the
>> value in that output file:
>>
>> https://github.com/cclib/cclib/blob/master/data/QChem/basicQChem4.2/water_mp4sdq.out#L97
>>
>> Perhaps including it as a method with cclib would be a good solution?
>>
>> Cheers,
>> Karol
>>
>>
>> On Mon, Oct 20, 2014 at 10:29 PM, Karol Langner <kar...@gm...>
>> wrote:
>>
>>> Hi Martin,
>>>
>>> That is not parsed currently. It could be included, but if I'm not
>>> mistaken it's very straightforward to calculate it based on parsed
>>> coordinates and nuclear charges, right?
>>>
>>> Karol
>>>
>>> On Mon, Oct 20, 2014 at 9:37 PM, Martin Rahm <mar...@gm...>
>>> wrote:
>>>
>>>> This is a very simple thing, but one I'm not sure cclib can do. Have I
>>>> simply missed it, or could it be included?
>>>>
>>>> Thanks,
>>>> Martin
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Comprehensive Server Monitoring with Site24x7.
>>>> Monitor 10 servers for $9/Month.
>>>> Get alerted through email, SMS, voice calls or mobile push
>>>> notifications.
>>>> Take corrective actions from your mobile device.
>>>> http://p.sf.net/sfu/Zoho
>>>> _______________________________________________
>>>> cclib-users mailing list
>>>> ccl...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>>
>>>>
>>>
>>
>

Re: [cclib-users] Can cclib extract nuclear repulsion energy?

[Martin R. <mar...@gm...>]

Works like charm, thanks a bunch for the quick reply. And yes, why not
include it as a method, saves code space!

Cheers,
Martin

On Mon, Oct 20, 2014 at 10:49 PM, Karol Langner <kar...@gm...>
wrote:

> I wrote up a gist showing how the NRE can be calculated:
> https://gist.github.com/langner/ac912b36122c367c5ab4
>
> If you run that, it should print around 8.88 hartress, which is also the
> value in that output file:
>
> https://github.com/cclib/cclib/blob/master/data/QChem/basicQChem4.2/water_mp4sdq.out#L97
>
> Perhaps including it as a method with cclib would be a good solution?
>
> Cheers,
> Karol
>
>
> On Mon, Oct 20, 2014 at 10:29 PM, Karol Langner <kar...@gm...>
> wrote:
>
>> Hi Martin,
>>
>> That is not parsed currently. It could be included, but if I'm not
>> mistaken it's very straightforward to calculate it based on parsed
>> coordinates and nuclear charges, right?
>>
>> Karol
>>
>> On Mon, Oct 20, 2014 at 9:37 PM, Martin Rahm <mar...@gm...>
>> wrote:
>>
>>> This is a very simple thing, but one I'm not sure cclib can do. Have I
>>> simply missed it, or could it be included?
>>>
>>> Thanks,
>>> Martin
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Comprehensive Server Monitoring with Site24x7.
>>> Monitor 10 servers for $9/Month.
>>> Get alerted through email, SMS, voice calls or mobile push notifications.
>>> Take corrective actions from your mobile device.
>>> http://p.sf.net/sfu/Zoho
>>> _______________________________________________
>>> cclib-users mailing list
>>> ccl...@li...
>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>
>>>
>>
>

Re: [cclib-users] Can cclib extract nuclear repulsion energy?

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

I wrote up a gist showing how the NRE can be calculated:
https://gist.github.com/langner/ac912b36122c367c5ab4

If you run that, it should print around 8.88 hartress, which is also the
value in that output file:
https://github.com/cclib/cclib/blob/master/data/QChem/basicQChem4.2/water_mp4sdq.out#L97

Perhaps including it as a method with cclib would be a good solution?

Cheers,
Karol


On Mon, Oct 20, 2014 at 10:29 PM, Karol Langner <kar...@gm...>
wrote:

> Hi Martin,
>
> That is not parsed currently. It could be included, but if I'm not
> mistaken it's very straightforward to calculate it based on parsed
> coordinates and nuclear charges, right?
>
> Karol
>
> On Mon, Oct 20, 2014 at 9:37 PM, Martin Rahm <mar...@gm...>
> wrote:
>
>> This is a very simple thing, but one I'm not sure cclib can do. Have I
>> simply missed it, or could it be included?
>>
>> Thanks,
>> Martin
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Comprehensive Server Monitoring with Site24x7.
>> Monitor 10 servers for $9/Month.
>> Get alerted through email, SMS, voice calls or mobile push notifications.
>> Take corrective actions from your mobile device.
>> http://p.sf.net/sfu/Zoho
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>>
>

Re: [cclib-users] Can cclib extract nuclear repulsion energy?

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

Hi Martin,

That is not parsed currently. It could be included, but if I'm not mistaken
it's very straightforward to calculate it based on parsed coordinates and
nuclear charges, right?

Karol

On Mon, Oct 20, 2014 at 9:37 PM, Martin Rahm <mar...@gm...> wrote:

> This is a very simple thing, but one I'm not sure cclib can do. Have I
> simply missed it, or could it be included?
>
> Thanks,
> Martin
>
>
>
> ------------------------------------------------------------------------------
> Comprehensive Server Monitoring with Site24x7.
> Monitor 10 servers for $9/Month.
> Get alerted through email, SMS, voice calls or mobile push notifications.
> Take corrective actions from your mobile device.
> http://p.sf.net/sfu/Zoho
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>

[cclib-users] Can cclib extract nuclear repulsion energy?

[Martin R. <mar...@gm...>]

This is a very simple thing, but one I'm not sure cclib can do. Have I
simply missed it, or could it be included?

Thanks,
Martin

[cclib-users] cclib v1.3b released

[Adam T. <ate...@gm...>]

On behalf of the cclib development team, we are pleased to announce the
release of cclib 1.3b, which is now available for download from
http://cclib.github.io. This version includes three new parsers (for
NWchem, Psi and QChem), as well as a number of bug fixes and improvements
(see below).

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

Among other data, cclib extracts:

    * coordinates and energies
    * information about geometry optimization
    * atomic orbital information
    * molecular orbital information
    * information on vibrational modes
    * the results of a TD-DFT calculation
    * charges and mutlipole moments

(For a complete list see http://cclib.github.io/data.html).

cclib also provides some calculation methods for interpreting the
electronic properties of molecules using analyses such as:

    * Mulliken and Lowdin population analyses
    * Overlap population analysis
    * Calculation of Mayer's bond orders.

(For a complete list see http://cclib.github.io/methods.html).

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

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

If your published work uses cclib, please support its development by citing
the following article:
    N. M. O'Boyle, A. L. Tenderholt, K. M. Langner, cclib: a library for
package-independent computational chemistry algorithms, J. Comp. Chem. 29
(5), 839-845 (2008).


Regards,

 The cclib development team

——-

Major changes since cclib 1.2:

Features:
* New parser: cclib can now parse NWChem files
* New parser: cclib can now parse Psi (versions 3 and 4) files
* New parser: cclib can now parse QChem files (by Eric Berquist)
    * Replace PC-GAMESS tests with Firefly versions
    * Many bugfixes, thanks to Martin Rahm, Russell Johnson, Matt Ernst and
others

Re: [cclib-users] cclib 1.3 optdone boolean/list

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

Right, that was confusing. It shouls now be more consistent. Plus, I added
the examples to the data notes:
http://cclib.github.io/data_notes.html#optdone

Thanks for raising this issue. Please continue to do so!

Best,
Karol


On Wed, Oct 1, 2014 at 11:29 AM, Johannes Wagner <joh...@h-...>
wrote:

> Hello Adam and Karol,
> glad to hear that the optdone list is planned to be future default. I used
> the ccopen argument and works as it should!
> Maybe it’s useful to include the argument usage in the optdone ‘parsed
> data notes’ on the github page.
> Also the ‘parsed data’ still (or already) says optdone is a list whereas
> the ‘parsed data notes' says it’s boolean.
>
> Thank you very much!
>
> Johannes
>
>
> --
> Dipl. Phys. Johannes Wagner
> PhD Student, MBM Group
> Heidelberg Institut for Theoretical Studies
> HITS gGmbH
> Schloß-Wolfsbrunnenweg 35
> 69118 Heidelberg
> Germany
>
> phone: +49-6221-533254
> fax: +49 6221 533298
> email: joh...@h-...
>
> http://www.h-its.org
> _________________________________________________
>
> Amtsgericht Mannheim / HRB 337446
> Managing Directors:
> Dr. h.c. Klaus Tschira
> Prof. Dr.-Ing. Andreas Reuter
>
> On Sep 30, 2014, at 8:10 PM, Karol Langner <kar...@gm...>
> wrote:
>
> I would just add that the option is available to ccget, too. See here for
> code:
> https://github.com/cclib/cclib/issues/122#issuecomment-57356881
>
> On Tue, Sep 30, 2014 at 12:06 PM, Johannes Wagner <
> joh...@h-...> wrote:
>
>> Hello together,
>> don’t know if this mailing list is dead since the move to github.io…
>>
>> I wanted to update from 1.2 to 1.3, but found the issue with the new
>> optdone set as boolean. Is there a way to maintain the old optdone list? On
>> http://cclib.github.io/ I couldn’t find any hint. I also wonder why it’s
>> changed in the first place...
>>
>> I would like to write out the optimized energy and the coordinates as xyz
>> file. The old optdone list this made this quite easy to handle with
>> atomcoords[optdone] and scfenergies[optdone]. The boolean version of course
>> can be made to work the same way, but I have to use if conditions and then
>> take the last scfenergies and atomcoords and also modify all my scripts
>> using cclib.
>>
>> Thanks for any answer!
>>
>> cheers, Johannes
>>
>> --
>> Dipl. Phys. Johannes Wagner
>> PhD Student, MBM Group
>> Heidelberg Institut for Theoretical Studies
>> HITS gGmbH
>> Schloß-Wolfsbrunnenweg 35
>> 69118 Heidelberg
>> Germany
>>
>> phone: +49-6221-533254
>> fax: +49 6221 533298
>> email: joh...@h-...
>>
>> http://www.h-its.org
>> _________________________________________________
>>
>> Amtsgericht Mannheim / HRB 337446
>> Managing Directors:
>> Dr. h.c. Klaus Tschira
>> Prof. Dr.-Ing. Andreas Reuter
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
>> Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
>> Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
>> Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>>
>
>

Re: [cclib-users] cclib 1.3 optdone boolean/list

[Johannes W. <joh...@h-...>]

Hello Adam and Karol,
glad to hear that the optdone list is planned to be future default. I used the ccopen argument and works as it should!
Maybe it’s useful to include the argument usage in the optdone ‘parsed data notes’ on the github page. 
Also the ‘parsed data’ still (or already) says optdone is a list whereas the ‘parsed data notes' says it’s boolean.

Thank you very much!

Johannes


--
Dipl. Phys. Johannes Wagner
PhD Student, MBM Group
Heidelberg Institut for Theoretical Studies 
HITS gGmbH
Schloß-Wolfsbrunnenweg 35
69118 Heidelberg
Germany

phone: +49-6221-533254
fax: +49 6221 533298
email: joh...@h-...

http://www.h-its.org
_________________________________________________

Amtsgericht Mannheim / HRB 337446
Managing Directors:
Dr. h.c. Klaus Tschira
Prof. Dr.-Ing. Andreas Reuter

> On Sep 30, 2014, at 8:10 PM, Karol Langner <kar...@gm...> wrote:
> 
> I would just add that the option is available to ccget, too. See here for code:
> https://github.com/cclib/cclib/issues/122#issuecomment-57356881 <https://github.com/cclib/cclib/issues/122#issuecomment-57356881>
> 
> On Tue, Sep 30, 2014 at 12:06 PM, Johannes Wagner <joh...@h-... <mailto:joh...@h-...>> wrote:
> Hello together,
> don’t know if this mailing list is dead since the move to github.io <http://github.io/>… 
> 
> I wanted to update from 1.2 to 1.3, but found the issue with the new optdone set as boolean. Is there a way to maintain the old optdone list? On http://cclib.github.io/ <http://cclib.github.io/> I couldn’t find any hint. I also wonder why it’s changed in the first place...
> 
> I would like to write out the optimized energy and the coordinates as xyz file. The old optdone list this made this quite easy to handle with atomcoords[optdone] and scfenergies[optdone]. The boolean version of course can be made to work the same way, but I have to use if conditions and then take the last scfenergies and atomcoords and also modify all my scripts using cclib.
> 
> Thanks for any answer!
> 
> cheers, Johannes
> 
> --
> Dipl. Phys. Johannes Wagner
> PhD Student, MBM Group
> Heidelberg Institut for Theoretical Studies 
> HITS gGmbH
> Schloß-Wolfsbrunnenweg 35
> 69118 Heidelberg
> Germany
> 
> phone: +49-6221-533254 <tel:%2B49-6221-533254>
> fax: +49 6221 533298 <tel:%2B49%206221%20533298>
> email: joh...@h-... <mailto:joh...@h-...>
> 
> http://www.h-its.org <http://www.h-its.org/>
> _________________________________________________
> 
> Amtsgericht Mannheim / HRB 337446
> Managing Directors:
> Dr. h.c. Klaus Tschira
> Prof. Dr.-Ing. Andreas Reuter
> 
> 
> ------------------------------------------------------------------------------
> Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
> Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
> Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
> Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
> http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk <http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk>
> _______________________________________________
> cclib-users mailing list
> ccl...@li... <mailto:ccl...@li...>
> https://lists.sourceforge.net/lists/listinfo/cclib-users <https://lists.sourceforge.net/lists/listinfo/cclib-users>
> 
> 

Re: [cclib-users] cclib 1.3 optdone boolean/list

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

I would just add that the option is available to ccget, too. See here for
code:
https://github.com/cclib/cclib/issues/122#issuecomment-57356881

On Tue, Sep 30, 2014 at 12:06 PM, Johannes Wagner <joh...@h-...
> wrote:

> Hello together,
> don’t know if this mailing list is dead since the move to github.io…
>
> I wanted to update from 1.2 to 1.3, but found the issue with the new
> optdone set as boolean. Is there a way to maintain the old optdone list? On
> http://cclib.github.io/ I couldn’t find any hint. I also wonder why it’s
> changed in the first place...
>
> I would like to write out the optimized energy and the coordinates as xyz
> file. The old optdone list this made this quite easy to handle with
> atomcoords[optdone] and scfenergies[optdone]. The boolean version of course
> can be made to work the same way, but I have to use if conditions and then
> take the last scfenergies and atomcoords and also modify all my scripts
> using cclib.
>
> Thanks for any answer!
>
> cheers, Johannes
>
> --
> Dipl. Phys. Johannes Wagner
> PhD Student, MBM Group
> Heidelberg Institut for Theoretical Studies
> HITS gGmbH
> Schloß-Wolfsbrunnenweg 35
> 69118 Heidelberg
> Germany
>
> phone: +49-6221-533254
> fax: +49 6221 533298
> email: joh...@h-...
>
> http://www.h-its.org
> _________________________________________________
>
> Amtsgericht Mannheim / HRB 337446
> Managing Directors:
> Dr. h.c. Klaus Tschira
> Prof. Dr.-Ing. Andreas Reuter
>
>
>
> ------------------------------------------------------------------------------
> Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
> Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
> Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
> Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
>
> http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>

Re: [cclib-users] cclib 1.3 optdone boolean/list

[Adam T. <ate...@gm...>]

Hi Johannes,

This list is still alive, although it doesn't see much action!

As far as your question, optdone was supposed to be a bool for v1.2 and
then we switched it to a list in the git master branch. Because we didn't
want to break the API by changing from a bool to a list for a point release
(i.e. 1.2 -> 1.3), we opted for a bit of magic to smooth the transition.

You should be able to access the optdone list as follows:

from cclib.parser import ccopen
parser = ccopen("filename", optdone_as_list=True) // could also do
future=True instead of optdone_as_list
data = parser.parse()

Please let us know if that doesn't work.

Adam



On Tue, Sep 30, 2014 at 9:06 AM, Johannes Wagner <joh...@h-...>
wrote:

> Hello together,
> don’t know if this mailing list is dead since the move to github.io…
>
> I wanted to update from 1.2 to 1.3, but found the issue with the new
> optdone set as boolean. Is there a way to maintain the old optdone list? On
> http://cclib.github.io/ I couldn’t find any hint. I also wonder why it’s
> changed in the first place...
>
> I would like to write out the optimized energy and the coordinates as xyz
> file. The old optdone list this made this quite easy to handle with
> atomcoords[optdone] and scfenergies[optdone]. The boolean version of course
> can be made to work the same way, but I have to use if conditions and then
> take the last scfenergies and atomcoords and also modify all my scripts
> using cclib.
>
> Thanks for any answer!
>
> cheers, Johannes
>
> --
> Dipl. Phys. Johannes Wagner
> PhD Student, MBM Group
> Heidelberg Institut for Theoretical Studies
> HITS gGmbH
> Schloß-Wolfsbrunnenweg 35
> 69118 Heidelberg
> Germany
>
> phone: +49-6221-533254
> fax: +49 6221 533298
> email: joh...@h-...
>
> http://www.h-its.org
> _________________________________________________
>
> Amtsgericht Mannheim / HRB 337446
> Managing Directors:
> Dr. h.c. Klaus Tschira
> Prof. Dr.-Ing. Andreas Reuter
>
>
>
> ------------------------------------------------------------------------------
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> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>

[cclib-users] cclib 1.3 optdone boolean/list

[Johannes W. <joh...@h-...>]

Hello together,
don’t know if this mailing list is dead since the move to github.io… 

I wanted to update from 1.2 to 1.3, but found the issue with the new optdone set as boolean. Is there a way to maintain the old optdone list? On http://cclib.github.io/ <http://cclib.github.io/> I couldn’t find any hint. I also wonder why it’s changed in the first place...

I would like to write out the optimized energy and the coordinates as xyz file. The old optdone list this made this quite easy to handle with atomcoords[optdone] and scfenergies[optdone]. The boolean version of course can be made to work the same way, but I have to use if conditions and then take the last scfenergies and atomcoords and also modify all my scripts using cclib.

Thanks for any answer!

cheers, Johannes

--
Dipl. Phys. Johannes Wagner
PhD Student, MBM Group
Heidelberg Institut for Theoretical Studies 
HITS gGmbH
Schloß-Wolfsbrunnenweg 35
69118 Heidelberg
Germany

phone: +49-6221-533254
fax: +49 6221 533298
email: joh...@h-...

http://www.h-its.org
_________________________________________________

Amtsgericht Mannheim / HRB 337446
Managing Directors:
Dr. h.c. Klaus Tschira
Prof. Dr.-Ing. Andreas Reuter

Re: [cclib-users] problem parsing GAMESS output

[Martin R. <mar...@gm...>]

Nope that doesn't seem to work either. I'm still stuck with "1.2b". The
test all.py script now produces a different error (below).

:cclib-master martin$ sudo python setup.py install -f

running install

running build

running build_py

running build_scripts

running install_lib

copying build/lib/cclib/__init__.py ->
/Library/Python/2.7/site-packages/cclib

copying build/lib/cclib/bridge/__init__.py ->
/Library/Python/2.7/site-packages/cclib/bridge

copying build/lib/cclib/bridge/cclib2biopython.py ->
/Library/Python/2.7/site-packages/cclib/bridge

copying build/lib/cclib/bridge/cclib2openbabel.py ->
/Library/Python/2.7/site-packages/cclib/bridge

copying build/lib/cclib/bridge/cclib2pyquante.py ->
/Library/Python/2.7/site-packages/cclib/bridge

copying build/lib/cclib/method/__init__.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/method/calculationmethod.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/method/cda.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/method/cspa.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/method/density.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/method/fragments.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/method/lpa.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/method/mbo.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/method/mpa.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/method/opa.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/method/population.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/method/volume.py ->
/Library/Python/2.7/site-packages/cclib/method

copying build/lib/cclib/parser/__init__.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/adfparser.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/ccopen.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/data.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/gamessparser.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/gamessukparser.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/gaussianparser.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/jaguarparser.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/logfileparser.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/molproparser.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/nwchemparser.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/orcaparser.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/psiparser.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/qchemparser.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/parser/utils.py ->
/Library/Python/2.7/site-packages/cclib/parser

copying build/lib/cclib/progress/__init__.py ->
/Library/Python/2.7/site-packages/cclib/progress

copying build/lib/cclib/progress/qt4progress.py ->
/Library/Python/2.7/site-packages/cclib/progress

copying build/lib/cclib/progress/textprogress.py ->
/Library/Python/2.7/site-packages/cclib/progress

byte-compiling /Library/Python/2.7/site-packages/cclib/__init__.py to
__init__.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/bridge/__init__.py
to __init__.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/bridge/cclib2biopython.py to
cclib2biopython.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/bridge/cclib2openbabel.py to
cclib2openbabel.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/bridge/cclib2pyquante.py to
cclib2pyquante.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/method/__init__.py
to __init__.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/method/calculationmethod.py to
calculationmethod.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/method/cda.py to
cda.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/method/cspa.py to
cspa.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/method/density.py to
density.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/method/fragments.py
to fragments.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/method/lpa.py to
lpa.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/method/mbo.py to
mbo.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/method/mpa.py to
mpa.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/method/opa.py to
opa.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/method/population.py
to population.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/method/volume.py to
volume.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/parser/__init__.py
to __init__.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/parser/adfparser.py
to adfparser.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/parser/ccopen.py to
ccopen.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/parser/data.py to
data.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/parser/gamessparser.py to
gamessparser.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/parser/gamessukparser.py to
gamessukparser.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/parser/gaussianparser.py to
gaussianparser.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/parser/jaguarparser.py to
jaguarparser.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/parser/logfileparser.py to
logfileparser.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/parser/molproparser.py to
molproparser.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/parser/nwchemparser.py to
nwchemparser.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/parser/orcaparser.py
to orcaparser.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/parser/psiparser.py
to psiparser.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/parser/qchemparser.py to
qchemparser.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/parser/utils.py to
utils.pyc

byte-compiling /Library/Python/2.7/site-packages/cclib/progress/__init__.py
to __init__.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/progress/qt4progress.py to
qt4progress.pyc

byte-compiling
/Library/Python/2.7/site-packages/cclib/progress/textprogress.py to
textprogress.pyc

running install_scripts

copying build/scripts-2.7/ccget -> /usr/local/bin

copying build/scripts-2.7/cda -> /usr/local/bin

changing mode of /usr/local/bin/ccget to 755

changing mode of /usr/local/bin/cda to 755

running install_egg_info

Removing /Library/Python/2.7/site-packages/cclib-1.2-py2.7.egg-info

Writing /Library/Python/2.7/site-packages/cclib-1.2-py2.7.egg-info


:cclib-master martin$ python

Python 2.7.5 (default, Mar  9 2014, 22:15:05)

[GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.0.68)] on darwin

Type "help", "copyright", "credits" or "license" for more information.

>>> import cclib

>>> cclib.__version__

'1.2b'


:cclib-master martin$ python test/testall.py

Traceback (most recent call last):

  File "test/testall.py", line 16, in <module>

    from cclib.parser import (ADF, GAMESS, GAMESSUK, Gaussian,

ImportError: cannot import name NWChem

On Tue, Sep 16, 2014 at 7:46 AM, Karol M. Langner <kar...@gm...>
wrote:

> I think you might be running in to the fact that Python does not overwrite
> files
> by default when it installs. But it will if you add the appropriate flag:
>
> sudo python set.py install -f
>
> Also, I'll be clear and point out that this fix is not in any release yet,
> and
> you will need to download the development source code. You can get it
> directly
> from the github repository or via this link:
> https://github.com/cclib/cclib/archive/master.zip
>
> Let us know if that helps,
> Karol
>
> On Sep 15 2014, Martin Rahm wrote:
> > I'm at a bit of a loss now, since I can't install the new version. I seem
> > stuck with the 1.2b version.
> >
> > $ sudo python setup.py build
> >
> > running build
> >
> > running build_py
> >
> > running build_scripts
> >
> > :cclib-1.2 martin$ sudo python setup.py install
> >
> > running install
> >
> > running build
> >
> > running build_py
> >
> > running build_scripts
> >
> > running install_lib
> >
> > running install_scripts
> >
> > changing mode of /usr/local/bin/ccget to 755
> >
> > changing mode of /usr/local/bin/cda to 755
> >
> > running install_egg_info
> >
> > Removing /Library/Python/2.7/site-packages/cclib-1.2-py2.7.egg-info
> >
> > Writing /Library/Python/2.7/site-packages/cclib-1.2-py2.7.egg-info
> >
> > :cclib-1.2 martin$ python
> >
> > Python 2.7.5 (default, Mar  9 2014, 22:15:05)
> >
> > [GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.0.68)] on darwin
> >
> > Type "help", "copyright", "credits" or "license" for more information.
> >
> > >>> import cclib
> >
> > >>> cclib.__version__
> >
> > '1.2b'
> >
> > This has to the best of my knowledge always worked before. What am I
> > missing? Is it that Python is only 2.7.5?
> >
> > The test script returns the following:
> >
> > :test martin$ python testall.py
> >
> > Traceback (most recent call last):
> >
> >   File "testall.py", line 216, in <module>
> >
> >     tests = testall(chosen_parsers, chosen_modules)
> >
> >   File "testall.py", line 151, in testall
> >
> >     testdata = gettestdata(module)
> >
> >   File "testall.py", line 71, in gettestdata
> >
> >     lines = open(testdatadir+'/testdata').readlines()
> >
> > IOError: [Errno 2] No such file or directory:
> > '/Applications/cclib-1.2/test/testdata'
> >
> >
> > Thanks,
> >
> > Martin
> >
> > On Mon, Sep 15, 2014 at 5:05 PM, Karol M. Langner <
> kar...@gm...>
> > wrote:
> >
> > > Hi,
> > >
> > > This should be fixed in master now.
> > >
> > > Thanks for reporting,
> > > Karol
> > >
> > > On Sep 10 2014, Martin Rahm wrote:
> > > > Hi,
> > > >
> > > > I am trying a script that is working fine with both gaussian and orca
> > > > output. I wish to print out the alpha and beta orbital energies of
> the
> > > > nitrogen atom (here in the quartet ground state). The script prints
> out
> > > > beta instead of alpha, and then returns "IndexError: list index out
> of
> > > > range".
> > > >
> > > > I hope this is something stupefyingly simple, and would really
> appreciate
> > > > the help! The output file is attached if anyone would like to give
> it a
> > > > try.
> > > >
> > > > Many thanks,
> > > > Martin
> > > >
> > > > My script:
> > > > ---------------
> > > > from numpy import *
> > > > from cclib.parser import ccopen
> > > > import cclib
> > > > import sys
> > > >
> > > > inputfile = sys.argv
> > > > data = ccopen(inputfile)
> > > > data = data.parse()
> > > >
> > > > print "alpha:"
> > > > print data.moenergies[0]
> > > > print "beta:"
> > > > print data.moenergies[1]
> > > > print "done"
> > > > ------------
> > > >
> > > > My output:
> > > > --------------
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > > atomcoords[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > atomnos[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> gbasis[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> nbasis:
> > > 20
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> charge:
> > > 0
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> mult: 4
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> homos[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> natom: 1
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > > scftargets[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > scfvalues[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > > scfenergies[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > > moenergies[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> mosyms[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> nmo: 20
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > mocoeffs[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > atombasis[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > aonames[]
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > > atomcharges: {}
> > > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > > coreelectrons[]
> > > > alpha:
> > > > [-423.94520709  -19.75274401    3.43679786    3.43679786
> 3.43679786
> > > >    15.00163627   15.19755824   15.19755824   15.19755824
>  59.89225728
> > > >    59.89225728   59.89225728   61.45146962   68.88017758
>  68.88017758
> > > >    68.88017758   68.88017758   68.88017758  162.94721266
> 976.48325392]
> > > > beta:
> > > > Traceback (most recent call last):
> > > >   File "./analyze.py", line 21, in <module>
> > > >     print data.moenergies[1]
> > > > IndexError: list index out of range
> > > > -----------
> > >
> > >
> > > >
> > >
> ------------------------------------------------------------------------------
> > > > Want excitement?
> > > > Manually upgrade your production database.
> > > > When you want reliability, choose Perforce
> > > > Perforce version control. Predictably reliable.
> > > >
> > >
> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
> > >
> > > > _______________________________________________
> > > > cclib-users mailing list
> > > > ccl...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/cclib-users
> > >
> > >
> > > --
> > > written by Karol M. Langner
> > > Mon Sep 15 17:05:04 EDT 2014
> > >
>
> --
> written by Karol M. Langner
> Tue Sep 16 07:42:17 EDT 2014
>

Re: [cclib-users] problem parsing GAMESS output

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

I think you might be running in to the fact that Python does not overwrite files
by default when it installs. But it will if you add the appropriate flag:

sudo python set.py install -f

Also, I'll be clear and point out that this fix is not in any release yet, and
you will need to download the development source code. You can get it directly
from the github repository or via this link:
https://github.com/cclib/cclib/archive/master.zip

Let us know if that helps,
Karol

On Sep 15 2014, Martin Rahm wrote:
> I'm at a bit of a loss now, since I can't install the new version. I seem
> stuck with the 1.2b version.
> 
> $ sudo python setup.py build
> 
> running build
> 
> running build_py
> 
> running build_scripts
> 
> :cclib-1.2 martin$ sudo python setup.py install
> 
> running install
> 
> running build
> 
> running build_py
> 
> running build_scripts
> 
> running install_lib
> 
> running install_scripts
> 
> changing mode of /usr/local/bin/ccget to 755
> 
> changing mode of /usr/local/bin/cda to 755
> 
> running install_egg_info
> 
> Removing /Library/Python/2.7/site-packages/cclib-1.2-py2.7.egg-info
> 
> Writing /Library/Python/2.7/site-packages/cclib-1.2-py2.7.egg-info
> 
> :cclib-1.2 martin$ python
> 
> Python 2.7.5 (default, Mar  9 2014, 22:15:05)
> 
> [GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.0.68)] on darwin
> 
> Type "help", "copyright", "credits" or "license" for more information.
> 
> >>> import cclib
> 
> >>> cclib.__version__
> 
> '1.2b'
> 
> This has to the best of my knowledge always worked before. What am I
> missing? Is it that Python is only 2.7.5?
> 
> The test script returns the following:
> 
> :test martin$ python testall.py
> 
> Traceback (most recent call last):
> 
>   File "testall.py", line 216, in <module>
> 
>     tests = testall(chosen_parsers, chosen_modules)
> 
>   File "testall.py", line 151, in testall
> 
>     testdata = gettestdata(module)
> 
>   File "testall.py", line 71, in gettestdata
> 
>     lines = open(testdatadir+'/testdata').readlines()
> 
> IOError: [Errno 2] No such file or directory:
> '/Applications/cclib-1.2/test/testdata'
> 
> 
> Thanks,
> 
> Martin
> 
> On Mon, Sep 15, 2014 at 5:05 PM, Karol M. Langner <kar...@gm...>
> wrote:
> 
> > Hi,
> >
> > This should be fixed in master now.
> >
> > Thanks for reporting,
> > Karol
> >
> > On Sep 10 2014, Martin Rahm wrote:
> > > Hi,
> > >
> > > I am trying a script that is working fine with both gaussian and orca
> > > output. I wish to print out the alpha and beta orbital energies of the
> > > nitrogen atom (here in the quartet ground state). The script prints out
> > > beta instead of alpha, and then returns "IndexError: list index out of
> > > range".
> > >
> > > I hope this is something stupefyingly simple, and would really appreciate
> > > the help! The output file is attached if anyone would like to give it a
> > > try.
> > >
> > > Many thanks,
> > > Martin
> > >
> > > My script:
> > > ---------------
> > > from numpy import *
> > > from cclib.parser import ccopen
> > > import cclib
> > > import sys
> > >
> > > inputfile = sys.argv
> > > data = ccopen(inputfile)
> > > data = data.parse()
> > >
> > > print "alpha:"
> > > print data.moenergies[0]
> > > print "beta:"
> > > print data.moenergies[1]
> > > print "done"
> > > ------------
> > >
> > > My output:
> > > --------------
> > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > atomcoords[]
> > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > atomnos[]
> > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute gbasis[]
> > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute nbasis:
> > 20
> > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute charge:
> > 0
> > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute mult: 4
> > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute homos[]
> > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute natom: 1
> > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > scftargets[]
> > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > scfvalues[]
> > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > scfenergies[]
> > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > moenergies[]
> > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute mosyms[]
> > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute nmo: 20
> > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > mocoeffs[]
> > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > atombasis[]
> > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > aonames[]
> > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > atomcharges: {}
> > > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > > coreelectrons[]
> > > alpha:
> > > [-423.94520709  -19.75274401    3.43679786    3.43679786    3.43679786
> > >    15.00163627   15.19755824   15.19755824   15.19755824   59.89225728
> > >    59.89225728   59.89225728   61.45146962   68.88017758   68.88017758
> > >    68.88017758   68.88017758   68.88017758  162.94721266  976.48325392]
> > > beta:
> > > Traceback (most recent call last):
> > >   File "./analyze.py", line 21, in <module>
> > >     print data.moenergies[1]
> > > IndexError: list index out of range
> > > -----------
> >
> >
> > >
> > ------------------------------------------------------------------------------
> > > Want excitement?
> > > Manually upgrade your production database.
> > > When you want reliability, choose Perforce
> > > Perforce version control. Predictably reliable.
> > >
> > http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
> >
> > > _______________________________________________
> > > cclib-users mailing list
> > > ccl...@li...
> > > https://lists.sourceforge.net/lists/listinfo/cclib-users
> >
> >
> > --
> > written by Karol M. Langner
> > Mon Sep 15 17:05:04 EDT 2014
> >

-- 
written by Karol M. Langner
Tue Sep 16 07:42:17 EDT 2014

Re: [cclib-users] problem parsing GAMESS output

[Martin R. <mar...@gm...>]

I'm at a bit of a loss now, since I can't install the new version. I seem
stuck with the 1.2b version.

$ sudo python setup.py build

running build

running build_py

running build_scripts

:cclib-1.2 martin$ sudo python setup.py install

running install

running build

running build_py

running build_scripts

running install_lib

running install_scripts

changing mode of /usr/local/bin/ccget to 755

changing mode of /usr/local/bin/cda to 755

running install_egg_info

Removing /Library/Python/2.7/site-packages/cclib-1.2-py2.7.egg-info

Writing /Library/Python/2.7/site-packages/cclib-1.2-py2.7.egg-info

:cclib-1.2 martin$ python

Python 2.7.5 (default, Mar  9 2014, 22:15:05)

[GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.0.68)] on darwin

Type "help", "copyright", "credits" or "license" for more information.

>>> import cclib

>>> cclib.__version__

'1.2b'

This has to the best of my knowledge always worked before. What am I
missing? Is it that Python is only 2.7.5?

The test script returns the following:

:test martin$ python testall.py

Traceback (most recent call last):

  File "testall.py", line 216, in <module>

    tests = testall(chosen_parsers, chosen_modules)

  File "testall.py", line 151, in testall

    testdata = gettestdata(module)

  File "testall.py", line 71, in gettestdata

    lines = open(testdatadir+'/testdata').readlines()

IOError: [Errno 2] No such file or directory:
'/Applications/cclib-1.2/test/testdata'


Thanks,

Martin

On Mon, Sep 15, 2014 at 5:05 PM, Karol M. Langner <kar...@gm...>
wrote:

> Hi,
>
> This should be fixed in master now.
>
> Thanks for reporting,
> Karol
>
> On Sep 10 2014, Martin Rahm wrote:
> > Hi,
> >
> > I am trying a script that is working fine with both gaussian and orca
> > output. I wish to print out the alpha and beta orbital energies of the
> > nitrogen atom (here in the quartet ground state). The script prints out
> > beta instead of alpha, and then returns "IndexError: list index out of
> > range".
> >
> > I hope this is something stupefyingly simple, and would really appreciate
> > the help! The output file is attached if anyone would like to give it a
> > try.
> >
> > Many thanks,
> > Martin
> >
> > My script:
> > ---------------
> > from numpy import *
> > from cclib.parser import ccopen
> > import cclib
> > import sys
> >
> > inputfile = sys.argv
> > data = ccopen(inputfile)
> > data = data.parse()
> >
> > print "alpha:"
> > print data.moenergies[0]
> > print "beta:"
> > print data.moenergies[1]
> > print "done"
> > ------------
> >
> > My output:
> > --------------
> > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > atomcoords[]
> > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> atomnos[]
> > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute gbasis[]
> > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute nbasis:
> 20
> > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute charge:
> 0
> > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute mult: 4
> > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute homos[]
> > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute natom: 1
> > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > scftargets[]
> > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> scfvalues[]
> > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > scfenergies[]
> > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > moenergies[]
> > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute mosyms[]
> > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute nmo: 20
> > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> mocoeffs[]
> > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> atombasis[]
> > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> aonames[]
> > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > atomcharges: {}
> > [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> > coreelectrons[]
> > alpha:
> > [-423.94520709  -19.75274401    3.43679786    3.43679786    3.43679786
> >    15.00163627   15.19755824   15.19755824   15.19755824   59.89225728
> >    59.89225728   59.89225728   61.45146962   68.88017758   68.88017758
> >    68.88017758   68.88017758   68.88017758  162.94721266  976.48325392]
> > beta:
> > Traceback (most recent call last):
> >   File "./analyze.py", line 21, in <module>
> >     print data.moenergies[1]
> > IndexError: list index out of range
> > -----------
>
>
> >
> ------------------------------------------------------------------------------
> > Want excitement?
> > Manually upgrade your production database.
> > When you want reliability, choose Perforce
> > Perforce version control. Predictably reliable.
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
>
> > _______________________________________________
> > cclib-users mailing list
> > ccl...@li...
> > https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>
> --
> written by Karol M. Langner
> Mon Sep 15 17:05:04 EDT 2014
>

Re: [cclib-users] problem parsing GAMESS output

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

Hi,

This should be fixed in master now.

Thanks for reporting,
Karol

On Sep 10 2014, Martin Rahm wrote:
> Hi,
> 
> I am trying a script that is working fine with both gaussian and orca
> output. I wish to print out the alpha and beta orbital energies of the
> nitrogen atom (here in the quartet ground state). The script prints out
> beta instead of alpha, and then returns "IndexError: list index out of
> range".
> 
> I hope this is something stupefyingly simple, and would really appreciate
> the help! The output file is attached if anyone would like to give it a
> try.
> 
> Many thanks,
> Martin
> 
> My script:
> ---------------
> from numpy import *
> from cclib.parser import ccopen
> import cclib
> import sys
> 
> inputfile = sys.argv
> data = ccopen(inputfile)
> data = data.parse()
> 
> print "alpha:"
> print data.moenergies[0]
> print "beta:"
> print data.moenergies[1]
> print "done"
> ------------
> 
> My output:
> --------------
> [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> atomcoords[]
> [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute atomnos[]
> [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute gbasis[]
> [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute nbasis: 20
> [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute charge: 0
> [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute mult: 4
> [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute homos[]
> [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute natom: 1
> [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> scftargets[]
> [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute scfvalues[]
> [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> scfenergies[]
> [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> moenergies[]
> [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute mosyms[]
> [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute nmo: 20
> [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute mocoeffs[]
> [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute atombasis[]
> [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute aonames[]
> [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> atomcharges: {}
> [GAMESS ['./analyze.py', 'N-d-UHF.out'] INFO] Creating attribute
> coreelectrons[]
> alpha:
> [-423.94520709  -19.75274401    3.43679786    3.43679786    3.43679786
>    15.00163627   15.19755824   15.19755824   15.19755824   59.89225728
>    59.89225728   59.89225728   61.45146962   68.88017758   68.88017758
>    68.88017758   68.88017758   68.88017758  162.94721266  976.48325392]
> beta:
> Traceback (most recent call last):
>   File "./analyze.py", line 21, in <module>
>     print data.moenergies[1]
> IndexError: list index out of range
> -----------


> ------------------------------------------------------------------------------
> Want excitement?
> Manually upgrade your production database.
> When you want reliability, choose Perforce
> Perforce version control. Predictably reliable.
> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk

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


-- 
written by Karol M. Langner
Mon Sep 15 17:05:04 EDT 2014