cclib-users — Help and support for cclib users

Re: [cclib-users] Fwd: How to do Population analysis

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

Hi all,

Adam is right, you can get orbital occupations by summing the appropriate atomic orbital
contributions, which are stored in aoresults after doing the calculation. it goes like this
in the interpretor:

>>> import cclib
>>> d = cclib.parser.ccopen("H20_sp_STO3G.log").parse()
(...)
>>> m = cclib.method.MPA(d)
>>> m.calculate()
(...)
>>> 2*m.aoresults[0][:d.homos[0]+1].sum(axis=0)
array([ 1.99731828,  1.84988399,  2.        ,  1.06865696,  1.44716636,
        0.81846894,  0.81846894])

and there you have the same number that Gaussian prints. Note that I just did d.homos[0]
to get the index of the HOMO automatically.

I suppose you were looking at the fragment charge contributions from MOs:
>>> m.fragresults
[array([[  1.00083418e+00,  -4.19328593e-04,  -4.19328593e-04],
[  7.84491789e-01,   1.07751544e-01,   1.07751544e-01],
[  5.34328481e-01,   2.32831101e-01,   2.32831101e-01],
[  8.61858340e-01,   6.90711521e-02,   6.90711521e-02],
[  1.00000000e+00,   0.00000000e+00,   0.00000000e+00],
[  3.52808101e-01,   3.23597395e-01,   3.23597395e-01],
[  4.65660941e-01,   2.67165641e-01,   2.67165641e-01]])]
where I see the number you had in you email, but this is a different
thing than the orbital occupotion. It is the contribution of MOs to the
charge of particular fragments.

Hope this helps,
Karol                                          

On Oct 27 2011, Adam Tenderholt wrote:
> Hi Martin,
> 
> I don't quite understand how you reformatted your cclib output. I went ahead ran your logfile through cclib:
> 
> parser = ccopen("H20_sp_STO3G.log")
> data = parser.parse()
> method = MPA(data)
> method.calculate()
> numpy.savetxt("H20_sp_STO3G.csv",method.aoresults[0]) #it's a restricted calc, so save "first" element
> 
> Attached is a spreadsheet with those values, along with the orbital occupations (i.e. for each atomic "orbital", sum from MO 1 through the HOMO, and multiply by 2). I get the same values as the Gaussian output file.
> 
> Hope that helps, and let me know if you have any further questions/problems.
> 
> Take care,
> 
> Adam
> 


> 
> 
> On Oct 25, 2011, at 3:53 PM, Martin Rahm wrote:
> 
> > Thank you Adam, 
> > 
> > That worked like a charm. However, as I ran a trial run on H2O with a STO-3G basis set (attached), I noticed that even though the MPA of cclib generates the exact same atomic charges as MPA of Gaussian09, the occupation of the p-electrons does not match! 
> > 
> > The results from g09 are:
> > 
> > Gross orbital populations:                         
> >   1 1   O  1S         1.99733
> >   2          2S         1.84988
> >   3        2PX         2.00000
> >   4        2PY         1.06867
> >   5        2PZ         1.44717
> >   6 2   H  1S          0.81848
> >   7 3   H  1S          0.81848
> > 
> > Whereas cclib generates (I reformated the output to that below): 
> > 
> >   O	          H	          H
> > 1S	1.001	0.000	0.000
> > 2S	0.784	0.108	0.108
> > P	0.534	0.233	0.233
> > P	0.862	0.069	0.069
> > P	1.000	0.000	0.000
> > S	0.353	0.324	0.324
> > S	0.466	0.267	0.267
> > 
> > which multiplied by two gives
> > 
> > P	1.069
> > P	1.724
> > P	2.000
> > 
> > Thus, the contribution from one p-orbital (they also seem to have switched order) is different between g09 and cclib. Overall 57.3% p-character in cclib, and 54.0% in g09. 
> > 
> > Does anyone have any explanation to this? Also is there a neat way of keeping track of which number in the result array that corresponds to which type of AO? (I had a very small list of AOs and pasted them next to the list from the G09 output, but one p-AO had still changed place)
> > 
> > Many thanks, 
> > Martin 
> > 
> > 
> > On Tue, Oct 25, 2011 at 4:08 AM, Noel O'Boyle <bao...@gm...> wrote:
> > > ---------- Forwarded message ----------
> > > From: Adam Tenderholt <ate...@gm...>
> > > Date: 25 October 2011 06:31
> > > Subject: Fwd: [cclib-users] How to do Population analysis
> > > To: Noel O'Boyle <bao...@gm...>, "Karol M. Langner"
> > > <kar...@gm...>
> > >
> > > I replied, cc'ing the cclib-users list, but it got rejected.
> > >
> > > The wiki probably hasn't been updated since Karol's refactoring. I
> > > think Martin's problem is missing data = parser.parse() and passing
> > > the data object to the MPA constructor.
> > >
> > > Take care,
> > >
> > > Adam
> > >
> > > ------------------------------------------------------------------------------
> > > The demand for IT networking professionals continues to grow, and the
> > > demand for specialized networking skills is growing even more rapidly.
> > > Take a complimentary Learning@Cisco Self-Assessment and learn
> > > about Cisco certifications, training, and career opportunities.
> > > http://p.sf.net/sfu/cisco-dev2dev
> > > _______________________________________________
> > > cclib-users mailing list
> > > ccl...@li...
> > > https://lists.sourceforge.net/lists/listinfo/cclib-users
> > >
> > 
> > <H20_sp_STO3G.log>------------------------------------------------------------------------------
> > The demand for IT networking professionals continues to grow, and the
> > demand for specialized networking skills is growing even more rapidly.
> > Take a complimentary Learning@Cisco Self-Assessment and learn 
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> > http://p.sf.net/sfu/cisco-dev2dev_______________________________________________
> > cclib-users mailing list
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> > https://lists.sourceforge.net/lists/listinfo/cclib-users
> 

> ------------------------------------------------------------------------------
> The demand for IT networking professionals continues to grow, and the
> demand for specialized networking skills is growing even more rapidly.
> Take a complimentary Learning@Cisco Self-Assessment and learn 
> about Cisco certifications, training, and career opportunities. 
> http://p.sf.net/sfu/cisco-dev2dev

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


-- 
written by Karol Langner
Thu Oct 27 18:39:41 CEST 2011

Re: [cclib-users] Fwd: How to do Population analysis

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

Hi Martin,

I don't quite understand how you reformatted your cclib output. I went ahead ran your logfile through cclib:

parser = ccopen("H20_sp_STO3G.log")
data = parser.parse()
method = MPA(data)
method.calculate()
numpy.savetxt("H20_sp_STO3G.csv",method.aoresults[0]) #it's a restricted calc, so save "first" element

Attached is a spreadsheet with those values, along with the orbital occupations (i.e. for each atomic "orbital", sum from MO 1 through the HOMO, and multiply by 2). I get the same values as the Gaussian output file.

Hope that helps, and let me know if you have any further questions/problems.

Take care,

Adam

[cclib-users] Fwd: How to do Population analysis

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

---------- Forwarded message ----------
From: Adam Tenderholt <ate...@gm...>
Date: 25 October 2011 06:31
Subject: Fwd: [cclib-users] How to do Population analysis
To: Noel O'Boyle <bao...@gm...>, "Karol M. Langner"
<kar...@gm...>

I replied, cc'ing the cclib-users list, but it got rejected.

The wiki probably hasn't been updated since Karol's refactoring. I
think Martin's problem is missing data = parser.parse() and passing
the data object to the MPA constructor.

Take care,

Adam

[cclib-users] How to do Population analysis

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

Dear List,

I'm a newbie when it comes to python, so I might have missed something
trivial. I've followed the "tutorial" by the letter, and am trying to
perform an MPA (and Löwdin=LPA?) on one of the testfiles
(dvb_un_sp.out in basicGaussian03, and others), but it fails. I have
run the testscript, and everything seems to check out there.

I have also tried the same on other testfiles (both from g03 and
g09),which had the following input:
#p gfinput iop(6/7=3) iop(3/33=1,3/36=-1) pop=full rb3lyp/6-31+g(d,p),
with the same results.

Python 2.7.1 (r271:86882M, Nov 30 2010, 10:35:34)
[GCC 4.2.1 (Apple Inc. build 5664)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from cclib.parser import Gaussian
>>> from cclib.method import MPA
>>> parser=Gaussian("dvb_un_sp.out")
>>> analysis=MPA(parser)
>>> analysis.calculate()
[MPA Gaussian log file dvb_un_sp.out ERROR] Missing mocoeffs
False
>>>

Very thankful for any help.

Martin

Re: [cclib-users] Any Gaussian users familiar with PBC?

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

On 14 October 2011 15:56, Manuel Melle Franco <man...@gm...> wrote:
> HI Karol,
>
> Crystal uses K points, I also have my own software that does graphitic
> materials in reciprocal state.
>
> Kpoints are points in reciprocal space typically defined by four
> numbers  kx, ky,kz, wk
> where wk is the relative weight.
>
> the DOS are basically a list of the eigenvalues for each kpoint
> broadened with a gaussian and weighted (in "intensity") by the
> relative weight of each kpoint.
>
> The projected dos, if I remember right, are based on the contribution
> of an atom to the DOS (list of eigenvalues) based on the relative
> mulliken population for each eigenvalue for that atom.
>
> Does it make sense?
>
> I have used gaussian with PBC's but since I know how to use crystal I
> prefer it,otherwise I would have already scripts that do that,
> sorry,:D.

This is very useful. I didn't realise about the relative weight - I'd
better check for that in the Gaussian output.

Is there anything special about k-point 0 0 0? Gaussian seems to treat
that one specially by printing out the full eigenvalues and AO
contributions to the MOs.

My other question is probably dumb. Are the corresponding orbitals at
each k-point identical in terms of composition of the AOs? I realise
that they have different energies, and so I guess the answer is no.
(But if it's no, it means that I can't do the PDOS as Gaussian only
prints out one set of AO contributions, the point at k-point 0 0 0)

> To test you may follow this:
> http://scuseria.rice.edu/gau/gdv_pbc/pbc_guide.html#dos_f2

I have already seen this. It seems to be by the guys who wrote the PBC
code in Gaussian. However, they seem to be using a patched version of
Gaussian in order to get output for the PDOS :-/

- Noel

Re: [cclib-users] Any Gaussian users familiar with PBC?

[Manuel M. F. <man...@gm...>]

HI Karol,

Crystal uses K points, I also have my own software that does graphitic
materials in reciprocal state.


Kpoints are points in reciprocal space typically defined by four
numbers  kx, ky,kz, wk
where wk is the relative weight.


the DOS are basically a list of the eigenvalues for each kpoint
broadened with a gaussian and weighted (in "intensity") by the
relative weight of each kpoint.

The projected dos, if I remember right, are based on the contribution
of an atom to the DOS (list of eigenvalues) based on the relative
mulliken population for each eigenvalue for that atom.

Does it make sense?

I have used gaussian with PBC's but since I know how to use crystal I
prefer it,otherwise I would have already scripts that do that,
sorry,:D.

To test you may follow this:
http://scuseria.rice.edu/gau/gdv_pbc/pbc_guide.html#dos_f2

regards

Manu

____________________________________________________________

Mohandas K. Gandhi often changed his mind publicly.  An aide once asked
him how he could so freely contradict this week what he had said just
last week.  The great man replied that it was because this week he knew
better.

____________________________________________________________

Manuel Melle-Franco, Ph.D.
Investigador Auxiliar
Centro de Ciências e Tecnologias de Computação, CCTC
Universidade do Minho
Campus de Gualtar
4710-057 Braga
PORTUGAL

---------------------------------------------------------

A mind all logic is like a knife all blade. It makes the hand bleed
that uses it.
Rabindranath Tagore

---------------------------------------------------------



On Fri, Oct 14, 2011 at 3:43 PM, Noel O'Boyle <bao...@gm...> wrote:
> Hi Manuel,
>
> The user wants a DOS (and possibly a Projected DOS). A typical
> Gaussian output file is at
> http://cclib.sourceforge.net/data/Gaussian/Gaussian03/maheshkumar.log.gz
>
> Does Crystal use the concept of k-points?
>
> - Noel
>
> On 14 October 2011 15:30, Manuel Melle Franco <man...@gm...> wrote:
>> Hi Noel,
>>
>> I have experience with PBC calculations but not with gaussian but with
>> crystal that has a similar methodology (LCAO+PBCs). what has the user
>> exactly asked you to output? just the orbitals?
>>
>> regards
>>
>> Manuel
>>
>>
>>
>> ____________________________________________________________
>>
>> Mohandas K. Gandhi often changed his mind publicly.  An aide once asked
>> him how he could so freely contradict this week what he had said just
>> last week.  The great man replied that it was because this week he knew
>> better.
>>
>> ____________________________________________________________
>>
>> Manuel Melle-Franco, Ph.D.
>> Investigador Auxiliar
>> Centro de Ciências e Tecnologias de Computação, CCTC
>> Universidade do Minho
>> Campus de Gualtar
>> 4710-057 Braga
>> PORTUGAL
>>
>> ---------------------------------------------------------
>>
>> A mind all logic is like a knife all blade. It makes the hand bleed
>> that uses it.
>> Rabindranath Tagore
>>
>> ---------------------------------------------------------
>>
>>
>>
>> On Fri, Oct 14, 2011 at 3:18 PM, Noel O'Boyle <bao...@gm...> wrote:
>>> Well, I haven't had any help from anyone, so I'm not sure that I'm
>>> going to be adding anything. If I were, then yes, I would plan to
>>> create an additional attribute or two.
>>>
>>> - Noel
>>>
>>> On 14 October 2011 15:10, Karol M. Langner <kar...@gm...> wrote:
>>>> Hi Noel,
>>>>
>>>>  I don't know enough about PBC calculations to help you here, but are
>>>> similar outputs available for the other programs we support? Do you plan
>>>> on creating some attribute for this?
>>>>
>>>> Best,
>>>> Karol
>>>>
>>>> On Oct 12 2011, Noel O'Boyle wrote:
>>>>> Hey there,
>>>>>
>>>>> A GaussSum user was asking me about extracting the orbitals at
>>>>> k-points in PBC calculations. Any of you familiar with these types of
>>>>> calculations? I'd like to add support but I am a bit confused by the
>>>>> data in the output file and need some advice.
>>>>>
>>>>> For example, there are several k-points, each with different
>>>>> associated orbitals. However the pop analysis just writes out the
>>>>> orbitals for the 0 0 0 k-point. Should GaussSum just plot these
>>>>> orbitals, or should it try to plot all of the k-point orbitals?
>>>>>
>>>>> - Noel
>>>>
>>>> --
>>>> written by Karol M. Langner
>>>> Fri Oct 14 16:09:15 CEST 2011
>>>>
>>>
>>> ------------------------------------------------------------------------------
>>> All the data continuously generated in your IT infrastructure contains a
>>> definitive record of customers, application performance, security
>>> threats, fraudulent activity and more. Splunk takes this data and makes
>>> sense of it. Business sense. IT sense. Common sense.
>>> http://p.sf.net/sfu/splunk-d2d-oct
>>> _______________________________________________
>>> cclib-users mailing list
>>> ccl...@li...
>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>
>>
>

Re: [cclib-users] Any Gaussian users familiar with PBC?

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

Hi Manuel,

The user wants a DOS (and possibly a Projected DOS). A typical
Gaussian output file is at
http://cclib.sourceforge.net/data/Gaussian/Gaussian03/maheshkumar.log.gz

Does Crystal use the concept of k-points?

- Noel

On 14 October 2011 15:30, Manuel Melle Franco <man...@gm...> wrote:
> Hi Noel,
>
> I have experience with PBC calculations but not with gaussian but with
> crystal that has a similar methodology (LCAO+PBCs). what has the user
> exactly asked you to output? just the orbitals?
>
> regards
>
> Manuel
>
>
>
> ____________________________________________________________
>
> Mohandas K. Gandhi often changed his mind publicly.  An aide once asked
> him how he could so freely contradict this week what he had said just
> last week.  The great man replied that it was because this week he knew
> better.
>
> ____________________________________________________________
>
> Manuel Melle-Franco, Ph.D.
> Investigador Auxiliar
> Centro de Ciências e Tecnologias de Computação, CCTC
> Universidade do Minho
> Campus de Gualtar
> 4710-057 Braga
> PORTUGAL
>
> ---------------------------------------------------------
>
> A mind all logic is like a knife all blade. It makes the hand bleed
> that uses it.
> Rabindranath Tagore
>
> ---------------------------------------------------------
>
>
>
> On Fri, Oct 14, 2011 at 3:18 PM, Noel O'Boyle <bao...@gm...> wrote:
>> Well, I haven't had any help from anyone, so I'm not sure that I'm
>> going to be adding anything. If I were, then yes, I would plan to
>> create an additional attribute or two.
>>
>> - Noel
>>
>> On 14 October 2011 15:10, Karol M. Langner <kar...@gm...> wrote:
>>> Hi Noel,
>>>
>>>  I don't know enough about PBC calculations to help you here, but are
>>> similar outputs available for the other programs we support? Do you plan
>>> on creating some attribute for this?
>>>
>>> Best,
>>> Karol
>>>
>>> On Oct 12 2011, Noel O'Boyle wrote:
>>>> Hey there,
>>>>
>>>> A GaussSum user was asking me about extracting the orbitals at
>>>> k-points in PBC calculations. Any of you familiar with these types of
>>>> calculations? I'd like to add support but I am a bit confused by the
>>>> data in the output file and need some advice.
>>>>
>>>> For example, there are several k-points, each with different
>>>> associated orbitals. However the pop analysis just writes out the
>>>> orbitals for the 0 0 0 k-point. Should GaussSum just plot these
>>>> orbitals, or should it try to plot all of the k-point orbitals?
>>>>
>>>> - Noel
>>>
>>> --
>>> written by Karol M. Langner
>>> Fri Oct 14 16:09:15 CEST 2011
>>>
>>
>> ------------------------------------------------------------------------------
>> All the data continuously generated in your IT infrastructure contains a
>> definitive record of customers, application performance, security
>> threats, fraudulent activity and more. Splunk takes this data and makes
>> sense of it. Business sense. IT sense. Common sense.
>> http://p.sf.net/sfu/splunk-d2d-oct
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>

Re: [cclib-users] Any Gaussian users familiar with PBC?

[Manuel M. F. <man...@gm...>]

Hi Noel,

I have experience with PBC calculations but not with gaussian but with
crystal that has a similar methodology (LCAO+PBCs). what has the user
exactly asked you to output? just the orbitals?

regards

Manuel



____________________________________________________________

Mohandas K. Gandhi often changed his mind publicly.  An aide once asked
him how he could so freely contradict this week what he had said just
last week.  The great man replied that it was because this week he knew
better.

____________________________________________________________

Manuel Melle-Franco, Ph.D.
Investigador Auxiliar
Centro de Ciências e Tecnologias de Computação, CCTC
Universidade do Minho
Campus de Gualtar
4710-057 Braga
PORTUGAL

---------------------------------------------------------

A mind all logic is like a knife all blade. It makes the hand bleed
that uses it.
Rabindranath Tagore

---------------------------------------------------------



On Fri, Oct 14, 2011 at 3:18 PM, Noel O'Boyle <bao...@gm...> wrote:
> Well, I haven't had any help from anyone, so I'm not sure that I'm
> going to be adding anything. If I were, then yes, I would plan to
> create an additional attribute or two.
>
> - Noel
>
> On 14 October 2011 15:10, Karol M. Langner <kar...@gm...> wrote:
>> Hi Noel,
>>
>>  I don't know enough about PBC calculations to help you here, but are
>> similar outputs available for the other programs we support? Do you plan
>> on creating some attribute for this?
>>
>> Best,
>> Karol
>>
>> On Oct 12 2011, Noel O'Boyle wrote:
>>> Hey there,
>>>
>>> A GaussSum user was asking me about extracting the orbitals at
>>> k-points in PBC calculations. Any of you familiar with these types of
>>> calculations? I'd like to add support but I am a bit confused by the
>>> data in the output file and need some advice.
>>>
>>> For example, there are several k-points, each with different
>>> associated orbitals. However the pop analysis just writes out the
>>> orbitals for the 0 0 0 k-point. Should GaussSum just plot these
>>> orbitals, or should it try to plot all of the k-point orbitals?
>>>
>>> - Noel
>>
>> --
>> written by Karol M. Langner
>> Fri Oct 14 16:09:15 CEST 2011
>>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2d-oct
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>

Re: [cclib-users] Any Gaussian users familiar with PBC?

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

Well, I haven't had any help from anyone, so I'm not sure that I'm
going to be adding anything. If I were, then yes, I would plan to
create an additional attribute or two.

- Noel

On 14 October 2011 15:10, Karol M. Langner <kar...@gm...> wrote:
> Hi Noel,
>
>  I don't know enough about PBC calculations to help you here, but are
> similar outputs available for the other programs we support? Do you plan
> on creating some attribute for this?
>
> Best,
> Karol
>
> On Oct 12 2011, Noel O'Boyle wrote:
>> Hey there,
>>
>> A GaussSum user was asking me about extracting the orbitals at
>> k-points in PBC calculations. Any of you familiar with these types of
>> calculations? I'd like to add support but I am a bit confused by the
>> data in the output file and need some advice.
>>
>> For example, there are several k-points, each with different
>> associated orbitals. However the pop analysis just writes out the
>> orbitals for the 0 0 0 k-point. Should GaussSum just plot these
>> orbitals, or should it try to plot all of the k-point orbitals?
>>
>> - Noel
>
> --
> written by Karol M. Langner
> Fri Oct 14 16:09:15 CEST 2011
>

Re: [cclib-users] Any Gaussian users familiar with PBC?

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

Hi Noel,

 I don't know enough about PBC calculations to help you here, but are
similar outputs available for the other programs we support? Do you plan
on creating some attribute for this?

Best,
Karol

On Oct 12 2011, Noel O'Boyle wrote:
> Hey there,
> 
> A GaussSum user was asking me about extracting the orbitals at
> k-points in PBC calculations. Any of you familiar with these types of
> calculations? I'd like to add support but I am a bit confused by the
> data in the output file and need some advice.
> 
> For example, there are several k-points, each with different
> associated orbitals. However the pop analysis just writes out the
> orbitals for the 0 0 0 k-point. Should GaussSum just plot these
> orbitals, or should it try to plot all of the k-point orbitals?
> 
> - Noel

-- 
written by Karol M. Langner
Fri Oct 14 16:09:15 CEST 2011

[cclib-users] Any Gaussian users familiar with PBC?

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

Hey there,

A GaussSum user was asking me about extracting the orbitals at
k-points in PBC calculations. Any of you familiar with these types of
calculations? I'd like to add support but I am a bit confused by the
data in the output file and need some advice.

For example, there are several k-points, each with different
associated orbitals. However the pop analysis just writes out the
orbitals for the 0 0 0 k-point. Should GaussSum just plot these
orbitals, or should it try to plot all of the k-point orbitals?

- Noel

Re: [cclib-users] cclib Debian package

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

Jeff is correct, and it took a bit of work to figure how to reasonably separate
the components of cclib into two parts for main and non-free. It seems,
however, that the log files might night even be OK for non-free due
to these license issues. It might be easier to just discard all unittests
and log files from the Debian packages. Most users don't care about them anyway.

We will see,
Karol

On Mon, Aug 01, 2011 at 05:58:09PM -0500, Jeff Hammond wrote:
> You can learn more about Debian's rules of inclusion from
> <http://en.wikipedia.org/wiki/Debian_Free_Software_Guidelines>.
> Gaussian log files are definitely not compliant with #1 since a
> licensee cannot share them with a competitor of Gaussian (e.g. me).
> If you interpret #2 and #4 to mean that one must have the source code
> used to generate an output file, then this is a clear requirement that
> log files cannot be included without the source of the program used to
> create them, thus, output files from any non-free code must be
> excluded.
> 
> On Debian, Firefox is renamed and uses a different logo because the
> Firefox logo is subject to restrictions that the Debian folks can't
> accept.  They are, of course, happy with the code itself though, since
> it is GPL.  See
> http://en.wikipedia.org/wiki/Mozilla_Corporation_software_rebranded_by_the_Debian_project
> for details.
> 
> Jeff
> 
> On Mon, Aug 1, 2011 at 2:14 PM, Noel O'Boyle <bao...@gm...> wrote:
> > Non-free? Surprised to hear that. What do they require to be free?
> >
> > On 29 July 2011 17:56, Karol M. Langner <kar...@gm...> wrote:
> >> Hi,
> >>
> >> I'm happy to say that cclib 1.0.1 is in the official Debian archive:
> >> http://packages.debian.org/sid/cclib
> >>
> >> For copyright reasons, the log files (and therefore also unit tests)
> >> were separated into the package cclib-data and moved to the non-free
> >> section of Debian. This package isn't available yet.
> >>
> >> Cheers,
> >> Karol
> >>
> >> --
> >> written by Karol M. Langner
> >> Fri Jul 29 18:52:32 CEST 2011
> >>
> >> ------------------------------------------------------------------------------
> >> Got Input?   Slashdot Needs You.
> >> Take our quick survey online.  Come on, we don't ask for help often.
> >> Plus, you'll get a chance to win $100 to spend on ThinkGeek.
> >> http://p.sf.net/sfu/slashdot-survey
> >> _______________________________________________
> >> cclib-users mailing list
> >> ccl...@li...
> >> https://lists.sourceforge.net/lists/listinfo/cclib-users
> >>
> >
> > ------------------------------------------------------------------------------
> > BlackBerry&reg; DevCon Americas, Oct. 18-20, San Francisco, CA
> > The must-attend event for mobile developers. Connect with experts.
> > Get tools for creating Super Apps. See the latest technologies.
> > Sessions, hands-on labs, demos & much more. Register early & save!
> > http://p.sf.net/sfu/rim-blackberry-1
> > _______________________________________________
> > cclib-users mailing list
> > ccl...@li...
> > https://lists.sourceforge.net/lists/listinfo/cclib-users
> >
> 
> 
> 
> -- 
> Jeff Hammond
> Argonne Leadership Computing Facility
> University of Chicago Computation Institute
> jha...@al... / (630) 252-5381
> http://www.linkedin.com/in/jeffhammond
> https://wiki.alcf.anl.gov/index.php/User:Jhammond

-- 
written by Karol M. Langner
Tue Aug  2 18:36:48 CEST 2011

Re: [cclib-users] cclib Debian package

[Jeff H. <jha...@al...>]

You can learn more about Debian's rules of inclusion from
<http://en.wikipedia.org/wiki/Debian_Free_Software_Guidelines>.
Gaussian log files are definitely not compliant with #1 since a
licensee cannot share them with a competitor of Gaussian (e.g. me).
If you interpret #2 and #4 to mean that one must have the source code
used to generate an output file, then this is a clear requirement that
log files cannot be included without the source of the program used to
create them, thus, output files from any non-free code must be
excluded.

On Debian, Firefox is renamed and uses a different logo because the
Firefox logo is subject to restrictions that the Debian folks can't
accept.  They are, of course, happy with the code itself though, since
it is GPL.  See
http://en.wikipedia.org/wiki/Mozilla_Corporation_software_rebranded_by_the_Debian_project
for details.

Jeff

On Mon, Aug 1, 2011 at 2:14 PM, Noel O'Boyle <bao...@gm...> wrote:
> Non-free? Surprised to hear that. What do they require to be free?
>
> On 29 July 2011 17:56, Karol M. Langner <kar...@gm...> wrote:
>> Hi,
>>
>> I'm happy to say that cclib 1.0.1 is in the official Debian archive:
>> http://packages.debian.org/sid/cclib
>>
>> For copyright reasons, the log files (and therefore also unit tests)
>> were separated into the package cclib-data and moved to the non-free
>> section of Debian. This package isn't available yet.
>>
>> Cheers,
>> Karol
>>
>> --
>> written by Karol M. Langner
>> Fri Jul 29 18:52:32 CEST 2011
>>
>> ------------------------------------------------------------------------------
>> Got Input?   Slashdot Needs You.
>> Take our quick survey online.  Come on, we don't ask for help often.
>> Plus, you'll get a chance to win $100 to spend on ThinkGeek.
>> http://p.sf.net/sfu/slashdot-survey
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>
> ------------------------------------------------------------------------------
> BlackBerry&reg; DevCon Americas, Oct. 18-20, San Francisco, CA
> The must-attend event for mobile developers. Connect with experts.
> Get tools for creating Super Apps. See the latest technologies.
> Sessions, hands-on labs, demos & much more. Register early & save!
> http://p.sf.net/sfu/rim-blackberry-1
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>



-- 
Jeff Hammond
Argonne Leadership Computing Facility
University of Chicago Computation Institute
jha...@al... / (630) 252-5381
http://www.linkedin.com/in/jeffhammond
https://wiki.alcf.anl.gov/index.php/User:Jhammond

Re: [cclib-users] cclib Debian package

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

And I forgot to say, well done on getting it in! Our world-domination
plan is continuing.

- Noel

On 1 August 2011 20:14, Noel O'Boyle <bao...@gm...> wrote:
> Non-free? Surprised to hear that. What do they require to be free?
>
> On 29 July 2011 17:56, Karol M. Langner <kar...@gm...> wrote:
>> Hi,
>>
>> I'm happy to say that cclib 1.0.1 is in the official Debian archive:
>> http://packages.debian.org/sid/cclib
>>
>> For copyright reasons, the log files (and therefore also unit tests)
>> were separated into the package cclib-data and moved to the non-free
>> section of Debian. This package isn't available yet.
>>
>> Cheers,
>> Karol
>>
>> --
>> written by Karol M. Langner
>> Fri Jul 29 18:52:32 CEST 2011
>>
>> ------------------------------------------------------------------------------
>> Got Input?   Slashdot Needs You.
>> Take our quick survey online.  Come on, we don't ask for help often.
>> Plus, you'll get a chance to win $100 to spend on ThinkGeek.
>> http://p.sf.net/sfu/slashdot-survey
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>

Re: [cclib-users] cclib Debian package

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

Non-free? Surprised to hear that. What do they require to be free?

On 29 July 2011 17:56, Karol M. Langner <kar...@gm...> wrote:
> Hi,
>
> I'm happy to say that cclib 1.0.1 is in the official Debian archive:
> http://packages.debian.org/sid/cclib
>
> For copyright reasons, the log files (and therefore also unit tests)
> were separated into the package cclib-data and moved to the non-free
> section of Debian. This package isn't available yet.
>
> Cheers,
> Karol
>
> --
> written by Karol M. Langner
> Fri Jul 29 18:52:32 CEST 2011
>
> ------------------------------------------------------------------------------
> Got Input?   Slashdot Needs You.
> Take our quick survey online.  Come on, we don't ask for help often.
> Plus, you'll get a chance to win $100 to spend on ThinkGeek.
> http://p.sf.net/sfu/slashdot-survey
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>

[cclib-users] cclib Debian package

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

Hi,

I'm happy to say that cclib 1.0.1 is in the official Debian archive:
http://packages.debian.org/sid/cclib

For copyright reasons, the log files (and therefore also unit tests)
were separated into the package cclib-data and moved to the non-free
section of Debian. This package isn't available yet.

Cheers,
Karol

-- 
written by Karol M. Langner
Fri Jul 29 18:52:32 CEST 2011

[cclib-users] Gaussian cclib examples

[Dan-thomas M. <Dan...@bi...>]

Hi,
where can I find some simple as well as advanced example python scripts of how to use cclib with gaussian?
Thanks,
Dan


Dan T Major (PhD)
Chemistry Department
Bar-Ilan University
Ramat-Gan 52900
Israel

Phone: 972-3-5317392
Fax: 972-3-7384053
e-mail: ma...@ma... (ma...@bi... or Dan...@bi...)

[cclib-users] Test email

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

Please ignore. Just checking to see that the mailing list is working...

- Noel

Re: [cclib-users] Installation of cclib 1.0 requires user intervention on Ubuntu 10.04

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

On Sun, Feb 27, 2011 at 04:57:35PM -0600, Jim Parker wrote:
> I agree the sudo su root is unusual, but doing it that way, the
> installer then placed all documents in the dist-packages directory
> rather than splitting some into site-packages which is not a default
> path.  Not a big issue as one can just add it as you mention to
> .bashrc or other startup script.
> 
> Cheers,
> --Jim
> 
> On Sun, Feb 27, 2011 at 3:32 PM, Noel O'Boyle <bao...@gm...> wrote:
> > "sudo python setup.py install" was the correct way to install it.
> > site-packages is the correct location, not dist-packages. The latter
> > is a directly for packages from your distribution; the former for ones
> > you install yourself. You should add site-packages to PYTHONPATH in
> > your startup script (.bashrc or so), or complain to Ubuntu! :-)

Noel is right. I also find this annoying, and what I do on Debian when manually
installing Python modules is to always put them in /usr/local, where I additionally
link site-packages to dist-packages in order to bypass this irritating behavior.

You can do this by adding the --prefix option, like so:
python setup.py install --prefix=/usr/local

Note that you need to make the symbolic link from /usr/local/lib/python2.x/site-packages
to /usr/local/lib/python2.x/dist-packages before this.

- Karol

-- 
written by Karol Langner
Sat Mar 26 16:22:36 CET 2011

Re: [cclib-users] Installation of cclib 1.0 requires user intervention on Ubuntu 10.04

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

On Wed, Mar 16, 2011 at 09:54:35AM +0000, Noel O'Boyle wrote:
> Regarding getting cclib into Debian, I suggest contacting Debichem as
> they have already packaged GaussSum and will probably want to
> coordinate on this.

Packaging is under way.

-- 
written by Karol Langner
Fri Mar 25 23:50:01 CET 2011

Re: [cclib-users] Installation of cclib 1.0 requires user intervention on Ubuntu 10.04

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

I think I must have made the release on Windows :-/

Regarding getting cclib into Debian, I suggest contacting Debichem as
they have already packaged GaussSum and will probably want to
coordinate on this.

- Noel

On 16 March 2011 09:41, Karol M. Langner <kar...@gm...> wrote:
> Wow, I'm surprised such a problem came up :)
>
> Thanks Noel for working on the new release. Maybe this is a good time
> to think about packaging cclib for Debian? I already make debs
> for my own use, so it is a question of getting it into the repository.
>
> - Karol
>
> On Mon, Feb 28, 2011 at 08:48:52PM -0600, Jim Parker wrote:
>> You're welcome.  Thank you for making the program...
>>
>> Cheers,
>> --Jim
>>
>> On Mon, Feb 28, 2011 at 1:59 PM, Noel O'Boyle <bao...@gm...> wrote:
>> > I just checked this myself, and I find the problem is even worse. I
>> > can't even cd into the cclib-1.0 folder after untarring the .tar.gz,
>> > due to permissions problems.
>> >
>> > Thanks for letting us know. I badly need to make a new release...
>> >
>> > - Noel
>> >
>> > On 27 February 2011 22:57, Jim Parker <jim...@gm...> wrote:
>> >> Noel,
>> >>  The permissions problem I'm having is that all files are installed
>> >> with 750 + setuid bit (or in symbols: rwxr-s--- ).  This occurs when I
>> >> use
>> >> $> sudo python setup.py install
>> >> or
>> >> $> sudo su root
>> >> #> python setup.py install
>> >>
>> >> Thus when I run as a user and attempt to import cclib, the file isn't found.
>> >>
>> >> I agree the sudo su root is unusual, but doing it that way, the
>> >> installer then placed all documents in the dist-packages directory
>> >> rather than splitting some into site-packages which is not a default
>> >> path.  Not a big issue as one can just add it as you mention to
>> >> .bashrc or other startup script.
>> >>
>> >> Cheers,
>> >> --Jim
>> >>
>> >> On Sun, Feb 27, 2011 at 3:32 PM, Noel O'Boyle <bao...@gm...> wrote:
>> >>> Hi Jim,
>> >>>
>> >>> We're just using the standard installer for Python packages.
>> >>>
>> >>> "sudo python setup.py install" was the correct way to install it.
>> >>> site-packages is the correct location, not dist-packages. The latter
>> >>> is a directly for packages from your distribution; the former for ones
>> >>> you install yourself. You should add site-packages to PYTHONPATH in
>> >>> your startup script (.bashrc or so), or complain to Ubuntu! :-)
>> >>>
>> >>> You didn't say what the permissions problem was exactly, but I expect
>> >>> that it results from use of "sudo su root", which looks like a very
>> >>> dangerous command. Just the regular "sudo" will do the trick.
>> >>>
>> >>> - Noel
>> >>>
>> >>> On 27 February 2011 21:12, Jim Parker <jim...@gm...> wrote:
>> >>>> This library looks to be very useful for me, and I'd like to thank the
>> >>>> developers.
>> >>>>
>> >>>> I didn't see this in the archives and regret if it is a repeat of
>> >>>> another post, but the release version of cclib-1.0 will not install
>> >>>> correctly using the INSTALL notes on Ubuntu 10.04.  The user must
>> >>>> recursively change the permissions of the installed files.  Ideally,
>> >>>> the installer would do this and remove the group "staff" from the new
>> >>>> install.
>> >>>>
>> >>>> My steps.
>> >>>> 1.  Ensure python, python-dev, and numpy are installed per INSTALL directions
>> >>>> 2.  as user,
>> >>>> $> python setup.py build
>> >>>> 3.  change to root, and install
>> >>>> $> sudo su root
>> >>>> $> python setup.py install
>> >>>> Note: giving the command
>> >>>> $> sudo python setup.py install
>> >>>> will install to /usr/local/lib/pythonx.x/site-packages rather than
>> >>>> /usr/local/lib/pythonx.x/dist-packages.  The difference is that
>> >>>> dist-packages is loaded into PYTHONPATH by default in Ubuntu 10.04,
>> >>>> site-packages is not.
>> >>>>
>> >>>> --Additional steps required beyond INSTALL directions.
>> >>>> 4. Fix permissions
>> >>>> $> cd /usr/local/lib/pythonx.x/
>> >>>> $> sudo chmod --recursive 755 *  (not best, but if you want you can
>> >>>> change the *.py files to 644)
>> >>>> 5. Remove "staff" group
>> >>>> $> sudo chgrp --recursive root *
>> >>>>
>> >>>> HTH some other new user.
>> >>>>
>> >>>> Cheers,
>> >>>> --Jim
>> >>>>
>> >>>> ------------------------------------------------------------------------------
>> >>>> Free Software Download: Index, Search & Analyze Logs and other IT data in
>> >>>> Real-Time with Splunk. Collect, index and harness all the fast moving IT data
>> >>>> generated by your applications, servers and devices whether physical, virtual
>> >>>> or in the cloud. Deliver compliance at lower cost and gain new business
>> >>>> insights. http://p.sf.net/sfu/splunk-dev2dev
>> >>>> _______________________________________________
>> >>>> cclib-users mailing list
>> >>>> ccl...@li...
>> >>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>> >>>>
>> >>>
>> >>
>> >
>>
>> ------------------------------------------------------------------------------
>> Free Software Download: Index, Search & Analyze Logs and other IT data in
>> Real-Time with Splunk. Collect, index and harness all the fast moving IT data
>> generated by your applications, servers and devices whether physical, virtual
>> or in the cloud. Deliver compliance at lower cost and gain new business
>> insights. http://p.sf.net/sfu/splunk-dev2dev
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>

Re: [cclib-users] Installation of cclib 1.0 requires user intervention on Ubuntu 10.04

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

Wow, I'm surprised such a problem came up :)

Thanks Noel for working on the new release. Maybe this is a good time
to think about packaging cclib for Debian? I already make debs
for my own use, so it is a question of getting it into the repository.

- Karol

On Mon, Feb 28, 2011 at 08:48:52PM -0600, Jim Parker wrote:
> You're welcome.  Thank you for making the program...
> 
> Cheers,
> --Jim
> 
> On Mon, Feb 28, 2011 at 1:59 PM, Noel O'Boyle <bao...@gm...> wrote:
> > I just checked this myself, and I find the problem is even worse. I
> > can't even cd into the cclib-1.0 folder after untarring the .tar.gz,
> > due to permissions problems.
> >
> > Thanks for letting us know. I badly need to make a new release...
> >
> > - Noel
> >
> > On 27 February 2011 22:57, Jim Parker <jim...@gm...> wrote:
> >> Noel,
> >>  The permissions problem I'm having is that all files are installed
> >> with 750 + setuid bit (or in symbols: rwxr-s--- ).  This occurs when I
> >> use
> >> $> sudo python setup.py install
> >> or
> >> $> sudo su root
> >> #> python setup.py install
> >>
> >> Thus when I run as a user and attempt to import cclib, the file isn't found.
> >>
> >> I agree the sudo su root is unusual, but doing it that way, the
> >> installer then placed all documents in the dist-packages directory
> >> rather than splitting some into site-packages which is not a default
> >> path.  Not a big issue as one can just add it as you mention to
> >> .bashrc or other startup script.
> >>
> >> Cheers,
> >> --Jim
> >>
> >> On Sun, Feb 27, 2011 at 3:32 PM, Noel O'Boyle <bao...@gm...> wrote:
> >>> Hi Jim,
> >>>
> >>> We're just using the standard installer for Python packages.
> >>>
> >>> "sudo python setup.py install" was the correct way to install it.
> >>> site-packages is the correct location, not dist-packages. The latter
> >>> is a directly for packages from your distribution; the former for ones
> >>> you install yourself. You should add site-packages to PYTHONPATH in
> >>> your startup script (.bashrc or so), or complain to Ubuntu! :-)
> >>>
> >>> You didn't say what the permissions problem was exactly, but I expect
> >>> that it results from use of "sudo su root", which looks like a very
> >>> dangerous command. Just the regular "sudo" will do the trick.
> >>>
> >>> - Noel
> >>>
> >>> On 27 February 2011 21:12, Jim Parker <jim...@gm...> wrote:
> >>>> This library looks to be very useful for me, and I'd like to thank the
> >>>> developers.
> >>>>
> >>>> I didn't see this in the archives and regret if it is a repeat of
> >>>> another post, but the release version of cclib-1.0 will not install
> >>>> correctly using the INSTALL notes on Ubuntu 10.04.  The user must
> >>>> recursively change the permissions of the installed files.  Ideally,
> >>>> the installer would do this and remove the group "staff" from the new
> >>>> install.
> >>>>
> >>>> My steps.
> >>>> 1.  Ensure python, python-dev, and numpy are installed per INSTALL directions
> >>>> 2.  as user,
> >>>> $> python setup.py build
> >>>> 3.  change to root, and install
> >>>> $> sudo su root
> >>>> $> python setup.py install
> >>>> Note: giving the command
> >>>> $> sudo python setup.py install
> >>>> will install to /usr/local/lib/pythonx.x/site-packages rather than
> >>>> /usr/local/lib/pythonx.x/dist-packages.  The difference is that
> >>>> dist-packages is loaded into PYTHONPATH by default in Ubuntu 10.04,
> >>>> site-packages is not.
> >>>>
> >>>> --Additional steps required beyond INSTALL directions.
> >>>> 4. Fix permissions
> >>>> $> cd /usr/local/lib/pythonx.x/
> >>>> $> sudo chmod --recursive 755 *  (not best, but if you want you can
> >>>> change the *.py files to 644)
> >>>> 5. Remove "staff" group
> >>>> $> sudo chgrp --recursive root *
> >>>>
> >>>> HTH some other new user.
> >>>>
> >>>> Cheers,
> >>>> --Jim
> >>>>
> >>>> ------------------------------------------------------------------------------
> >>>> Free Software Download: Index, Search & Analyze Logs and other IT data in
> >>>> Real-Time with Splunk. Collect, index and harness all the fast moving IT data
> >>>> generated by your applications, servers and devices whether physical, virtual
> >>>> or in the cloud. Deliver compliance at lower cost and gain new business
> >>>> insights. http://p.sf.net/sfu/splunk-dev2dev
> >>>> _______________________________________________
> >>>> cclib-users mailing list
> >>>> ccl...@li...
> >>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
> >>>>
> >>>
> >>
> >
> 
> ------------------------------------------------------------------------------
> Free Software Download: Index, Search & Analyze Logs and other IT data in 
> Real-Time with Splunk. Collect, index and harness all the fast moving IT data 
> generated by your applications, servers and devices whether physical, virtual
> or in the cloud. Deliver compliance at lower cost and gain new business 
> insights. http://p.sf.net/sfu/splunk-dev2dev 
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users

[cclib-users] ANN: cclib 1.0.1

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

Hello all,

cclib 1.0.1 is now available for download from http://cclib.sf.net.
This is largely a bug fix release (thanks to everyone that reported
bugs or supplied patches). We've also taken the opportunity to
(finally!) add instructions on the command-line application 'ccget' to
our wiki, so check it out, as it's quite handy.

Thanks to everyone that cited the cclib paper in the past - we really
appreciate it. This paper was the 2nd most cited J Comp Chem paper in
2009.

Changes since cclib-1.0:

Features:
	* New attribute atommasses - atomic masses in Dalton
	* Added support for Gaussian geometry optimisations that change
	the number of linearly independent basis functions over the
	course of the calculation

Bugfixes:
	* Handle triplet PM3 calculations in Gaussian03 (Greg Magoon)
	* Some Gaussian09 calculations were missing atomnos (Marius Retegan)
	* Handle multiple pseudopotentials in Gaussian03 (Tiago Silva)
	* Handle Gaussian calculations with >999 basis functions
	* ADF versions > 2007 no longer print overlap info by default
	* Handle parsing Firefly calculations that fail
	* Fix parsing of ORCA calculation (Marius Retegan)

Regards,
   Noel (on behalf of the cclib dev team)

Re: [cclib-users] Installation of cclib 1.0 requires user intervention on Ubuntu 10.04

[Jim P. <jim...@gm...>]

You're welcome.  Thank you for making the program...

Cheers,
--Jim

On Mon, Feb 28, 2011 at 1:59 PM, Noel O'Boyle <bao...@gm...> wrote:
> I just checked this myself, and I find the problem is even worse. I
> can't even cd into the cclib-1.0 folder after untarring the .tar.gz,
> due to permissions problems.
>
> Thanks for letting us know. I badly need to make a new release...
>
> - Noel
>
> On 27 February 2011 22:57, Jim Parker <jim...@gm...> wrote:
>> Noel,
>>  The permissions problem I'm having is that all files are installed
>> with 750 + setuid bit (or in symbols: rwxr-s--- ).  This occurs when I
>> use
>> $> sudo python setup.py install
>> or
>> $> sudo su root
>> #> python setup.py install
>>
>> Thus when I run as a user and attempt to import cclib, the file isn't found.
>>
>> I agree the sudo su root is unusual, but doing it that way, the
>> installer then placed all documents in the dist-packages directory
>> rather than splitting some into site-packages which is not a default
>> path.  Not a big issue as one can just add it as you mention to
>> .bashrc or other startup script.
>>
>> Cheers,
>> --Jim
>>
>> On Sun, Feb 27, 2011 at 3:32 PM, Noel O'Boyle <bao...@gm...> wrote:
>>> Hi Jim,
>>>
>>> We're just using the standard installer for Python packages.
>>>
>>> "sudo python setup.py install" was the correct way to install it.
>>> site-packages is the correct location, not dist-packages. The latter
>>> is a directly for packages from your distribution; the former for ones
>>> you install yourself. You should add site-packages to PYTHONPATH in
>>> your startup script (.bashrc or so), or complain to Ubuntu! :-)
>>>
>>> You didn't say what the permissions problem was exactly, but I expect
>>> that it results from use of "sudo su root", which looks like a very
>>> dangerous command. Just the regular "sudo" will do the trick.
>>>
>>> - Noel
>>>
>>> On 27 February 2011 21:12, Jim Parker <jim...@gm...> wrote:
>>>> This library looks to be very useful for me, and I'd like to thank the
>>>> developers.
>>>>
>>>> I didn't see this in the archives and regret if it is a repeat of
>>>> another post, but the release version of cclib-1.0 will not install
>>>> correctly using the INSTALL notes on Ubuntu 10.04.  The user must
>>>> recursively change the permissions of the installed files.  Ideally,
>>>> the installer would do this and remove the group "staff" from the new
>>>> install.
>>>>
>>>> My steps.
>>>> 1.  Ensure python, python-dev, and numpy are installed per INSTALL directions
>>>> 2.  as user,
>>>> $> python setup.py build
>>>> 3.  change to root, and install
>>>> $> sudo su root
>>>> $> python setup.py install
>>>> Note: giving the command
>>>> $> sudo python setup.py install
>>>> will install to /usr/local/lib/pythonx.x/site-packages rather than
>>>> /usr/local/lib/pythonx.x/dist-packages.  The difference is that
>>>> dist-packages is loaded into PYTHONPATH by default in Ubuntu 10.04,
>>>> site-packages is not.
>>>>
>>>> --Additional steps required beyond INSTALL directions.
>>>> 4. Fix permissions
>>>> $> cd /usr/local/lib/pythonx.x/
>>>> $> sudo chmod --recursive 755 *  (not best, but if you want you can
>>>> change the *.py files to 644)
>>>> 5. Remove "staff" group
>>>> $> sudo chgrp --recursive root *
>>>>
>>>> HTH some other new user.
>>>>
>>>> Cheers,
>>>> --Jim
>>>>
>>>> ------------------------------------------------------------------------------
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Re: [cclib-users] Parsing Gaussian 09 .out does not find normal modes (vibdisps)

[Jim P. <jim...@gm...>]

Noel,
  Attached are 2 files.  The changes to gaussianparser.py and the .out
file from a Gaussian 09 run.  I'm fine with this file being in the
public domain.

Cheers,
--Jim


On Mon, Feb 28, 2011 at 7:06 AM, Noel O'Boyle <bao...@gm...> wrote:
> Please do. We can't assess the patch without a test file. Please note
> also that we ask that are test files are placed in the public domain.
> Are you happy with this?
>
> - Noel
>
> On 28 February 2011 11:57, Jim Parker <jim...@gm...> wrote:
>> Noel,
>>  I can, but I think it is OBE. I made some changes to the
>> gaussianparser.py that allowed the parser to read the file.  I posted
>> the changes to cclib-users.
>>
>> Cheers,
>> --Jim
>>
>> On Mon, Feb 28, 2011 at 3:09 AM, Noel O'Boyle <bao...@gm...> wrote:
>>> Hi Jim,
>>>
>>> Could you resend your email on the above topic, but this time zip the file?
>>>
>>> - Noel
>>>
>>
>