cclib-users — Help and support for cclib users

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

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

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
>>>
>>
>

Re: [cclib-users] Parsing Gaussian 09 .out does not find normal modes (vibdisps)

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

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
>>
>

[cclib-users] Fix (kludge?) for vibdisps and Gaussian 09 .out files

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

I was unable to parse my Gaussian 09 files for normal mode info.  The
parser skipped that part of the file.  I checked the code and replaced
the following in gaussianparser.py (release version 1.0)

Line 579
if line[1:29] == "Atom  AN      X      Y      Z":

with--

vibdispre = re.compile('^Atom  AN      X      Y      Z')
if vibdispre.search(line.strip()):

Apparently there is an extra space in the Gaussian 09 files which is
causing the previous version to fail.  I believe this will work for
versions 03 & 09 of Gaussian.

Cheers,
--Jim Parker

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

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

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
>>
>

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

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

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
>

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

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

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

Re: [cclib-users] Gaussian 09

[Pavlo S. <psolntse@d.umn.edu>]

Thank you for your direction. 
My small script works just fine. Unfortunately, i have some problem with
qmforge. But this is another story. 

Thanks again. 

Best. Pavel.




On Tue, 2010-08-17 at 16:31 +0100, Noel O'Boyle wrote: 
> Does the development version work for you? See the instructions at
> http://cclib.sourceforge.net/wiki/index.php/Install#Getting_the_latest_version
> 
> - Noel
> 
> On 17 August 2010 16:25, Pavlo Solntsev <psolntse@d.umn.edu> wrote:
> > I use MOForge and found what its doesn't read output file from
> > Gassian09. I also wrote very simple script:
> > #!/usr/bin/python
> >
> > import sys
> > from cclib.parser import ccopen
> > from cclib.progress  import TextProgress
> > import logging
> >
> > progress = TextProgress()
> > myfile = ccopen(sys.argv[1],progress,logging.ERROR)
> >
> > data = myfile.parse()
> > coord = data.atomcoords
> >
> > print "Number of atoms is %d " % data.natom
> > print "Mult = %d " % data.mult
> > print "NMO = %d" % data.nmo
> >
> > for j in range(0,  data.natom):
> >  print "%f\t\t%f\t\t%f" % (coord[-1,  j, 0] ,  coord[-1,  j, 1],
> > coord[-1,  j, 2])
> >
> > # END
> > This script works fine with Gaussian 03 files, but with Gaussian 09 i
> > got error:
> > [----------]   0%    QM convergenceTraceback (most recent call last):
> >  File "./hello.py", line 11, in <module>
> >    data = myfile.parse()
> >  File
> > "/usr/local/lib/python2.6/dist-packages/cclib/parser/logfileparser.py",
> > line 221, in parse
> >    self.extract(inputfile, line)
> >  File
> > "/usr/local/lib/python2.6/dist-packages/cclib/parser/gaussianparser.py",
> > line 851, in extract
> >    atomname = "%s%s" % (parts[2], parts[1])
> > IndexError: list index out of range
> > # END
> >
> > and script stopped. Are you going to make Gaussian 09 files working in
> > the cclib or you already done this? How can i fix this problem?
> >
> > Best, Pavlo.
> >
> >
> >
> >
> > ------------------------------------------------------------------------------
> > This SF.net email is sponsored by
> >
> > Make an app they can't live without
> > Enter the BlackBerry Developer Challenge
> > http://p.sf.net/sfu/RIM-dev2dev
> > _______________________________________________
> > cclib-users mailing list
> > ccl...@li...
> > https://lists.sourceforge.net/lists/listinfo/cclib-users
> >

Re: [cclib-users] Gaussian 09

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

Does the development version work for you? See the instructions at
http://cclib.sourceforge.net/wiki/index.php/Install#Getting_the_latest_version

- Noel

On 17 August 2010 16:25, Pavlo Solntsev <psolntse@d.umn.edu> wrote:
> I use MOForge and found what its doesn't read output file from
> Gassian09. I also wrote very simple script:
> #!/usr/bin/python
>
> import sys
> from cclib.parser import ccopen
> from cclib.progress  import TextProgress
> import logging
>
> progress = TextProgress()
> myfile = ccopen(sys.argv[1],progress,logging.ERROR)
>
> data = myfile.parse()
> coord = data.atomcoords
>
> print "Number of atoms is %d " % data.natom
> print "Mult = %d " % data.mult
> print "NMO = %d" % data.nmo
>
> for j in range(0,  data.natom):
>  print "%f\t\t%f\t\t%f" % (coord[-1,  j, 0] ,  coord[-1,  j, 1],
> coord[-1,  j, 2])
>
> # END
> This script works fine with Gaussian 03 files, but with Gaussian 09 i
> got error:
> [----------]   0%    QM convergenceTraceback (most recent call last):
>  File "./hello.py", line 11, in <module>
>    data = myfile.parse()
>  File
> "/usr/local/lib/python2.6/dist-packages/cclib/parser/logfileparser.py",
> line 221, in parse
>    self.extract(inputfile, line)
>  File
> "/usr/local/lib/python2.6/dist-packages/cclib/parser/gaussianparser.py",
> line 851, in extract
>    atomname = "%s%s" % (parts[2], parts[1])
> IndexError: list index out of range
> # END
>
> and script stopped. Are you going to make Gaussian 09 files working in
> the cclib or you already done this? How can i fix this problem?
>
> Best, Pavlo.
>
>
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by
>
> Make an app they can't live without
> Enter the BlackBerry Developer Challenge
> http://p.sf.net/sfu/RIM-dev2dev
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>

[cclib-users] Gaussian 09

[Pavlo S. <psolntse@d.umn.edu>]

I use MOForge and found what its doesn't read output file from
Gassian09. I also wrote very simple script:
#!/usr/bin/python

import sys
from cclib.parser import ccopen
from cclib.progress  import TextProgress        
import logging

progress = TextProgress()
myfile = ccopen(sys.argv[1],progress,logging.ERROR)

data = myfile.parse()
coord = data.atomcoords

print "Number of atoms is %d " % data.natom
print "Mult = %d " % data.mult
print "NMO = %d" % data.nmo

for j in range(0,  data.natom):
  print "%f\t\t%f\t\t%f" % (coord[-1,  j, 0] ,  coord[-1,  j, 1],
coord[-1,  j, 2])

# END
This script works fine with Gaussian 03 files, but with Gaussian 09 i
got error:
[----------]   0%    QM convergenceTraceback (most recent call last): 
  File "./hello.py", line 11, in <module>
    data = myfile.parse()
  File
"/usr/local/lib/python2.6/dist-packages/cclib/parser/logfileparser.py",
line 221, in parse
    self.extract(inputfile, line)
  File
"/usr/local/lib/python2.6/dist-packages/cclib/parser/gaussianparser.py",
line 851, in extract
    atomname = "%s%s" % (parts[2], parts[1])
IndexError: list index out of range
# END

and script stopped. Are you going to make Gaussian 09 files working in
the cclib or you already done this? How can i fix this problem?

Best, Pavlo.

[cclib-users] ANN: cclib 1.0 now available

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

Hello everyone,

cclib 1.0 is now available for download from http://cclib.sf.net. It's
been some time since the last release, so we recommend you to upgrade
to this version.

Changes since cclib-0.9:

Features:
	* Handle PBC calculations from Gaussian
	* Updates to handle Gaussian09
	* Support TDDFT calculations from ADF
	* A number of improvements for GAMESS support
	* ccopen now supports any file-like object with a read() method, so it
	can parse across HTTP

Bugfixes:
	* Many many additional files parsed thanks to bugs reported by users

Remember to cite cclib if you use it to obtain results for
publication. This encourages us to keep doing what we do.

Regards,
   The cclib development team

Re: [cclib-users] cclib-0.91 bug Gaussian parser does not parse Vibsyms correctly if T symm

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

(Please cc to list)

The official release will be this weekend (and the webpage will be
updated), but you can get the files right now from our SourceForge
download page at https://sourceforge.net/projects/cclib/files/ under
cclib version 1.0b.

- Noel

On 5 March 2010 12:32, Klemens Noga <kn...@ch...> wrote:
> Dear Noel,
>
> I apologize for delay in reply, today I've got big mount of issues to deal
> with.
> Now parsed data are correct:). When or from where could I get fixed cclib
> version?
>
> Best regads,
>
> Klemens
>
>
> On 5 Mar 2010, at 10:46, Noel O'Boyle wrote:
>
>> Using the current beta release, cclib-1.0b, I don't see any problem:
>>
>>> python C:\Python26\Scripts\ccget vibsyms *.log
>>
>> Attempting to parse ccl4631gpd.freq.log
>> vibsyms:
>> ['E', 'E', 'T2', 'T2', 'T2', 'A1', 'T2', 'T2', 'T2']
>> Attempting to parse ccl4AnD631gpd.freq.log
>> vibsyms:
>> ['T2', 'T2', 'T2', 'E', 'E', 'A1', 'T2', 'T2', 'T2']
>>
>> Is this correct?
>>
>> - Noel
>>
>> On 5 March 2010 09:39, Noel O'Boyle <bao...@gm...> wrote:
>>>
>>> Hello Klemens,
>>>
>>> Thanks for letting us know. To fix bugs we need public domain test
>>> files - are you happy to place your attached files in the public
>>> domain? If not, we'd appreciate if you could generate some small test
>>> files that reproduce the problem.
>>>
>>> I've leave the others to discuss Turbomole.
>>>
>>> - Noel
>>>
>>> On 5 March 2010 07:32, Klemens Noga <kn...@ch...> wrote:
>>>>
>>>> Dear all,
>>>>
>>>> My name is Klemens Noga and I'm PhD student in Theoretical Chemistry at
>>>> Jagiellonian University in Krakow, Poland. I've started using cclib to
>>>> parse
>>>> data from GAMESS and Gaussian output files and I probably found bug.
>>>> When
>>>> there are vibrations with T symmetry they aren't parsed into vibsyms
>>>> list
>>>> correctly. You could check it in attached example files. Is there any
>>>> simple
>>>> solution?
>>>> Secondly, I'm interested in parsing data from Turbomole outputs. I've
>>>> heard
>>>> that cclib development team is working at this issue but i've found only
>>>> very old information and I'm curious about progress.
>>>>
>>>> Best regads,
>>>>
>>>> Klemens
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Klemens Noga
>>>> Ph.D. student
>>>> Department of Theoretical Chemistry
>>>> Faculty of Chemistry, Jagiellonian University
>>>> Ingardena st. 3, 30-060 Krakow, Poland
>>>> tel. +48-12-6632023
>>>> e.mail: kn...@ch...
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Download Intel&#174; Parallel Studio Eval
>>>> Try the new software tools for yourself. Speed compiling, find bugs
>>>> proactively, and fine-tune applications for parallel performance.
>>>> See why Intel Parallel Studio got high marks during beta.
>>>> http://p.sf.net/sfu/intel-sw-dev
>>>> _______________________________________________
>>>> cclib-users mailing list
>>>> ccl...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>>>
>>>>
>>>
>
> Klemens Noga
> Ph.D. student
> Department of Theoretical Chemistry
> Faculty of Chemistry, Jagiellonian University
> Ingardena st. 3, 30-060 Krakow, Poland
> tel. +48-12-6632023
> e.mail: kn...@ch...
>
>
>

Re: [cclib-users] cclib-0.91 bug Gaussian parser does not parse Vibsyms correctly if T symm

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

Using the current beta release, cclib-1.0b, I don't see any problem:

>python C:\Python26\Scripts\ccget vibsyms *.log
Attempting to parse ccl4631gpd.freq.log
vibsyms:
['E', 'E', 'T2', 'T2', 'T2', 'A1', 'T2', 'T2', 'T2']
Attempting to parse ccl4AnD631gpd.freq.log
vibsyms:
['T2', 'T2', 'T2', 'E', 'E', 'A1', 'T2', 'T2', 'T2']

Is this correct?

- Noel

On 5 March 2010 09:39, Noel O'Boyle <bao...@gm...> wrote:
> Hello Klemens,
>
> Thanks for letting us know. To fix bugs we need public domain test
> files - are you happy to place your attached files in the public
> domain? If not, we'd appreciate if you could generate some small test
> files that reproduce the problem.
>
> I've leave the others to discuss Turbomole.
>
> - Noel
>
> On 5 March 2010 07:32, Klemens Noga <kn...@ch...> wrote:
>> Dear all,
>>
>> My name is Klemens Noga and I'm PhD student in Theoretical Chemistry at
>> Jagiellonian University in Krakow, Poland. I've started using cclib to parse
>> data from GAMESS and Gaussian output files and I probably found bug. When
>> there are vibrations with T symmetry they aren't parsed into vibsyms list
>> correctly. You could check it in attached example files. Is there any simple
>> solution?
>> Secondly, I'm interested in parsing data from Turbomole outputs. I've heard
>> that cclib development team is working at this issue but i've found only
>> very old information and I'm curious about progress.
>>
>> Best regads,
>>
>> Klemens
>>
>>
>>
>>
>>
>> Klemens Noga
>> Ph.D. student
>> Department of Theoretical Chemistry
>> Faculty of Chemistry, Jagiellonian University
>> Ingardena st. 3, 30-060 Krakow, Poland
>> tel. +48-12-6632023
>> e.mail: kn...@ch...
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Download Intel&#174; Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev
>> _______________________________________________
>> cclib-users mailing list
>> ccl...@li...
>> https://lists.sourceforge.net/lists/listinfo/cclib-users
>>
>>
>

Re: [cclib-users] cclib-0.91 bug Gaussian parser does not parse Vibsyms correctly if T symm

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

Hello Klemens,

Thanks for letting us know. To fix bugs we need public domain test
files - are you happy to place your attached files in the public
domain? If not, we'd appreciate if you could generate some small test
files that reproduce the problem.

I've leave the others to discuss Turbomole.

- Noel

On 5 March 2010 07:32, Klemens Noga <kn...@ch...> wrote:
> Dear all,
>
> My name is Klemens Noga and I'm PhD student in Theoretical Chemistry at
> Jagiellonian University in Krakow, Poland. I've started using cclib to parse
> data from GAMESS and Gaussian output files and I probably found bug. When
> there are vibrations with T symmetry they aren't parsed into vibsyms list
> correctly. You could check it in attached example files. Is there any simple
> solution?
> Secondly, I'm interested in parsing data from Turbomole outputs. I've heard
> that cclib development team is working at this issue but i've found only
> very old information and I'm curious about progress.
>
> Best regads,
>
> Klemens
>
>
>
>
>
> Klemens Noga
> Ph.D. student
> Department of Theoretical Chemistry
> Faculty of Chemistry, Jagiellonian University
> Ingardena st. 3, 30-060 Krakow, Poland
> tel. +48-12-6632023
> e.mail: kn...@ch...
>
>
>
> ------------------------------------------------------------------------------
> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>

[cclib-users] cclib-0.91 bug Gaussian parser does not parse Vibsyms correctly if T symm

[Klemens N. <kn...@ch...>]

Dear all,

My name is Klemens Noga and I'm PhD student in Theoretical Chemistry  
at Jagiellonian University in Krakow, Poland. I've started using cclib  
to parse data from GAMESS and Gaussian output files and I probably  
found bug. When there are vibrations with T symmetry they aren't  
parsed into vibsyms list correctly. You could check it in attached  
example files. Is there any simple solution?
Secondly, I'm interested in parsing data from Turbomole outputs. I've  
heard that cclib development team is working at this issue but i've  
found only very old information and I'm curious about progress.

Best regads,

Klemens

Re: [cclib-users] GAMESS-US and mpenergies

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

Hello Paulo,

Sounds like a bug.

Could you provide us with a public domain test file? That is, this
should be a test file which you are happy for us to share with the
world.

- Noel

On 25 February 2010 12:16, Paulo E. Abreu <pau...@ci...> wrote:
> Hello,
> I have been using cclib for my parsers and just noticed something odd about
> GAMESS-US files with MP2 calculations.
> According to http://cclib.sourceforge.net/wiki/index.php/Parsed_Data and
>  http://cclib.sourceforge.net/wiki/index.php/Mpenergies
> this is available for GAMESS-US output files. The problem is that I cannot
> access this information. The logging after parsing the file
> does not show any mpenergies and consequently when I try to use it I get an
> error
> AttributeError: 'ccData' object has no attribute 'mpenergies'
> Is there something which I am missing here ?
> ===begin code snippet
> myfile = ccopen("mp2.out")
> data = myfile.parse()
> print data.mpenergies
> ===end code snippet
> Thanks a lot
> --
> Paulo E. Abreu
> Professor Auxiliar
> Departamento de Química
> Faculdade de Ciências e Tecnologia da Universidade de Coimbra
>
> ------------------------------------------------------------------------------
> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> cclib-users mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>

[cclib-users] GAMESS-US and mpenergies

[Paulo E. A. <pau...@ci...>]

Hello,

I have been using cclib for my parsers and just noticed something odd about
GAMESS-US files with MP2 calculations.
According to http://cclib.sourceforge.net/wiki/index.php/Parsed_Data and
http://cclib.sourceforge.net/wiki/index.php/Mpenergies
this is available for GAMESS-US output files. The problem is that I cannot
access this information. The logging after parsing the file
does not show any mpenergies and consequently when I try to use it I get an
error

AttributeError: 'ccData' object has no attribute 'mpenergies'

Is there something which I am missing here ?

===begin code snippet
myfile = ccopen("mp2.out")
data = myfile.parse()
print data.mpenergies
===end code snippet
Thanks a lot

-- 
Paulo E. Abreu
Professor Auxiliar
Departamento de Química
Faculdade de Ciências e Tecnologia da Universidade de Coimbra

Re: [cclib-users] GaussSum/cclib once more

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

2009/11/24 Xaver Wurzenberger <xav...@we...>:
> Hi,
>> It can handle anything that *behaves* like a file. So you need to
>> convert your string to a StringIO.StringIO. I use this trick myself to
>> read strings.
>
> perfect, that's what I was looking for. BTW, it speeds up by just parsing e.
> g. one line instead of a whole log file in my case.
>
> Three more questions:
>
> - There's no information extracted about the "steps" needed to get SCF
> convergence, right? Gaussian seems to mix up the words steps and cycles. What
> I mean is not the number of geometry points=SCF energies but the numer of
> iterations made to get one SCF energy. Gaussian writes this in the log file
> as
>  SCF Done:  E(UB+HF-LYP) =  -1721.919     a.u. after   31 cycles
> (and I want the 31). Could this be included in a future release?

These values are available as the dimension of the arrays in
scfvalues: http://cclib.sourceforge.net/wiki/index.php/Scfvalues

> - What about having the SCF energy array also contain E/Hartree and E/kJ/mol
> as second and third column?

We store a single value in a defined unit. You can convert the values
using our handy converter (cclib.parser.utils.convertor or something).

> - What is the best way to tell from ccopen() which calculation type (Gaussian,
> GAMESS, ...) it recognized? There's no field for that, right?

To check whether object A is an instance of class B, use isinstance(A)
== B. B in this case would be gaussianparser.GaussianParser or so.

Hope this helps. BTW, could you cc cclib questions to our mailing list.

- Noel

> Thanks,
> Xaver
>
>
> Am Tuesday 24 November 2009 09:57:47 schrieben Sie:
>> Hell Xaver,
>>
>> 2009/11/23 Xaver Wurzenberger <xav...@we...>:
>> > Hi Noel,
>> >
>> > in case you don't remember me, I'm the guy who kept thinking about
>> > forking GaussSum in the spring this year and finally decided to just do
>> > his own thing ;-)
>> > I hope you're fine... you seem to, as I saw a pretty recent GaussSum
>> > version a few days ago. So your making-gausssum-rock-stable-project is
>> > moving foward! For me, it has been as with a lot of projects in my life,
>> > I start overly- motivated, oversize it all a little, and am out of power
>> > at 85% progress of the thing *g But this time, I'm gonna finish it and
>> > half a year later, I'm back at it. To my defense, I had to publish a
>> > (hopefully) big paper in the mean time, as an academic you'll know what I
>> > mean.
>>
>> Of course :-)
>>
>> > But enough chit-chat, I am of course writing to get a little help from
>> > you once more! I admit this light-heartedly, because I honestly belief
>> > that someday I'll repay by contributing to cclib or some other cc open
>> > source project.
>> > As for the former, I am once more thinking about using it. Since you're
>> > the first name on the cclib page, I think these questions are rightly
>> > adressed at you (sometimes my english is funny, I know ;-) ):
>> > Is - or will be - cclib able to parse
>> > a) simple text/strings or just files? Could I trick it by writing my
>> > snippet into a temp file?
>>
>> It can handle anything that *behaves* like a file. So you need to
>> convert your string to a StringIO.StringIO. I use this trick myself to
>> read strings.
>>
>> > b) for only specific data, say, SCF energies?
>> > What might be the pitfalls? Could small source code changes make it
>> > possible?
>>
>> This isn't possible. We go through the whole file once, and use "if"
>> statements to find matches. You could simply comment out many of the
>> "if" statements and see if it still works. In many cases it will. The
>> speed will improve somewhat.
>>
>> > Both is in the end intended to drastically reduce parsing time.
>>
>> I can't see how step (a) would speed anything up, but (b) will have
>> some effect.
>>
>> > BTW, does testall.py of cclib have to pass every test with OK? Because I
>> > got some fails and errors:
>> > ********* SUMMARY OF EVERYTHING **************
>> > TOTAL: 522      PASSED: 492     FAILED: 6       ERRORS: 3       SKIPPED:
>> > 21 Are these bugs, should I send them to the sourceforge tracker?
>>
>> They aren't really bugs, but I forget what they are. There's no need
>> to file them as bugs.
>>
>> > Regards,
>> > Xaver
>
>
>

Re: [cclib-users] testing

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

I added this conditional import in revision 874, so this particular issue 
should be fixed in the trunk. That does not mean, however, that we support 
old Pythons!

Karol

On Friday 16 October 2009 13:40:47 Noel O'Boyle wrote:
> You are using an old version of Python, Python2.3. I think we only
> support Python 2.4+. However, if you want to fix this particular
> problem add the following to the start of logfileparser.py:
>
> from sets import Set as set
>
> - Noel
>
> 2009/10/16 ANUP THOMAS <anu...@gm...>:
> > Dear all.
> >
> >  i am new to cclib
> >
> > After installing cclib for running  the unit tests i executed the
> > following command
> >
> > python testall.py
> > but i am getting an error
> >
> >  File "/usr/lib/python2.3/site-packages/cclib/parser/logfileparser.py",
> > line 100, in parse
> >     _nodelete = list(set(self.__dict__.keys()))
> > NameError: global name 'set' is not defined
> >
> > What will be the probable cause  of this error. Thank you for
> > consideration. --
> > Regards
> >
> > Anup Thomas
> > SRF 7123
> > Computational Chemistry Lab of I and PC Division
> > Indian Institute of Chemical Technology
> > Hyderabad 500007
> > India

-- 
written by Karol Langner
Wed Oct 21 14:33:21 CEST 2009

Re: [cclib-users] testing

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

You are using an old version of Python, Python2.3. I think we only
support Python 2.4+. However, if you want to fix this particular
problem add the following to the start of logfileparser.py:

from sets import Set as set

- Noel

2009/10/16 ANUP THOMAS <anu...@gm...>:
> Dear all.
>
>  i am new to cclib
>
> After installing cclib for running  the unit tests i executed the following
> command
>
> python testall.py
> but i am getting an error
>
>  File "/usr/lib/python2.3/site-packages/cclib/parser/logfileparser.py", line
> 100, in parse
>     _nodelete = list(set(self.__dict__.keys()))
> NameError: global name 'set' is not defined
>
> What will be the probable cause  of this error. Thank you for consideration.
> --
> Regards
>
> Anup Thomas
> SRF 7123
> Computational Chemistry Lab of I and PC Division
> Indian Institute of Chemical Technology
> Hyderabad 500007
> India
>
> ------------------------------------------------------------------------------
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> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>

[cclib-users] testing

[ANUP T. <anu...@gm...>]

Dear all.

 i am new to cclib

After installing cclib for running  the unit tests i executed the following
command

python testall.py
 but i am getting an error

 File "/usr/lib/python2.3/site-packages/cclib/parser/logfileparser.py", line
100, in parse
    _nodelete = list(set(self.__dict__.keys()))
NameError: global name 'set' is not defined

What will be the probable cause  of this error. Thank you for consideration.

-- 
Regards

Anup Thomas
SRF 7123
Computational Chemistry Lab of I and PC Division
Indian Institute of Chemical Technology
Hyderabad 500007
India

Re: [cclib-users] Problems parsing Gaussian03 TD-DFT calc.

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

On Friday 25 September 2009 06:18:08 Steve George wrote:
> I am trying to generate the UV-Vis spectra from a Gaussian03 .log
> file.  I was able to do this in Gausssum 2.1.4, but get parsing errors
> from cclib in 2.1.6.
>
> Any help would be appreciated.
>
> Steve George

I think Noel will be the best person to help you. However, if you could 
show us the log file and place it in the public domain, we could also use 
it for regression testing and fix the supposed bug in cclib.

Chers,
Karol

-- 
written by Karol Langner
Fri Sep 25 09:57:52 CEST 2009

[cclib-users] Problems parsing Gaussian03 TD-DFT calc.

[Steve G. <spg...@uc...>]

I am trying to generate the UV-Vis spectra from a Gaussian03 .log  
file.  I was able to do this in Gausssum 2.1.4, but get parsing errors  
from cclib in 2.1.6.

Any help would be appreciated.

Steve George 
  

Re: [cclib-users] Forces from gaussian job (feature request)

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

Uh, seems I skipped over this part of the thread. Sorry for overlapping 
comments.

Karol

On Monday 18 May 2009 17:32:11 Noel O'Boyle wrote:
> In that case, for sure we'd welcome the code.
>
> - Noel
>
> 2009/5/16 Hugh Chaffey-Millar <hug...@ch...>:
> > On Friday 15 May 2009 15:01:09 Noel O'Boyle wrote:
> >> Looking at http://cclib.sourceforge.net/wiki/index.php/Parsed_Data,
> >> there's the hessian. Is this what you're looking for?
> >
> > No. I'm looking for the vector dE/dx, i.e. the first derivatives of the
> > energy with respect to atomic coordinates.
> >
> > Regard
> > Hugh

-- 
written by Karol Langner
Fri Jun 12 00:56:16 CEST 2009

Re: [cclib-users] g03 oniom

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

Hello Manuel,

Can you send us a public domain test file so we can see what the problem is?

Are you saying that there is a bug, or are you requesting a new feature?

Regards,
    Noel

2009/6/4 Manuel Melle Franco <man...@gm...>:
> Dear Users,
>
> Any chance of parsing g03 output in oniom calculations in the future?
>
> if not, do you think is it feasible to modify the existing parser to add the
> funcionality?
>
> best 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,
> Investigador Auxiliar do Requimte
> Chemistry Department
> Faculty of Sciences
> University of Porto
> Rua do Campo Alegre,687
> 4169-007 Porto
> Portugal.
> Portuguese mobile : 00351-918817917
> Portuguese work    : 00351-220402526
> Spanish mobile:     : 0034-651754516
> Italian mobile:        : 0039-3283647205
>
> ---------------------------------------------------------
>
> A mind all logic is like a knife all blade. It makes the hand bleed that
> uses it.
> Rabindranath Tagore
>
> ---------------------------------------------------------
>
> ------------------------------------------------------------------------------
> OpenSolaris 2009.06 is a cutting edge operating system for enterprises
> looking to deploy the next generation of Solaris that includes the latest
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> _______________________________________________
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> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-users
>
>

[cclib-users] g03 oniom

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

Dear Users,

Any chance of parsing g03 output in oniom calculations in the future?

if not, do you think is it feasible to modify the existing parser to add the
funcionality?

best 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,
Investigador Auxiliar do Requimte
Chemistry Department
Faculty of Sciences
University of Porto
Rua do Campo Alegre,687
4169-007 Porto
Portugal.
Portuguese mobile : 00351-918817917
Portuguese work    : 00351-220402526
Spanish mobile:     : 0034-651754516
Italian mobile:        : 0039-3283647205

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

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

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