cclib-devel — Developer's mailing list

[cclib-devel] svn status

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

When I run 'svn status' in my cclib trunk, I get:

?      data/ADF/ADF2006.01

This directory was created by the script that download the regression files. 
How come the other regression file paths don't appear here, only this one?

Karol

-- 
written by Karol Langner
Fri Mar 23 12:16:53 CET 2007

Re: [cclib-devel] CCL:G: ANN: cclib 0.7 released

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

Cher Jerome,

On 22/03/07, Jerome Kieffer <jer...@te...> wrote:
>
> Interresting ...
> but it crashes on a Jaguar 6.5 out-file :(
Schrodinger has just given cclib a year's licence for Jaguar 6.5.
However, we haven't had any access to Jaguar for the last six months
so, as you found, the parser is not quite 100% bug-free. :-)

Could you describe the error message that occurs, and  send me a .zip
file of the input and output file that caused the problem? Please note
that by sending me these files, you agree to place these files in the
public domain (i.e. freely accessible to anyone). If you are not happy
with this, please send me some other test file that exhibits the same
problem, and which you *are* happy to place in the public domain.

> I wrote a wrapper to read =ABCAChe=BB CSF files, but it is neither
> complete, nor =ABpublishable=BB as my code is rather ugly. Nevertheless
> you could be interested in incorporating it in a futur release of CClib.
We are always interested in expanding cclib. However, since none of
the core developers have access to CAChe, you would have to get
involved to maintain that code (I assume the code is written in
Python?). If you are interested, we would be happy to help you get
involved and 'show you the ropes'.

...the only problem is, after some googling I cannot find out whether
CAChe is still available. It seems like CAChe Scientific by bought by
Oxford Molecular which was bought by Accelrys...but I don't know what
has happened to the CAChe software. Here is the Accelrys page:
   http://www.accelrys.com/solutions/compchem/

Anyway, send me the bug report and we'll sort that out...

Regards,
   Noel

> Regards.
> --
> J=E9r=F4me KIEFFER  : http://www.terre-adelie.org
>

Re: [cclib-devel] Release of 0.7 final

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

On Wednesday 21 of March 2007 18:59, Adam Tenderholt wrote:
> > As ever if you feel strongly, I can work on those bugs tonight
> > instead...I will probably take a look in any case. Otherwise, we can
> > do a 0.71 release at a later date, which will just contain bug fixes -
> > at least this will allow us to start on the refactoring necessary for
> > 0.8.
>
> I don't feel strongly about it. And now that I think about it, there
> are two (minor) problems with the ADF parser: we haven't added
> support for the 2006.01 version or spin-orbit calculations. Fixing
> the first is like adding support for a new parse, while fixing the
> second is like adding support for a completely different type of
> calculation (eg. mp energies). Both of which should be minor updates
> as they involve slight modifications to our current adf parser and
> can go in a 0.7.1 release.
>
> Adam

I'm all for getting 0.7 out as soon as possible and later releasing 0.7.1 - 
that would probably make the fixes more solid. I'll be happy to help with the 
ADF parser, too, especially since I've been wanting to start using the 
program for a while now. In my case, I will have a some more time to spare 
for cclib after Friday.

Karol

-- 
written by Karol Langner
Wed Mar 21 23:02:32 CET 2007

[cclib-devel] ANN: cclib 0.7 released

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

cclib 0.7 is now available for download from http://cclib.sf.net.

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

Among other data, cclib extracts:

    * coordinates
    * atomic orbital information
    * molecular orbital information
    * information on vibrational modes
    * the results of a TD-DFT calculation

(For a complete list see http://cclib.sf.net/wiki/index.php/Parsed_Data).

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

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

(For a complete list see
http://cclib.sf.net/wiki/index.php/Calculation_Methods).

For information on how to use cclib, see
      http://cclib.sf.net/wiki/index.php/Using_cclib.

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

Regards,

 The cclib development team

Re: [cclib-devel] Release of 0.7 final

[Adam T. <a-t...@st...>]

> As ever if you feel strongly, I can work on those bugs tonight
> instead...I will probably take a look in any case. Otherwise, we can
> do a 0.71 release at a later date, which will just contain bug fixes -
> at least this will allow us to start on the refactoring necessary for
> 0.8.

I don't feel strongly about it. And now that I think about it, there  
are two (minor) problems with the ADF parser: we haven't added  
support for the 2006.01 version or spin-orbit calculations. Fixing  
the first is like adding support for a new parse, while fixing the  
second is like adding support for a completely different type of  
calculation (eg. mp energies). Both of which should be minor updates  
as they involve slight modifications to our current adf parser and  
can go in a 0.7.1 release.

Adam

Re: [cclib-devel] Release of 0.7 final

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

Well...in an ideal world yes, but my ideals are starting to become
more pragmatic :-) I have time tonight to get things done, which I
won't have for the next few days. Also, I think we should try and
stick to a reasonably timely release schedule even if it means that
particular bugs don't make it.

As ever if you feel strongly, I can work on those bugs tonight
instead...I will probably take a look in any case. Otherwise, we can
do a 0.71 release at a later date, which will just contain bug fixes -
at least this will allow us to start on the refactoring necessary for
0.8.

Regards,
   Noel

On 21/03/07, Adam Tenderholt <a-t...@st...> wrote:
> You didn't want to wait until the ADF bugs were fixed?
>
> Noel O'Boyle wrote:
> > I plan to create a release of 0.7 final this evening. To be safe, I'm
> > going to apply the minimum number of patches:
> >
> > r574, r575 which are basically documentation patches (but welcome all
> > the same :-) )
> >
> > This release will be announced on the CCL, so we might even get some feedback.
> >
> > Regards,
> >    Noel
> >
> > -------------------------------------------------------------------------
> > Take Surveys. Earn Cash. Influence the Future of IT
> > Join SourceForge.net's Techsay panel and you'll get the chance to share your
> > opinions on IT & business topics through brief surveys-and earn cash
> > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> > _______________________________________________
> > cclib-devel mailing list
> > ccl...@li...
> > https://lists.sourceforge.net/lists/listinfo/cclib-devel
>

Re: [cclib-devel] Release of 0.7 final

[Adam T. <a-t...@st...>]

You didn't want to wait until the ADF bugs were fixed?

Noel O'Boyle wrote:
> I plan to create a release of 0.7 final this evening. To be safe, I'm
> going to apply the minimum number of patches:
> 
> r574, r575 which are basically documentation patches (but welcome all
> the same :-) )
> 
> This release will be announced on the CCL, so we might even get some feedback.
> 
> Regards,
>    Noel
> 
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
> opinions on IT & business topics through brief surveys-and earn cash
> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> _______________________________________________
> cclib-devel mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-devel

[cclib-devel] Release of 0.7 final

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

I plan to create a release of 0.7 final this evening. To be safe, I'm
going to apply the minimum number of patches:

r574, r575 which are basically documentation patches (but welcome all
the same :-) )

This release will be announced on the CCL, so we might even get some feedback.

Regards,
   Noel

Re: [cclib-devel] jaguar on krypton

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

> On a related note - is the plan to repeat all the Jaguar tests for the current
> version and replace the test files in the trunk?

I guess so - doesn't this seem reasonable. And also, to fill any gaps
in our Jaguar coverage.

> Karol
>
> --
> written by Karol Langner
> Tue Mar 20 17:59:43 CET 2007
>

Re: [cclib-devel] ADF output error again

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

On Tuesday 20 of March 2007 22:29, Adam Tenderholt wrote:
> > OK, I see that now, but don't know how to fix it. I did just submit
> > a little
> > fix for the code that parses mocoeff, although I'm not sure I relly
> > fixed
> > anything (looks nicer, though).
>
> Nor do I. I'm a bit busy right now, but I'll keep it in the back of
> my mind and hopefully think of a fix soon.
>
> Adam

I have an idea. There is a "SYMMETRY, ELECTRONS" section in the output, in two 
places - the second one is after building the fragments or something(?). 
Anyways, it looks like this the second time around for Nuno's "Au2.out":

=====================================
 S Y M M E T R Y ,   E L E C T R O N S
 =====================================
  
 Symmetry: D(LIN)

 Irreducible Representations, including subspecies
 -------------------------------------------------
 SIGMA.g
 SIGMA.u
 PI.g:x  PI.g:y
 PI.u:x  PI.u:y
 DELTA.g:x2-y2  DELTA.g:xy
 DELTA.u:x2-y2  DELTA.u:xy
 PHI.g:x3-3xy2  PHI.g:3x2y-y3
 PHI.u:x3-3xy2  PHI.u:3x2y-y3

...which should work nicely for counting the number of irreducible 
representations, I think.

I don't think I understand where the mocoeffs are read in for ADF, though..... 
the attribute, together with mosyms, is parsed when "Orbital Energies, all 
Irreps" is found on some line - and this, again, happens twice. As it turns 
out, the second one is not parsed (there's an 'and not hasattr(self, 
"mosyms")' addition to the parsing condition. Is this correct? I wonder, 
because these energies are different, and the MO coefficients are printed 
only once, after the second MO energies output. This is all because I'm not 
oriented much with ADF.

Karol

-- 
written by Karol Langner
Tue Mar 20 22:45:10 CET 2007

Re: [cclib-devel] ADF output error again

[Adam T. <a-t...@st...>]

> OK, I see that now, but don't know how to fix it. I did just submit  
> a little
> fix for the code that parses mocoeff, although I'm not sure I relly  
> fixed
> anything (looks nicer, though).

Nor do I. I'm a bit busy right now, but I'll keep it in the back of  
my mind and hopefully think of a fix soon.

Adam

Re: [cclib-devel] ADF output error again

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

On Tuesday 20 of March 2007 21:57, Adam Tenderholt wrote:
> > For "Au2.out", besides the code that parses mocoeffs failing (the
> > new output
> > files don't have two lines of comment that were there before),
> > there seems to
> > be a problem with the number of MOs. Adding some debugging code
> > before the
> >
> > mocoeffs section gives this:
> >>> from cclib.parser import ccopen
> >>> a = ccopen("Au2.out")
> >>> a.parse()
> >
> > nbasis: 108
> > len(moenergies[0]) 170
> > len(mosyms[0]) 170
> > mosyms: [['SIGMAg', 'SIGMAu', 'SIGMAg', 'SIGMAu', 'PIu', 'PIu', 'PIu',
> >  ....... more lines .....
> >  'SIGMAg', 'SIGMAu']]
>
> I think it's not correctly adding up the degeneracies of orbitals for
> SIGMA, PI, and DELTA symmetries. In the "all Irreps" section, where
> moenergies and mosyms are set, you have to know that PI (x and y
> "sub"-symmetries) and DELTA (xy and x2-y2 "sub"-symmetries) orbitals
> are degenerate (occupations with 4 electrons are allowed) and I'm
> guessing it's not adding this section up correctly. The mocoeffs
> section (and nbasis section) already splits this up, so nbasis == 108
> is correct and len(moenergies) == 170 is probably wrong.

OK, I see that now, but don't know how to fix it. I did just submit a little 
fix for the code that parses mocoeff, although I'm not sure I relly fixed 
anything (looks nicer, though).

> > Hope this helps somehow,
>
> It does. I didn't realize that the parser was this broken. I'll try
> to get around running this file in ADF2004.01 and see if we have a
> similar problem. My guess is we do because I don't work with linear
> molecules and so this case wasn't expected.
>
> Adam

-- 
written by Karol Langner
Tue Mar 20 22:18:34 CET 2007

Re: [cclib-devel] ADF output error again

[Adam T. <a-t...@st...>]

> For "Au2.out", besides the code that parses mocoeffs failing (the  
> new output
> files don't have two lines of comment that were there before),  
> there seems to
> be a problem with the number of MOs. Adding some debugging code  
> before the
> mocoeffs section gives this:
>
>>> from cclib.parser import ccopen
>>> a = ccopen("Au2.out")
>>> a.parse()
> nbasis: 108
> len(moenergies[0]) 170
> len(mosyms[0]) 170
> mosyms: [['SIGMAg', 'SIGMAu', 'SIGMAg', 'SIGMAu', 'PIu', 'PIu', 'PIu',
>  ....... more lines .....
>  'SIGMAg', 'SIGMAu']]

I think it's not correctly adding up the degeneracies of orbitals for  
SIGMA, PI, and DELTA symmetries. In the "all Irreps" section, where  
moenergies and mosyms are set, you have to know that PI (x and y  
"sub"-symmetries) and DELTA (xy and x2-y2 "sub"-symmetries) orbitals  
are degenerate (occupations with 4 electrons are allowed) and I'm  
guessing it's not adding this section up correctly. The mocoeffs  
section (and nbasis section) already splits this up, so nbasis == 108  
is correct and len(moenergies) == 170 is probably wrong.

> Hope this helps somehow,

It does. I didn't realize that the parser was this broken. I'll try  
to get around running this file in ADF2004.01 and see if we have a  
similar problem. My guess is we do because I don't work with linear  
molecules and so this case wasn't expected.

Adam

Re: [cclib-devel] ADF output error again

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

I'm not too well familiar with ADF, but also tried running Nuno's files 
through the parser.

For "Au2.out", besides the code that parses mocoeffs failing (the new output 
files don't have two lines of comment that were there before), there seems to 
be a problem with the number of MOs. Adding some debugging code before the 
mocoeffs section gives this:

>>from cclib.parser import ccopen
>>a = ccopen("Au2.out")
>>a.parse()
nbasis: 108
len(moenergies[0]) 170
len(mosyms[0]) 170
mosyms: [['SIGMAg', 'SIGMAu', 'SIGMAg', 'SIGMAu', 'PIu', 'PIu', 'PIu', 
 ....... more lines .....
 'SIGMAg', 'SIGMAu']]
[ADF Au2.out INFO] Creating attribute mocoeffs: array[]
Traceback (most recent call last):
  File "./test", line 6, in <module>
    a.parse()
  File 
"/home/langner/apps/python/lib/python2.5/site-packages/cclib/parser/logfileparser.py", 
line 118, in parse
    self.extract(inputfile, fupdate=fupdate, cupdate=cupdate)
  File 
"/home/langner/apps/python/lib/python2.5/site-packages/cclib/parser/adfparser.py", 
line 696, in extract
    self.mocoeffs[spin][aolist[i+base], row + symoffset] = float(cols[i + 1])
IndexError: invalid index

Notice that there are more MOs than basis functions (SFOs for ADF, I guess). 
Is this norml? Now, since mocoeffs is created as Numeric.zeros((self.nbasis, 
self.nbasis), "d") there will always be a problem with filling it in this 
particular case.

Hope this helps somehow,
Karol

-- 
written by Karol Langner
Tue Mar 20 21:10:26 CET 2007

[cclib-devel] Fwd: Re: jaguar on krypton

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

On Monday 19 of March 2007 15:16, you wrote:
> With Cygwin/X it worked faster, and there's no need for the "-SGL" if
> you use "ssh -Y" instead of "ssh -X" (presumably, this is also true
> for Linux).
>
> Noel

Yes, the same is true for Linux on my laptop, although  I probably won't be
using maestro.

On a related note - is the plan to repeat all the Jaguar tests for the
 current version and replace the test files in the trunk?

Karol

-- 
written by Karol Langner
Tue Mar 20 18:01:23 CET 2007

Re: [cclib-devel] downloadwiki.py

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

Still works for me.

Noel

On 19/03/07, Karol Langner <kar...@kn...> wrote:
> Yes, the problem is probably a different version - I have BeautifulSoup 1.1
> installed (the one Debian stable has in the repository. It works if I call
> the read() method on urllib.urlopen("....") first. I submitted that, but I'm
> not sure to what extent the problem is version-specific. If it fails for the
> newer version now (can you check?), I'll make a more specific fix.
>
> Karol
>
> On Sunday 18 of March 2007 20:03, Noel O'Boyle wrote:
> > Works for me. ??
> >
> > (1) I downloaded BeautifulSoup 3.0.3 from the web and placed it in my
> > cclib trunk directory.
> > (2) Running "python downloadwiki.py" (Python 2.4.3 on Windows) gives:
> > [u'Announce', u'Aonames', u'Aooverlaps', u'Atomcoords', u'Atomnos',
> > u'C_squared' , u'Calculation_Methods', u'Cclib', u'Changelog',
> > u'Charge_Decomposition_Analysi s', u'Cheesecake_index', u'Complife06',
> > u'Coreelectrons', u'Density', u'Develope rs', u'Development',
> > u'Development_methods', u'Development_parsed_data', u'Etene rgies',
> > u'Etsecs', u'Fonames', u'Fooverlaps', u'Gbasis', u'Geotargets', u'Geoval
> > ues', u'Hessian', u'Homos', u'Install', u'Instructions', u'Main_Page',
> > u'Mocoeff s', u'Moenergies', u'Mosyms', u'Mpenergies', u'Mulliken',
> > u'Natom', u'Nbasis', u 'Nmo', u'Parsed_Data', u'Parsed_data', u'Progress',
> > u'Scfenergies', u'Scftargets ', u'Scfvalues', u'Tests', u'Using_cclib',
> > u'Vibcarts', u'Vibdisps']
> >
> > and the file backup.xml is created.
> >
> > I assume the problem is a different version of BeautifulSoup. I will
> > doublecheck on Monday whether this works on Linux for me.
> >
> > On 09/03/07, Karol Langner <kar...@kn...> wrote:
> > > I can't seem to use the script downloadwiki.py. After installing
> > > BesutifulSoup, I get the following error:
> > >
> > > langner@slim:~/tmp/python/cclib/trunk$ python2.3 downloadwiki.py
> > > Traceback (most recent call last):
> > >   File "downloadwiki.py", line 8, in ?
> > >     soup = BeautifulSoup(allpages)
> > >   File "/usr/lib/python2.3/site-packages/BeautifulSoup.py", line 307, in
> > > __init__
> > >     self.feed(text)
> > >   File "/usr/lib/python2.3/site-packages/BeautifulSoup.py", line 310, in
> > > feed SGMLParser.feed(self, text)
> > >   File "/usr/lib/python2.3/sgmllib.py", line 94, in feed
> > >     self.rawdata = self.rawdata + data
> > > TypeError: cannot concatenate 'str' and 'instance' objects
> > >
> > > Does the script actually work?
> > >
> > > --
> > > written by Karol Langner
> > > Fri Mar  9 17:50:42 CET 2007
> > >
> > > -------------------------------------------------------------------------
> > > Take Surveys. Earn Cash. Influence the Future of IT
> > > Join SourceForge.net's Techsay panel and you'll get the chance to share
> > > your opinions on IT & business topics through brief surveys-and earn cash
> > > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> > > _______________________________________________
> > > cclib-devel mailing list
> > > ccl...@li...
> > > https://lists.sourceforge.net/lists/listinfo/cclib-devel
>
> --
> written by Karol Langner
> Mon Mar 19 11:10:03 CET 2007
>

Re: [cclib-devel] Mediawiki and equations/images

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

On Sunday 18 of March 2007 19:57, Noel O'Boyle wrote:
> (Regarding instant message question from Karol)
>
> Mediawiki on sourceforge is a pain to set up. I was happy to get it
> working in the first place (after several attempts).
>
> OpenBabel have both images and equations working: see for example,
> http://openbabel.sourceforge.net/wiki/OBForceFieldGhemical
>
> I am not really interested in spending more time on configuring
> Mediawiki, especially as I am worried about losing all of the wiki
> data. Feel free to experiment yourself if you feel confident, although
> let me know if you are trying something major so that I can export the
> database.

Why are you worried about losing all of the wiki data?

I have set up a few mediawikis in the past, but if it's a pain on sourceforge 
then I'm also not eager to spend time on it. On the other hand, if OpenBabel 
has it working, then shouldn't it be possible to simply copy their 
configuration?

I'm often frustrated by the speed at which the wiki works...

> P.S. I haven't yet checked the exportwiki python script. It did work;
> the problem may be due to categories, which weren't present when I
> wrote the script.

-- 
written by Karol Langner
Mon Mar 19 10:45:13 CET 2007

Re: [cclib-devel] downloadwiki.py

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

Yes, the problem is probably a different version - I have BeautifulSoup 1.1 
installed (the one Debian stable has in the repository. It works if I call 
the read() method on urllib.urlopen("....") first. I submitted that, but I'm 
not sure to what extent the problem is version-specific. If it fails for the 
newer version now (can you check?), I'll make a more specific fix.

Karol

On Sunday 18 of March 2007 20:03, Noel O'Boyle wrote:
> Works for me. ??
>
> (1) I downloaded BeautifulSoup 3.0.3 from the web and placed it in my
> cclib trunk directory.
> (2) Running "python downloadwiki.py" (Python 2.4.3 on Windows) gives:
> [u'Announce', u'Aonames', u'Aooverlaps', u'Atomcoords', u'Atomnos',
> u'C_squared' , u'Calculation_Methods', u'Cclib', u'Changelog',
> u'Charge_Decomposition_Analysi s', u'Cheesecake_index', u'Complife06',
> u'Coreelectrons', u'Density', u'Develope rs', u'Development',
> u'Development_methods', u'Development_parsed_data', u'Etene rgies',
> u'Etsecs', u'Fonames', u'Fooverlaps', u'Gbasis', u'Geotargets', u'Geoval
> ues', u'Hessian', u'Homos', u'Install', u'Instructions', u'Main_Page',
> u'Mocoeff s', u'Moenergies', u'Mosyms', u'Mpenergies', u'Mulliken',
> u'Natom', u'Nbasis', u 'Nmo', u'Parsed_Data', u'Parsed_data', u'Progress',
> u'Scfenergies', u'Scftargets ', u'Scfvalues', u'Tests', u'Using_cclib',
> u'Vibcarts', u'Vibdisps']
>
> and the file backup.xml is created.
>
> I assume the problem is a different version of BeautifulSoup. I will
> doublecheck on Monday whether this works on Linux for me.
>
> On 09/03/07, Karol Langner <kar...@kn...> wrote:
> > I can't seem to use the script downloadwiki.py. After installing
> > BesutifulSoup, I get the following error:
> >
> > langner@slim:~/tmp/python/cclib/trunk$ python2.3 downloadwiki.py
> > Traceback (most recent call last):
> >   File "downloadwiki.py", line 8, in ?
> >     soup = BeautifulSoup(allpages)
> >   File "/usr/lib/python2.3/site-packages/BeautifulSoup.py", line 307, in
> > __init__
> >     self.feed(text)
> >   File "/usr/lib/python2.3/site-packages/BeautifulSoup.py", line 310, in
> > feed SGMLParser.feed(self, text)
> >   File "/usr/lib/python2.3/sgmllib.py", line 94, in feed
> >     self.rawdata = self.rawdata + data
> > TypeError: cannot concatenate 'str' and 'instance' objects
> >
> > Does the script actually work?
> >
> > --
> > written by Karol Langner
> > Fri Mar  9 17:50:42 CET 2007
> >
> > -------------------------------------------------------------------------
> > Take Surveys. Earn Cash. Influence the Future of IT
> > Join SourceForge.net's Techsay panel and you'll get the chance to share
> > your opinions on IT & business topics through brief surveys-and earn cash
> > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> > _______________________________________________
> > cclib-devel mailing list
> > ccl...@li...
> > https://lists.sourceforge.net/lists/listinfo/cclib-devel

-- 
written by Karol Langner
Mon Mar 19 11:10:03 CET 2007

Re: [cclib-devel] Mediawiki and equations/images

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

On 19/03/07, Karol Langner <kar...@kn...> wrote:
> On Sunday 18 of March 2007 19:57, Noel O'Boyle wrote:
> > (Regarding instant message question from Karol)
> >
> > Mediawiki on sourceforge is a pain to set up. I was happy to get it
> > working in the first place (after several attempts).
> >
> > OpenBabel have both images and equations working: see for example,
> > http://openbabel.sourceforge.net/wiki/OBForceFieldGhemical
> >
> > I am not really interested in spending more time on configuring
> > Mediawiki, especially as I am worried about losing all of the wiki
> > data. Feel free to experiment yourself if you feel confident, although
> > let me know if you are trying something major so that I can export the
> > database.
>
> Why are you worried about losing all of the wiki data?
I have never reimported the wiki database, so I have no idea whether
it works or whether I am using the correct export options.

> I have set up a few mediawikis in the past, but if it's a pain on sourceforge
> then I'm also not eager to spend time on it. On the other hand, if OpenBabel
> has it working, then shouldn't it be possible to simply copy their
> configuration?
I think you will understand better the problems if you try to
configure the wiki yourself, although if you have experience with
mediawiki you may find it easier than I did. I think you will need
some passwords and permissions first though. Please let me know what
you need. Note that part of the problem setting up mediawiki on
sourceforge is that you need to use a series of workarounds as SF
prevents certain actions required by mediawiki. The series of
workarounds I used is slightly different than those used by OpenBabel.

> I'm often frustrated by the speed at which the wiki works...
I don't think anything can be done about this. OpenBabel is the same.
SF is good, but slow, even for html web sites with a few images.

> > P.S. I haven't yet checked the exportwiki python script. It did work;
> > the problem may be due to categories, which weren't present when I
> > wrote the script.
>
> --
> written by Karol Langner
> Mon Mar 19 10:45:13 CET 2007
>

Re: [cclib-devel] ADF output error again

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

On 18/03/07, Nuno A. G. Bandeira <nun...@is...> wrote:
> I just noticed, browsing through the ADF manual that SFO analysis is not
> produced with spin orbit runs so naturally there will be nothing for the
> parser to read in that case.

Even so, it's still a bug in cclib - the parser shouldn't exit with an error.

>
>
> --
> Nuno A. G. Bandeira, AMRSC
> Graduate researcher and molecular sculptor
> Inorganic and Theoretical Chemistry Group,
> Faculty of Science
> University of Lisbon - C8 building, Campo Grande,
> 1749-016 Lisbon,Portugal
> http://cqb.fc.ul.pt/intheochem/nuno.html
> Doctoral student @ IST,Lisbon
> --
>

Re: [cclib-devel] ADF output error again

[Nuno A. G. B. <nun...@is...>]

I just noticed, browsing through the ADF manual that SFO analysis is not 
produced with spin orbit runs so naturally there will be nothing for the 
parser to read in that case.



-- 
Nuno A. G. Bandeira, AMRSC
Graduate researcher and molecular sculptor
Inorganic and Theoretical Chemistry Group,
Faculty of Science
University of Lisbon - C8 building, Campo Grande,
1749-016 Lisbon,Portugal
http://cqb.fc.ul.pt/intheochem/nuno.html
Doctoral student @ IST,Lisbon
--

Re: [cclib-devel] ADF output error again

[Adam T. <a-t...@st...>]

Nuno,

 From what I can tell, the errors for the first file is related to  
ADF 2006.01 (I have yet to switch from 2004.01). The symmetry labels  
are uppercase in your test files, but our parser only looks for the  
first letter being capitalized. I'd guess this is a simple fix, but  
I'm not positive that there aren't other issues we'd have to deal with.

> Also spin orbit runs give another error message:
>
> Traceback (most recent call last):
>    File "PyMOlyze", line 28, in ?
>    File "pymolyze\pymolyze.pyc", line 140, in open
>    File "cclib\parser\adfparser.pyc", line 555, in parse
> IndexError: list index out of range

Spin orbit relativistic calculations print the info in a slightly  
different format than the non-relativistic and scalar relativistic  
calcs do. This may take a bit of time to write the extra parsing code.

Sorry for the inconvenience and thanks for reporting the bugs.

Adam

Re: [cclib-devel] ADF output error again

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

On 18/03/07, Nuno A. G. Bandeira <nun...@is...> wrote:
> Hi,
>
> Some months ago I'd emailed the development team sending some sample ADF
> outputs to improve cclib operability. Have they been used ? I don't see
> them on the present cclib distribution.
As discussed at the time (around 18/8/06), using your files we solved
several problems. However, the FeCl4.zip you sent (24/06/06) was
parsed correctly by cclib, and so was not included in the
distribution. Our policy is to only include those files that (at some
time) break our parser. Note that in any case you won't find these
files in the regular cclib-0.x download. Due to the size of the files,
they are provided separately (since they are mainly for testing
purposes) on the sourceforge download site
(http://www.sf.net/projects/cclib).

> Also I got this error message when running a simple ADF example file:
>
>
>     File "PyMOlyze", line 28, in ?
>     File "pymolyze\pymolyze.pyc", line 140, in open
>     File "cclib\parser\adfparser.pyc", line 728, in parse
> IndexError: invalid index
>
> The file is attached.
>
> Also spin orbit runs give another error message:
>
> Traceback (most recent call last):
>     File "PyMOlyze", line 28, in ?
>     File "pymolyze\pymolyze.pyc", line 140, in open
>     File "cclib\parser\adfparser.pyc", line 555, in parse
> IndexError: list index out of range

We will look into these...

> Any help would be appreciated. If you'd like more input files I can
> provide as many as you wish.
That's great - once we fix this bug, you could run 'ccget --list
*.adfout' over all of your adf files to see whether they are all
parsed without errors.

> Regards,
>
> --
> Nuno A. G. Bandeira, AMRSC
> Graduate researcher and molecular sculptor
> Inorganic and Theoretical Chemistry Group,
> Faculty of Science
> University of Lisbon - C8 building, Campo Grande,
> 1749-016 Lisbon,Portugal
> http://cqb.fc.ul.pt/intheochem/nuno.html
> Doctoral student @ IST,Lisbon
> --

[cclib-devel] ADF output error again

[Nuno A. G. B. <nun...@is...>]

Hi,

Some months ago I'd emailed the development team sending some sample ADF
outputs to improve cclib operability. Have they been used ? I don't see
them on the present cclib distribution.

Also I got this error message when running a simple ADF example file:


    File "PyMOlyze", line 28, in ?
    File "pymolyze\pymolyze.pyc", line 140, in open
    File "cclib\parser\adfparser.pyc", line 728, in parse
IndexError: invalid index

The file is attached.

Also spin orbit runs give another error message:

Traceback (most recent call last):
    File "PyMOlyze", line 28, in ?
    File "pymolyze\pymolyze.pyc", line 140, in open
    File "cclib\parser\adfparser.pyc", line 555, in parse
IndexError: list index out of range

Any help would be appreciated. If you'd like more input files I can 
provide as many as you wish.

Regards,

-- 
Nuno A. G. Bandeira, AMRSC
Graduate researcher and molecular sculptor
Inorganic and Theoretical Chemistry Group,
Faculty of Science
University of Lisbon - C8 building, Campo Grande,
1749-016 Lisbon,Portugal
http://cqb.fc.ul.pt/intheochem/nuno.html
Doctoral student @ IST,Lisbon
--

Re: [cclib-devel] downloadwiki.py

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

Works for me. ??

(1) I downloaded BeautifulSoup 3.0.3 from the web and placed it in my
cclib trunk directory.
(2) Running "python downloadwiki.py" (Python 2.4.3 on Windows) gives:
[u'Announce', u'Aonames', u'Aooverlaps', u'Atomcoords', u'Atomnos', u'C_squared'
, u'Calculation_Methods', u'Cclib', u'Changelog', u'Charge_Decomposition_Analysi
s', u'Cheesecake_index', u'Complife06', u'Coreelectrons', u'Density', u'Develope
rs', u'Development', u'Development_methods', u'Development_parsed_data', u'Etene
rgies', u'Etsecs', u'Fonames', u'Fooverlaps', u'Gbasis', u'Geotargets', u'Geoval
ues', u'Hessian', u'Homos', u'Install', u'Instructions', u'Main_Page', u'Mocoeff
s', u'Moenergies', u'Mosyms', u'Mpenergies', u'Mulliken', u'Natom', u'Nbasis', u
'Nmo', u'Parsed_Data', u'Parsed_data', u'Progress', u'Scfenergies', u'Scftargets
', u'Scfvalues', u'Tests', u'Using_cclib', u'Vibcarts', u'Vibdisps']

and the file backup.xml is created.

I assume the problem is a different version of BeautifulSoup. I will
doublecheck on Monday whether this works on Linux for me.

On 09/03/07, Karol Langner <kar...@kn...> wrote:
> I can't seem to use the script downloadwiki.py. After installing
> BesutifulSoup, I get the following error:
>
> langner@slim:~/tmp/python/cclib/trunk$ python2.3 downloadwiki.py
> Traceback (most recent call last):
>   File "downloadwiki.py", line 8, in ?
>     soup = BeautifulSoup(allpages)
>   File "/usr/lib/python2.3/site-packages/BeautifulSoup.py", line 307, in
> __init__
>     self.feed(text)
>   File "/usr/lib/python2.3/site-packages/BeautifulSoup.py", line 310, in feed
>     SGMLParser.feed(self, text)
>   File "/usr/lib/python2.3/sgmllib.py", line 94, in feed
>     self.rawdata = self.rawdata + data
> TypeError: cannot concatenate 'str' and 'instance' objects
>
> Does the script actually work?
>
> --
> written by Karol Langner
> Fri Mar  9 17:50:42 CET 2007
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
> opinions on IT & business topics through brief surveys-and earn cash
> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> _______________________________________________
> cclib-devel mailing list
> ccl...@li...
> https://lists.sourceforge.net/lists/listinfo/cclib-devel
>