cclib-devel Mailing List for cclib

Hi Adam,

1) Yes, this is an over sight on my behalf, i can easily add this.

2) AS you mention this is some what complicated. 

The for rigid scan case the calculation is basically a series of single point energies, and cclib correctly collects these coordinates in the atom coords section. For this case i suggest we copy the atomcoords array to a scancoords array for clarity and completeness.

The situation for a relaxed scan is much more complicated. 
Gaussian outputs the geometries as values for a z-matrix. While it is fairly simple to extract these values converting them into xyz coordinates this would require parsing the input z matrix and converting the z-matrix with open babel (i guess)
As the scan is now a series of optimisations cclib does not correctly collect all geometries as the parser halts after the first optimisation has completed.

I think the best solution for the relaxed scan problem is to avoid converting the z-mat and extent the code that searches for geometries to look for more than 1 optimisation step in scan jobs. My reasoning for choosing this option is that it avoids additional dependancies (open babel) and the coded would also be useful for other jobs that are expected to be a series of optimisations (IRC jobs for example).

I'll probably have some time over the next weekend to work on this code.

Yours

Ed Holland 
 
On 21 Jan 2012, at 18:06, Adam Tenderholt wrote:

> Hi Ed,
> 
> Thanks for the patch. Your changes look pretty straight-forward. A
> couple of questions:
> 
> 1) Do you think the names of the variables should also be stored? This
> would probably be important if it's a multi-dimensional scan.
> 2) Do you have interest in trying to parse the final xyz coordinates
> at each point? If I remember correctly, this is somewhat complicated
> but something that cclib should probably handle.
> 
> Thanks again,
> 
> Adam
> 
> 
> On Wed, Jan 18, 2012 at 7:14 AM, Edward Holland <hol...@ca...> wrote:
>> helps if i attach the file!!
>> 
>> 
>> 
>> On 18 Jan 2012, at 15:13, Edward Holland wrote:
>> 
>>> Hi All,
>>> 
>>> I've finally had some free time (read: I didn't want to write my thesis) to write the patch for extracting data from rigid scans in gaussian. I attach the patch, as you can see its fairly simple and I hope it fits with the coding style. If you have any questions please get in touch.
>>> 
>>> I've also been writing some code to extract data from IRC calculations in gaussian so if people are interested i could write another patch some time.
>>> 
>>> Yours
>>> 
>>> Ed Holland
>> 
>> 
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Hi Ed,

Thanks for the patch. Your changes look pretty straight-forward. A
couple of questions:

1) Do you think the names of the variables should also be stored? This
would probably be important if it's a multi-dimensional scan.
2) Do you have interest in trying to parse the final xyz coordinates
at each point? If I remember correctly, this is somewhat complicated
but something that cclib should probably handle.

Thanks again,

Adam


On Wed, Jan 18, 2012 at 7:14 AM, Edward Holland <hol...@ca...> wrote:
> helps if i attach the file!!
>
>
>
> On 18 Jan 2012, at 15:13, Edward Holland wrote:
>
>> Hi All,
>>
>> I've finally had some free time (read: I didn't want to write my thesis) to write the patch for extracting data from rigid scans in gaussian. I attach the patch, as you can see its fairly simple and I hope it fits with the coding style. If you have any questions please get in touch.
>>
>> I've also been writing some code to extract data from IRC calculations in gaussian so if people are interested i could write another patch some time.
>>
>> Yours
>>
>> Ed Holland
>
>
> ------------------------------------------------------------------------------
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Bugs item #3476063, was opened at 2012-01-19 06:23
Message generated for change (Comment added) made by langner
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=819222&aid=3476063&group_id=161285

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: None
Status: Open
>Resolution: Fixed
Priority: 5
Private: No
Submitted By: Karol Langner (langner)
Assigned to: Karol Langner (langner)
Summary: Failed hessian parsing for newer GAMESS-US

Initial Comment:
Chengju Wang reported this on the cclib-users list.

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

>Comment By: Karol Langner (langner)
Date: 2012-01-19 06:49

Message:
Fixed with commit r951. The log file now parses.

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=819222&aid=3476063&group_id=161285

Bugs item #3476063, was opened at 2012-01-19 06:23
Message generated for change (Tracker Item Submitted) made by langner
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=819222&aid=3476063&group_id=161285

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Karol Langner (langner)
Assigned to: Karol Langner (langner)
Summary: Failed hessian parsing for newer GAMESS-US

Initial Comment:
Chengju Wang reported this on the cclib-users list.

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=819222&aid=3476063&group_id=161285

helps if i attach the file!!

Hi All,

I've finally had some free time (read: I didn't want to write my thesis) to write the patch for extracting data from rigid scans in gaussian. I attach the patch, as you can see its fairly simple and I hope it fits with the coding style. If you have any questions please get in touch.

I've also been writing some code to extract data from IRC calculations in gaussian so if people are interested i could write another patch some time.

Yours

Ed Holland

Any thoughts? It's a bit hard since we don't have the actual logfile.

Adam



Begin forwarded message:

> From: Chengju Wang <fra...@gm...>
> Date: January 12, 2012 11:20:05 PM PST
> To: Adam Tenderholt <ate...@gm...>
> Cc: ccl...@li...
> Subject: Re: [cclib-users] cclib.method
> 
> Hi, Adam and other folks.
> 
> Attached please find the requested file, which was given by
> "
> >>> f=open("aonames.txt",'w')
> >>> import pickle
> >>> pickle.dump(ps.aonames,f)
> >>> f.close()
> "
> following the previous email.
> 
> By tail this file, one will get
> " tail aonames.txt
> p3711
> aS'H40_S'
> p3712
> aS'H40_X'
> p3713
> aS'H40_Y'
> p3714
> aS'H40_Z'
> p3715
> a."
> 
> This file is incomplete. I think this is problem but I don't how to solve it. :P
> 
> thanks for your attention.
> 
> Best.
> 
> Chengju
> 
> On Wed, Jan 4, 2012 at 3:24 PM, Adam Tenderholt <ate...@gm...> wrote:
> Hi Chengju,
> 
> Sorry for the late reply. Your error is a bit odd, and I'm not sure
> where the code is failing. Can you send us the aonames parsed by
> cclib? If that's not available, send fonames.
> 
> Cheers,
> 
> Adam
> 
> 
> On Thu, Dec 29, 2011 at 9:30 PM, Chengju Wang
> <fra...@gm...> wrote:
> > Dear all.
> >
> > I hope someone here can help me to analysis my GAMESS log file. Thank you.
> >
> > I tried to use cclib to extract the pdos, but have met with the following
> > problem.
> >
> >  >>> from cclib.parser import GAMESS
> >  >>> from cclib.method import CSPA
> >  >>> s=GAMESS("test.log")
> >  >>> ps=s.parse()
> >  [GAMESS test.log INFO] Creating attribute atomcoords[]
> >  [GAMESS test.log INFO] Creating attribute atomnos[]
> >  [GAMESS test.log INFO] Creating attribute gbasis[]
> >  [GAMESS test.log INFO] Creating attribute nbasis: 2343
> >  [GAMESS test.log INFO] Creating attribute charge: 0
> >  [GAMESS test.log INFO] Creating attribute mult: 1
> >  [GAMESS test.log INFO] Creating attribute homos[]
> >  [GAMESS test.log INFO] Creating attribute natom: 340
> >  [GAMESS test.log INFO] Creating attribute aooverlaps[]
> >  [GAMESS test.log INFO] Creating attribute scftargets[]
> >  [GAMESS test.log INFO] Creating attribute scfvalues[]
> >  [GAMESS test.log INFO] Creating attribute scfenergies[]
> >  [GAMESS test.log INFO] Creating attribute moenergies[]
> >  [GAMESS test.log INFO] Creating attribute mosyms[]
> >  [GAMESS test.log INFO] Creating attribute nmo: 2343
> >  [GAMESS test.log INFO] Creating attribute mocoeffs[]
> >  [GAMESS test.log INFO] Creating attribute atombasis[]
> >  [GAMESS test.log INFO] Creating attribute aonames[]
> >  [GAMESS test.log INFO] Creating attribute coreelectrons[]
> >  >>> m=CSPA(ps)
> >  >>>>>> len(m.fragresults[0])
> >  2343
> >  >>> len(m.fragresults[0][0])
> >  204
> >
> > Why is it not 340 here?
> >
> >
> > Sorry, the log file is too big to be attached.
> >
> >
> > My input key words:
> >
> >  $CONTRL SCFTYP=RHF RUNTYP=ENERGY MAXIT=60 MULT=1 $END
> >  $CONTRL MOLPLT=.TRUE. PLTORB=.TRUE. NPRINT=3 $END
> >  $SYSTEM TIMLIM=525600 MWORDS=9000 $END
> >  $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END
> >  $SCF DIRSCF=.TRUE. $END
> >  $STATPT OPTTOL=0.0001 NSTEP=2000 $END
> >  $DATA
> >
> > There is no such problem found for my testing runs on smaller systems
> > (~100), i.e.: len(m.fragresults[0][0] always equals to natom.
> >
> >
> >
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>