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Re: [cclib-devel] Turbomole parser
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From: Noel O'B. <bao...@gm...> - 2007-07-12 12:40:14
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The important thing is now to get you coding. I've created a branch
for the turbomoleparser called um, turbomoleparser or something. We
can test out on this branch how to include multiple files, but I
recommend that in the meanwhile you pick your favourite file and start
working on that.
It might help at this point if you can say what OS you are working on
(I think we have one developer at the moment on Linux, one on Windows,
one on Mac), and how familiar are you with the following:
(1) Open source devel
(2) Subversion
(3) Python
This will let us know how much we should explain things. Feel free of
course to ask any questions, and don't worry about making mistakes.
Oh yes, and don't forget to create a Sourceforge (SF) account and send
me the name...
Regards,
Noel
On 11/07/07, Christopher Rowley <cro...@uo...> wrote:
> I've attached a zip of the turbomole output files for the optimization
> of ethene.
>
> I have a summary of the important files here:
>
> control - this is a ascii file that specifies the type of calculation to
> run. It also contains keywords that specify the location of other files
> related to the calculation
> ie. $basis file=basis
>
> basis - ascii file containing all the basis functions used in the
> calculation
> ie:
> $basis
> *
> c def2-TZVPP
> # c (11s6p2d1f) / [5s3p2d1f] {62111/411/11/1}
> *
> 6 s
> 13575.349682 0.22245814352E-03
> 2035.2333680 0.17232738252E-02
> 463.22562359 0.89255715314E-02
> 131.20019598 0.35727984502E-01
> 42.853015891 0.11076259931
> 15.584185766 0.24295627626
> 2 s
> ...
> $end
>
> energy - ascii file containing the final SCF energy for each
> optimization step
> $energy SCF SCFKIN SCFPOT
> 1 -78.62006391840 78.22049121937 -156.84055513777
> ...
> 5 -78.62016433199 78.17813647354 -156.79830080553
> $end
>
> gradient - ascii file containing the final SCF energy, the norm of the
> gradient, the cartesian coordinates,
> and the gradient at each optimization step
>
> $grad cartesian gradients
> cycle = 1 SCF energy = -78.6200639184 |dE/dxyz| =
> 0.007787
> -12.43305554870021 1.45676390273213 0.00000001455089 c
> -11.46168130574795 -0.34900040894297 -0.00000002588925 h
> -14.48255219706143 1.39416928077853 -0.00000005914843 h
> -11.17787929057337 3.63195569944202 -0.00000000094486 c
> -12.14925477129624 5.43772016116137 -0.00000002135391 h
> -9.12838183435422 3.69454983309038 -0.00000005461309 h
> 0.37240190690901D-03 0.57948431095057D-03 0.38853271069288D-08
> -.18362345421673D-02 0.34133613968580D-02 -.97583915002572D-09
> 0.38481666111819D-02 0.11765947797167D-03 -.22974479052215D-08
> -.37249153523038D-03 -.57960132610911D-03 0.12907959533087D-08
> 0.18360651045835D-02 -.34131936211959D-02 -.29052983458520D-09
> -.38479075912553D-02 -.11771021861143D-03 -.16148640940085D-08
> ...
> $end
>
> mos - Contains the MO energies and coefficients in 4d20.14 format
>
> $scfmo scfconv=6 format(4d20.14)
> # SCF total energy is -78.6201643320 a.u.
> #
> 1 a eigenvalue=-.98998832838354D+01 nsaos=118
> 0.33525257887995D+000.43483755824514D+000.29687028164704D-010.1443675670
> 3553D-01
> 0.52678143243858D-02-.10363028095958D-060.11827623499659D-03-.1226611495
> 0504D-10
> 0.13566446246138D-05-.13171691954860D-01-.21677290745517D-09-.4112147855
> 9874D-06
> -.28603744354330D-03-.85454212224573D-11-.14708011769907D-020.6148298791
> 2470D-10
> 0.20389102757828D-100.20796546607765D-060.72089304597414D-03-.3544240520
> 8995D-02
> 0.41175724483158D-090.55184920814757D-10-.79343053802777D-060.7001808373
> 3727D-02
> 0.36597788268211D-10-.49165972048646D-070.13379843496344D-02-.9468926087
> 0386D-10
> -.26197917829845D-100.85579464932607D-060.15672280349784D-020.2630723827
> 4649D-04
> -.17447811306186D-01-.16629360526852D-020.11032161215752D-02-.6181968637
> 1091D-03
> 0.14490807816497D-100.66606858738943D-02-.55586812728540D-020.3203660664
> 0502D-10
> ...
>
> For open shell systems, there are two separate files for the MO
> coefficients, alpha and beta
>
> job.last - each optimization step writes output to a file job.x on the
> details of the calculation,
> such as SCF iteractions. Additional output, such as dipole moments, is
> also written here. This is analogous to a log file like in other
> programs.
>
> hessian - ascii file - for frequency analysis calculations, this file
> contains the hessian (I'm not immediately sure what the format is)
>
> -----Original Message-----
> From: Noel O'Boyle [mailto:bao...@gm...]
> Sent: Wednesday, July 11, 2007 2:54 AM
> To: Adam Tenderholt
> Cc: Christopher Rowley; ccl...@li...
> Subject: Re: [cclib-devel] Turbomole parser
>
> Hello Chris,
>
> Good to hear from you and welcome to cclib. We welcome all the help we
> can get so there's really no question about approval. Our only
> standard is that the code works before we release it, and we have a
> number of tests that try to ensure this is the case.
>
> On 11/07/07, Adam Tenderholt <a-t...@st...> wrote:
> > > Ok, I'll try to set aside some time do to it once there's approval.
> I
> > > have a project needs automated CDA analysis with turbomole, so I'd
> be
> > > looking get parser for the MO coefficients working first.
> >
> > I too generally focus on MO coeffs, so if you want help, let me know.
> > One of the first steps you could take is to have a look at our basic
> > test datafiles, and start running calculations with those.
> > Specifically, you should run dvb_sp and dvb_un_sp. Both are
> > calculations on di-vinylbenzene, and I believe you can find xyz
> > coordinates in the input files of other calculations. The SP calc is
> > a restricted single-point calc with no net charge and the UN_SP calc
> > is an unrestricted single-point with a positive charge and a
> > multiplicity of 2.
> >
> > > I took a look at the other parsers and I don't think it will be that
> > > difficult to get turbomole working. The only significant problem is
> > > that
> > > turbomole doesn't put all its output in a single file. I generally
> > > keep
> > > a separate directory for each turbomole calculation. The simplest
> > > way to
> > > do it would be to pass the path of a directory containing the
> > > output of
> > > a turbomole job to the parser instead of the filename of the output
> > > file.
> > >
> > > This would be inconsistent with all the other parsers, so it's a
> > > little
> > > unattractive. The other route I can see is to have a separate
> > > utility to
> > > merge the various turbomole output files into a single output file
> > > that
> > > could be read in by the parser.
> >
> > I'd suggest using cat to combine all of the files into one, although
> > this probably isn't the best option for our windows-using friends.
> > Perhaps we should handle zip or tar files (we already handle gz and
> > bzip2, as I recall). Noel, Karol, any comments? I'm willing to help
> > add any logfiles or code to a branch in the svn tree during the next
> > few days, so if you have anything ready, let me know.
>
> Perhaps Chris, you could describe in detail the typical output from a
> Turbomole calculation; that is, what files are created, what do they
> contain (in general terms), are they ASCII files or binary. It might
> make sense if you send to this list a .zip file of results of a small
> example calculation.
>
> One possibility is that we have several parsers for several files. At
> first this may seem messy, but we are moving towards separating the
> parsers and the results, and it will be trivial for the user to add
> the results together. But let's take a look at the actual output first
> before we think about this too much.
>
> Some bookkeeping now. Can you create an account on SourceForge and
> send me the name? I will need this to make you a developer.
>
> > Adam
> >
> >
> >
> >
> >
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>
>
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