Re: [cclib-devel] Q-Chem and ORCA parsers

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

Hi Martin,

That's true, technically it is not hard. I was thinking more about integration
with the rest of cclib. Binary files will not be "parsed" in the sense logfiles
are, that is the task is not one of reading a text file line by line and
extracting useful information. Rather, it is one of reading data that is stored
in a predefined format. This is obvious, but it implies some design choices
that have not been discussed here. Above all, the line-by-line paradigm
used in the class LogFile (inherited by all parsers) is not useful and
we cannot just pass one extra file.

Anyway, this can definitely be done, I'm just saying it needs a little
bit of forethought.

Cheers,
Karol

On Aug 18 2014, Martin Blood-Forsythe wrote:
> I'll have to look at the way that the multiple file parse is implemented
> for Molpro, but at least for ORCA and Q-Chem adding a binary file parser
> wouldn't require much different than the way a text based multiple file
> parsing works. I've had a lot of success parsing these files using
> numpy.fromfile and numpy.frombuffer.  Typically the only required knowledge
> is the number of orbitals (to determine the array shape to dump into) and
> the file name.
> 
> -Martin
> 
> 
> 
> 
> On Mon, Aug 18, 2014 at 1:52 PM, Karol Langner <kar...@gm...>
> wrote:
> 
> > Well, we do support parsing multiple files for one job, although this has
> > been limited so far to Molpro if I recall correctly (it was probably also
> > in the works for Turbomole, but this is not an officially supported parser
> > ATM). We have not been parsing binary files at all, though, so that might
> > involve a major change in the way cclib works. It is worth doing, however,
> > or the reasons you mentioned as well as others.
> >
> > Karol
> >
> >
> > On Mon, Aug 18, 2014 at 10:44 AM, Martin Blood-Forsythe <
> > mbl...@ph...> wrote:
> >
> >> Sounds great.  I'll take a look at your qchem branch and see if there are
> >> areas that I think I can add to.  Would there be interest in my adding
> >> parsers for some quantities directly from the binary save files that qchem
> >> leaves around (with an if file exists condition of course)? The primary
> >> advantage of this is getting everything in float precision, but it can also
> >> capture output that the user did not request be printed to the .out file.
> >>
> >> -Martin
> >>
> >>
> >> ---------------------------------------------------
> >> Martin Blood-Forsythe
> >> Graduate Student in Physics
> >> Harvard University
> >> Aspuru-Guzik Lab
> >>
> >>
> >> On Mon, Aug 18, 2014 at 10:14 AM, Eric Berquist <er...@pi...> wrote:
> >>
> >>> Hi Karol and Martin,
> >>>
> >>> My Q-Chem parser is currently working on many "difficult" files in
> >>> addition to some tests that I've made. It hasn't been merged in yet since
> >>> the Travis CI build fails for a silly reason, which I will get to by the
> >>> end of the week. It has to do with there being no regression folder/data in
> >>> the cclib_data repository; I'm going to find a trouble file somewhere and
> >>> add that.
> >>>
> >>> If anyone would like to test out the parser and submit pull requests, my
> >>> GitHub username is `berquist`, and I've created a `qchem` branch.
> >>>
> >>> Eric
> >>>
> >>> On Thursday, August 14, 2014, Karol M. Langner <kar...@gm...>
> >>> wrote:
> >>>
> >>>> Hi Martin,
> >>>>
> >>>> Nice to hear from you. We actually upport ORCA in the newest release of
> >>>> cclib,
> >>>> which would be 1.2 -- have you looked at the repostiory at
> >>>> https://github.com/cclib/cclib ?
> >>>> Of course, there is still some work to do for ORCA.
> >>>>
> >>>> As far as Q-Chem is concerned, I am fairly certain someone else has
> >>>> recently
> >>>> expressed interest in contributing to that (on this ML), so you would
> >>>> not be alone.
> >>>> Contributing unit test output is already tremendous, since it gives a
> >>>> starting
> >>>> point to get the parser working.
> >>>>
> >>>> In any case, you are more than welcome to fork from our git repository
> >>>> and put in
> >>>> pull requests. In fact, we would be tremendously happy to merge new
> >>>> features.
> >>>>
> >>>> Developmentwise, cclib has been quiet during this summer.
> >>>>
> >>>> You might also want to look at the new docs: http://cclib.github.io/
> >>>>
> >>>> The sourceforge website and wiki is now obsolete, and will probably be
> >>>> soon offline.
> >>>>
> >>>> Best,
> >>>> Karol
> >>>>
> >>>> On Aug 12 2014, Martin Blood-Forsythe wrote:
> >>>> > Hi cclib developers,
> >>>> > I'm interested in contributing towards the efforts to get Q-Chem and
> >>>> ORCA
> >>>> > parsers supported in cclib.  I'd be happy to contribute unit test
> >>>> output
> >>>> > files for ORCA 2.9.1, 3.0.1, 3.0.2, and Q-Chem 4.1.2.  I have some
> >>>> > experience with writing python parsers for both the text-based and
> >>>> binary
> >>>> > output files from both ORCA and Q-Chem, so I'm happy to help in any
> >>>> way I
> >>>> > can.
> >>>> > Best wishes,
> >>>> > -Martin
> >>>> >
> >>>> > ---------------------------------------------------
> >>>> > Martin Blood-Forsythe
> >>>> > Graduate Student in Physics
> >>>> > Harvard University
> >>>>
> >>>> >
> >>>> ------------------------------------------------------------------------------
> >>>>
> >>>> > _______________________________________________
> >>>> > cclib-devel mailing list
> >>>> > ccl...@li...
> >>>> > https://lists.sourceforge.net/lists/listinfo/cclib-devel
> >>>>
> >>>>
> >>>> --
> >>>> written by Karol M. Langner
> >>>> Thu Aug 14 22:06:25 EDT 2014
> >>>>
> >>>>
> >>>> ------------------------------------------------------------------------------
> >>>> _______________________________________________
> >>>> cclib-devel mailing list
> >>>> ccl...@li...
> >>>> https://lists.sourceforge.net/lists/listinfo/cclib-devel
> >>>>
> >>>
> >>
> >

-- 
written by Karol M. Langner
Mon Aug 18 20:35:25 EDT 2014