[ghemical-devel] hello

[Jean Bréfort]

Le mardi 25 octobre 2005 à 12:43 +0300, Tommi Hassinen a écrit :
> On Mon, 24 Oct 2005, Maria Pinjanainen wrote:
> 
> > Hi!
> > I am trying to find new good programs for chemists
> > here in Åbo Akademi.  :-)
> > Ghemical looks very fine and is user-friendly too.
> 
> Ok, thanks ; I hope you will find it useful...  :)
> 
> > I have compiled it into Debian Sarge and I have found one problem.
> > When we are using MPQC Ghemical is writing temporaryfile into /tmp/xxxx.
> > If something happens and another user logs into machine and tries to use
> > Ghemical and MPQC she/he have no permission to write that file....
> 
> Yes, the way how both MOPAC7 and MPQC are used from ghemical/libghemical 
> is through a temporary input file that is read in by MOPAC7/MPQC programs.
> 
> > So, my idea is to modify a bit a string in eng1_qm_mpqc.cpp, but how?
> > Of cource there is a line 110 in libghemical-1.90's src, where is possible to
> > tell about the temp file... Fast way is to use straight users home, but that
> > is not best solution, I think.
> 
> The solution which uses the /tmp directory is not perhaps the best one in 
> all cases. It seems to me that it is safe to edit the line 110, so that 
> the input file is created in elsewhere ; since the path ~/ is interpreted 
> as the user's home directory, then
> 
>          str << "~/mpqc" << setfill('0') << setw(4) << ifile_name_counter++ << ".in" << ends;
>                 ^^^
> would make the files in user's home directory (haven't tried this though).

This will not work. ~ is HOME only in the terminal. You must retrieve
the HOME directory with getenv("HOME");

> > I am interesting to use Ghemical in amd64, too, but perhaps need to wait a bit
> > if wants to use MOPAC....
> >
> > My plans are find how to give users an easy way export/import jobs, when
> > she/he can use a "supermachine" for bigger jobs.
> 
> That has been on my "wish list" as well, but has so far not progressed 
> very well due to my other tasks. Let's see if we find good ideas about 
> this.
> 
> About amd64, the ghemical app (and it's graphics code to be precise) was 
> just recently patched for 64-bit systems ; the fixes will be released as 
> v1.91 soon (in November) and the fixes already exist at the 
> bioinformatics.org CVS server.
> 
> Regards,
> 
>  	Tommi
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