[ghemical-devel] hello

[Tommi Hassinen]

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).

> 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