Re: [SPAM] Re: XFS, EXT3 or some other?

On 6/22/06, Francesco Pietra <frapietra@alice.it> wrote:

On Thursday 22 June 2006 14:46, Lennart Sorensen wrote:
> On Thu, Jun 22, 2006 at 06:03:09AM +0200, Francesco Pietra wrote:
> > Out of SuSe - which I do not know - may I ask about debian etch (32 and
> > 64): reiser3, reiser4, or even some other reiser#? Just because I took
> > that, as reiserfs, for good (and I am long using it at 32bit without
> > problems; now also at 64bit). Presently my problems are not there; they
> > are about putting mpqc at work with "difficult" molecules: so far -
> > despite my initial enthusiasm - it has failed badly.
>
> So what kind of problems is mpqc giving you? I know nothing about
> quantum chemistry, but I am pretty good at fixing software. :)

Hi Lennart:
This is a most welcome invitation.

Below is pasted a message that I addressed this morning (8.38 UTC) to the
mpqc community. As such, it could only trigger response from experts in mpqc.
However, to let you investigating the matter, I could send you files of
successful and unsuccessful computations. The version of mpqc is just the one
currently on debian etch amd64.

I don't know if it is a problem of software. It may well be that I am putting
mpqc to work the wrong way. In particular, I do not undestand whether the
flexibility of the molecule poses problems to the software, stopping it under
certain conditions. I do not know how exactly mpcq works, the manual is
detailed as to commands but I have not found a description of how it works.
Perhaps, to understand fully, one should look at the source. But, as an
object oriented program, it must be a hard way. I must also add that what I
am trying to do is putting quantum calculation on the very hard way; I wonder
whether other dare so. Not evident from the publications. The problems I am
investigating are rather for molecular mechanics, and I do so. But molecular
mechanics tells nothing about most properties of the molecule, except the
shape and relative energies of conformers.

What will never finish to surprise me is that tout le monde - or about so -
does such computations with a commercial software, released (at a very high
price) for commercial Linux under the understanding that installation of
Linux must be that of the CD, no variations. Sic. It surprises me because I
can not figure how users can understand what they are doing with such
inmperscrutable packages. At any event, these computations end on the most
respectable chemical journals.

Tell me what you want.

cheers
francesco
______________
Although this may well be a premature ask for help, it might result in
suggesting me a general approach.

mpqc 2.3.0 runs correctly (amd64 debian etch, parallel mode with four nodes,
dual opteron) for simple molecules, B3LYP simple input, as given in the
manual with water.in. For example, the energy difference between the two ax
and eq conformers of methylcyclohexane (input from molecular-mechanics
minimized structures) is evaluated 1.8 kcal/mol, in accordance with the
experimental value. In both cases the calculation reached convergence
extremely rapidly and the energy was furnished as "Molecular Energy".

With molecules of the size C22H25NO6 involving benzene ring, unsaturated
conjugated ring and helicity problems, so far I was unable to reach
convergence. Either one of the two most stable conformers used for input with
the water template (basis set 3-21G* or higher) with coordinates furnished as
described above for the methylcyclohexanes, was not brought to conclusion. In
most instances the calculation hangs after a few cycles of iterations and the
prompt is not furnished; I can examine from the *.out file "each molecule"
for each iteration set and found it correct, with all atoms - including
hydrogens - where they should be. Also, the general conformation was not much
changed, except for minor details.

In another instance the above calculations went farther (about four hours),
for some twenty cycles of iteration and it did not hang: the prompt was
furnished. However, no "Molecular Energy" was furnished, only scf energy and
it was clearly stated that convergence was not reached. Comparing scf energy,
from input as bove for the two most stable conformers, resulted in a far too
large energy difference between them (5 kcal/mol; absurd because I can see
both them by NMR at r.t.).

I was unable to tell the story in fewer words. I do not expect anything easy
for complex systems. Before putting the hands further on files I am trying to
figure out a plan how to move.

Thanks for your kind attention.

francesco pietra
____________________-
>
> Len Sorensen