Re: [SPAM] Re: XFS, EXT3 or some other?
On Thu, Jun 22, 2006 at 02:23:22PM +0200, Francesco Pietra wrote:
> 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.
Well there is a version 2.3.1 which is supposed to contain some bug
fixes. I wonder if there is any chance that one of the fixed bugs is
what is causing your problem.
The mpqc changelog has this:
2006-03-22: MPQC-2.3.1
* MCSearch added for cubic interpolation during quasi-Newton line searches.
* Added KMLYP method.
* Updated libtool to version 1.5.22.
* SumDenFunctional returns correct HF exchange coefficient when
using nested ACM functionals. This could change the results from
certain, uncommon inputs.
* Other minor bug fixes, enhancements, and
* documentation improvements.
Debian doesn't have 2.3.1 built yet, but it wouldn't be hard to do. I
can try and build a debian package of 2.3.1 if you want to try that.
Len Sorensen
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