[CPMD-list] problem with path integrals restart

[Marek Naryniecki]

Hi All

Thank You for Your suggestions. Now I know i must recalculate it.
many thnaks

Marek Naryniecki
Wydzial Chemii
Uniwersytet Wroclawski

On Thu, 3 Apr 2008, Axel Kohlmeyer wrote:

> marek,
>
> i had a closer look at the PI code (while debugging something related)
> and found that those "spurious" NaNs and Infinities can come from
> when you are not using a thermostat and thus the target temperature
> is not defined. if just you put a TEMPERATURE statement into
> the &CPMD section, even though it will be ignored when restarting
> with velocities, those denormalized (information only) numbers go away.
>
> now as a result this brings up the question: does it make sense at all
> to run an NVE path-integrals run and if yes, how to handle this case?
> should one compute the instantenous temperature? or just skip that output?
>
> cheers,
>     axel.
> 2008/4/2 Marek Naryniecki <marek at elrond.chem.uni.wroc.pl>:
> >
> >  Dear  Axel and Serge
> >
> >  I know DIPOLE shouldn't apeare in PI calculation. My mistake.
> >  Calculation without DIPOLE produce the same problem.
> >  I put 2 replicas for fast check of the problem on varius machines and
> >  pseudos. This problem also occure with 8 replicas in 120K. I know it is
> >  small number but more replicas is to expensive for me. I'll try some short
> >  calculation with 32 replicas.
> >
> >
> >   > On Wed, 2 Apr 2008, Marek Naryniecki wrote:
> >  >
> >  > MN> Dear All
> >  >
> >  > dear marek,
> >
> > >
> >  > MN> ***************************************************************
> >  > MN>  *                    CHARACTERISTIC RADII                     *
> >  > MN>  ***************************************************************
> >
> > > MN>    SPECIES  R OF GYRATION  FREE PARTICLE  (IN ANGSTROM)
> >  > MN>    1   P    0.06799       Infinity
> >  > MN>    2   O    0.05446       Infinity
> >  > MN>    3   K    0.08015       Infinity
> >  > MN>    4   H    0.12800       Infinity
> >  >
> >
> > > looks like a division by zero somewhere.
> >  >
> >  > [...]
> >  >
> >
> > > MN> what is the reason of that? After that calculations go on and average
> >  > MN> values for bonds seems to be good.
> >  > MN> I looked into cpmd code but without  succes.
> >  >
> >
> > > you're neither giving enough information to reproduce
> >
> > > that run somewhere else (full input!) nor enough details
> >
> > I'm sorry, I thought it will be easier to read. Now I know it was stupid.
> >
> > I attached inputs for replicas generation and dynamic. if I stop dynamic
> >
> > and then restart it this problem occures.
> >
> > > to narrow it down. what machine are you running on?
> >
> > > does the error happen in serial or in parallel?
> >
> > it happen in serial and in parallel. I chacked on several machines i was
> >
> > able and the problem happen.
> >  >
> >
> > > looking at the code itself may not be enough.
> >
> > > compile cpmd with debug info, find the code
> >
> > > where the properties from above are computed,
> >
> > > set a breakpoint and try to figure out where the
> >
> > > denormalized numbers are coming from...
> >
> > I'm not familar with fortran, but I will try
> >  >
> >
> > > MN>     100.0
> >  > MN>  &END
> >  > MN> ..
> >  > MN> &PIMD
> >  > MN>    TROTTER DIMENSION
> >  >
> >
> > > it has become a very bad habit on this list lately to
> >
> > > exclude vital information from inputs posted. if you
> >
> > > don't make it easy to reproduce your problem, you'll
> >
> > > have to solve it by yourself.
> >
> > ok, You're right.
> >  >
> >  > [...]
> >  > MN>
> >  > MN> Please help me.
> >
> > >
> >  > quid pro quo. you have to help us to help you.
> >  >
> >
> > Thank You very much for reply. I'm still trying to figure out what
> >
> > is wrong. I thought someone tell me what can this mean physically.
> >
> >
> > Many Thanks
> >   marek
> >  > cheers,
> >  >    axel.
> >  >
> >
> > > MN>
> >  > MN> Best Regards,
> >  > MN>
> >  > MN>
> >
> > > MN> Marek Naryniecki
> >  > MN> Wydzial Chemii
> >
> > > MN> Uniwersytet Wroclawski
> >  > MN>
> >  > MN>
> >  > MN>
> >  > MN> _______________________________________________
> >
> > > MN> CPMD-list mailing list
> >  > MN> CPMD-list at cpmd.org
> >  > MN> http://cpmd.org/mailman/listinfo/cpmd-list
> >  > MN>
> >  >
> >  > --
> >
> >
> > > =======================================================================
> >  > Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
> >  >    Center for Molecular Modeling   --   University of Pennsylvania
> >  > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> >  > tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
> >  > =======================================================================
> >  > If you make something idiot-proof, the universe creates a better idiot.
> >  >
> >
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> >  http://cpmd.org/mailman/listinfo/cpmd-list
> >
> >
>
>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
>  Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>