[gmx-developers] Re: gmx-developers digest, Vol 1 #324 - 6 msgs

Jason DeJoannis jdejoan at emory.edu
Fri Apr 23 15:45:49 CEST 2004

> Subject: Re: [gmx-developers] insertion-deletion
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> To: gmx-developers at gromacs.org
> Date: Fri, 23 Apr 2004 08:47:04 +0200
> Reply-To: gmx-developers at gromacs.org
> On Thu, 2004-04-22 at 22:36, Jason DeJoannis wrote:
> > Dear All,
> >
> > Consider a lennard-jones fluid. I want to perform insertions
> > and deletions provided
> >
> >             1 < n < n0
> >
> > where n  is the number of atoms
> >       n0 is the number of atoms in the starting config
> >
> >
> > All I do is change top->atoms.nr and all the other measures of
> > the number of atoms (i.e. inside mdatoms,top->atoms,top->blocks,nsb).
> > Directly afterwards a new neighbor search is performed.
> >
> > Unfortunately after a dozen or so steps, one or more of the forces
> > becomes "nan". Right now I am running in serial mode with 10 atoms to
> > keep things simple.
> >
> > Any idea what is killing my forces?
> How about the lengths of the force arrays, coordinate arrays and son on?
That is the point of keeping the number of particles less than or equal
to the starting config. The arrays have a fixed length of n0. At first
I tried using srenew(array,newsize) to expand the arrays but it proved
difficult to find everything that needs expansion.

I am looking into the neighbor search right now. I'm thinking that
maybe the search is still including the deleted particles somehow.
But even so, it should not produce a force error, right? I think the
appropriate lists are in fr->nlist_sr[eNL_VDW].jindex[*]? Since it
is an LJ-fluid there are no charges, and I am not using dual-range
cutoffs (i.e. rlist=rvdw).


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