[lammps-users] PPPM calculation

Paul will repsond to the PPPM question. Re: xmovie,
it does not re-order your snapshots in a dump file. So it
is not responsible for swapping steps 50 and 100.

Steve

Dongsheng,

The tolerance on your PPPM solve isn't small enough. You've got:

kspace_style pppm 0.001

Try:

kspace_style pppm 0.000001

I typically do long runs of large systems with:

kspace_style pppm 0.0001

but acknowledge that this setting introduces some error, and would be
particularly bad for a two atom system. If you want essentially exact
results, especially for a two atom system use Ewald. See:
http://lammps.sandia.gov/doc/kspace_style.html

Paul

Dongsheng,

Also note that there is a very important difference between the model
used for a cutoff fluid versus that for Ewald or PPPM. The former
models an isolated periodic box, and the latter models a periodic
infinitely replicated system where the primary box is replicated in
all directions out to infinity. So you wouldn't expect to get the same
answer since you are simulating a fundamentally different thing. Read
Allen and Tildesley's description of the Ewald sum.

Paul

Hi. I am trying to do the following with a recent version of LAMMPS.

dump 1 all custom 500000 configs.equilib.4 tag mol type x y z ix iy iz

When I run, I get the error

LAMMPS (12 Feb 2007)
ERROR: Dumping an atom quantity that isn't allocated

"mol" should work, but it doesn't. When I change the command to

dump 1 all custom 500000 configs.equilib.4 tag type x y z ix iy iz

the simulation runs, with output

LAMMPS (12 Feb 2007)
Reading restart file ...
WARNING: Restart file version does not match LAMMPS version
   restart file = 12 Apr 2006, LAMMPS = 12 Feb 2007
WARNING: Restart file used different # of processors
   orthogonal box = (-125 -125 -0.0001) to (125 125 128.206)
   restart file = 12 Apr 2006, LAMMPS = 12 Feb 2007
WARNING: Restart file version does not match LAMMPS version
   restart file = 12 Apr 2006, LAMMPS = 12 Feb 2007
WARNING: Restart file version does not match LAMMPS version
   restart file = 12 Apr 2006, LAMMPS = 12 Feb 2007
   2 by 2 by 1 processor grid
   250500 atoms
   250000 bonds
Finding 1-2 1-3 1-4 neighbors ...
   2 = max # of 1-2 neighbors
   2 = max # of special neighbors
500 atoms in group ends
250000 atoms in group notends
Setting up run ...
Memory usage per processor = 19.095 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
15000000 0.99560498 0.024870383 20.713135 22.231407 -0.00031911119 8012894.9
15000100 0.9951811 0.02467336 20.713056 22.230495 -0.00037047244 7984119.4

But the image values in the dump file configs.equilib.4 are messed up:

ITEM: TIMESTEP
15000000
ITEM: NUMBER OF ATOMS
250500
ITEM: BOX BOUNDS
-125 125
-0.0001 128.206
ITEM: ATOMS
1003 1 -116.117 -85.7444 0 -492 -190 -35
1004 2 -116.666 -85.1762 0.610642 -492 -190 -35
1005 2 -117.446 -85.2011 1.18932 -492 -190 -35
1006 2 -116.638 -84.7063 1.60567 -492 -190 -35
1007 2 -116.014 -85.3735 1.30212 -492 -190 -35
1008 2 -115.788 -85.5984 2.22241 -492 -190 -35

This is for a system of tethered chains, so these image numbers are nonsense. I seem to recall this being an issue a while back, but I don't remember if there was a workaround.

Help?

Thanks!
Rob

Doing restart2data on the old restart file and working from the new data file fixes the image problem, but the "mol" problem remains.

Thanks,
Rob

The error check that produces this should not trigger if you
have an atom style that includes molecule tags (e.g. bond, molecular, full).

If this is not the problem, then send a simple input script
that reproduces the error ...

Steve