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Re: [lammps-users] problem in combining dump file
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Re: [lammps-users] problem in combining dump file


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Fri, 7 Jul 2017 15:17:36 -0400

On Fri, Jul 7, 2017 at 3:06 PM, Mathur Nil <nilmathur786@...24...> wrote:
> hello all,
>
> i am trying to do two phase simulation..
>
> first i equilibrate atoms  at certain temp with periodic boundary condition
> and npt ensemble..i used simulation box size 0 20 0 20 -21 -1
>
> then i equilibrate atoms at another temp with periodic boundary condition
> and npt ensemble.. i used simulation box size 0 20 0 20 0 20
>
> then i read this dump file to another simulation box and equilibrate it with
> certain temp with periodic boundary conditions . simulation box size is 0 20
> 0 20 -21 20 . i used npt ensemble .

this is a bad protocol, especially since you have periodic boundary
conditions. image flags and thus positions will be invalid after
merging the systems. even, if you correct for that (or use fixed
boundaries with walls in z-direction), you are creating a high
potential energy area near the interfaces.

a) compute your target density for the entire system and determine a
suitable simulation cell size
b) build a system that has both phases already included. define each
phase into a separate group
c) run a minimization to remove close contacts and thus high potential
energy collisions.
d) set up a simulation with fix nve and fix langevin or fix temp/csld
that operates at only one of the two subsystems, the other remains
immobile
e) switch fix nve and the thermostat fix to the other subsystem and
equilibrate that for a bit, while keeping the other part immobile.
f) repeat steps d) and e) a couple of times while starting with a
rather short Tdamp and increasing it for each iteration.
g) switch to fix nvt for the whole system for a bit and only then
switch to fix npt.

this is simpler, faster, and safer.

axel.

> problem is dump file it creates is not shows two different region. they
> mixed with each other
> boundary        p p p
>
> lattice            fcc 4.046
> region whole block 0 20 0 20 -21 20 units box
> create_box 2 whole
>
> region solid block 0 20 0 20 -21 -1 units box
> create_atoms 1 region solid
> mass 1 26.98
>
> region liquid block 0 20 0 20 0 20 units box
> create_atoms 2 region liquid
> mass 2 26.98
>
> read_dump dump_solid 80000 type vx vy vz box yes replace yes
> read_dump dump_liquid 79990 type vx vy vz box yes replace yes
>
> echo screen
>
> group solid type 1
> group liquid type 2
>
>
>
>
> dump             5 all custom 10 dump_liquidrelax id type x y z vx vy vz
>
>
>
> thanks in advance
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-- 
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.