I am trying to simulate a simple phase separated system. I set up a system with 2 LJ atoms. However I keep getting the error:
ERROR: Lost atoms: original 7400 current 7349 (…/thermo.cpp:442)
In addition I have the warning:
WARNING: One or more atoms are time integrated more than once (…/modify.cpp:279)
I also tried to use a soft interaction between the 2 atom types, but it didn’t solve the problem (though it decreased a little bit the number of the lost atoms).
Here is my input file:
units lj
dimension 2
boundary p p p
atom_style atomic
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
lattice hex 0.5
region simbox block 0 80 0 40 -0.1 0.1
create_box 2 simbox
create_atoms 1 random 1000 2225 NULL
create_atoms 2 box
mass 1 1.0
mass 2 10.0
velocity all create 0.05 11111
pair_style hybrid lj/cut 2.5 soft 1.0
pair_coeff 1 1 lj/cut 1.0 1.0 2.5
pair_coeff 2 2 lj/cut 1.0 1.0 2.5
pair_coeff 1 2 soft 1.0
fix 1 all nvt temp 0.25 0.25 1.0
fix 2 all nvt temp 0.25 0.25 1.0
dump 1 all atom 250 dump2.lammpstrj
thermo 100
run 1000
I am trying to simulate a simple phase separated system. I set up a system
with 2 LJ atoms. However I keep getting the error:
ERROR: Lost atoms: original 7400 current 7349 (../thermo.cpp:442)
In addition I have the warning:
WARNING: One or more atoms are time integrated more than once
(../modify.cpp:279)
this is the problem, that you have to resolve. the solution is *very*
obvious!
axel.
It’s not obvious to me how to create initial conditions of interleaved particles as shown in this movie: https://www.youtube.com/watch?v=AliZxq-I2ho
Looks like the movie has random initial conditions.
If I use:
create_atoms 1 random 100 1500 NULL
create_atoms 2 random 100 3000 NULL
They will clash again. How do I prevent it?
It's not obvious to me how to create initial conditions of interleaved
particles as shown in this movie: https://www.youtube.
com/watch?v=AliZxq-I2ho
simple: create first only atoms of one type. melt/equilibrate your system.
that is what is shown as initial configuration. then you can use the "set"
command with the "type/fraction" option to set the required fraction of
atoms to the second type. of course, you also need suitable parameters to
have the phase separation behavior, but that is not a LAMMPS question, but
a question of the science.
axel.
I am not sure we are on the same page. I want to have 2 atoms shifted on a hex lattice. But LAMMPS doesn’t like the input I give it:
lattice hex 0.5
region whole block 0 10 0 10 -0.1 0.1
create_box 2 whole
lattice hex 0.5
create_atoms 1 region whole
lattice hex 0.5 origin 0.5 0.5 0.5
create_atoms 2 region whole
Shouldn’t the above work?
I get: ERROR: Lattice settings are not compatible with 2d simulation (…/lattice.cpp:241)
Sorry this is the error I get:
units lj
dimension 2
boundary p p p
atom_style atomic
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
lattice hex 0.5
region simbox block 0 80 0 40 -0.1 0.1
create_box 2 simbox
lattice hex 0.5
create_atoms 1 region simbox
lattice hex 0.5 origin 0.5 0.5
create_atoms 2 region simbox
https://github.com/lammps/lammps/blob/master/src/lattice.cpp#L152
LAMMPS (22 Feb 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (…/comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 1.51967 2.63215 1.51967
Created orthogonal box = (0 0 -0.151967) to (121.574 105.286 0.151967)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 1.51967 2.63215 1.51967
Created 6400 atoms
Time spent = 0.000982046 secs
ERROR: Illegal lattice command (…/lattice.cpp:152)
Last command: lattice hex 0.5 origin 0.5 0.5
Is it a bug in the engine?
I am not sure we are on the same page. I want to have 2 atoms shifted on a
hex lattice. But LAMMPS doesn't like the input I give it:
if you change your story every time you post a question, then nobody will
be able to give a satisfactory answer.
axel.
I am not sure we are on the same page. I want to have 2 atoms shifted on a
hex lattice. But LAMMPS doesn't like the input I give it:
*lattice hex 0.5*
*region whole block 0 10 0 10 -0.1 0.1*
*create_box 2 whole *
*lattice hex 0.5*
*create_atoms 1 region whole *
*lattice hex 0.5 origin 0.5 0.5 0.5 *
*create_atoms 2 region whole *
Shouldn't the above work?
no. with 2d geometries the z component of "origin" must be 0.0
axel.