Joh_Nop
December 1, 2018, 12:47am
1
While trying to simulate phase separation, using DPD particles.
My input configuration is as follows:
units lj
timestep 0.001
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 50 0 25 -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 0
create_atoms 2 region simbox
mass 1 1
mass 2 1
comm_modify vel yes
velocity all create ${temp} 123456 dist gaussian
pair_style hybrid dpd 1 2.5 123456 soft 0.5
pair_coeff 1 1 dpd 0.7 2.5 12345
pair_coeff 2 2 dpd 0.7 2.5 12346
pair_coeff 1 2 soft 0.5
fix 1 all nvt temp 0.7 0.7 0.1
dump 1 all atom 5000 out/dump.lammpstrj
write_data dpd_data.all
thermo 500
run 5000000
But when I run the above I get the following error:
LAMMPS (2 Aug 2018)
Lattice spacing in x,y,z = 1.51967 2.63215 1.51967
Created orthogonal box = (0 0 -0.151967) to (75.9836 65.8037 0.151967)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 1.51967 2.63215 1.51967
Created 2500 atoms
Time spent = 0.000518799 secs
Lattice spacing in x,y,z = 1.51967 2.63215 1.51967
Created 2500 atoms
Time spent = 0.00031805 secs
System init for write_data ...
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.28239e+06
ghost atom cutoff = 8.28239e+06
binsize = 4.14119e+06, bins = 1 1 1
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair dpd, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
ERROR on proc 0: Cannot open dump file (../dump.cpp:603)
Last command: write_data dpd_data.all
What am I missing?
Hi Johana,
Hello Dezhao, and thank you.
I did create it, I am sorry I pasted the wrong output: all I can see is the following, it doesn’t do anything.
LAMMPS (2 Aug 2018)
Lattice spacing in x,y,z = 1.51967 2.63215 1.51967
Created orthogonal box = (0 0 -0.151967) to (75.9836 65.8037 0.151967)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 1.51967 2.63215 1.51967
Created 2500 atoms
Time spent = 0.00096488 secs
Lattice spacing in x,y,z = 1.51967 2.63215 1.51967
Created 2500 atoms
Time spent = 0.000313997 secs
System init for write_data ...
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.28239e+06
ghost atom cutoff = 8.28239e+06
binsize = 4.14119e+06, bins = 1 1 1
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair dpd, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
The third argument in pair_coeff for dpd is an interaction cutoff. Setting it to such a ridiculously high value cannot end well.
Michał
Joh_Nop
December 2, 2018, 12:49am
5
But here https://lammps.sandia.gov/doc/pair_dpd.html it says:
pair_style dpd T cutoff seed
Why does this get stuck?
The doc says pair_style dpd Temp Cutoff seed
comm_modify vel yes
velocity all create ${temp} 123456 dist gaussian
pair_style hybrid dpd 1 2.5 123456 soft 0.5
pair_coeff 1 1 dpd 0.7 2.5 12345
pair_coeff 2 2 dpd 0.7 2.5 12346
Michal flagged the issue, which is in your pair_coeff command, not
Steve
