Hi
I am using fix/deform command using scale and I have to restart the simulation after few steps. LAMMPS reads the restart file, but instead of calculating the final box sizes from the initial box size, LAMMPS calculates the final box sizes from the restart box size and hence the deformation rate is changed. LAMMPS adjusts the steps to account for the already simulated timesteps after the first run but the final box size, which is calculated first is already modified to a higher value.
I am pasting a small portion of the output code to show what is happening:
begin output
part of the input script
orthogonal box = (-102.248 -70.8392 0.0) to (102.248 70.8392 62.6136)
pair_style eam
pair_coeff * * /potentials/Cu.eam
timestep 0.000812
thermo_style custom step lx
thermo 1
fix sim-nvt all nvt 100 100 0.1
dump 11 all custom 200 dat.*.gz xs ys zs tag epair centro
restart 1000 file_restart1 file_restart2
fix vol-rescale all deform 1 x scale 1.06 y scale 1.06
I have tried using everything else, like using only, “10000 upto stop 10000”, “10000 upto start 0”, “start 0 stop 10000” but the result is the same
run 10000 upto start 0 stop 10000
unfix vol-rescale
run 50000 upto
Output from the lammps: run before the simulation had to be stopped
Step Lx
2390 207.42774
2391 207.42897
2392 207.4302
2393 207.43142
2394 207.43265
2395 207.43388
2396 207.43511
2397 207.43633
2398 207.43756
2399 207.43879
2400 207.44001 ### 1.01440 times initial X dimension
simulation stopped and then restarted
the restart script file --begin
read_restart file_restart2
pair_style eam
pair_coeff * * /potentials/Cu.eam
timestep 0.000812
thermo_style custom step pe etotal vol temp lx cpu
thermo 1
fix sim-nvt all nvt 100 100 0.1
dump 11 all custom 200 dat.*.gz xs ys zs tag epair centro
restart 1000 file_restart1 file_restart2
fix vol-rescale all deform 1 x scale 1.06 yscale 1.06
run 10000 upto start 0 stop 10000
I have tried using everything else, like using only, “10000 upto stop 10000”, “10000 upto start 0”, “start 0 stop 10000”
unfix vol-rescale
run 50000 upto
the restart script file --end
restart simulation output
LAMMPS (22 Jun 2007)
Reading restart file …
WARNING: Resetting unit_style to restart file value
WARNING: Resetting boundary settings to restart file values
orthogonal box = (-103.72 -71.8593 0.0437496) to (103.72 71.8593 62.5859)
1 by 1 by 1 processor grid
158720 atoms
Setting up run …
Memory usage per processor = 187.396 Mbytes
Step Lx
2400 207.44001
2401 210.42839 ### 1.01440 times X dimension at timestep = 2400
2402 210.42964
2403 210.43088
2404 210.43213
2405 210.43337
2406 210.43462
2407 210.43586
2408 210.43711
2409 210.43835
end output
Is there anything wrong in my script ? Kindly suggest.
Thank you,
Kedar.
Kedarnath Kolluri
Ph.D Candidate, Dept of Chemical Engineering
University of Massachusetts, Amherst, MA 01003
Ph: 413-577-0136
kedar@…424…