Dear lammps user,
My lammps version is 29 Sep 2021.
I am trying to compute the mean square displacement “MSD” using the “compute msd” command.
When I submit the below script to run 200 times in the computer cluster at my university, most of the runs generate reasonable MSD values but a few runs generate unreasonable MSD values.
I attached a plot of the MSD versus time in the log-log scale for different runs of the below script.
In the attached Figure, for example, msd.167 means the run number 167 out of 200 runs of the below script. This run, number 167, outputs unreasonable values for MSD at short time scales while the other runs generate reasonable values as it is clear from the Figure in the attached file
I run the script using :
lmp -in in.ellipsoids -screen none -var a “some integer”
Could you please tell me what could be wrong?
Thanks in advance
Mohammed
Here is the script
*************************************
units lj
dimension 3
boundary p p p
atom_style ellipsoid
lattice sc 0.0001
region box block 0.0 13.0 0.0 13.0 0.0 13.0 units lattice
create_box 1 box
create_atoms 1 box
set type 1 shape 2.5 1 1
set type 1 quat 0 0 1 0
velocity all create 1.0 ${seed1} mom yes rot yes dist gaussian
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
pair_style gayberne_rep 1.0 1.0 1.0 5.0 # gamma upsilon mu cutoff
pair_coeff 1 1 1 1 1.0 1.0 1.0 1.0 1.0 1.0
variable t_log equal logfreq2(1,45,10)
variable fixed_angle equal 0
timestep 0.0001
set type 1 quat 0 0 1 ${fixed_angle}
velocity all create 1.0 ${seed2} mom yes rot yes dist gaussian
fix 213 all brownian/asphere 1.0 ${seed3} gamma_t_eigen 1.089 1.089 0.859 gamma_r_eigen 9.351 9.351 1.667 rng gaussian
run 50000
reset_timestep 0
timestep 0.0001
set type 1 quat 0 0 1 ${fixed_angle}
compute msd all msd com yes
variable twopoint equal c_msd[4]/6/(step*dt+1.0e-6)
fix 9 all vector 10 c_msd[4]
variable fitslope equal slope(f_9)/6/(10*dt)
variable msd_var_x equal c_msd[1]
variable msd_var_y equal c_msd[2]
variable msd_var_z equal c_msd[3]
variable msd_var equal c_msd[4]
fix msdlog all print v_t_log "$(step) $(v_msd_var_x:%6.11f) $(v_msd_var_y:%6.11f) $(v_msd_var_z:%6.11f) $(v_msd_var:%6.11f)" file msdMe.$a
dump 222 all custom 100 coordMe.$a id x y z c_orient[*]
dump_modify 222 every v_t_log first yes pbc yes sort id
run 1000000
