This program works fine in small-scale simulations (4 nm), but when the scale is expanded to 30 nm, the output becomes nan when pressed down. Does anyone know what caused this?
units metal
atom_style atomic
boundary p p s
read_data Si_sphere_110.lmp
mass 1 28.0855
neighbor 2.0 bin
neigh_modify every 5 delay 10 check yes
pair_style tersoff
pair_coeff * * Si.tersoff Si
minimize 1.0e-4 1.0e-6 1000 100000
compute sample_temp all temp
fix nvt all nvt temp 10.0 10.0 0.1
fix_modify nvt temp sample_temp
fix momentum all momentum 10 linear 0 0 1
compute msd_all all msd
timestep 0.0001
thermo 1000
thermo_style custom step c_sample_temp ke pe etotal c_msd_all[4] pxx pyy pzz pxy pxz pyz
dump relax all custom 1000 dump.relax.lammpstrj id type x y z
dump_modify relax sort id
run 100000
undump relax
variable z_top equal 308.224-0.15step
variable z_bottom equal -1+0.15step
fix indenter_top all indent 1000.0 plane z v_z_top hi units box
fix indenter_bottom all indent 1000.0 plane z v_z_bottom lo units box
variable force_z_top equal f_indenter_top[3]
variable force_z_bottom equal f_indenter_bottom[3]
thermo_modify lost warn
thermo 1000
thermo_style custom step c_sample_temp ke pe etotal v_force_z_top v_force_z_bottom c_msd_all[4] vol lx ly lz pxx pyy pzz pxy pxz pyz f_indenter_top[3] f_indenter_bottom[3] v_z_top v_z_bottom
dump compress all custom 1000 dump.compress.lammpstrj id type x y z vx vy vz fx fy fz
dump_modify compress sort id
run 100000
Per MPI rank memory allocation (min/avg/max) = 3.366 | 3.485 | 3.634 Mbytes
Step c_sample_temp KinEng PotEng TotEng v_force_z_top v_force_z_bottom c_msd_all[4] Volume Lx Ly Lz Pxx Pyy Pzz Pxy Pxz Pyz f_indenter_top[3] f_indenter_bottom[3] v_z_top v_z_bottom
100001 9.9932652 912.50196 -3241731.4 -3240818.9 1.5569086e+17 -1.5569086e+17 0.0021299618 40001906 307.22375 434.48 299.67885 101.87494 101.87494 101.87494 -1.1148576e-06 1.7674167e-09 1.3972206e-06 1.5569086e+17 -1.5569086e+17 -14691.926 14999.15
101000 nan nan nan nan nan nan -nan 40001906 307.22375 434.48 299.67885 -nan -nan nan -nan -nan -nan nan nan -14841.776 15149
102000 nan nan nan nan nan nan -nan 40001906 307.22375 434.48 299.67885 -nan -nan nan -nan -nan -nan nan nan -14991.776 15299