I printed out lots of diagnostics every time step.
thermo 1 setting:
The Result:
Step Temp TotEng Volume E_pair Press PotEng
0 2 3.8689479e+24 1706.6667 3.8689479e+24 -1.2642773e+27 3.8689479e+24
1 inf inf 0 0 nan 0
2 nan nan nan 0 nan 0
3 nan nan nan 0 nan 0
4 nan nan nan 0 nan 0
5 nan nan nan 0 nan 0
6 nan nan nan 0 nan 0
7 nan nan nan 0 nan 0
…
I tried another way. I didn’t thermostat with fix deform. I Just used it to get the correct density. unfix deform. Then run with thermostat. The input script is the following. İt is giving the error (NaNs) again when I ran with thermostat its.
units lj
atom_style ellipsoid
lattice sc 0.01
region box block 0 8 0 8 0 8
create_box 1 box
create_atoms 1 box
set group all quat/random 982381
mass 1 1.5
shape 1 1 1 3
compute rot all temp/asphere
group spheroid type 1
variable dof equal count(spheroid)+2
compute_modify rot extra ${dof}
velocity all create 2.0 41787 loop geom
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 1.0 1.0 1.0 1.0 0.2 1.0 1.0 0.2 4.0
neighbor 0.3 bin
timestep 0.002
thermo_style custom step temp etotal vol epair press pe
thermo 100
fix 1 all deform 10 x final 0 11.95 y final 0 11.95 z final 0 11.95 units box
restart 1000000 restart_*.dat
run 5000000 upto
This unfix is to remove the box rescaling
unfix 1
Now actually run the simulation at the target concentration
fix 2 all npt/asphere 2.0 2.0 0.5 xyz 0.0 8.0 0.5
compute_modify 2_temp extra ${dof}
run 5100000 upto
unfix 2
fix 3 all npt/asphere 2.0 2.0 0.5 xyz 8.0 8.0 0.5
compute_modify 3_temp extra ${dof}
run 5200000 upto
What should I do?
Thanks in advance