Nan for thermo_style quantities

Dear users,

I used to apply DLPOLY to simulate my models. Currently, I am moving to LAMMPS. To this aim, I transferred my data from DLPOLY format (e.g. CONFIG file) to LAMMPS format by providing a fortran code. When I run my simulation model (SPC/E water inside two carbon atom surfaces) to reach the equilibrate state I get “Nan ” error for temp, etotal, pe…(via thermo_style command).

I am also using the “fix adapt ” command to flee from “overlapping” issue. However, the “Nan” values are regularly happening.

So that, when try it with DLPOLY there is no error at all.

I’d be appreciated anybody explains the other possible reasons for this problem.

My input

***************** Initialization *********************

units real
dimension 3
boundary p p p
atom_style full
read_data atm_data.dat

group oxygen type 1
group hydrogen type 2
group carbon type 3
group water type 1 2

#soft potential

pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
variable prefactor equal ramp(1.0,20.0)
fix 1 all adapt 1 pair soft a * * v_prefactor

set group oxygen charge -0.8476
set group hydrogen charge 0.4238
set group carbon charge 0.0000

unfix 1

#pair_style dpd/tstat 300.0 300.0 10.0 34387
#comm_style brick
#comm_modify vel yes

#pair_style hybrid lj/cut/coul/long 10.0 10.0 tersoff
pair_style lj/cut/coul/long 10.0 10.0
pair_coeff 1 1 0.155300 3.16900 #lj/cut/coul/long
pair_coeff 1 2 0.00000 0.00000
pair_coeff 1 3 0.093627 3.1900
pair_coeff 2 2 0.000000 0.0000
pair_coeff 2 3 0.000000 0.0000
pair_coeff 3 3 0.000000 0.0000
#pair_coeff * * tersoff SiC_1994.tersoff NULL NULL C

bond_style harmonic
bond_coeff 1 529.581 1.0
angle_style harmonic
angle_coeff 1 37.95 109.47

fix force_zero carbon setforce 0.0 0.0 0.0
fix vel_zero carbon move linear 0.0 0.0 0.0 units lattice

#velocity oxygen create 300.0 34387 rot yes dist gaussian # for Oxygen
#velocity hydrogen create 300.0 34387 rot yes dist gaussian # for Hydrogen
#velocity water create 300.0 34387 rot yes dist gaussian # for water

kspace_style ewald 1.0e-6

*************** Setting ******************************

neighbor 2.0 bin
neigh_modify delay 0 every 10 check yes

reset_timestep 0

thermo 100
thermo_style custom step temp pe etotal press vol
thermo_modify norm no flush yes

minimize 1.0e-4 1.0e-6 100 1000
min_style cg

fix ensemble_set all nvt temp 300.0 300.0 0.05
fix spce_model water shake 0.0001 20 0 b 1 a 1#

#compute 1 all pe/atom
dump trj all atom 500 wat.lammpstrj
#dump trj all cfg 100 wat_lammpstrj.*.cfg id type xs ys zs
#dump_modify trj element O H C

#write_data waterinfo.data
#write_restart waterinfo.restart

timestep 0.2
run 1000

The error,

Step Temp PotEng TotEng Press Volume
0 0 nan nan nan 18000
100 0 nan nan nan 18000
200 0 nan nan nan 18000
300 0 nan nan nan 18000
400 0 nan nan nan 18000
500 0 nan nan nan 18000
600 0 nan nan nan 18000
700 0 nan nan nan 18000
800 0 nan nan nan 18000
900 0 nan nan nan 18000
1000 0 nan nan nan 18000

Thanks in advance

Dear users,

I used to apply DLPOLY to simulate my models. Currently, I am moving to
LAMMPS. To this aim, I transferred my data from DLPOLY format (e.g. CONFIG
file) to LAMMPS format by providing a fortran code. When I run my simulation
model (SPC/E water inside two carbon atom surfaces) to reach the equilibrate
state I get “Nan ” error for temp, etotal, pe....(via thermo_style command).

I am also using the “fix adapt ” command to flee from “overlapping” issue.

no, you don't. there is no run command before the pair style is
switched and fix adapt is unfixed. with the ridiculous cutoff and
unreasonably (for real units) potential parameter ramp, it would
likely not work as expected anyway.

However, the “Nan” values are regularly happening.

So that, when try it with DLPOLY there is no error at all.

what does it matter what DLPOLY does, when the data you feed to LAMMPS is crap?

I'd be appreciated anybody explains the other possible reasons for this
problem.

possible reasons for that have been discussed without end on this
mailing list. most likely you have a bad initial configuration (i.e.
your conversion tool is crap).
MD is "garbage in, garbage out". so you will have to make certain that
all the data is proper and in the way LAMMPS expects it.

axel