Hi:
I am modeling perfluoropolyether/carbon bi-layer system. I build up the model in Materials Studio, converted to LAMMPS input via “msi2lmp” tool with pcff potential. Then I am equilibrating the model via classII forcefield. Some of my input script is as follows. However, I met energy ‘nan’ problem at minimize step as below. I check the dump file output & find that only one atom has the force vector as ‘nan’ at “timestep 0”.
I have carefully checked the coordinates of atoms & believe there is no overlapping or over-close pair of atoms. The atom shown (in dump file) with ‘nan’ force vectors actually has a distance of 2.01 Anstrong to the nearest neighbor. To avoid random reason, I have tried to set the zero force at the beginning (fix setforce), but the problem still exists.
I believe there is no coordinate overlapping because only one atom shows force as ‘nan’. Because any actual overlapping atom pairs will at least cause two ‘nan’ cases.
Would highly appreciate if any advise!
Input script:
……
Forcefield
pair_style lj/class2/coul/cut 10.
bond_style class2
angle_style class2
dihedral_style class2
improper_style class2
Atom definition
read_data NS.inp
Parameter of simulation
neighbor 5 bin
neigh_modify every 10 delay 0 check yes
timestep 0.1
……
Minimize
minimize 0.0 1.0e-8 1000 100000
Equilibration
fix 1 all nvt temp 300.0 300.0 100.0
run 10000
Output (log.lammmps):
……….
Minimize
minimize 0.0 1.0e-8 1000 100000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 90.6056 Mbytes
Step Temp E_pair E_mol TotEng Press
0 209.32771 55407.949 nan nan nan
1 209.32771 55407.949 nan nan nan
Dump data:
ITEM: TIMESTEP
0
ITEM: ATOMS id type x y z vx vy vz fx fy fz mol
….
10968 4 6.8552 1.0056 22.2926 4.9888e-03 -5.6215e-03 -6.4112e-03 0.0000 0.0000 0.0000 31
10997 4 0.6333 4.8765 22.0531 -1.9312e-03 -1.7868e-03 1.6617e-03 0.0000 0.0000 0.0000 31
1 1 17.6363 6.9447 28.9946 -7.5721e-03 -6.0609e-03 1.7162e-03 nan nan nan 1
2 2 19.0314 6.5512 28.8435 6.0839e-03 -2.1043e-03 -7.8102e-03 -28.2966 22.3860 13.3885 1
3 3 19.3154 5.5499 29.7162 -2.0617e-03 -1.4510e-04 -5.4143e-04 2.9177 -21.2351 16.9181 1
………
Thanks & Best Regards!
Dai Ling
Scientist
Institue of High Performance Computing, A*STAR
Singapore
Tel: +65-64191428