Dear Sir
I want to simulate MoS2 sheet using lammps, for this purpose i use material studio for structure generation and i use msi2lmp tool to convert .car and .mdf file from material studio output into lammps data file. (MoS2.data) then i read this data file using lammps input script and start to perform simulation but simulation stop at the start by error as i mentioned below. I have attached data file along with this email. Can any body please helps me to figure out whats wrong in thee setting? the input script i have used is also shown below
Output
LAMMPS (10 Feb 2015)
WARNING: OMP_NUM_THREADS environment is not set. (…/comm.cpp:89)
using 1 OpenMP thread(s) per MPI task
Reading data file …
triclinic box = (-4.48942 -0.152469 3.081) to (14.5246 16.3141 27.729) with tilt (-9.507 0 0)
1 by 2 by 2 MPI processor grid
WARNING: Atom style in data file differs from currently defined atom style (…/read_data.cpp:261)
reading atoms …
108 atoms
scanning bonds …
6 = max bonds/atom
scanning angles …
15 = max angles/atom
scanning dihedrals …
60 = max dihedrals/atom
scanning impropers …
1 = max impropers/atom
reading bonds …
216 bonds
reading angles …
756 angles
reading dihedrals …
2160 dihedrals
reading impropers …
72 impropers
Finding 1-2 1-3 1-4 neighbors …
6 = max # of 1-2 neighbors
15 = max # of 1-3 neighbors
72 = max # of 1-4 neighbors
30 = max # of special neighbors
Setting atom values …
108 settings made for charge
Setting atom values …
0 settings made for charge
PPPM initialization …
WARNING: System is not charge neutral, net charge = 82.08 (…/kspace.cpp:293)
G vector (1/distance) = 0.26965
grid = 20 30 24
stencil order = 5
estimated absolute RMS force accuracy = 8.09549e-07
estimated relative force accuracy = 8.09549e-07
using double precision FFTs
3d grid and FFT values/proc = 8500 3600
Neighbor list info …
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
master list distance cutoff = 12.63
Setting up run …
WARNING: Inconsistent image flags (…/domain.cpp:678)
WARNING: Bond/angle/dihedral extent > half of periodic box length (…/domain.cpp:799)
Memory usage per processor = 35.2421 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5 -nan 66.865658 -nan -nan
MoS2.data (125 KB)