LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task # Using KIM Simulator Model : Sim_LAMMPS_SNAP_ChenDengTran_2017_Mo__SM_003882782678_000 # For Simulator : LAMMPS 12 Dec 2018 # Running on : LAMMPS 7 Aug 2019 # Lattice spacing in x,y,z = 3.15999 3.15999 3.15999 Created orthogonal box = (0 -39.0901 0) to (18.4257 39.0901 4.4689) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.41934 5.36487 4.4689 Created 206 atoms create_atoms CPU = 0.000296831 secs 206 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.41934 5.36487 4.4689 Created 206 atoms create_atoms CPU = 0.000140905 secs 206 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXKVn9xg/Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18 SNAP Element = Mo, Radius 0.5, Weight 1 Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXKVn9xg/Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18 SNAP keyword rcutfac 4.615858 SNAP keyword twojmax 6 System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.61586 ghost atom cutoff = 6.61586 binsize = 3.30793, bins = 6 24 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair snap, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 404 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.61586 ghost atom cutoff = 6.61586 binsize = 3.30793, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair snap, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.72 | 4.72 | 4.72 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9011.401 0 -9011.401 7744.8098 32 0 -9033.8075 0 -9033.8075 -3000.6891 Loop time of 3.7135 on 1 procs for 32 steps with 404 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9011.40098387 -9033.801833 -9033.80750818 Force two-norm initial, final = 38.2176 0.240084 Force max component initial, final = 11.365 0.047261 Final line search alpha, max atom move = 1 0.047261 Iterations, force evaluations = 32 54 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7107 | 3.7107 | 3.7107 | 0.0 | 99.93 Neigh | 0.0010221 | 0.0010221 | 0.0010221 | 0.0 | 0.03 Comm | 0.0010335 | 0.0010335 | 0.0010335 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007091 | | | 0.02 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2456 ave 2456 max 2456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25896 ave 25896 max 25896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25896 Ave neighs/atom = 64.099 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.722 | 4.722 | 4.722 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -9033.8075 0 -9033.8075 -3000.6891 6437.5655 33 0 -9033.8133 0 -9033.8133 -926.26249 6432.353 Loop time of 0.191677 on 1 procs for 1 steps with 404 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9033.80750818 -9033.80750818 -9033.81332263 Force two-norm initial, final = 13.4194 6.41659 Force max component initial, final = 13.3919 6.40049 Final line search alpha, max atom move = 7.46718e-05 0.000477936 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19151 | 0.19151 | 0.19151 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 4.6968e-05 | 4.6968e-05 | 4.6968e-05 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000124 | | | 0.06 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2416 ave 2416 max 2416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25924 ave 25924 max 25924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25924 Ave neighs/atom = 64.1683 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.61586 ghost atom cutoff = 6.61586 binsize = 3.30793, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair snap, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (3) compute pair/local, occasional, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.353 | 4.353 | 4.353 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9033.8133 0 -9033.8133 -926.26249 Loop time of 1.19209e-06 on 1 procs for 0 steps with 404 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.192e-06 | | |100.00 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2416 ave 2416 max 2416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25924 ave 25924 max 25924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25924 Ave neighs/atom = 64.1683 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.353 | 4.353 | 4.353 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -9033.8133 -9033.8133 18.426717 78.180111 4.4650427 -926.26249 -926.26249 1594.324 -4469.5279 96.416488 2.5056735 371.3432 Loop time of 9.53674e-07 on 1 procs for 0 steps with 404 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2416 ave 2416 max 2416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12962 ave 12962 max 12962 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25924 ave 25924 max 25924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25924 Ave neighs/atom = 64.1683 Neighbor list builds = 0 Dangerous builds = 0 404 -2054.39180311289 eV 2.50567350948257 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04