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 Lattice spacing in x,y,z = 3.17012 3.17012 3.17012 Created orthogonal box = (0 -42.0596 0) to (14.8692 42.0596 4.48323) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.40698 4.77914 4.48323 Created 178 atoms create_atoms CPU = 0.000178814 secs 178 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.40698 4.77914 4.48323 Created 178 atoms create_atoms CPU = 6.8903e-05 secs 178 atoms in group lower Displacing atoms ... 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 = 7.2 ghost atom cutoff = 7.2 binsize = 3.6, bins = 5 24 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 7.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 350 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 = 7.2 ghost atom cutoff = 7.2 binsize = 3.6, bins = 5 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.2 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) = 4.446 | 4.446 | 4.446 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3748.1159 0 -3748.1159 16892.123 37 0 -3782.3224 0 -3782.3224 -3322.5955 Loop time of 4.73052 on 1 procs for 37 steps with 350 atoms 79.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3748.11586378 -3782.31865385 -3782.32240857 Force two-norm initial, final = 67.0956 0.181416 Force max component initial, final = 27.1666 0.0247045 Final line search alpha, max atom move = 1 0.0247045 Iterations, force evaluations = 37 58 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7273 | 4.7273 | 4.7273 | 0.0 | 99.93 Neigh | 0.0010941 | 0.0010941 | 0.0010941 | 0.0 | 0.02 Comm | 0.0013225 | 0.0013225 | 0.0013225 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007627 | | | 0.02 Nlocal: 350 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3247 ave 3247 max 3247 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: 38224 ave 38224 max 38224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38224 Ave neighs/atom = 109.211 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 : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.446 | 4.446 | 4.446 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -3782.3224 0 -3782.3224 -3322.5955 5607.5504 41 0 -3782.3658 0 -3782.3658 2033.966 5596.0345 Loop time of 0.676241 on 1 procs for 4 steps with 350 atoms 59.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3782.32240857 -3782.36555545 -3782.36579084 Force two-norm initial, final = 35.2814 0.224868 Force max component initial, final = 34.0994 0.0397502 Final line search alpha, max atom move = 0.000321534 1.27811e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.67574 | 0.67574 | 0.67574 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012469 | 0.00012469 | 0.00012469 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003796 | | | 0.06 Nlocal: 350 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3245 ave 3245 max 3245 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: 38272 ave 38272 max 38272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38272 Ave neighs/atom = 109.349 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 = 7.2 ghost atom cutoff = 7.2 binsize = 3.6, bins = 5 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.584 | 4.584 | 4.584 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3782.3658 0 -3782.3658 2033.966 Loop time of 9.53674e-07 on 1 procs for 0 steps with 350 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: 350 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3245 ave 3245 max 3245 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: 38272 ave 38272 max 38272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38272 Ave neighs/atom = 109.349 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) = 4.584 | 4.584 | 4.584 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 -3782.3658 -3782.3658 14.87913 84.119173 4.4710329 2033.966 2033.966 -1.2319038 6099.4229 3.7071343 2.4986829 369.14566 Loop time of 1.90735e-06 on 1 procs for 0 steps with 350 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 | | 1.907e-06 | | |100.00 Nlocal: 350 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3245 ave 3245 max 3245 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19136 ave 19136 max 19136 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 38272 ave 38272 max 38272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38272 Ave neighs/atom = 109.349 Neighbor list builds = 0 Dangerous builds = 0 350 -2303.45967129705 eV 2.49868287959146 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05