LAMMPS (24 Dec 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -55.458454 0.0000000) to (33.959072 55.458454 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4772697 5.3666064 5.7504086 Created 1494 atoms create_atoms CPU = 0.001 seconds 1494 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4772697 5.3666064 5.7504086 Created 1494 atoms create_atoms CPU = 0.001 seconds 1494 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 35 3 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 36 atoms, new total = 2952 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 35 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.711 | 5.711 | 5.711 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13034.355 0 -13034.355 3930.1883 21 0 -13090.626 0 -13090.626 -7014.3279 Loop time of 1.71511 on 1 procs for 21 steps with 2952 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 = -13034.3551766504 -13090.6142746462 -13090.6257755307 Force two-norm initial, final = 77.065917 0.39292363 Force max component initial, final = 15.555285 0.051511823 Final line search alpha, max atom move = 1.0000000 0.051511823 Iterations, force evaluations = 21 36 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7115 | 1.7115 | 1.7115 | 0.0 | 99.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016816 | 0.0016816 | 0.0016816 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001974 | | | 0.12 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8801.00 ave 8801 max 8801 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 254484.0 ave 254484 max 254484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 254484 Ave neighs/atom = 86.207317 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Setting up cg style minimization ... Unit style : metal Current step : 21 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.711 | 5.711 | 5.711 Mbytes Step Temp E_pair E_mol TotEng Press Volume 21 0 -13090.626 0 -13090.626 -7014.3279 32489.538 24 0 -13090.813 0 -13090.813 -1808.6405 32397.828 Loop time of 0.279501 on 1 procs for 3 steps with 2952 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13090.6257755308 -13090.8118771007 -13090.8129420773 Force two-norm initial, final = 178.60248 0.43121229 Force max component initial, final = 147.27134 0.060761811 Final line search alpha, max atom move = 0.00012039584 7.3154691e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2783 | 0.2783 | 0.2783 | 0.0 | 99.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000249 | 0.000249 | 0.000249 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000957 | | | 0.34 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8792.00 ave 8792 max 8792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 258108.0 ave 258108 max 258108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258108 Ave neighs/atom = 87.434959 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 35 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.849 | 5.849 | 5.849 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13090.813 0 -13090.813 -1808.6405 Loop time of 2.00002e-06 on 1 procs for 0 steps with 2952 atoms 150.0% 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 | | 2e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8801.00 ave 8801 max 8801 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 258540.0 ave 258540 max 258540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258540 Ave neighs/atom = 87.581301 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) = 5.849 | 5.849 | 5.849 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 -13090.813 -13090.813 33.927723 110.91691 8.6092124 -1808.6405 -1808.6405 -2.9693808 -5421.6441 -1.3078975 2.2469785 968.19474 Loop time of 2.29999e-06 on 1 procs for 0 steps with 2952 atoms 130.4% 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 | | 2.3e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8801.00 ave 8801 max 8801 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 129270.0 ave 129270 max 129270 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 258540.0 ave 258540 max 258540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258540 Ave neighs/atom = 87.581301 Neighbor list builds = 0 Dangerous builds = 0 2952 -13090.8129420773 eV 2.24697851554244 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02