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 = 3.48714 3.48714 3.48714 Created orthogonal box = (0 -59.5918 0) to (29.7942 59.5918 3.48714) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.48953 4.48953 3.48714 Created 586 atoms create_atoms CPU = 0.000221968 secs 586 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.48953 4.48953 3.48714 Created 586 atoms create_atoms CPU = 0.000112057 secs 586 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 8 32 1 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 7.61876 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1156 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.61876 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) = 5.464 | 5.464 | 5.464 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5099.0819 0 -5099.0819 6360.7734 54 0 -5126.7141 0 -5126.7141 -7445.4343 Loop time of 1.21249 on 1 procs for 54 steps with 1156 atoms 100.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5099.08185354 -5126.71010379 -5126.71407998 Force two-norm initial, final = 59.0092 0.289578 Force max component initial, final = 16.6035 0.0841612 Final line search alpha, max atom move = 1 0.0841612 Iterations, force evaluations = 54 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1993 | 1.1993 | 1.1993 | 0.0 | 98.91 Neigh | 0.0039079 | 0.0039079 | 0.0039079 | 0.0 | 0.32 Comm | 0.0063291 | 0.0063291 | 0.0063291 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002954 | | | 0.24 Nlocal: 1156 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9659 ave 9659 max 9659 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: 201760 ave 201760 max 201760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201760 Ave neighs/atom = 174.533 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 : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.464 | 5.464 | 5.464 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -5126.7141 0 -5126.7141 -7445.4343 12382.775 57 0 -5126.8089 0 -5126.8089 -1372.5674 12339.211 Loop time of 0.058681 on 1 procs for 3 steps with 1156 atoms 102.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5126.71407998 -5126.8088648 -5126.80893514 Force two-norm initial, final = 76.1872 0.370686 Force max component initial, final = 56.8049 0.111475 Final line search alpha, max atom move = 0.00149025 0.000166125 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.057734 | 0.057734 | 0.057734 | 0.0 | 98.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026369 | 0.00026369 | 0.00026369 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006833 | | | 1.16 Nlocal: 1156 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9641 ave 9641 max 9641 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: 201864 ave 201864 max 201864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201864 Ave neighs/atom = 174.623 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.61876 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) = 5.602 | 5.602 | 5.602 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5126.8089 0 -5126.8089 -1372.5674 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1156 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: 1156 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9653 ave 9653 max 9653 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: 201892 ave 201892 max 201892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201892 Ave neighs/atom = 174.647 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) = 5.602 | 5.602 | 5.602 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 -5126.8089 -5126.8089 29.742057 119.18367 3.480965 -1372.5674 -1372.5674 -13.501364 -4116.2235 12.022784 2.2226734 443.48654 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1156 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: 1156 ave 1156 max 1156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9653 ave 9653 max 9653 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100946 ave 100946 max 100946 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 201892 ave 201892 max 201892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201892 Ave neighs/atom = 174.647 Neighbor list builds = 0 Dangerous builds = 0 1156 -5126.80893514177 eV 2.22267338864805 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01