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 = 3.16669 3.16669 3.16669 Created orthogonal box = (0 -49.4684 0) to (24.7326 49.4684 3.16669) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.45998 4.45998 3.16669 Created 245 atoms create_atoms CPU = 0.000164032 secs 245 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.45998 4.45998 3.16669 Created 245 atoms create_atoms CPU = 5.48363e-05 secs 245 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 = 6.7012 ghost atom cutoff = 6.7012 binsize = 3.3506, bins = 8 30 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 6.7012 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 488 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 = 6.7012 ghost atom cutoff = 6.7012 binsize = 3.3506, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7012 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) = 4.473 | 4.473 | 4.473 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 52.736447 0 52.736447 19097.632 93 0 11.002845 0 11.002845 4657.8101 Loop time of 18.5764 on 1 procs for 93 steps with 488 atoms 76.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = 52.7364471439 11.0028563059 11.0028454987 Force two-norm initial, final = 36.7353 0.0113717 Force max component initial, final = 11.1673 0.00216265 Final line search alpha, max atom move = 1 0.00216265 Iterations, force evaluations = 93 166 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.548 | 18.548 | 18.548 | 0.0 | 99.85 Neigh | 0.021245 | 0.021245 | 0.021245 | 0.0 | 0.11 Comm | 0.0045419 | 0.0045419 | 0.0045419 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002321 | | | 0.01 Nlocal: 488 ave 488 max 488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3826 ave 3826 max 3826 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: 31652 ave 31652 max 31652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31652 Ave neighs/atom = 64.8607 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 : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.474 | 4.474 | 4.474 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 11.002845 0 11.002845 4657.8101 7748.7705 96 0 10.98699 0 10.98699 1360.6282 7758.5401 Loop time of 0.667046 on 1 procs for 3 steps with 488 atoms 100.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = 11.0028454987 10.9869903802 10.9869900455 Force two-norm initial, final = 26.9667 0.122046 Force max component initial, final = 24.9042 0.102515 Final line search alpha, max atom move = 0.0678153 0.00695209 Iterations, force evaluations = 3 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.66638 | 0.66638 | 0.66638 | 0.0 | 99.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017571 | 0.00017571 | 0.00017571 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004926 | | | 0.07 Nlocal: 488 ave 488 max 488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3816 ave 3816 max 3816 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: 31616 ave 31616 max 31616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31616 Ave neighs/atom = 64.7869 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 = 6.7012 ghost atom cutoff = 6.7012 binsize = 3.3506, bins = 8 30 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7012 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) = 4.612 | 4.612 | 4.612 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 10.98699 0 10.98699 1360.6282 Loop time of 9.53674e-07 on 1 procs for 0 steps with 488 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: 488 ave 488 max 488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3816 ave 3816 max 3816 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: 31608 ave 31608 max 31608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31608 Ave neighs/atom = 64.7705 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) = 4.612 | 4.612 | 4.612 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 10.98699 10.98699 24.76424 98.936779 3.1666294 1360.6282 1360.6282 10.959378 4049.7558 21.169489 2.4636564 112.49476 Loop time of 9.53674e-07 on 1 procs for 0 steps with 488 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: 488 ave 488 max 488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3816 ave 3816 max 3816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15804 ave 15804 max 15804 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 31608 ave 31608 max 31608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31608 Ave neighs/atom = 64.7705 Neighbor list builds = 0 Dangerous builds = 0 488 -3345.01219923958 eV 2.46365640972352 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19