LAMMPS (24 Jan 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 = 3.14096 3.14096 3.14096 Created orthogonal box = (0 -55.4836 0) to (32.0317 55.4836 5.44031) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.92795 4.97902 5.44031 Created 626 atoms create_atoms CPU = 0.000910997 secs 626 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.92795 4.97902 5.44031 Created 627 atoms create_atoms CPU = 0.0007689 secs 627 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 6 20 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 11.5437 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 1246 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 6 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.5437 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) = 6.723 | 6.723 | 6.723 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8041.4788 0 -8041.4788 59339.02 325 0 -8427.1026 0 -8427.1026 3950.0269 Loop time of 16.2156 on 1 procs for 325 steps with 1246 atoms 73.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8041.47884673 -8427.09440895 -8427.10259179 Force two-norm initial, final = 423.4 0.539595 Force max component initial, final = 89.2871 0.115736 Final line search alpha, max atom move = 0.286374 0.0331437 Iterations, force evaluations = 325 632 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.903 | 15.903 | 15.903 | 0.0 | 98.07 Neigh | 0.21348 | 0.21348 | 0.21348 | 0.0 | 1.32 Comm | 0.070433 | 0.070433 | 0.070433 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0287 | | | 0.18 Nlocal: 1246 ave 1246 max 1246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12321 ave 12321 max 12321 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: 514534 ave 514534 max 514534 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 514534 Ave neighs/atom = 412.949 Neighbor list builds = 9 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : metal Current step : 325 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.723 | 6.723 | 6.723 Mbytes Step Temp E_pair E_mol TotEng Press Volume 325 0 -8427.1026 0 -8427.1026 3950.0269 19337.377 340 0 -8434.2549 0 -8434.2549 -25792.913 19531.015 Loop time of 0.592992 on 1 procs for 15 steps with 1246 atoms 45.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8427.10259179 -8434.25437751 -8434.25490021 Force two-norm initial, final = 1037.27 4.12745 Force max component initial, final = 1035.92 1.90865 Final line search alpha, max atom move = 0.000146831 0.00028025 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.58695 | 0.58695 | 0.58695 | 0.0 | 98.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015287 | 0.0015287 | 0.0015287 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004517 | | | 0.76 Nlocal: 1246 ave 1246 max 1246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12331 ave 12331 max 12331 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: 514474 ave 514474 max 514474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 514474 Ave neighs/atom = 412.9 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 6 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.5437 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) = 6.859 | 6.859 | 6.859 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8434.2549 0 -8434.2549 -25792.913 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1246 atoms 157.3% 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: 1246 ave 1246 max 1246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12249 ave 12249 max 12249 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: 510636 ave 510636 max 510636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 510636 Ave neighs/atom = 409.82 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) = 6.859 | 6.859 | 6.859 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 -8434.2549 -8434.2549 31.907213 110.96721 5.5162162 -25792.913 -25792.913 76.319467 -77613.814 158.75622 2.6179775 7741.5225 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1246 atoms 139.8% 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 | | 2.146e-06 | | |100.00 Nlocal: 1246 ave 1246 max 1246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12249 ave 12249 max 12249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 255318 ave 255318 max 255318 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 510636 ave 510636 max 510636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 510636 Ave neighs/atom = 409.82 Neighbor list builds = 0 Dangerous builds = 0 1246 -8434.25490021091 eV 2.61797746437343 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17