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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -44.805806 0.0000000) to (31.680000 44.805806 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8666667 6.0842611 4.9780318 Created 650 atoms create_atoms CPU = 0.001 seconds 650 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8666667 6.0842611 4.9780318 Created 650 atoms create_atoms CPU = 0.001 seconds 650 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 ghost atom cutoff = 6 binsize = 3, bins = 11 30 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1288 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 ghost atom cutoff = 6 binsize = 3, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.033 | 5.033 | 5.033 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5673.8614 0 -5673.8614 11390.818 63 0 -5718.9722 0 -5718.9722 -6308.0766 Loop time of 2.37167 on 1 procs for 63 steps with 1288 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5673.86139879479 -5718.96664670507 -5718.97224480694 Force two-norm initial, final = 59.605917 0.23524716 Force max component initial, final = 16.054093 0.048959645 Final line search alpha, max atom move = 1.0000000 0.048959645 Iterations, force evaluations = 63 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3621 | 2.3621 | 2.3621 | 0.0 | 99.60 Neigh | 0.002671 | 0.002671 | 0.002671 | 0.0 | 0.11 Comm | 0.0036378 | 0.0036378 | 0.0036378 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003227 | | | 0.14 Nlocal: 1288.00 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5271.00 ave 5271 max 5271 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: 100476.0 ave 100476 max 100476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100476 Ave neighs/atom = 78.009317 Neighbor list builds = 1 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 : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.033 | 5.033 | 5.033 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -5718.9722 0 -5718.9722 -6308.0766 14132.114 65 0 -5718.9976 0 -5718.9976 -3385.9293 14110.113 Loop time of 0.127328 on 1 procs for 2 steps with 1288 atoms 96.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5718.97224480693 -5718.99751852869 -5718.99762628022 Force two-norm initial, final = 45.393821 0.24491268 Force max component initial, final = 34.909572 0.052313854 Final line search alpha, max atom move = 0.00067861194 3.5500806e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12655 | 0.12655 | 0.12655 | 0.0 | 99.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001586 | 0.0001586 | 0.0001586 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006161 | | | 0.48 Nlocal: 1288.00 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5279.00 ave 5279 max 5279 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: 100396.0 ave 100396 max 100396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100396 Ave neighs/atom = 77.947205 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 ghost atom cutoff = 6 binsize = 3, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.171 | 5.171 | 5.171 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5718.9976 0 -5718.9976 -3385.9293 Loop time of 2.2e-06 on 1 procs for 0 steps with 1288 atoms 136.4% 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 | | 2.2e-06 | | |100.00 Nlocal: 1288.00 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5279.00 ave 5279 max 5279 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: 100404.0 ave 100404 max 100404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100404 Ave neighs/atom = 77.953416 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) = 5.171 | 5.171 | 5.171 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 -5718.9976 -5718.9976 31.650639 89.611612 4.9748926 -3385.9293 -3385.9293 0.40340792 -10152.255 -5.9363928 2.3168714 456.84216 Loop time of 2.1e-06 on 1 procs for 0 steps with 1288 atoms 190.5% 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 | | 2.1e-06 | | |100.00 Nlocal: 1288.00 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5279.00 ave 5279 max 5279 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50202.0 ave 50202 max 50202 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 100404.0 ave 100404 max 100404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100404 Ave neighs/atom = 77.953416 Neighbor list builds = 0 Dangerous builds = 0 1288 -5718.99762628022 eV 2.31687144207719 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02