LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 4.0415970 4.0415970 4.0415970 Created orthogonal box = (0.0000000 -63.647134 0.0000000) to (38.975750 63.647134 9.8998505) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2864113 6.1594000 6.5999003 Created 1486 atoms using lattice units in orthogonal box = (0.0000000 -63.647134 0.0000000) to (38.975750 63.647134 9.8998505) create_atoms CPU = 0.003 seconds 1486 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2864113 6.1594000 6.5999003 Created 1492 atoms using lattice units in orthogonal box = (0.0000000 -63.647134 0.0000000) to (38.975750 63.647134 9.8998505) create_atoms CPU = 0.002 seconds 1492 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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 13 43 4 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, ghost, cut 6.04112 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 4 atoms, new total = 2974 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_992900971352_000#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 13 43 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.04112 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 6.275 | 6.275 | 6.275 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9605.614 0 -9605.614 18833.919 82 0 -9995.0618 0 -9995.0618 9869.23 Loop time of 43.28 on 1 procs for 82 steps with 2974 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 = -9605.61396118249 -9995.05212629563 -9995.0618438892 Force two-norm initial, final = 280.32577 0.29040535 Force max component initial, final = 45.650085 0.021394025 Final line search alpha, max atom move = 1.0000000 0.021394025 Iterations, force evaluations = 82 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 43.204 | 43.204 | 43.204 | 0.0 | 99.83 Neigh | 0.044364 | 0.044364 | 0.044364 | 0.0 | 0.10 Comm | 0.010347 | 0.010347 | 0.010347 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0208 | | | 0.05 Nlocal: 2974.00 ave 2974 max 2974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6337.00 ave 6337 max 6337 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: 160016.0 ave 160016 max 160016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160016 Ave neighs/atom = 53.804976 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 13 43 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.04112 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.278 | 6.278 | 6.278 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -9995.0618 0 -9995.0618 9869.23 49117.015 89 0 -9996.2913 0 -9996.2913 -14.289901 49448.253 Loop time of 2.08971 on 1 procs for 7 steps with 2974 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 = -9995.06184388913 -9996.29052448743 -9996.2913262867 Force two-norm initial, final = 551.98728 2.0942219 Force max component initial, final = 440.84890 1.9311972 Final line search alpha, max atom move = 9.6030146e-05 0.00018545315 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0857 | 2.0857 | 2.0857 | 0.0 | 99.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00046774 | 0.00046774 | 0.00046774 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003524 | | | 0.17 Nlocal: 2974.00 ave 2974 max 2974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6575.00 ave 6575 max 6575 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: 160128.0 ave 160128 max 160128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160128 Ave neighs/atom = 53.842636 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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 13 43 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.04112 pair build: full/bin/ghost stencil: full/ghost/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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.416 | 6.416 | 6.416 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9996.2913 0 -9996.2913 -14.289901 Loop time of 1.976e-06 on 1 procs for 0 steps with 2974 atoms 151.8% 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 | | 1.976e-06 | | |100.00 Nlocal: 2974.00 ave 2974 max 2974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6536.00 ave 6536 max 6536 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: 160068.0 ave 160068 max 160068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160068 Ave neighs/atom = 53.822461 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 = 6.04112 ghost atom cutoff = 6.04112 binsize = 3.02056, bins = 13 43 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.04112 pair build: full/bin/ghost stencil: full/ghost/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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.416 | 6.416 | 6.416 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 -9996.2913 -9996.2913 39.015406 128.05929 9.8970038 -14.289901 -14.289901 -62.636527 17.981244 1.7855812 2.5571437 1466.6223 Loop time of 2.156e-06 on 1 procs for 0 steps with 2974 atoms 185.5% 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 | | 2.156e-06 | | |100.00 Nlocal: 2974.00 ave 2974 max 2974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6536.00 ave 6536 max 6536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 80034.0 ave 80034 max 80034 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 160068.0 ave 160068 max 160068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160068 Ave neighs/atom = 53.822461 Neighbor list builds = 0 Dangerous builds = 0 2974 -9996.2913262867 eV 2.55714365228569 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:46