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 = 4.0469996 4.0469996 4.0469996 Created orthogonal box = (0.0000000 -46.851454 0.0000000) to (33.126119 46.851454 5.7233217) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4274559 6.9921503 5.7233217 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -46.851454 0.0000000) to (33.126119 46.851454 5.7233217) create_atoms CPU = 0.001 seconds 538 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4274559 6.9921503 5.7233217 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -46.851454 0.0000000) to (33.126119 46.851454 5.7233217) create_atoms CPU = 0.001 seconds 538 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 10 27 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 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 1062 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_958395190627_001#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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 4.611 | 4.611 | 4.611 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3532.0766 0 -3532.0766 4556.1097 75 0 -3561.2879 0 -3561.2879 -5373.0205 Loop time of 6.11904 on 1 procs for 75 steps with 1062 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3532.07657712127 -3561.28472887325 -3561.28785252953 Force two-norm initial, final = 23.389630 0.16630805 Force max component initial, final = 5.8249911 0.029893435 Final line search alpha, max atom move = 1.0000000 0.029893435 Iterations, force evaluations = 75 136 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.0918 | 6.0918 | 6.0918 | 0.0 | 99.55 Neigh | 0.012736 | 0.012736 | 0.012736 | 0.0 | 0.21 Comm | 0.0075837 | 0.0075837 | 0.0075837 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006911 | | | 0.11 Nlocal: 1062.00 ave 1062 max 1062 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5056.00 ave 5056 max 5056 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: 90588.0 ave 90588 max 90588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90588 Ave neighs/atom = 85.299435 Neighbor list builds = 2 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.611 | 4.611 | 4.611 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -3561.2879 0 -3561.2879 -5373.0205 17765.269 79 0 -3561.4322 0 -3561.4322 -1076.6356 17666.932 Loop time of 0.268965 on 1 procs for 4 steps with 1062 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 = -3561.28785252953 -3561.43128289728 -3561.43219729732 Force two-norm initial, final = 73.867506 2.2860776 Force max component initial, final = 56.648640 2.1224329 Final line search alpha, max atom move = 0.00027474421 0.00058312616 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26761 | 0.26761 | 0.26761 | 0.0 | 99.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002358 | 0.0002358 | 0.0002358 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001116 | | | 0.42 Nlocal: 1062.00 ave 1062 max 1062 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5056.00 ave 5056 max 5056 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: 90580.0 ave 90580 max 90580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90580 Ave neighs/atom = 85.291902 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.749 | 4.749 | 4.749 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3561.4322 0 -3561.4322 -1076.6356 Loop time of 1.621e-06 on 1 procs for 0 steps with 1062 atoms 185.1% 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 | | 1.621e-06 | | |100.00 Nlocal: 1062.00 ave 1062 max 1062 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5056.00 ave 5056 max 5056 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: 90688.0 ave 90688 max 90688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90688 Ave neighs/atom = 85.393597 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.749 | 4.749 | 4.749 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 -3561.4322 -3561.4322 33.012366 93.702908 5.7112532 -1076.6356 -1076.6356 74.843818 -3496.8237 192.07306 2.5414162 671.44068 Loop time of 1.671e-06 on 1 procs for 0 steps with 1062 atoms 119.7% 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 | | 1.671e-06 | | |100.00 Nlocal: 1062.00 ave 1062 max 1062 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5056.00 ave 5056 max 5056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45344.0 ave 45344 max 45344 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 90688.0 ave 90688 max 90688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90688 Ave neighs/atom = 85.393597 Neighbor list builds = 0 Dangerous builds = 0 1062 -3561.43219729732 eV 2.54141624152501 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06