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 = 2.8826503 2.8826503 2.8826503 Created orthogonal box = (0.0000000 -40.766831 0.0000000) to (20.383415 40.766831 2.8826503) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.2613465 3.2613465 2.8826503 Created 200 atoms using lattice units in orthogonal box = (0.0000000 -40.766831 0.0000000) to (20.383415 40.766831 2.8826503) create_atoms CPU = 0.001 seconds 200 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.2613465 3.2613465 2.8826503 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -40.766831 0.0000000) to (20.383415 40.766831 2.8826503) create_atoms CPU = 0.001 seconds 202 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 5 19 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 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 402 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_331285495617_004#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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 4.881 | 4.881 | 4.881 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1290.3991 0 -1290.3991 107573.67 58 0 -1552.4019 0 -1552.4019 15699.54 Loop time of 1.26735 on 1 procs for 58 steps with 402 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1290.39910306763 -1552.40059105223 -1552.40189372955 Force two-norm initial, final = 446.67855 0.15774309 Force max component initial, final = 102.61743 0.020457928 Final line search alpha, max atom move = 1.0000000 0.020457928 Iterations, force evaluations = 58 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2315 | 1.2315 | 1.2315 | 0.0 | 97.17 Neigh | 0.012857 | 0.012857 | 0.012857 | 0.0 | 1.01 Comm | 0.014534 | 0.014534 | 0.014534 | 0.0 | 1.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008498 | | | 0.67 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5879.00 ave 5879 max 5879 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: 98528.0 ave 98528 max 98528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98528 Ave neighs/atom = 245.09453 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.882 | 4.882 | 4.882 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -1552.4019 0 -1552.4019 15699.54 4790.7759 97 0 -1553.6819 0 -1553.6819 688.33678 4833.4068 Loop time of 0.509594 on 1 procs for 39 steps with 402 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1552.40189372955 -1553.68116685239 -1553.68191707333 Force two-norm initial, final = 93.266581 3.9300010 Force max component initial, final = 68.668253 2.5066715 Final line search alpha, max atom move = 0.0011197099 0.0028067449 Iterations, force evaluations = 39 40 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47495 | 0.47495 | 0.47495 | 0.0 | 93.20 Neigh | 0.012794 | 0.012794 | 0.012794 | 0.0 | 2.51 Comm | 0.0056411 | 0.0056411 | 0.0056411 | 0.0 | 1.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01621 | | | 3.18 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6272.00 ave 6272 max 6272 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: 96440.0 ave 96440 max 96440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96440 Ave neighs/atom = 239.90050 Neighbor list builds = 1 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 4.640 | 4.640 | 4.640 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1553.6819 0 -1553.6819 688.33678 Loop time of 6.495e-06 on 1 procs for 0 steps with 402 atoms 169.4% 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 | | 6.495e-06 | | |100.00 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6219.00 ave 6219 max 6219 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: 94160.0 ave 94160 max 94160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94160 Ave neighs/atom = 234.22886 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 4.640 | 4.640 | 4.640 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 -1553.6819 -1553.6819 20.855646 82.904627 2.7954448 688.33678 688.33678 706.43957 552.79648 805.77428 2.379057 247.20662 Loop time of 6.906e-06 on 1 procs for 0 steps with 402 atoms 231.7% 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 | | 6.906e-06 | | |100.00 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6219.00 ave 6219 max 6219 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47080.0 ave 47080 max 47080 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 94160.0 ave 94160 max 94160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94160 Ave neighs/atom = 234.22886 Neighbor list builds = 0 Dangerous builds = 0 402 -1553.68191707334 eV 2.37905695413416 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02