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 = 2.8603420 2.8603420 2.8603420 Created orthogonal box = (0.0000000 -39.326061 0.0000000) to (10.702420 39.326061 7.0063784) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5867513 4.3692446 4.6709189 Created 254 atoms using lattice units in orthogonal box = (0.0000000 -39.326061 0.0000000) to (10.702420 39.326061 7.0063784) create_atoms CPU = 0.001 seconds 254 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5867513 4.3692446 4.6709189 Created 254 atoms using lattice units in orthogonal box = (0.0000000 -39.326061 0.0000000) to (10.702420 39.326061 7.0063784) create_atoms CPU = 0.000 seconds 254 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 3 21 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 500 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 3 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.546 | 4.546 | 4.546 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2118.7635 0 -2118.7635 3459.5057 347 0 -2173.2537 0 -2173.2537 2618.183 Loop time of 2.69728 on 1 procs for 347 steps with 500 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 = -2118.76346256973 -2173.25172956795 -2173.25371215265 Force two-norm initial, final = 54.787016 0.20182175 Force max component initial, final = 18.790150 0.050661126 Final line search alpha, max atom move = 1.0000000 0.050661126 Iterations, force evaluations = 347 671 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6241 | 2.6241 | 2.6241 | 0.0 | 97.29 Neigh | 0.038352 | 0.038352 | 0.038352 | 0.0 | 1.42 Comm | 0.020505 | 0.020505 | 0.020505 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01435 | | | 0.53 Nlocal: 500.000 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4222.00 ave 4222 max 4222 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: 83382.0 ave 83382 max 83382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83382 Ave neighs/atom = 166.76400 Neighbor list builds = 7 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 3 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 347 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.546 | 4.546 | 4.546 Mbytes Step Temp E_pair E_mol TotEng Press Volume 347 0 -2173.2537 0 -2173.2537 2618.183 5897.7454 367 0 -2176.4035 0 -2176.4035 -3606.5037 5906.5501 Loop time of 0.0906026 on 1 procs for 20 steps with 500 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 = -2173.25371215265 -2176.40303835902 -2176.40352385277 Force two-norm initial, final = 240.82660 1.0596393 Force max component initial, final = 196.23463 0.31345886 Final line search alpha, max atom move = 0.00048882972 0.00015322801 Iterations, force evaluations = 20 21 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.087113 | 0.087113 | 0.087113 | 0.0 | 96.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00062268 | 0.00062268 | 0.00062268 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002867 | | | 3.16 Nlocal: 500.000 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4109.00 ave 4109 max 4109 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: 83836.0 ave 83836 max 83836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83836 Ave neighs/atom = 167.67200 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 3 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.686 | 4.686 | 4.686 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2176.4035 0 -2176.4035 -3606.5037 Loop time of 2.004e-06 on 1 procs for 0 steps with 500 atoms 99.8% 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 | | 2.004e-06 | | |100.00 Nlocal: 500.000 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4348.00 ave 4348 max 4348 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: 83562.0 ave 83562 max 83562 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83562 Ave neighs/atom = 167.12400 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 3 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.686 | 4.686 | 4.686 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 -2176.4035 -2176.4035 10.908403 78.652123 6.8843397 -3606.5037 -3606.5037 -86.663493 -10786.843 53.995641 2.3563442 1744.2898 Loop time of 2.873e-06 on 1 procs for 0 steps with 500 atoms 174.0% 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 | | 2.873e-06 | | |100.00 Nlocal: 500.000 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4348.00 ave 4348 max 4348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 41781.0 ave 41781 max 41781 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 83562.0 ave 83562 max 83562 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83562 Ave neighs/atom = 167.12400 Neighbor list builds = 0 Dangerous builds = 0 500 -2176.40352385277 eV 2.35634418111139 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03