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 = 3.4986965 3.4986965 3.4986965 Created orthogonal box = (0.0000000 -38.329799 0.0000000) to (7.8233233 38.329799 8.5700212) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6939940 5.1101734 5.7133475 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -38.329799 0.0000000) to (7.8233233 38.329799 8.5700212) create_atoms CPU = 0.002 seconds 242 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6939940 5.1101734 5.7133475 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -38.329799 0.0000000) to (7.8233233 38.329799 8.5700212) create_atoms CPU = 0.001 seconds 242 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 3 21 3 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 474 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 3 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.558 | 4.558 | 4.558 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1909.2124 0 -1909.2124 33984.278 69 0 -1941.3309 0 -1941.3309 -7894.0542 Loop time of 1.26264 on 1 procs for 69 steps with 474 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1909.21237778613 -1941.32952376257 -1941.33086132968 Force two-norm initial, final = 99.115829 0.19978034 Force max component initial, final = 42.086706 0.058266099 Final line search alpha, max atom move = 1.0000000 0.058266099 Iterations, force evaluations = 69 133 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2304 | 1.2304 | 1.2304 | 0.0 | 97.45 Neigh | 0.010644 | 0.010644 | 0.010644 | 0.0 | 0.84 Comm | 0.011659 | 0.011659 | 0.011659 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009935 | | | 0.79 Nlocal: 474.000 ave 474 max 474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4189.00 ave 4189 max 4189 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: 82304.0 ave 82304 max 82304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82304 Ave neighs/atom = 173.63713 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 3 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.558 | 4.558 | 4.558 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -1941.3309 0 -1941.3309 -7894.0542 5139.723 73 0 -1941.4154 0 -1941.4154 -665.66833 5107.5066 Loop time of 0.0574693 on 1 procs for 4 steps with 474 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1941.33086132968 -1941.41451690805 -1941.4153570948 Force two-norm initial, final = 37.975991 0.76402197 Force max component initial, final = 27.487622 0.63862860 Final line search alpha, max atom move = 0.00029934441 0.00019116991 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.055323 | 0.055323 | 0.055323 | 0.0 | 96.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00046754 | 0.00046754 | 0.00046754 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001678 | | | 2.92 Nlocal: 474.000 ave 474 max 474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4166.00 ave 4166 max 4166 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: 82288.0 ave 82288 max 82288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82288 Ave neighs/atom = 173.60338 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 3 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.696 | 4.696 | 4.696 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1941.4154 0 -1941.4154 -665.66833 Loop time of 6.135e-06 on 1 procs for 0 steps with 474 atoms 179.3% 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 | | 6.135e-06 | | |100.00 Nlocal: 474.000 ave 474 max 474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4179.00 ave 4179 max 4179 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: 82368.0 ave 82368 max 82368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82368 Ave neighs/atom = 173.77215 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 3 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.696 | 4.696 | 4.696 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 -1941.4154 -1941.4154 7.7965819 76.659598 8.5455133 -665.66833 -665.66833 -80.408053 -2116.3558 199.75886 2.2430367 262.62718 Loop time of 6.345e-06 on 1 procs for 0 steps with 474 atoms 315.2% 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 | | 6.345e-06 | | |100.00 Nlocal: 474.000 ave 474 max 474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4179.00 ave 4179 max 4179 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 41184.0 ave 41184 max 41184 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 82368.0 ave 82368 max 82368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82368 Ave neighs/atom = 173.77215 Neighbor list builds = 0 Dangerous builds = 0 474 -1941.4153570948 eV 2.24303666152365 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01