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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -48.936337 0.0000000) to (59.934528 48.936337 9.9204336) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7471465 6.0332470 6.6136224 Created 1748 atoms using lattice units in orthogonal box = (0.0000000 -48.936337 0.0000000) to (59.934528 48.936337 9.9204336) create_atoms CPU = 0.007 seconds 1748 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7471465 6.0332470 6.6136224 Created 1754 atoms using lattice units in orthogonal box = (0.0000000 -48.936337 0.0000000) to (59.934528 48.936337 9.9204336) create_atoms CPU = 0.007 seconds 1754 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 16 26 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 3478 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_418978237058_005#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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.519 | 6.519 | 6.519 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11193.181 0 -11193.181 10456.029 126 0 -11671.477 0 -11671.477 -400.35207 Loop time of 8.73384 on 1 procs for 126 steps with 3478 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 = -11193.181135883 -11671.4657782546 -11671.4770831229 Force two-norm initial, final = 183.77798 0.21819581 Force max component initial, final = 26.396916 0.034149704 Final line search alpha, max atom move = 1.0000000 0.034149704 Iterations, force evaluations = 126 215 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.3443 | 8.3443 | 8.3443 | 0.0 | 95.54 Neigh | 0.26088 | 0.26088 | 0.26088 | 0.0 | 2.99 Comm | 0.050929 | 0.050929 | 0.050929 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07773 | | | 0.89 Nlocal: 3478.00 ave 3478 max 3478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9483.00 ave 9483 max 9483 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: 450768.0 ave 450768 max 450768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 450768 Ave neighs/atom = 129.60552 Neighbor list builds = 4 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 126 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.517 | 6.517 | 6.517 Mbytes Step Temp E_pair E_mol TotEng Press Volume 126 0 -11671.477 0 -11671.477 -400.35207 58192.793 129 0 -11671.511 0 -11671.511 3.7365883 58163.774 Loop time of 0.270758 on 1 procs for 3 steps with 3478 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 = -11671.4770831229 -11671.5114486267 -11671.5114538578 Force two-norm initial, final = 42.913236 0.35158080 Force max component initial, final = 30.624204 0.23528719 Final line search alpha, max atom move = 0.0032941829 0.00077507906 Iterations, force evaluations = 3 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26314 | 0.26314 | 0.26314 | 0.0 | 97.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014253 | 0.0014253 | 0.0014253 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006195 | | | 2.29 Nlocal: 3478.00 ave 3478 max 3478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9209.00 ave 9209 max 9209 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: 452358.0 ave 452358 max 452358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 452358 Ave neighs/atom = 130.06268 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.655 | 6.655 | 6.655 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11671.511 0 -11671.511 3.7365883 Loop time of 7.517e-06 on 1 procs for 0 steps with 3478 atoms 0.0% 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 | | 7.517e-06 | | |100.00 Nlocal: 3478.00 ave 3478 max 3478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9227.00 ave 9227 max 9227 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: 452404.0 ave 452404 max 452404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 452404 Ave neighs/atom = 130.07591 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.655 | 6.655 | 6.655 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 -11671.511 -11671.511 59.874201 97.99767 9.9128172 3.7365883 3.7365883 6.474686 2.0163418 2.7187371 2.6491323 2381.2123 Loop time of 6.815e-06 on 1 procs for 0 steps with 3478 atoms 264.1% 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 | | 6.815e-06 | | |100.00 Nlocal: 3478.00 ave 3478 max 3478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9227.00 ave 9227 max 9227 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 226202.0 ave 226202 max 226202 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 452404.0 ave 452404 max 452404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 452404 Ave neighs/atom = 130.07591 Neighbor list builds = 0 Dangerous builds = 0 3478 -11671.5114538578 eV 2.64913230214489 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10