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 = 3.6084290 3.6084290 3.6084290 Created orthogonal box = (0.0000000 -42.695508 0.0000000) to (52.291105 42.695508 8.8388099) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9761262 5.4894225 5.8925399 Created 1666 atoms using lattice units in orthogonal box = (0.0000000 -42.695508 0.0000000) to (52.291105 42.695508 8.8388099) create_atoms CPU = 0.003 seconds 1666 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9761262 5.4894225 5.8925399 Created 1690 atoms using lattice units in orthogonal box = (0.0000000 -42.695508 0.0000000) to (52.291105 42.695508 8.8388099) create_atoms CPU = 0.003 seconds 1690 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 18 29 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3356 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_549900287421_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.609 | 5.609 | 5.609 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13218.254 0 -13218.254 108670.47 516 0 -14263.224 0 -14263.224 1014.2379 Loop time of 109.376 on 1 procs for 516 steps with 3356 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 = -13218.2539696027 -14263.2113231974 -14263.2235914737 Force two-norm initial, final = 1199.2791 0.42742360 Force max component initial, final = 112.36971 0.19974899 Final line search alpha, max atom move = 0.63744297 0.12732859 Iterations, force evaluations = 516 992 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 108.88 | 108.88 | 108.88 | 0.0 | 99.55 Neigh | 0.25891 | 0.25891 | 0.25891 | 0.0 | 0.24 Comm | 0.089672 | 0.089672 | 0.089672 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1471 | | | 0.13 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7709.00 ave 7709 max 7709 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: 250872.0 ave 250872 max 250872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250872 Ave neighs/atom = 74.753278 Neighbor list builds = 12 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 516 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.611 | 5.611 | 5.611 Mbytes Step Temp E_pair E_mol TotEng Press Volume 516 0 -14263.224 0 -14263.224 1014.2379 39466.971 528 0 -14266.547 0 -14266.547 8.0412644 39488.592 Loop time of 1.58555 on 1 procs for 12 steps with 3356 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 = -14263.2235914737 -14266.5470970653 -14266.5471664578 Force two-norm initial, final = 488.97389 1.2872036 Force max component initial, final = 372.59484 0.72710630 Final line search alpha, max atom move = 0.00099867514 0.00072614299 Iterations, force evaluations = 12 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5775 | 1.5775 | 1.5775 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00095557 | 0.00095557 | 0.00095557 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007085 | | | 0.45 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7755.00 ave 7755 max 7755 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: 250646.0 ave 250646 max 250646 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250646 Ave neighs/atom = 74.685936 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.748 | 5.748 | 5.748 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14266.547 0 -14266.547 8.0412644 Loop time of 3.896e-06 on 1 procs for 0 steps with 3356 atoms 179.7% 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 | | 3.896e-06 | | |100.00 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7719.00 ave 7719 max 7719 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: 251226.0 ave 251226 max 251226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 251226 Ave neighs/atom = 74.858760 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.748 | 5.748 | 5.748 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 -14266.547 -14266.547 51.721362 85.893078 8.8888081 8.0412644 8.0412644 7.1597366 -12.703813 29.667869 2.2261478 8921.9991 Loop time of 2.126e-06 on 1 procs for 0 steps with 3356 atoms 282.2% 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 | | 2.126e-06 | | |100.00 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7719.00 ave 7719 max 7719 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 125613.0 ave 125613 max 125613 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 251226.0 ave 251226 max 251226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 251226 Ave neighs/atom = 74.858760 Neighbor list builds = 0 Dangerous builds = 0 3356 -14266.5471664578 eV 2.22614779379794 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:51