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 = 3.5184747 3.5184747 3.5184747 Created orthogonal box = (0.0000000 -37.401899 0.0000000) to (37.401899 37.401899 3.5184747) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9648538 4.9648538 3.5184747 Created 452 atoms using lattice units in orthogonal box = (0.0000000 -37.401899 0.0000000) to (37.401899 37.401899 3.5184747) create_atoms CPU = 0.001 seconds 452 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9648538 4.9648538 3.5184747 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -37.401899 0.0000000) to (37.401899 37.401899 3.5184747) create_atoms CPU = 0.001 seconds 454 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 ghost atom cutoff = 8 binsize = 4, bins = 10 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 906 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_922363340570_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 10 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.003 | 5.003 | 5.003 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3619.6885 0 -3619.6885 122284.51 80 0 -3925.9739 0 -3925.9739 7331.522 Loop time of 1.30818 on 1 procs for 80 steps with 906 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 = -3619.68850333173 -3925.97079674786 -3925.97388441157 Force two-norm initial, final = 564.32979 0.18524202 Force max component initial, final = 167.96146 0.039527286 Final line search alpha, max atom move = 1.0000000 0.039527286 Iterations, force evaluations = 80 139 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2708 | 1.2708 | 1.2708 | 0.0 | 97.15 Neigh | 0.020407 | 0.020407 | 0.020407 | 0.0 | 1.56 Comm | 0.0099647 | 0.0099647 | 0.0099647 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006957 | | | 0.53 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7729.00 ave 7729 max 7729 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: 179668.0 ave 179668 max 179668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179668 Ave neighs/atom = 198.30905 Neighbor list builds = 2 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 ghost atom cutoff = 8 binsize = 4, bins = 10 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.002 | 5.002 | 5.002 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -3925.9739 0 -3925.9739 7331.522 9844.0026 86 0 -3926.1959 0 -3926.1959 -195.81683 9881.8015 Loop time of 0.0895209 on 1 procs for 6 steps with 906 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 = -3925.97388441156 -3926.19534204752 -3926.19586325216 Force two-norm initial, final = 99.745903 3.1413807 Force max component initial, final = 92.900747 2.8000122 Final line search alpha, max atom move = 0.00026868680 0.00075232630 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.086264 | 0.086264 | 0.086264 | 0.0 | 96.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056825 | 0.00056825 | 0.00056825 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002689 | | | 3.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7729.00 ave 7729 max 7729 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: 179704.0 ave 179704 max 179704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179704 Ave neighs/atom = 198.34879 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 ghost atom cutoff = 8 binsize = 4, bins = 10 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.140 | 5.140 | 5.140 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3926.1959 0 -3926.1959 -195.81683 Loop time of 1.906e-06 on 1 procs for 0 steps with 906 atoms 157.4% 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 | | 1.906e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 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: 179364.0 ave 179364 max 179364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179364 Ave neighs/atom = 197.97351 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 ghost atom cutoff = 8 binsize = 4, bins = 10 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.140 | 5.140 | 5.140 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 -3926.1959 -3926.1959 37.35737 75.172119 3.5188685 -195.81683 -195.81683 79.796407 -213.21876 -454.02813 2.2100561 132.84585 Loop time of 2.217e-06 on 1 procs for 0 steps with 906 atoms 180.4% 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 | | 2.217e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 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: 89682.0 ave 89682 max 89682 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 179364.0 ave 179364 max 179364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179364 Ave neighs/atom = 197.97351 Neighbor list builds = 0 Dangerous builds = 0 906 -3926.19586325216 eV 2.21005605643203 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01