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 -47.230712 0.0000000) to (23.615356 47.230712 4.0500001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5565544 5.5565544 4.0500001 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -47.230712 0.0000000) to (23.615356 47.230712 4.0500001) create_atoms CPU = 0.002 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5565544 5.5565544 4.0500001 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -47.230712 0.0000000) to (23.615356 47.230712 4.0500001) create_atoms CPU = 0.001 seconds 274 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 6 23 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 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 546 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_678952612413_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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 6 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 4.520 | 4.520 | 4.520 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1794.6354 0 -1794.6354 7067.3675 61 0 -1828.3186 0 -1828.3186 7358.7429 Loop time of 1.28784 on 1 procs for 61 steps with 546 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 = -1794.63543165594 -1828.31678485643 -1828.3185996144 Force two-norm initial, final = 18.875258 0.11873965 Force max component initial, final = 2.9002262 0.023895604 Final line search alpha, max atom move = 1.0000000 0.023895604 Iterations, force evaluations = 61 111 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2649 | 1.2649 | 1.2649 | 0.0 | 98.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.012819 | 0.012819 | 0.012819 | 0.0 | 1.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01013 | | | 0.79 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4989.00 ave 4989 max 4989 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: 77520.0 ave 77520 max 77520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77520 Ave neighs/atom = 141.97802 Neighbor list builds = 0 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 6 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.520 | 4.520 | 4.520 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -1828.3186 0 -1828.3186 7358.7429 9034.498 76 0 -1828.8474 0 -1828.8474 2.6931899 9118.318 Loop time of 0.227063 on 1 procs for 15 steps with 546 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 = -1828.3185996144 -1828.84658209747 -1828.84743191114 Force two-norm initial, final = 87.015790 0.45508896 Force max component initial, final = 81.334176 0.18496261 Final line search alpha, max atom move = 0.00054297522 0.00010043011 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20632 | 0.20632 | 0.20632 | 0.0 | 90.87 Neigh | 0.011542 | 0.011542 | 0.011542 | 0.0 | 5.08 Comm | 0.0022919 | 0.0022919 | 0.0022919 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006907 | | | 3.04 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4959.00 ave 4959 max 4959 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: 76860.0 ave 76860 max 76860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76860 Ave neighs/atom = 140.76923 Neighbor list builds = 1 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 6 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 4.658 | 4.658 | 4.658 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1828.8474 0 -1828.8474 2.6931899 Loop time of 6.555e-06 on 1 procs for 0 steps with 546 atoms 183.1% 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 | | 6.555e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4959.00 ave 4959 max 4959 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: 76864.0 ave 76864 max 76864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76864 Ave neighs/atom = 140.77656 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 6 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 4.658 | 4.658 | 4.658 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 -1828.8474 -1828.8474 23.546016 95.838935 4.040688 2.6931899 2.6931899 32.404289 -12.733934 -11.590785 2.575787 401.01629 Loop time of 7.327e-06 on 1 procs for 0 steps with 546 atoms 218.4% 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 | | 7.327e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4959.00 ave 4959 max 4959 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38432.0 ave 38432 max 38432 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 76864.0 ave 76864 max 76864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76864 Ave neighs/atom = 140.77656 Neighbor list builds = 0 Dangerous builds = 0 546 -1828.84743191114 eV 2.57578702863743 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02