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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -46.248236 0.0000000) to (23.122313 46.248236 3.6110985) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0756296 5.0756296 3.6110985 Created 329 atoms using lattice units in orthogonal box = (0.0000000 -46.248236 0.0000000) to (23.122313 46.248236 3.6110985) create_atoms CPU = 0.002 seconds 329 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0756296 5.0756296 3.6110985 Created 329 atoms using lattice units in orthogonal box = (0.0000000 -46.248236 0.0000000) to (23.122313 46.248236 3.6110985) create_atoms CPU = 0.001 seconds 329 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 8 29 2 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 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 654 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_343168101490_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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 8 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 4.521 | 4.521 | 4.521 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2728.9363 0 -2728.9363 20188.406 43 0 -2767.4711 0 -2767.4711 -647.75693 Loop time of 4.97217 on 1 procs for 43 steps with 654 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 = -2728.93630919262 -2767.46855183892 -2767.47111851673 Force two-norm initial, final = 40.550369 0.17337303 Force max component initial, final = 13.444967 0.047274240 Final line search alpha, max atom move = 1.0000000 0.047274240 Iterations, force evaluations = 43 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.9466 | 4.9466 | 4.9466 | 0.0 | 99.49 Neigh | 0.0096839 | 0.0096839 | 0.0096839 | 0.0 | 0.19 Comm | 0.0084819 | 0.0084819 | 0.0084819 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007376 | | | 0.15 Nlocal: 654.000 ave 654 max 654 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5121.00 ave 5121 max 5121 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: 56178.0 ave 56178 max 56178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56178 Ave neighs/atom = 85.899083 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 8 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.521 | 4.521 | 4.521 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -2767.4711 0 -2767.4711 -647.75693 7723.1732 53 0 -2767.6939 0 -2767.6939 -3112.5006 7734.2306 Loop time of 0.863315 on 1 procs for 10 steps with 654 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 = -2767.47111851673 -2767.69368585773 -2767.69386730929 Force two-norm initial, final = 36.620683 0.99521445 Force max component initial, final = 26.804178 0.71486174 Final line search alpha, max atom move = 0.0066189569 0.0047316391 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.85749 | 0.85749 | 0.85749 | 0.0 | 99.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012633 | 0.0012633 | 0.0012633 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004563 | | | 0.53 Nlocal: 654.000 ave 654 max 654 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5116.00 ave 5116 max 5116 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: 56212.0 ave 56212 max 56212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56212 Ave neighs/atom = 85.951070 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 8 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 4.659 | 4.659 | 4.659 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2767.6939 0 -2767.6939 -3112.5006 Loop time of 6.435e-06 on 1 procs for 0 steps with 654 atoms 170.9% 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 | | 6.435e-06 | | |100.00 Nlocal: 654.000 ave 654 max 654 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5126.00 ave 5126 max 5126 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: 56188.0 ave 56188 max 56188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56188 Ave neighs/atom = 85.914373 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 8 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 4.659 | 4.659 | 4.659 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 -2767.6939 -2767.6939 22.943004 92.496472 3.6445312 -3112.5006 -3112.5006 113.00298 -9301.0472 -149.45747 2.3106898 155.34494 Loop time of 6.626e-06 on 1 procs for 0 steps with 654 atoms 271.7% 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 | | 6.626e-06 | | |100.00 Nlocal: 654.000 ave 654 max 654 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5126.00 ave 5126 max 5126 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28094.0 ave 28094 max 28094 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 56188.0 ave 56188 max 56188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56188 Ave neighs/atom = 85.914373 Neighbor list builds = 0 Dangerous builds = 0 654 -2767.69386730929 eV 2.31068975007377 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06