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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -54.987678 0.0000000) to (27.492079 54.987678 3.5200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9575880 4.9575880 3.5200000 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -54.987678 0.0000000) to (27.492079 54.987678 3.5200000) create_atoms CPU = 0.002 seconds 490 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9575880 4.9575880 3.5200000 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -54.987678 0.0000000) to (27.492079 54.987678 3.5200000) create_atoms CPU = 0.002 seconds 490 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 26 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 972 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_103383163946_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.429 | 5.429 | 5.429 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4285.1218 0 -4285.1218 12988.879 58 0 -4315.7067 0 -4315.7067 -3457.2549 Loop time of 2.65602 on 1 procs for 58 steps with 972 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 = -4285.12176091428 -4315.70332120262 -4315.70668215309 Force two-norm initial, final = 37.880359 0.18201863 Force max component initial, final = 12.476985 0.014013290 Final line search alpha, max atom move = 1.0000000 0.014013290 Iterations, force evaluations = 58 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6203 | 2.6203 | 2.6203 | 0.0 | 98.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.021445 | 0.021445 | 0.021445 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01431 | | | 0.54 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8955.00 ave 8955 max 8955 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: 217796.0 ave 217796 max 217796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217796 Ave neighs/atom = 224.06996 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.430 | 5.430 | 5.430 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -4315.7067 0 -4315.7067 -3457.2549 10642.548 60 0 -4315.7275 0 -4315.7275 -1142.1492 10628.798 Loop time of 0.119798 on 1 procs for 2 steps with 972 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4315.70668215308 -4315.72456836439 -4315.72751604922 Force two-norm initial, final = 31.004541 1.3885869 Force max component initial, final = 29.244469 1.0164347 Final line search alpha, max atom move = 0.00019237953 0.00019554123 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11598 | 0.11598 | 0.11598 | 0.0 | 96.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0009522 | 0.0009522 | 0.0009522 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002871 | | | 2.40 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9033.00 ave 9033 max 9033 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: 218120.0 ave 218120 max 218120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 218120 Ave neighs/atom = 224.40329 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.568 | 5.568 | 5.568 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4315.7275 0 -4315.7275 -1142.1492 Loop time of 8.219e-06 on 1 procs for 0 steps with 972 atoms 158.2% 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 | | 8.219e-06 | | |100.00 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9033.00 ave 9033 max 9033 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: 218208.0 ave 218208 max 218208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 218208 Ave neighs/atom = 224.49383 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.568 | 5.568 | 5.568 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 -4315.7275 -4315.7275 27.449129 109.97536 3.5209529 -1142.1492 -1142.1492 152.97719 -3719.2427 139.81793 2.2355601 147.55698 Loop time of 6.906e-06 on 1 procs for 0 steps with 972 atoms 304.1% 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 | | 6.906e-06 | | |100.00 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9033.00 ave 9033 max 9033 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 109104.0 ave 109104 max 109104 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 218208.0 ave 218208 max 218208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 218208 Ave neighs/atom = 224.49383 Neighbor list builds = 0 Dangerous builds = 0 972 -4289.25867650842 eV 2.23556014147933 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03