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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -50.941536 0.0000000) to (12.006182 50.941536 5.1194532) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4573554 6.1742928 5.1194532 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -50.941536 0.0000000) to (12.006182 50.941536 5.1194532) create_atoms CPU = 0.002 seconds 266 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4573554 6.1742928 5.1194532 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -50.941536 0.0000000) to (12.006182 50.941536 5.1194532) create_atoms CPU = 0.002 seconds 266 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 27 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 526 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_803527979660_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.544 | 4.544 | 4.544 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1841.4102 0 -1841.4102 9361.2505 42 0 -1857.0528 0 -1857.0528 107.30068 Loop time of 0.786463 on 1 procs for 42 steps with 526 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 = -1841.41015822731 -1857.05103055466 -1857.05277001804 Force two-norm initial, final = 27.227571 0.12173494 Force max component initial, final = 7.5237513 0.016664935 Final line search alpha, max atom move = 1.0000000 0.016664935 Iterations, force evaluations = 42 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.76602 | 0.76602 | 0.76602 | 0.0 | 97.40 Neigh | 0.010074 | 0.010074 | 0.010074 | 0.0 | 1.28 Comm | 0.0062879 | 0.0062879 | 0.0062879 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004077 | | | 0.52 Nlocal: 526.000 ave 526 max 526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5018.00 ave 5018 max 5018 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: 91400.0 ave 91400 max 91400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91400 Ave neighs/atom = 173.76426 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.544 | 4.544 | 4.544 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -1857.0528 0 -1857.0528 107.30068 6262.2518 43 0 -1857.0539 0 -1857.0539 909.16499 6258.5313 Loop time of 0.0303026 on 1 procs for 1 steps with 526 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 = -1857.05277001804 -1857.05277001804 -1857.05387112167 Force two-norm initial, final = 5.0518486 1.1213848 Force max component initial, final = 4.4075895 0.97805909 Final line search alpha, max atom move = 0.00022688138 0.00022190340 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.029377 | 0.029377 | 0.029377 | 0.0 | 96.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022519 | 0.00022519 | 0.00022519 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007004 | | | 2.31 Nlocal: 526.000 ave 526 max 526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5026.00 ave 5026 max 5026 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: 91612.0 ave 91612 max 91612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91612 Ave neighs/atom = 174.16730 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.682 | 4.682 | 4.682 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1857.0539 0 -1857.0539 909.16499 Loop time of 2.901e-06 on 1 procs for 0 steps with 526 atoms 137.9% 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 | | 2.901e-06 | | |100.00 Nlocal: 526.000 ave 526 max 526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5026.00 ave 5026 max 5026 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: 91612.0 ave 91612 max 91612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91612 Ave neighs/atom = 174.16730 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.682 | 4.682 | 4.682 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 -1857.0539 -1857.0539 12.001607 101.88307 5.1183619 909.16499 909.16499 -136.81637 2613.9828 250.32858 2.3393455 260.1004 Loop time of 3.073e-06 on 1 procs for 0 steps with 526 atoms 162.7% 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 | | 3.073e-06 | | |100.00 Nlocal: 526.000 ave 526 max 526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5026.00 ave 5026 max 5026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45806.0 ave 45806 max 45806 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 91612.0 ave 91612 max 91612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91612 Ave neighs/atom = 174.16730 Neighbor list builds = 0 Dangerous builds = 0 526 -1857.05387112167 eV 2.33934547757575 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01