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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -63.778638 0.0000000) to (22.547909 63.778638 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0494390 5.4442173 4.9800000 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -63.778638 0.0000000) to (22.547909 63.778638 4.9800000) create_atoms CPU = 0.002 seconds 658 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0494390 5.4442173 4.9800000 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -63.778638 0.0000000) to (22.547909 63.778638 4.9800000) create_atoms CPU = 0.001 seconds 658 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 8 41 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1304 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 8 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.073 | 5.073 | 5.073 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5763.4483 0 -5763.4483 3599.3952 53 0 -5792.3284 0 -5792.3284 -7667.6005 Loop time of 4.25544 on 1 procs for 53 steps with 1304 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5763.44828098003 -5792.32311476923 -5792.3283599254 Force two-norm initial, final = 44.794687 0.25575533 Force max component initial, final = 14.074236 0.060581642 Final line search alpha, max atom move = 1.0000000 0.060581642 Iterations, force evaluations = 53 97 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2408 | 4.2408 | 4.2408 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0075119 | 0.0075119 | 0.0075119 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007125 | | | 0.17 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6487.00 ave 6487 max 6487 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: 111868.0 ave 111868 max 111868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111868 Ave neighs/atom = 85.788344 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 8 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.074 | 5.074 | 5.074 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -5792.3284 0 -5792.3284 -7667.6005 14323.226 56 0 -5792.4037 0 -5792.4037 -3078.573 14287.571 Loop time of 0.262613 on 1 procs for 3 steps with 1304 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 = -5792.32835992539 -5792.40257665731 -5792.40365664709 Force two-norm initial, final = 72.302506 0.26541598 Force max component initial, final = 66.123387 0.058645822 Final line search alpha, max atom move = 0.00014222177 8.3407128e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26082 | 0.26082 | 0.26082 | 0.0 | 99.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031926 | 0.00031926 | 0.00031926 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001474 | | | 0.56 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6508.00 ave 6508 max 6508 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: 112236.0 ave 112236 max 112236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112236 Ave neighs/atom = 86.070552 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 8 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.212 | 5.212 | 5.212 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5792.4037 0 -5792.4037 -3078.573 Loop time of 2.078e-06 on 1 procs for 0 steps with 1304 atoms 144.4% 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 | | 2.078e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6508.00 ave 6508 max 6508 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: 112236.0 ave 112236 max 112236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112236 Ave neighs/atom = 86.070552 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 8 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.212 | 5.212 | 5.212 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 -5792.4037 -5792.4037 22.539042 127.55728 4.9695576 -3078.573 -3078.573 -1.2333301 -9236.5306 2.0450567 2.3232061 416.61096 Loop time of 1.825e-06 on 1 procs for 0 steps with 1304 atoms 164.4% 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 | | 1.825e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6508.00 ave 6508 max 6508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56118.0 ave 56118 max 56118 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 112236.0 ave 112236 max 112236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112236 Ave neighs/atom = 86.070552 Neighbor list builds = 0 Dangerous builds = 0 1304 -5792.40365664709 eV 2.32320612979525 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04