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 -42.549138 0.0000000) to (52.111839 42.549138 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9970257 5.2457842 5.7504086 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -42.549138 0.0000000) to (52.111839 42.549138 8.6256130) create_atoms CPU = 0.002 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9970257 5.2457842 5.7504086 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -42.549138 0.0000000) to (52.111839 42.549138 8.6256130) create_atoms CPU = 0.002 seconds 1756 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 17 27 3 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 3503 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_115454747503_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 17 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 6.106 | 6.106 | 6.106 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13142.06 0 -13142.06 133203.83 109 0 -15523.641 0 -15523.641 9527.4177 Loop time of 29.4661 on 1 procs for 109 steps with 3503 atoms 97.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13142.0601090757 -15523.6259064423 -15523.6409380315 Force two-norm initial, final = 1512.1283 0.52337792 Force max component initial, final = 182.89755 0.20880917 Final line search alpha, max atom move = 0.73560636 0.15360135 Iterations, force evaluations = 109 177 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 29.275 | 29.275 | 29.275 | 0.0 | 99.35 Neigh | 0.12803 | 0.12803 | 0.12803 | 0.0 | 0.43 Comm | 0.024863 | 0.024863 | 0.024863 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03864 | | | 0.13 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9114.00 ave 9114 max 9114 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: 312374.0 ave 312374 max 312374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 312374 Ave neighs/atom = 89.173280 Neighbor list builds = 5 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 17 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 109 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.106 | 6.106 | 6.106 Mbytes Step Temp E_pair E_mol TotEng Press Volume 109 0 -15523.641 0 -15523.641 9527.4177 38251.382 117 0 -15525.081 0 -15525.081 34.228389 38444.171 Loop time of 1.8731 on 1 procs for 8 steps with 3503 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 = -15523.6409380315 -15525.0811859204 -15525.0812891434 Force two-norm initial, final = 484.38875 1.7085319 Force max component initial, final = 452.42715 1.0178401 Final line search alpha, max atom move = 0.00035318361 0.00035948443 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8646 | 1.8646 | 1.8646 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00099247 | 0.00099247 | 0.00099247 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007477 | | | 0.40 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9193.00 ave 9193 max 9193 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: 312032.0 ave 312032 max 312032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 312032 Ave neighs/atom = 89.075649 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 17 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 6.244 | 6.244 | 6.244 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15525.081 0 -15525.081 34.228389 Loop time of 2.581e-06 on 1 procs for 0 steps with 3503 atoms 193.7% 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 | | 2.581e-06 | | |100.00 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9239.00 ave 9239 max 9239 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: 309802.0 ave 309802 max 309802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 309802 Ave neighs/atom = 88.439052 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 17 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 6.244 | 6.244 | 6.244 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 -15525.081 -15525.081 52.089153 85.675357 8.6144445 34.228389 34.228389 28.847164 31.474028 42.363975 2.2118961 1493.4116 Loop time of 2.971e-06 on 1 procs for 0 steps with 3503 atoms 235.6% 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 | | 2.971e-06 | | |100.00 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9239.00 ave 9239 max 9239 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 154901.0 ave 154901 max 154901 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 309802.0 ave 309802 max 309802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 309802 Ave neighs/atom = 88.439052 Neighbor list builds = 0 Dangerous builds = 0 3503 -15525.0812891434 eV 2.21189614797377 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:32