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 = 4.0469996 4.0469996 4.0469996 Created orthogonal box = (0.0000000 -51.509895 0.0000000) to (12.140999 51.509895 5.7233217) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7449993 5.7233217 5.7233217 Created 216 atoms using lattice units in orthogonal box = (0.0000000 -51.509895 0.0000000) to (12.140999 51.509895 5.7233217) create_atoms CPU = 0.001 seconds 216 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7449993 5.7233217 5.7233217 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -51.509895 0.0000000) to (12.140999 51.509895 5.7233217) create_atoms CPU = 0.001 seconds 218 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 4 30 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 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 434 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_958395190627_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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 4 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 4.490 | 4.490 | 4.490 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1362.5792 0 -1362.5792 39507.795 58 0 -1454.9639 0 -1454.9639 6339.1112 Loop time of 2.26215 on 1 procs for 58 steps with 434 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 = -1362.57916111266 -1454.96259580002 -1454.96387021579 Force two-norm initial, final = 161.83085 0.097972427 Force max component initial, final = 41.833188 0.011220389 Final line search alpha, max atom move = 1.0000000 0.011220389 Iterations, force evaluations = 58 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2518 | 2.2518 | 2.2518 | 0.0 | 99.54 Neigh | 0.0029267 | 0.0029267 | 0.0029267 | 0.0 | 0.13 Comm | 0.0041586 | 0.0041586 | 0.0041586 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003268 | | | 0.14 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3353.00 ave 3353 max 3353 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: 37232.0 ave 37232 max 37232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37232 Ave neighs/atom = 85.788018 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 4 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 4.489 | 4.489 | 4.489 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -1454.9639 0 -1454.9639 6339.1112 7158.5197 66 0 -1455.1223 0 -1455.1223 -88.141221 7216.2362 Loop time of 0.203716 on 1 procs for 8 steps with 434 atoms 96.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1454.96387021579 -1455.12213314605 -1455.12227084722 Force two-norm initial, final = 51.763996 0.85698849 Force max component initial, final = 41.712336 0.67562108 Final line search alpha, max atom move = 0.00083971632 0.00056733005 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20228 | 0.20228 | 0.20228 | 0.0 | 99.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002702 | 0.0002702 | 0.0002702 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001167 | | | 0.57 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3291.00 ave 3291 max 3291 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: 37292.0 ave 37292 max 37292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37292 Ave neighs/atom = 85.926267 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 4 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 4.627 | 4.627 | 4.627 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1455.1223 0 -1455.1223 -88.141221 Loop time of 1.654e-06 on 1 procs for 0 steps with 434 atoms 181.4% 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 | | 1.654e-06 | | |100.00 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3283.00 ave 3283 max 3283 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: 37200.0 ave 37200 max 37200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37200 Ave neighs/atom = 85.714286 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 4 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 4.627 | 4.627 | 4.627 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 -1455.1223 -1455.1223 12.153056 103.7637 5.7224207 -88.141221 -88.141221 -112.22726 -2.2160282 -149.98038 2.6096138 360.47444 Loop time of 1.543e-06 on 1 procs for 0 steps with 434 atoms 129.6% 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 | | 1.543e-06 | | |100.00 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3283.00 ave 3283 max 3283 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18600.0 ave 18600 max 18600 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 37200.0 ave 37200 max 37200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37200 Ave neighs/atom = 85.714286 Neighbor list builds = 0 Dangerous builds = 0 434 -1455.12227084722 eV 2.60961376290364 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02