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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -51.800847 0.0000000) to (25.898401 51.800847 4.0446508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6850149 5.6850149 4.0446508 Created 330 atoms using lattice units in orthogonal box = (0.0000000 -51.800847 0.0000000) to (25.898401 51.800847 4.0446508) create_atoms CPU = 0.002 seconds 330 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6850149 5.6850149 4.0446508 Created 330 atoms using lattice units in orthogonal box = (0.0000000 -51.800847 0.0000000) to (25.898401 51.800847 4.0446508) create_atoms CPU = 0.001 seconds 330 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 = 8 32 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 652 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_616482358807_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 = 8 32 2 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) = 4.503 | 4.503 | 4.503 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2169.8874 0 -2169.8874 5556.3711 72 0 -2185.658 0 -2185.658 -2256.4836 Loop time of 6.85346 on 1 procs for 72 steps with 652 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 = -2169.88735748157 -2185.65611203336 -2185.65799475207 Force two-norm initial, final = 14.587381 0.11362289 Force max component initial, final = 4.1859358 0.023122255 Final line search alpha, max atom move = 1.0000000 0.023122255 Iterations, force evaluations = 72 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.8138 | 6.8138 | 6.8138 | 0.0 | 99.42 Neigh | 0.015074 | 0.015074 | 0.015074 | 0.0 | 0.22 Comm | 0.012318 | 0.012318 | 0.012318 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01226 | | | 0.18 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3752.00 ave 3752 max 3752 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: 49724.0 ave 49724 max 49724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49724 Ave neighs/atom = 76.263804 Neighbor list builds = 2 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 = 8 32 2 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 : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.503 | 4.503 | 4.503 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -2185.658 0 -2185.658 -2256.4836 10852.276 75 0 -2185.6804 0 -2185.6804 -248.86386 10824.448 Loop time of 0.320599 on 1 procs for 3 steps with 652 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 = -2185.65799475207 -2185.67946615189 -2185.68038461025 Force two-norm initial, final = 21.934489 0.11556520 Force max component initial, final = 18.322431 0.019454130 Final line search alpha, max atom move = 0.00042010055 8.1726907e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31837 | 0.31837 | 0.31837 | 0.0 | 99.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048052 | 0.00048052 | 0.00048052 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001751 | | | 0.55 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3752.00 ave 3752 max 3752 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: 49708.0 ave 49708 max 49708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49708 Ave neighs/atom = 76.239264 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 = 8 32 2 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) = 4.641 | 4.641 | 4.641 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2185.6804 0 -2185.6804 -248.86386 Loop time of 6.625e-06 on 1 procs for 0 steps with 652 atoms 181.1% 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 | | 6.625e-06 | | |100.00 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3756.00 ave 3756 max 3756 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: 49716.0 ave 49716 max 49716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49716 Ave neighs/atom = 76.251534 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 = 8 32 2 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) = 4.641 | 4.641 | 4.641 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 -2185.6804 -2185.6804 25.888792 103.60169 4.0357767 -248.86386 -248.86386 -1.2844012 -746.04598 0.73880639 2.5525936 182.12928 Loop time of 6.666e-06 on 1 procs for 0 steps with 652 atoms 240.0% 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 | | 6.666e-06 | | |100.00 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3756.00 ave 3756 max 3756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24858.0 ave 24858 max 24858 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 49716.0 ave 49716 max 49716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49716 Ave neighs/atom = 76.251534 Neighbor list builds = 0 Dangerous builds = 0 652 -2185.68038461025 eV 2.55259357446792 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07