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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -43.782243 0.0000000) to (35.748051 43.782243 8.8453488) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1068645 5.0632526 5.8968992 Created 1174 atoms using lattice units in orthogonal box = (0.0000000 -43.782243 0.0000000) to (35.748051 43.782243 8.8453488) create_atoms CPU = 0.002 seconds 1174 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1068645 5.0632526 5.8968992 Created 1182 atoms using lattice units in orthogonal box = (0.0000000 -43.782243 0.0000000) to (35.748051 43.782243 8.8453488) create_atoms CPU = 0.002 seconds 1182 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 = 11 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 4 atoms, new total = 2352 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_179420363944_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 = 11 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) = 5.535 | 5.535 | 5.535 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8672.4128 0 -8672.4128 91052.641 51 0 -9944.331 0 -9944.331 8341.2977 Loop time of 10.248 on 1 procs for 51 steps with 2352 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 = -8672.41282162496 -9944.32405088667 -9944.33103826466 Force two-norm initial, final = 1241.8254 0.41061735 Force max component initial, final = 166.59809 0.12373191 Final line search alpha, max atom move = 1.0000000 0.12373191 Iterations, force evaluations = 51 82 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.196 | 10.196 | 10.196 | 0.0 | 99.49 Neigh | 0.03443 | 0.03443 | 0.03443 | 0.0 | 0.34 Comm | 0.00702 | 0.00702 | 0.00702 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01075 | | | 0.10 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6589.00 ave 6589 max 6589 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: 205036.0 ave 205036 max 205036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205036 Ave neighs/atom = 87.175170 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 = 11 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 : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.535 | 5.535 | 5.535 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -9944.331 0 -9944.331 8341.2977 27688.239 58 0 -9945.1446 0 -9945.1446 394.97773 27815.143 Loop time of 1.14672 on 1 procs for 7 steps with 2352 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 = -9944.33103826467 -9945.1358242488 -9945.14461006032 Force two-norm initial, final = 286.95280 12.559854 Force max component initial, final = 248.01329 10.173878 Final line search alpha, max atom move = 6.1216862e-05 0.00062281287 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1423 | 1.1423 | 1.1423 | 0.0 | 99.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057355 | 0.00057355 | 0.00057355 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003804 | | | 0.33 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6591.00 ave 6591 max 6591 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: 206104.0 ave 206104 max 206104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206104 Ave neighs/atom = 87.629252 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 = 11 28 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) = 5.674 | 5.674 | 5.674 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9945.1446 0 -9945.1446 394.97773 Loop time of 2.29e-06 on 1 procs for 0 steps with 2352 atoms 174.7% 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 | | 2.29e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6591.00 ave 6591 max 6591 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: 205836.0 ave 205836 max 205836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205836 Ave neighs/atom = 87.515306 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 = 11 28 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) = 5.674 | 5.674 | 5.674 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 -9945.1446 -9945.1446 35.621271 87.75454 8.8982027 394.97773 394.97773 302.18553 587.29617 295.4515 2.2191905 2116.5757 Loop time of 2.618e-06 on 1 procs for 0 steps with 2352 atoms 305.6% 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 | | 2.618e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6591.00 ave 6591 max 6591 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 102918.0 ave 102918 max 102918 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 205836.0 ave 205836 max 205836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205836 Ave neighs/atom = 87.515306 Neighbor list builds = 0 Dangerous builds = 0 2352 -9945.14461006031 eV 2.2191905333053 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12