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 = 4.0320734 4.0320734 4.0320734 Created orthogonal box = (0.0000000 -59.259134 0.0000000) to (20.951268 59.259134 5.7022129) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4318102 6.5843483 5.7022129 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -59.259134 0.0000000) to (20.951268 59.259134 5.7022129) create_atoms CPU = 0.002 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4318102 6.5843483 5.7022129 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -59.259134 0.0000000) to (20.951268 59.259134 5.7022129) create_atoms CPU = 0.001 seconds 434 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 6 31 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 862 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 6 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 4.977 | 4.977 | 4.977 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2828.7119 0 -2828.7119 6562.0654 82 0 -2889.4106 0 -2889.4106 2790.085 Loop time of 0.899635 on 1 procs for 82 steps with 862 atoms 94.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2828.71190818677 -2889.40778635903 -2889.41060927732 Force two-norm initial, final = 34.919165 0.14358253 Force max component initial, final = 7.7085886 0.034375399 Final line search alpha, max atom move = 1.0000000 0.034375399 Iterations, force evaluations = 82 147 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.86981 | 0.86981 | 0.86981 | 0.0 | 96.69 Neigh | 0.014533 | 0.014533 | 0.014533 | 0.0 | 1.62 Comm | 0.0080187 | 0.0080187 | 0.0080187 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00727 | | | 0.81 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5365.00 ave 5365 max 5365 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: 113400.0 ave 113400 max 113400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113400 Ave neighs/atom = 131.55452 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 6 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.977 | 4.977 | 4.977 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -2889.4106 0 -2889.4106 2790.085 14159.21 88 0 -2889.5267 0 -2889.5267 -20.212225 14207.955 Loop time of 0.089648 on 1 procs for 6 steps with 862 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 = -2889.41060927732 -2889.52669309098 -2889.52671179589 Force two-norm initial, final = 52.927042 0.45307643 Force max component initial, final = 49.162716 0.38392234 Final line search alpha, max atom move = 0.0018876613 0.00072471532 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.085719 | 0.085719 | 0.085719 | 0.0 | 95.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00073277 | 0.00073277 | 0.00073277 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003196 | | | 3.57 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5336.00 ave 5336 max 5336 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: 113368.0 ave 113368 max 113368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113368 Ave neighs/atom = 131.51740 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 6 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.115 | 5.115 | 5.115 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2889.5267 0 -2889.5267 -20.212225 Loop time of 3.436e-06 on 1 procs for 0 steps with 862 atoms 378.3% 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 | | 3.436e-06 | | |100.00 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5387.00 ave 5387 max 5387 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: 113204.0 ave 113204 max 113204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113204 Ave neighs/atom = 131.32715 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 6 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.115 | 5.115 | 5.115 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 -2889.5267 -2889.5267 20.952852 119.10602 5.6931777 -20.212225 -20.212225 -43.296719 -16.082062 -1.2578958 2.6276394 574.59112 Loop time of 3.336e-06 on 1 procs for 0 steps with 862 atoms 149.9% 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 | | 3.336e-06 | | |100.00 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5387.00 ave 5387 max 5387 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56602.0 ave 56602 max 56602 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 113204.0 ave 113204 max 113204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113204 Ave neighs/atom = 131.32715 Neighbor list builds = 0 Dangerous builds = 0 862 -2889.52671179589 eV 2.62763935232875 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01