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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -59.005646 0.0000000) to (41.723293 59.005646 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2273571 5.7244284 5.0973115 Created 1072 atoms using lattice units in orthogonal box = (0.0000000 -59.005646 0.0000000) to (41.723293 59.005646 5.0973115) create_atoms CPU = 0.003 seconds 1072 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2273571 5.7244284 5.0973115 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -59.005646 0.0000000) to (41.723293 59.005646 5.0973115) create_atoms CPU = 0.003 seconds 1080 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 39 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 2136 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.216 | 5.216 | 5.216 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8760.3753 0 -8760.3753 46523.742 400 0 -9080.8756 0 -9080.8756 -12069.349 Loop time of 68.1187 on 1 procs for 400 steps with 2136 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 = -8760.37533177016 -9080.86776073037 -9080.87556822145 Force two-norm initial, final = 580.54147 0.26128198 Force max component initial, final = 100.84459 0.040154179 Final line search alpha, max atom move = 1.0000000 0.040154179 Iterations, force evaluations = 400 766 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 67.785 | 67.785 | 67.785 | 0.0 | 99.51 Neigh | 0.16078 | 0.16078 | 0.16078 | 0.0 | 0.24 Comm | 0.084888 | 0.084888 | 0.084888 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08852 | | | 0.13 Nlocal: 2136.00 ave 2136 max 2136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8151.00 ave 8151 max 8151 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: 151692.0 ave 151692 max 151692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 151692 Ave neighs/atom = 71.016854 Neighbor list builds = 12 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 400 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.219 | 5.219 | 5.219 Mbytes Step Temp E_pair E_mol TotEng Press Volume 400 0 -9080.8756 0 -9080.8756 -12069.349 25098.242 431 0 -9102.4218 0 -9102.4218 6.2583718 24878.521 Loop time of 3.6521 on 1 procs for 31 steps with 2136 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 = -9080.87556822147 -9102.42122477549 -9102.42184494065 Force two-norm initial, final = 1081.0882 5.6633360 Force max component initial, final = 768.46701 3.7130829 Final line search alpha, max atom move = 0.00098389559 0.0036532859 Iterations, force evaluations = 31 33 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5926 | 3.5926 | 3.5926 | 0.0 | 98.37 Neigh | 0.04 | 0.04 | 0.04 | 0.0 | 1.10 Comm | 0.0032756 | 0.0032756 | 0.0032756 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01627 | | | 0.45 Nlocal: 2136.00 ave 2136 max 2136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8355.00 ave 8355 max 8355 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: 147906.0 ave 147906 max 147906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147906 Ave neighs/atom = 69.244382 Neighbor list builds = 3 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.360 | 5.360 | 5.360 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9102.4218 0 -9102.4218 6.2583718 Loop time of 2.742e-06 on 1 procs for 0 steps with 2136 atoms 182.3% 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 | | 2.742e-06 | | |100.00 Nlocal: 2136.00 ave 2136 max 2136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8364.00 ave 8364 max 8364 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: 147820.0 ave 147820 max 147820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147820 Ave neighs/atom = 69.204120 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.360 | 5.360 | 5.360 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 -9102.4218 -9102.4218 41.169728 121.46257 4.9751263 6.2583718 6.2583718 235.94994 -4.7318695 -212.44295 2.377578 2412.7279 Loop time of 2.659e-06 on 1 procs for 0 steps with 2136 atoms 188.0% 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 | | 2.659e-06 | | |100.00 Nlocal: 2136.00 ave 2136 max 2136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8364.00 ave 8364 max 8364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73910.0 ave 73910 max 73910 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 147820.0 ave 147820 max 147820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147820 Ave neighs/atom = 69.204120 Neighbor list builds = 0 Dangerous builds = 0 2136 -9102.42184494065 eV 2.37757800085808 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:12