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 = 3.5200001 3.5200001 3.5200001 Created orthogonal box = (0.0000000 -41.649202 0.0000000) to (51.009647 41.649202 8.6222040) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8296739 5.3548975 5.7481360 Created 1660 atoms using lattice units in orthogonal box = (0.0000000 -41.649202 0.0000000) to (51.009647 41.649202 8.6222040) create_atoms CPU = 0.008 seconds 1660 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8296739 5.3548975 5.7481360 Created 1684 atoms using lattice units in orthogonal box = (0.0000000 -41.649202 0.0000000) to (51.009647 41.649202 8.6222040) create_atoms CPU = 0.007 seconds 1684 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 15 25 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 6.85 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 3316 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_776437554506_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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 15 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 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) = 6.500 | 6.500 | 6.500 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14586.537 0 -14586.537 3075.8388 183 0 -14694.671 0 -14694.671 -12882.4 Loop time of 12.8629 on 1 procs for 183 steps with 3316 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 = -14586.5368269626 -14694.6605480564 -14694.6712504275 Force two-norm initial, final = 66.859543 0.36074422 Force max component initial, final = 7.9671052 0.12605376 Final line search alpha, max atom move = 0.36521435 0.046036642 Iterations, force evaluations = 183 328 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.073 | 12.073 | 12.073 | 0.0 | 93.86 Neigh | 0.59918 | 0.59918 | 0.59918 | 0.0 | 4.66 Comm | 0.07864 | 0.07864 | 0.07864 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1124 | | | 0.87 Nlocal: 3316.00 ave 3316 max 3316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9299.00 ave 9299 max 9299 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: 437476.0 ave 437476 max 437476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 437476 Ave neighs/atom = 131.92883 Neighbor list builds = 9 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 15 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 183 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.500 | 6.500 | 6.500 Mbytes Step Temp E_pair E_mol TotEng Press Volume 183 0 -14694.671 0 -14694.671 -12882.4 36635.937 189 0 -14696.047 0 -14696.047 -408.42512 36371.67 Loop time of 0.293649 on 1 procs for 6 steps with 3316 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 = -14694.6712504275 -14696.0378082713 -14696.0470007688 Force two-norm initial, final = 530.41623 17.561234 Force max component initial, final = 411.36518 14.901141 Final line search alpha, max atom move = 5.1064708e-05 0.00076092244 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28415 | 0.28415 | 0.28415 | 0.0 | 96.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015976 | 0.0015976 | 0.0015976 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007898 | | | 2.69 Nlocal: 3316.00 ave 3316 max 3316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9284.00 ave 9284 max 9284 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: 437534.0 ave 437534 max 437534 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 437534 Ave neighs/atom = 131.94632 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 15 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 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) = 6.638 | 6.638 | 6.638 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14696.047 0 -14696.047 -408.42512 Loop time of 6.224e-06 on 1 procs for 0 steps with 3316 atoms 192.8% 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 | | 6.224e-06 | | |100.00 Nlocal: 3316.00 ave 3316 max 3316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9296.00 ave 9296 max 9296 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: 437922.0 ave 437922 max 437922 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 437922 Ave neighs/atom = 132.06333 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 15 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 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) = 6.638 | 6.638 | 6.638 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 -14696.047 -14696.047 50.972578 82.856495 8.6119221 -408.42512 -408.42512 -323.34903 -652.91481 -249.01152 2.1611527 1620.243 Loop time of 6.465e-06 on 1 procs for 0 steps with 3316 atoms 293.9% 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 | | 6.465e-06 | | |100.00 Nlocal: 3316.00 ave 3316 max 3316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9296.00 ave 9296 max 9296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 218961.0 ave 218961 max 218961 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 437922.0 ave 437922 max 437922 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 437922 Ave neighs/atom = 132.06333 Neighbor list builds = 0 Dangerous builds = 0 3316 -14696.0470007688 eV 2.16115271741188 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14