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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -67.341580 0.0000000) to (38.879679 67.341580 6.0968202) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7363461 5.1518149 6.0968202 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -67.341580 0.0000000) to (38.879679 67.341580 6.0968202) create_atoms CPU = 0.008 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7363461 5.1518149 6.0968202 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -67.341580 0.0000000) to (38.879679 67.341580 6.0968202) create_atoms CPU = 0.008 seconds 1466 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 35 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2926 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_820335782779_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.001 | 7.001 | 7.001 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12718.816 0 -12718.816 17096.451 161 0 -12974.657 0 -12974.657 5685.8298 Loop time of 17.6156 on 1 procs for 161 steps with 2926 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 = -12718.8163237701 -12974.6439863706 -12974.6567761872 Force two-norm initial, final = 403.27915 0.51378983 Force max component initial, final = 119.41479 0.087737490 Final line search alpha, max atom move = 1.0000000 0.087737490 Iterations, force evaluations = 161 305 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.144 | 17.144 | 17.144 | 0.0 | 97.32 Neigh | 0.28289 | 0.28289 | 0.28289 | 0.0 | 1.61 Comm | 0.098968 | 0.098968 | 0.098968 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0897 | | | 0.51 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12356.0 ave 12356 max 12356 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: 518920.0 ave 518920 max 518920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 518920 Ave neighs/atom = 177.34792 Neighbor list builds = 4 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 161 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.001 | 7.001 | 7.001 Mbytes Step Temp E_pair E_mol TotEng Press Volume 161 0 -12974.657 0 -12974.657 5685.8298 31925.621 165 0 -12975.016 0 -12975.016 360.77784 32015.393 Loop time of 0.335739 on 1 procs for 4 steps with 2926 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 = -12974.6567761874 -12975.0091998156 -12975.0160890891 Force two-norm initial, final = 236.27681 13.876149 Force max component initial, final = 220.72564 11.623163 Final line search alpha, max atom move = 4.7830963e-05 0.00055594707 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32813 | 0.32813 | 0.32813 | 0.0 | 97.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016481 | 0.0016481 | 0.0016481 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005966 | | | 1.78 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12349.0 ave 12349 max 12349 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: 516344.0 ave 516344 max 516344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 516344 Ave neighs/atom = 176.46753 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.139 | 7.139 | 7.139 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12975.016 0 -12975.016 360.77784 Loop time of 6.886e-06 on 1 procs for 0 steps with 2926 atoms 203.3% 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 | | 6.886e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12337.0 ave 12337 max 12337 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: 515804.0 ave 515804 max 515804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 515804 Ave neighs/atom = 176.28298 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.139 | 7.139 | 7.139 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 -12975.016 -12975.016 38.86709 135.11868 6.096231 360.77784 360.77784 153.11671 583.54982 345.66698 2.2659952 926.71144 Loop time of 7.026e-06 on 1 procs for 0 steps with 2926 atoms 355.8% 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 | | 7.026e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12337.0 ave 12337 max 12337 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 257902.0 ave 257902 max 257902 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 515804.0 ave 515804 max 515804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 515804 Ave neighs/atom = 176.28298 Neighbor list builds = 0 Dangerous builds = 0 2926 -12975.0160890891 eV 2.26599519194955 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19