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 = 4.0500004 4.0500004 4.0500004 Created orthogonal box = (0.0000000 -41.306112 0.0000000) to (35.768635 41.306112 7.0148065) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4200114 6.3541634 7.0148065 Created 627 atoms using lattice units in orthogonal box = (0.0000000 -41.306112 0.0000000) to (35.768635 41.306112 7.0148065) create_atoms CPU = 0.001 seconds 627 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4200114 6.3541634 7.0148065 Created 627 atoms using lattice units in orthogonal box = (0.0000000 -41.306112 0.0000000) to (35.768635 41.306112 7.0148065) create_atoms CPU = 0.001 seconds 627 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 22 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 26 atoms, new total = 1228 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 22 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) = 5.043 | 5.043 | 5.043 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4081.4279 0 -4081.4279 3523.966 74 0 -4109.3193 0 -4109.3193 -3536.5406 Loop time of 1.77835 on 1 procs for 74 steps with 1228 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4081.42787068982 -4109.31600160121 -4109.31931993137 Force two-norm initial, final = 26.869145 0.18151953 Force max component initial, final = 6.5158485 0.063044066 Final line search alpha, max atom move = 1.0000000 0.063044066 Iterations, force evaluations = 74 134 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7304 | 1.7304 | 1.7304 | 0.0 | 97.30 Neigh | 0.026664 | 0.026664 | 0.026664 | 0.0 | 1.50 Comm | 0.00925 | 0.00925 | 0.00925 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01207 | | | 0.68 Nlocal: 1228.00 ave 1228 max 1228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5033.00 ave 5033 max 5033 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: 160176.0 ave 160176 max 160176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160176 Ave neighs/atom = 130.43648 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 22 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 : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.043 | 5.043 | 5.043 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -4109.3193 0 -4109.3193 -3536.5406 20728.238 79 0 -4109.5079 0 -4109.5079 416.8159 20628.276 Loop time of 0.107448 on 1 procs for 5 steps with 1228 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 = -4109.31931993137 -4109.50520997621 -4109.5079309475 Force two-norm initial, final = 89.664828 3.4650274 Force max component initial, final = 79.025014 3.2143535 Final line search alpha, max atom move = 0.00013435910 0.00043187764 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10413 | 0.10413 | 0.10413 | 0.0 | 96.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052404 | 0.00052404 | 0.00052404 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002791 | | | 2.60 Nlocal: 1228.00 ave 1228 max 1228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5035.00 ave 5035 max 5035 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: 160044.0 ave 160044 max 160044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160044 Ave neighs/atom = 130.32899 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 22 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) = 5.181 | 5.181 | 5.181 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4109.5079 0 -4109.5079 416.8159 Loop time of 3.335e-06 on 1 procs for 0 steps with 1228 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 | | 3.335e-06 | | |100.00 Nlocal: 1228.00 ave 1228 max 1228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5036.00 ave 5036 max 5036 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: 160162.0 ave 160162 max 160162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160162 Ave neighs/atom = 130.42508 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 22 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) = 5.181 | 5.181 | 5.181 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 -4109.5079 -4109.5079 35.747924 82.612224 6.9850223 416.8159 416.8159 -98.057772 1597.1009 -248.59544 2.6209635 1355.9866 Loop time of 3.344e-06 on 1 procs for 0 steps with 1228 atoms 179.4% 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 | | 3.344e-06 | | |100.00 Nlocal: 1228.00 ave 1228 max 1228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5036.00 ave 5036 max 5036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 80081.0 ave 80081 max 80081 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 160162.0 ave 160162 max 160162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160162 Ave neighs/atom = 130.42508 Neighbor list builds = 0 Dangerous builds = 0 1228 -4109.5079309475 eV 2.62096345858879 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02