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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -62.203701 0.0000000) to (35.911290 62.203701 6.0992294) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5248139 5.5820674 6.0992294 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -62.203701 0.0000000) to (35.911290 62.203701 6.0992294) create_atoms CPU = 0.003 seconds 1251 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5248139 5.5820674 6.0992294 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -62.203701 0.0000000) to (35.911290 62.203701 6.0992294) create_atoms CPU = 0.002 seconds 1251 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 40 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 2480 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.712 | 5.712 | 5.712 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10957.535 0 -10957.535 4461.5382 35 0 -10997.539 0 -10997.539 -2827.4056 Loop time of 5.21357 on 1 procs for 35 steps with 2480 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10957.5350006192 -10997.5296895049 -10997.5389162481 Force two-norm initial, final = 62.383637 0.37843013 Force max component initial, final = 10.860564 0.090499215 Final line search alpha, max atom move = 1.0000000 0.090499215 Iterations, force evaluations = 35 65 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2002 | 5.2002 | 5.2002 | 0.0 | 99.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0055437 | 0.0055437 | 0.0055437 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007794 | | | 0.15 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8605.00 ave 8605 max 8605 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: 212836.0 ave 212836 max 212836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212836 Ave neighs/atom = 85.820968 Neighbor list builds = 0 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.712 | 5.712 | 5.712 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -10997.539 0 -10997.539 -2827.4056 27249.103 37 0 -10997.573 0 -10997.573 -769.18261 27218.815 Loop time of 0.393479 on 1 procs for 2 steps with 2480 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 = -10997.5389162481 -10997.5717738887 -10997.5733524152 Force two-norm initial, final = 68.109792 0.38607515 Force max component initial, final = 64.545943 0.094877660 Final line search alpha, max atom move = 9.4652447e-05 8.9804027e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39145 | 0.39145 | 0.39145 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029799 | 0.00029799 | 0.00029799 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001727 | | | 0.44 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8563.00 ave 8563 max 8563 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: 212582.0 ave 212582 max 212582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212582 Ave neighs/atom = 85.718548 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.849 | 5.849 | 5.849 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10997.573 0 -10997.573 -769.18261 Loop time of 2.178e-06 on 1 procs for 0 steps with 2480 atoms 137.7% 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 | | 2.178e-06 | | |100.00 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8563.00 ave 8563 max 8563 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: 212602.0 ave 212602 max 212602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212602 Ave neighs/atom = 85.726613 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.849 | 5.849 | 5.849 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 -10997.573 -10997.573 35.90881 124.4074 6.0928709 -769.18261 -769.18261 -3.358665 -2304.6249 0.43577567 2.2159237 943.83773 Loop time of 2.15e-06 on 1 procs for 0 steps with 2480 atoms 186.0% 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 | | 2.15e-06 | | |100.00 Nlocal: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8563.00 ave 8563 max 8563 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 106301.0 ave 106301 max 106301 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 212602.0 ave 212602 max 212602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212602 Ave neighs/atom = 85.726613 Neighbor list builds = 0 Dangerous builds = 0 2480 -10997.5733524152 eV 2.21592370062264 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06