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 -56.761258 0.0000000) to (34.759030 56.761258 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6062952 5.4930250 5.8858683 Created 1487 atoms using lattice units in orthogonal box = (0.0000000 -56.761258 0.0000000) to (34.759030 56.761258 8.8288024) create_atoms CPU = 0.002 seconds 1487 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6062952 5.4930250 5.8858683 Created 1493 atoms using lattice units in orthogonal box = (0.0000000 -56.761258 0.0000000) to (34.759030 56.761258 8.8288024) create_atoms CPU = 0.002 seconds 1493 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 ghost atom cutoff = 6 binsize = 3, bins = 12 38 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 11 atoms, new total = 2969 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_492310898779_001#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 ghost atom cutoff = 6 binsize = 3, bins = 12 38 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.579 | 5.579 | 5.579 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11254.484 0 -11254.484 114187.38 222 0 -12586.317 0 -12586.317 -2167.0451 Loop time of 43.158 on 1 procs for 222 steps with 2969 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 = -11254.4843298471 -12586.3048025738 -12586.3169724265 Force two-norm initial, final = 2302.4202 0.34054623 Force max component initial, final = 348.06995 0.062613473 Final line search alpha, max atom move = 1.0000000 0.062613473 Iterations, force evaluations = 222 404 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 42.934 | 42.934 | 42.934 | 0.0 | 99.48 Neigh | 0.11789 | 0.11789 | 0.11789 | 0.0 | 0.27 Comm | 0.0425 | 0.0425 | 0.0425 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06356 | | | 0.15 Nlocal: 2969.00 ave 2969 max 2969 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7434.00 ave 7434 max 7434 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: 225510.0 ave 225510 max 225510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225510 Ave neighs/atom = 75.954867 Neighbor list builds = 6 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 ghost atom cutoff = 6 binsize = 3, bins = 12 38 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 222 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.580 | 5.580 | 5.580 Mbytes Step Temp E_pair E_mol TotEng Press Volume 222 0 -12586.317 0 -12586.317 -2167.0451 34837.859 228 0 -12587.072 0 -12587.072 -18.355396 34790.326 Loop time of 0.866957 on 1 procs for 6 steps with 2969 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 = -12586.3169724265 -12587.0651081385 -12587.0716727694 Force two-norm initial, final = 214.67220 2.1428666 Force max component initial, final = 161.96499 1.3148518 Final line search alpha, max atom move = 7.3811623e-05 9.7051343e-05 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.86238 | 0.86238 | 0.86238 | 0.0 | 99.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055224 | 0.00055224 | 0.00055224 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004025 | | | 0.46 Nlocal: 2969.00 ave 2969 max 2969 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7438.00 ave 7438 max 7438 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: 225376.0 ave 225376 max 225376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225376 Ave neighs/atom = 75.909734 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 ghost atom cutoff = 6 binsize = 3, bins = 12 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.718 | 5.718 | 5.718 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12587.072 0 -12587.072 -18.355396 Loop time of 2.539e-06 on 1 procs for 0 steps with 2969 atoms 157.5% 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 | | 2.539e-06 | | |100.00 Nlocal: 2969.00 ave 2969 max 2969 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7427.00 ave 7427 max 7427 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: 225538.0 ave 225538 max 225538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225538 Ave neighs/atom = 75.964298 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 ghost atom cutoff = 6 binsize = 3, bins = 12 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.718 | 5.718 | 5.718 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 -12587.072 -12587.072 34.70972 112.94882 8.8741278 -18.355396 -18.355396 52.64085 -46.844152 -60.862884 2.3013354 3572.0979 Loop time of 2.221e-06 on 1 procs for 0 steps with 2969 atoms 315.2% 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 | | 2.221e-06 | | |100.00 Nlocal: 2969.00 ave 2969 max 2969 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7427.00 ave 7427 max 7427 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112769.0 ave 112769 max 112769 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 225538.0 ave 225538 max 225538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225538 Ave neighs/atom = 75.964298 Neighbor list builds = 0 Dangerous builds = 0 2969 -12587.0716727694 eV 2.30133535177409 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:44