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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -66.626249 0.0000000) to (33.313124 66.626249 3.6133156) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0949484 5.0949484 3.6133156 Created 680 atoms using lattice units in orthogonal box = (0.0000000 -66.626249 0.0000000) to (33.313124 66.626249 3.6133156) create_atoms CPU = 0.001 seconds 680 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0949484 5.0949484 3.6133156 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -66.626249 0.0000000) to (33.313124 66.626249 3.6133156) create_atoms CPU = 0.001 seconds 682 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 ghost atom cutoff = 7 binsize = 3.5, bins = 10 39 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1362 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_813575892799_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.080 | 5.080 | 5.080 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4609.468 0 -4609.468 38267.065 29 0 -4813.7672 0 -4813.7672 4809.9983 Loop time of 2.39302 on 1 procs for 29 steps with 1362 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4609.46801834176 -4813.76293653367 -4813.76724668777 Force two-norm initial, final = 301.90440 0.22369619 Force max component initial, final = 100.79608 0.042945264 Final line search alpha, max atom move = 1.0000000 0.042945264 Iterations, force evaluations = 29 48 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3834 | 2.3834 | 2.3834 | 0.0 | 99.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.005004 | 0.005004 | 0.005004 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004629 | | | 0.19 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8235.00 ave 8235 max 8235 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: 181880.0 ave 181880 max 181880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181880 Ave neighs/atom = 133.53891 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.080 | 5.080 | 5.080 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -4813.7672 0 -4813.7672 4809.9983 16039.714 34 0 -4813.9396 0 -4813.9396 -101.49467 16094.757 Loop time of 0.39745 on 1 procs for 5 steps with 1362 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 = -4813.76724668777 -4813.93865005762 -4813.9396184192 Force two-norm initial, final = 99.538035 3.7899793 Force max component initial, final = 89.727027 3.4251904 Final line search alpha, max atom move = 0.00013100229 0.00044870781 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39441 | 0.39441 | 0.39441 | 0.0 | 99.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055246 | 0.00055246 | 0.00055246 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002484 | | | 0.63 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8230.00 ave 8230 max 8230 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: 181824.0 ave 181824 max 181824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181824 Ave neighs/atom = 133.49780 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 ghost atom cutoff = 7 binsize = 3.5, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.218 | 5.218 | 5.218 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4813.9396 0 -4813.9396 -101.49467 Loop time of 2.376e-06 on 1 procs for 0 steps with 1362 atoms 126.3% 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 | | 2.376e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8230.00 ave 8230 max 8230 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: 181740.0 ave 181740 max 181740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181740 Ave neighs/atom = 133.43612 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 ghost atom cutoff = 7 binsize = 3.5, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.218 | 5.218 | 5.218 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 -4813.9396 -4813.9396 33.286071 133.77393 3.6145182 -101.49467 -101.49467 129.84602 -93.250868 -341.07915 2.3103223 156.93514 Loop time of 2.396e-06 on 1 procs for 0 steps with 1362 atoms 166.9% 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 | | 2.396e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8230.00 ave 8230 max 8230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90870.0 ave 90870 max 90870 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 181740.0 ave 181740 max 181740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181740 Ave neighs/atom = 133.43612 Neighbor list builds = 0 Dangerous builds = 0 1362 -4813.9396184192 eV 2.31032233833414 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03