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 = 3.1666864 3.1666864 3.1666864 Created orthogonal box = (0.0000000 -51.061284 0.0000000) to (25.530642 51.061284 3.1666864) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5350120 3.5350120 3.1666864 Created 260 atoms using lattice units in orthogonal box = (0.0000000 -51.061284 0.0000000) to (25.530642 51.061284 3.1666864) create_atoms CPU = 0.001 seconds 260 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5350120 3.5350120 3.1666864 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -51.061284 0.0000000) to (25.530642 51.061284 3.1666864) create_atoms CPU = 0.000 seconds 261 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 = 6.7012 ghost atom cutoff = 6.7012 binsize = 3.3506, bins = 8 31 1 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 6.7012 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 521 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_560387080449_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 = 6.7012 ghost atom cutoff = 6.7012 binsize = 3.3506, bins = 8 31 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7012 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) = 4.481 | 4.481 | 4.481 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 69.898603 0 69.898603 27343.558 64 0 15.335715 0 15.335715 13440.229 Loop time of 24.3497 on 1 procs for 64 steps with 521 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = 69.8986026603104 15.3357274804089 15.3357152146946 Force two-norm initial, final = 44.384933 0.012129837 Force max component initial, final = 9.1161260 0.0023072202 Final line search alpha, max atom move = 1.0000000 0.0023072202 Iterations, force evaluations = 64 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 24.336 | 24.336 | 24.336 | 0.0 | 99.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.006948 | 0.006948 | 0.006948 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006368 | | | 0.03 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3974.00 ave 3974 max 3974 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: 33924.0 ave 33924 max 33924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33924 Ave neighs/atom = 65.113244 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 = 6.7012 ghost atom cutoff = 6.7012 binsize = 3.3506, bins = 8 31 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7012 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.484 | 4.484 | 4.484 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 15.335715 0 15.335715 13440.229 8256.3581 75 0 14.98705 0 14.98705 -4.7280492 8299.2936 Loop time of 3.7569 on 1 procs for 11 steps with 521 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = 15.3357152146945 14.9870582142311 14.9870503890482 Force two-norm initial, final = 137.10126 0.26393484 Force max component initial, final = 122.12011 0.12873180 Final line search alpha, max atom move = 0.0043132444 0.00055525173 Iterations, force evaluations = 11 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7523 | 3.7523 | 3.7523 | 0.0 | 99.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00077712 | 0.00077712 | 0.00077712 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003778 | | | 0.10 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4396.00 ave 4396 max 4396 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: 33688.0 ave 33688 max 33688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33688 Ave neighs/atom = 64.660269 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 = 6.7012 ghost atom cutoff = 6.7012 binsize = 3.3506, bins = 8 31 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7012 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) = 4.622 | 4.622 | 4.622 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 14.98705 0 14.98705 -4.7280492 Loop time of 2.093e-06 on 1 procs for 0 steps with 521 atoms 191.1% 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 | | 2.093e-06 | | |100.00 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4391.00 ave 4391 max 4391 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: 33616.0 ave 33616 max 33616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33616 Ave neighs/atom = 64.522073 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 = 6.7012 ghost atom cutoff = 6.7012 binsize = 3.3506, bins = 8 31 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7012 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) = 4.622 | 4.622 | 4.622 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 14.98705 14.98705 25.501754 102.71748 3.1683031 -4.7280492 -4.7280492 17.179379 -6.4991973 -24.864329 2.5567085 121.25267 Loop time of 3.939e-06 on 1 procs for 0 steps with 521 atoms 203.1% 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 | | 3.939e-06 | | |100.00 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4391.00 ave 4391 max 4391 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16808.0 ave 16808 max 16808 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 33616.0 ave 33616 max 33616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33616 Ave neighs/atom = 64.522073 Neighbor list builds = 0 Dangerous builds = 0 521 -3567.95470702388 eV 2.55670849745981 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:29