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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -44.306930 0.0000000) to (9.0441142 44.306930 9.9073307) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4264685 5.9075906 6.6048871 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -44.306930 0.0000000) to (9.0441142 44.306930 9.9073307) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4264685 5.9075906 6.6048871 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -44.306930 0.0000000) to (9.0441142 44.306930 9.9073307) create_atoms CPU = 0.001 seconds 242 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 3 23 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 480 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_793141037706_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 3 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.505 | 4.505 | 4.505 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1564.2813 0 -1564.2813 18973.964 43 0 -1606.1107 0 -1606.1107 5138.9171 Loop time of 2.8304 on 1 procs for 43 steps with 480 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 = -1564.28128168691 -1606.10949188785 -1606.11073005172 Force two-norm initial, final = 82.043111 0.078069281 Force max component initial, final = 25.635500 0.012220743 Final line search alpha, max atom move = 1.0000000 0.012220743 Iterations, force evaluations = 43 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8249 | 2.8249 | 2.8249 | 0.0 | 99.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0027509 | 0.0027509 | 0.0027509 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002725 | | | 0.10 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3611.00 ave 3611 max 3611 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: 64048.0 ave 64048 max 64048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64048 Ave neighs/atom = 133.43333 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 3 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.504 | 4.504 | 4.504 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -1606.1107 0 -1606.1107 5138.9171 7940.0703 55 0 -1606.3648 0 -1606.3648 1.7756204 7990.8866 Loop time of 0.478827 on 1 procs for 12 steps with 480 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 = -1606.11073005172 -1606.36470235029 -1606.36477727149 Force two-norm initial, final = 54.478611 0.29794506 Force max component initial, final = 51.510696 0.10091026 Final line search alpha, max atom move = 0.0024517025 0.00024740193 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47254 | 0.47254 | 0.47254 | 0.0 | 98.69 Neigh | 0.004109 | 0.004109 | 0.004109 | 0.0 | 0.86 Comm | 0.00044989 | 0.00044989 | 0.00044989 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00173 | | | 0.36 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3461.00 ave 3461 max 3461 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: 63752.0 ave 63752 max 63752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63752 Ave neighs/atom = 132.81667 Neighbor list builds = 1 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 3 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.642 | 4.642 | 4.642 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1606.3648 0 -1606.3648 1.7756204 Loop time of 1.592e-06 on 1 procs for 0 steps with 480 atoms 125.6% 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 | | 1.592e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3461.00 ave 3461 max 3461 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: 63756.0 ave 63756 max 63756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63756 Ave neighs/atom = 132.82500 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 3 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.642 | 4.642 | 4.642 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 -1606.3648 -1606.3648 9.0250001 89.605318 9.8812975 1.7756204 1.7756204 15.67951 -20.458927 10.106278 2.5233453 350.80184 Loop time of 1.613e-06 on 1 procs for 0 steps with 480 atoms 248.0% 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 | | 1.613e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3461.00 ave 3461 max 3461 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31878.0 ave 31878 max 31878 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 63756.0 ave 63756 max 63756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63756 Ave neighs/atom = 132.82500 Neighbor list builds = 0 Dangerous builds = 0 480 -1606.36477727149 eV 2.52334527380615 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03