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 = 3.6533440 3.6533440 3.6533440 Created orthogonal box = (0.0000000 -46.499478 0.0000000) to (32.880096 46.499478 5.1666087) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0889067 6.3147440 5.1666087 Created 648 atoms using lattice units in orthogonal box = (0.0000000 -46.499478 0.0000000) to (32.880096 46.499478 5.1666087) create_atoms CPU = 0.005 seconds 648 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0889067 6.3147440 5.1666087 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -46.499478 0.0000000) to (32.880096 46.499478 5.1666087) create_atoms CPU = 0.005 seconds 650 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 8 22 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 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1298 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_673777079812_004#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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 5.506 | 5.506 | 5.506 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4005.3735 0 -4005.3735 33732.515 158 0 -4241.9724 0 -4241.9724 -1899.3514 Loop time of 8.78204 on 1 procs for 158 steps with 1298 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 = -4005.37348415711 -4241.96835755021 -4241.97238074082 Force two-norm initial, final = 291.65699 0.24808296 Force max component initial, final = 74.956262 0.020007269 Final line search alpha, max atom move = 1.0000000 0.020007269 Iterations, force evaluations = 158 300 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.6317 | 8.6317 | 8.6317 | 0.0 | 98.29 Neigh | 0.038538 | 0.038538 | 0.038538 | 0.0 | 0.44 Comm | 0.063712 | 0.063712 | 0.063712 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04807 | | | 0.55 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9239.00 ave 9239 max 9239 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: 292576.0 ave 292576 max 292576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292576 Ave neighs/atom = 225.40524 Neighbor list builds = 1 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 158 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.504 | 5.504 | 5.504 Mbytes Step Temp E_pair E_mol TotEng Press Volume 158 0 -4241.9724 0 -4241.9724 -1899.3514 15798.532 166 0 -4242.6764 0 -4242.6764 -17.561408 15775.852 Loop time of 0.294963 on 1 procs for 8 steps with 1298 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 = -4241.97238074083 -4242.67621612023 -4242.67635601406 Force two-norm initial, final = 173.39290 0.66303021 Force max component initial, final = 157.49987 0.35936573 Final line search alpha, max atom move = 0.00057718903 0.00020742196 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28606 | 0.28606 | 0.28606 | 0.0 | 96.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.002104 | 0.002104 | 0.002104 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006794 | | | 2.30 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9112.00 ave 9112 max 9112 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: 293564.0 ave 293564 max 293564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293564 Ave neighs/atom = 226.16641 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 5.641 | 5.641 | 5.641 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4242.6764 0 -4242.6764 -17.561408 Loop time of 6.255e-06 on 1 procs for 0 steps with 1298 atoms 175.9% 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 | | 6.255e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9061.00 ave 9061 max 9061 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: 294092.0 ave 294092 max 294092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 294092 Ave neighs/atom = 226.57319 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 5.641 | 5.641 | 5.641 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 -4242.6764 -4242.6764 32.984674 92.339814 5.1795454 -17.561408 -17.561408 -36.61283 -1.5321785 -14.539217 2.4179741 1347.7361 Loop time of 6.866e-06 on 1 procs for 0 steps with 1298 atoms 262.2% 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 | | 6.866e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9061.00 ave 9061 max 9061 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 147046.0 ave 147046 max 147046 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 294092.0 ave 294092 max 294092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 294092 Ave neighs/atom = 226.57319 Neighbor list builds = 0 Dangerous builds = 0 1298 -4242.67635601406 eV 2.41797405154056 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09