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 = 4.0452705 4.0452705 4.0452705 Created orthogonal box = (0.0000000 -52.432698 0.0000000) to (30.272032 52.432698 7.0066140) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4868641 6.2419879 7.0066140 Created 672 atoms using lattice units in orthogonal box = (0.0000000 -52.432698 0.0000000) to (30.272032 52.432698 7.0066140) create_atoms CPU = 0.002 seconds 672 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4868641 6.2419879 7.0066140 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -52.432698 0.0000000) to (30.272032 52.432698 7.0066140) create_atoms CPU = 0.001 seconds 676 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 23 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 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1344 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_658278549784_005#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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 5.916 | 5.916 | 5.916 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4438.4658 0 -4438.4658 18820.809 53 0 -4569.5202 0 -4569.5202 5438.5913 Loop time of 1.56866 on 1 procs for 53 steps with 1344 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 = -4438.46581363997 -4569.51605397985 -4569.52023528232 Force two-norm initial, final = 171.65584 0.13220709 Force max component initial, final = 31.299951 0.010826371 Final line search alpha, max atom move = 1.0000000 0.010826371 Iterations, force evaluations = 53 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5315 | 1.5315 | 1.5315 | 0.0 | 97.63 Neigh | 0.018859 | 0.018859 | 0.018859 | 0.0 | 1.20 Comm | 0.010352 | 0.010352 | 0.010352 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007957 | | | 0.51 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8954.00 ave 8954 max 8954 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: 294192.0 ave 294192 max 294192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 294192 Ave neighs/atom = 218.89286 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.915 | 5.915 | 5.915 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -4569.5202 0 -4569.5202 5438.5913 22242.417 62 0 -4569.9895 0 -4569.9895 2.8853669 22388.929 Loop time of 0.19048 on 1 procs for 9 steps with 1344 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 = -4569.52023528249 -4569.98942618784 -4569.98951534589 Force two-norm initial, final = 146.32682 0.41805124 Force max component initial, final = 128.80300 0.27526848 Final line search alpha, max atom move = 0.00052142517 0.00014353191 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18489 | 0.18489 | 0.18489 | 0.0 | 97.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00090777 | 0.00090777 | 0.00090777 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00468 | | | 2.46 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8958.00 ave 8958 max 8958 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: 296312.0 ave 296312 max 296312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296312 Ave neighs/atom = 220.47024 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 6.052 | 6.052 | 6.052 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4569.9895 0 -4569.9895 2.8853669 Loop time of 2.232e-06 on 1 procs for 0 steps with 1344 atoms 134.4% 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 | | 2.232e-06 | | |100.00 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8902.00 ave 8902 max 8902 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: 295328.0 ave 295328 max 295328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 295328 Ave neighs/atom = 219.73810 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 6.052 | 6.052 | 6.052 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 -4569.9895 -4569.9895 30.263057 105.69675 6.9993692 2.8853669 2.8853669 -12.810862 1.7888145 19.678148 2.6315994 968.0514 Loop time of 2.852e-06 on 1 procs for 0 steps with 1344 atoms 245.4% 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 | | 2.852e-06 | | |100.00 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8902.00 ave 8902 max 8902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 147664.0 ave 147664 max 147664 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 295328.0 ave 295328 max 295328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 295328 Ave neighs/atom = 219.73810 Neighbor list builds = 0 Dangerous builds = 0 1344 -4569.98951534589 eV 2.63159937203974 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02