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 = 3.6150017 3.6150017 3.6150017 Created orthogonal box = (0.0000000 -47.958417 0.0000000) to (29.368412 47.958417 8.8549095) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3397114 5.4498201 5.9032730 Created 1049 atoms using lattice units in orthogonal box = (0.0000000 -47.958417 0.0000000) to (29.368412 47.958417 8.8549095) create_atoms CPU = 0.002 seconds 1049 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3397114 5.4498201 5.9032730 Created 1073 atoms using lattice units in orthogonal box = (0.0000000 -47.958417 0.0000000) to (29.368412 47.958417 8.8549095) create_atoms CPU = 0.001 seconds 1073 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 7 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 2112 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_592013496703_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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 7 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 6.436 | 6.436 | 6.436 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7456.6252 0 -7456.6252 3596.1659 12 0 -7465.2379 0 -7465.2379 2883.45 Loop time of 0.499765 on 1 procs for 12 steps with 2112 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7456.62517753663 -7465.23214822871 -7465.23786740241 Force two-norm initial, final = 16.761224 0.12376497 Force max component initial, final = 1.7326654 0.010696435 Final line search alpha, max atom move = 1.0000000 0.010696435 Iterations, force evaluations = 12 24 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49521 | 0.49521 | 0.49521 | 0.0 | 99.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020802 | 0.0020802 | 0.0020802 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002478 | | | 0.50 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8940.00 ave 8940 max 8940 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: 425248.0 ave 425248 max 425248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 425248 Ave neighs/atom = 201.34848 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 7 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 12 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.436 | 6.436 | 6.436 Mbytes Step Temp E_pair E_mol TotEng Press Volume 12 0 -7465.2379 0 -7465.2379 2883.45 24943.617 18 0 -7465.5459 0 -7465.5459 191.94155 24991.441 Loop time of 0.165856 on 1 procs for 6 steps with 2112 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 = -7465.23786740238 -7465.54424179762 -7465.54593185962 Force two-norm initial, final = 119.02341 5.3785010 Force max component initial, final = 117.58569 4.1195564 Final line search alpha, max atom move = 0.00017881865 0.00073665353 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1617 | 0.1617 | 0.1617 | 0.0 | 97.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00065103 | 0.00065103 | 0.00065103 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003501 | | | 2.11 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8940.00 ave 8940 max 8940 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: 428010.0 ave 428010 max 428010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 428010 Ave neighs/atom = 202.65625 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 7 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 6.574 | 6.574 | 6.574 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7465.5459 0 -7465.5459 191.94155 Loop time of 2.031e-06 on 1 procs for 0 steps with 2112 atoms 147.7% 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 | | 2.031e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8949.00 ave 8949 max 8949 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: 423840.0 ave 423840 max 423840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 423840 Ave neighs/atom = 200.68182 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 7 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 6.574 | 6.574 | 6.574 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 -7465.5459 -7465.5459 29.297094 96.421228 8.8469606 191.94155 191.94155 139.43431 265.4895 170.90085 2.4247552 640.33733 Loop time of 2.25e-06 on 1 procs for 0 steps with 2112 atoms 266.7% 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 | | 2.25e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8949.00 ave 8949 max 8949 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 211920.0 ave 211920 max 211920 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 423840.0 ave 423840 max 423840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 423840 Ave neighs/atom = 200.68182 Neighbor list builds = 0 Dangerous builds = 0 2112 -7465.54593185962 eV 2.42475520023842 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01