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 = 3.6149602 3.6149602 3.6149602 Created orthogonal box = (0.0000000 -44.274039 0.0000000) to (6.2612947 44.274039 5.1123257) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2612947 5.9032052 5.1123257 Created 120 atoms using lattice units in orthogonal box = (0.0000000 -44.274039 0.0000000) to (6.2612947 44.274039 5.1123257) create_atoms CPU = 0.002 seconds 120 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2612947 5.9032052 5.1123257 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -44.274039 0.0000000) to (6.2612947 44.274039 5.1123257) create_atoms CPU = 0.002 seconds 122 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 = 8.3953378 ghost atom cutoff = 8.3953378 binsize = 4.1976689, bins = 2 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 8.395337773223552 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 240 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_950828638160_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 = 8.3953378 ghost atom cutoff = 8.3953378 binsize = 4.1976689, bins = 2 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337773223552 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) = 4.494 | 4.494 | 4.494 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -826.99546 0 -826.99546 29217.86 90 0 -847.48938 0 -847.48938 10257.878 Loop time of 1.08878 on 1 procs for 90 steps with 240 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 = -826.995461162314 -847.488544745862 -847.489377443942 Force two-norm initial, final = 46.635359 0.091971908 Force max component initial, final = 17.322132 0.018318856 Final line search alpha, max atom move = 1.0000000 0.018318856 Iterations, force evaluations = 90 171 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0557 | 1.0557 | 1.0557 | 0.0 | 96.96 Neigh | 0.0070272 | 0.0070272 | 0.0070272 | 0.0 | 0.65 Comm | 0.016227 | 0.016227 | 0.016227 | 0.0 | 1.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009876 | | | 0.91 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4244.00 ave 4244 max 4244 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: 48512.0 ave 48512 max 48512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48512 Ave neighs/atom = 202.13333 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 = 8.3953378 ghost atom cutoff = 8.3953378 binsize = 4.1976689, bins = 2 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337773223552 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.496 | 4.496 | 4.496 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -847.48938 0 -847.48938 10257.878 2834.4043 96 0 -847.57211 0 -847.57211 14.292492 2855.2723 Loop time of 0.0588893 on 1 procs for 6 steps with 240 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 = -847.489377443942 -847.571904649174 -847.572114649303 Force two-norm initial, final = 32.577863 0.18269557 Force max component initial, final = 22.155990 0.079885639 Final line search alpha, max atom move = 0.00084043340 6.7138559e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.055716 | 0.055716 | 0.055716 | 0.0 | 94.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00080061 | 0.00080061 | 0.00080061 | 0.0 | 1.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002373 | | | 4.03 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4485.00 ave 4485 max 4485 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: 48216.0 ave 48216 max 48216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48216 Ave neighs/atom = 200.90000 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 = 8.3953378 ghost atom cutoff = 8.3953378 binsize = 4.1976689, bins = 2 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337773223552 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) = 4.634 | 4.634 | 4.634 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -847.57211 0 -847.57211 14.292492 Loop time of 6.254e-06 on 1 procs for 0 steps with 240 atoms 191.9% 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 | | 6.254e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4485.00 ave 4485 max 4485 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: 48080.0 ave 48080 max 48080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48080 Ave neighs/atom = 200.33333 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 = 8.3953378 ghost atom cutoff = 8.3953378 binsize = 4.1976689, bins = 2 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337773223552 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) = 4.634 | 4.634 | 4.634 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 -847.57211 -847.57211 6.2843706 88.936418 5.1086495 14.292492 14.292492 -40.767327 38.850877 44.793927 2.4617172 161.28863 Loop time of 7.016e-06 on 1 procs for 0 steps with 240 atoms 228.1% 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 | | 7.016e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4485.00 ave 4485 max 4485 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24040.0 ave 24040 max 24040 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 48080.0 ave 48080 max 48080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48080 Ave neighs/atom = 200.33333 Neighbor list builds = 0 Dangerous builds = 0 240 -847.572114649303 eV 2.46171723258382 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01