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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -52.960623 0.0000000) to (24.965877 52.960623 5.7275650) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2559741 6.5039362 5.7275650 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -52.960623 0.0000000) to (24.965877 52.960623 5.7275650) create_atoms CPU = 0.004 seconds 454 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2559741 6.5039362 5.7275650 Created 462 atoms using lattice units in orthogonal box = (0.0000000 -52.960623 0.0000000) to (24.965877 52.960623 5.7275650) create_atoms CPU = 0.003 seconds 462 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 7 28 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 912 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_418978237058_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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 7 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 4.983 | 4.983 | 4.983 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3027.6811 0 -3027.6811 12386.115 28 0 -3060.5584 0 -3060.5584 6316.1092 Loop time of 0.588498 on 1 procs for 28 steps with 912 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 = -3027.68114983957 -3060.55552328049 -3060.55838284274 Force two-norm initial, final = 42.942103 0.10820480 Force max component initial, final = 7.9577779 0.0087786783 Final line search alpha, max atom move = 1.0000000 0.0087786783 Iterations, force evaluations = 28 52 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.57519 | 0.57519 | 0.57519 | 0.0 | 97.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0069412 | 0.0069412 | 0.0069412 | 0.0 | 1.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00637 | | | 1.08 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5459.00 ave 5459 max 5459 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: 120676.0 ave 120676 max 120676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120676 Ave neighs/atom = 132.32018 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 7 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 28 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.983 | 4.983 | 4.983 Mbytes Step Temp E_pair E_mol TotEng Press Volume 28 0 -3060.5584 0 -3060.5584 6316.1092 15146.069 39 0 -3061.0276 0 -3061.0276 40.63218 15265.581 Loop time of 0.166791 on 1 procs for 11 steps with 912 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 = -3060.55838284274 -3061.02740090077 -3061.02757423057 Force two-norm initial, final = 116.01982 0.72557756 Force max component initial, final = 102.49063 0.44588366 Final line search alpha, max atom move = 0.0010161362 0.00045307851 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1428 | 0.1428 | 0.1428 | 0.0 | 85.62 Neigh | 0.016124 | 0.016124 | 0.016124 | 0.0 | 9.67 Comm | 0.0019416 | 0.0019416 | 0.0019416 | 0.0 | 1.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005926 | | | 3.55 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5353.00 ave 5353 max 5353 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: 119552.0 ave 119552 max 119552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119552 Ave neighs/atom = 131.08772 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 7 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.120 | 5.120 | 5.120 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3061.0276 0 -3061.0276 40.63218 Loop time of 6.114e-06 on 1 procs for 0 steps with 912 atoms 196.3% 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 | | 6.114e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5353.00 ave 5353 max 5353 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: 119536.0 ave 119536 max 119536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119536 Ave neighs/atom = 131.07018 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 7 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.120 | 5.120 | 5.120 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 -3061.0276 -3061.0276 24.940608 106.99789 5.7204621 40.63218 40.63218 34.175492 40.982022 46.739024 2.6055802 660.63208 Loop time of 6.665e-06 on 1 procs for 0 steps with 912 atoms 255.1% 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 | | 6.665e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5353.00 ave 5353 max 5353 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59768.0 ave 59768 max 59768 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119536.0 ave 119536 max 119536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119536 Ave neighs/atom = 131.07018 Neighbor list builds = 0 Dangerous builds = 0 912 -3061.02757423057 eV 2.60558018441012 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01