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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -54.427998 0.0000000) to (38.483858 54.427998 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0763986 5.2514766 5.0973115 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -54.427998 0.0000000) to (38.483858 54.427998 5.0973115) create_atoms CPU = 0.002 seconds 916 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0763986 5.2514766 5.0973115 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -54.427998 0.0000000) to (38.483858 54.427998 5.0973115) create_atoms CPU = 0.002 seconds 916 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 37 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 1806 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_492310898779_001#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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.158 | 5.158 | 5.158 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7595.3086 0 -7595.3086 492.2371 184 0 -7657.2165 0 -7657.2165 -15081.775 Loop time of 22.7194 on 1 procs for 184 steps with 1806 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 = -7595.30861815942 -7657.20916507601 -7657.21651118112 Force two-norm initial, final = 41.379277 0.24030176 Force max component initial, final = 8.2184423 0.049230559 Final line search alpha, max atom move = 0.79549905 0.039162863 Iterations, force evaluations = 184 333 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.593 | 22.593 | 22.593 | 0.0 | 99.44 Neigh | 0.053946 | 0.053946 | 0.053946 | 0.0 | 0.24 Comm | 0.037709 | 0.037709 | 0.037709 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03486 | | | 0.15 Nlocal: 1806.00 ave 1806 max 1806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7289.00 ave 7289 max 7289 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: 136432.0 ave 136432 max 136432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136432 Ave neighs/atom = 75.543743 Neighbor list builds = 5 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 184 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.157 | 5.157 | 5.157 Mbytes Step Temp E_pair E_mol TotEng Press Volume 184 0 -7657.2165 0 -7657.2165 -15081.775 21353.65 193 0 -7658.4404 0 -7658.4404 -475.56792 21156.991 Loop time of 0.730851 on 1 procs for 9 steps with 1806 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 = -7657.21651118113 -7658.44011514454 -7658.44038877478 Force two-norm initial, final = 317.99865 0.39045633 Force max component initial, final = 283.94908 0.052541504 Final line search alpha, max atom move = 0.00021321615 1.1202697e-05 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.7261 | 0.7261 | 0.7261 | 0.0 | 99.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0007391 | 0.0007391 | 0.0007391 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004016 | | | 0.55 Nlocal: 1806.00 ave 1806 max 1806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7299.00 ave 7299 max 7299 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: 136300.0 ave 136300 max 136300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136300 Ave neighs/atom = 75.470653 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.295 | 5.295 | 5.295 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7658.4404 0 -7658.4404 -475.56792 Loop time of 1.876e-06 on 1 procs for 0 steps with 1806 atoms 159.9% 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 | | 1.876e-06 | | |100.00 Nlocal: 1806.00 ave 1806 max 1806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7321.00 ave 7321 max 7321 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: 136628.0 ave 136628 max 136628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136628 Ave neighs/atom = 75.652270 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.295 | 5.295 | 5.295 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 -7658.4404 -7658.4404 38.430484 108.856 5.0573811 -475.56792 -475.56792 -2.5339585 -1421.4064 -2.7633818 2.3328346 1419.2239 Loop time of 2.139e-06 on 1 procs for 0 steps with 1806 atoms 187.0% 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 | | 2.139e-06 | | |100.00 Nlocal: 1806.00 ave 1806 max 1806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7321.00 ave 7321 max 7321 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 68314.0 ave 68314 max 68314 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 136628.0 ave 136628 max 136628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136628 Ave neighs/atom = 75.652270 Neighbor list builds = 0 Dangerous builds = 0 1806 -7658.44038877478 eV 2.332834636791 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:23