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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -44.318670 0.0000000) to (9.0456848 44.318670 9.9090513) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4274109 5.9086166 6.6060342 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -44.318670 0.0000000) to (9.0456848 44.318670 9.9090513) create_atoms CPU = 0.001 seconds 242 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4274109 5.9086166 6.6060342 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -44.318670 0.0000000) to (9.0456848 44.318670 9.9090513) create_atoms CPU = 0.000 seconds 242 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 3 29 4 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 472 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 3 29 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.444 | 4.444 | 4.444 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1575.2922 0 -1575.2922 -2508.2063 41 0 -1579.471 0 -1579.471 -7673.7146 Loop time of 1.11298 on 1 procs for 41 steps with 472 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 = -1575.29223871608 -1579.46947742914 -1579.47101442379 Force two-norm initial, final = 5.7130011 0.083958392 Force max component initial, final = 1.8333681 0.013229366 Final line search alpha, max atom move = 1.0000000 0.013229366 Iterations, force evaluations = 41 73 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.109 | 1.109 | 1.109 | 0.0 | 99.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017084 | 0.0017084 | 0.0017084 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002251 | | | 0.20 Nlocal: 472.000 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2418.00 ave 2418 max 2418 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: 25252.0 ave 25252 max 25252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25252 Ave neighs/atom = 53.500000 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 3 29 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.443 | 4.443 | 4.443 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -1579.471 0 -1579.471 -7673.7146 7944.933 47 0 -1579.6308 0 -1579.6308 -1298.96 7874.3522 Loop time of 0.123517 on 1 procs for 6 steps with 472 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 = -1579.47101442379 -1579.63073802014 -1579.63075901321 Force two-norm initial, final = 50.231976 0.19156359 Force max component initial, final = 35.752713 0.075942395 Final line search alpha, max atom move = 0.0058659038 0.00044547078 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12256 | 0.12256 | 0.12256 | 0.0 | 99.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016069 | 0.00016069 | 0.00016069 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007942 | | | 0.64 Nlocal: 472.000 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2327.00 ave 2327 max 2327 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: 25560.0 ave 25560 max 25560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25560 Ave neighs/atom = 54.152542 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 3 29 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.581 | 4.581 | 4.581 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1579.6308 0 -1579.6308 -1298.96 Loop time of 1.982e-06 on 1 procs for 0 steps with 472 atoms 201.8% 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 | | 1.982e-06 | | |100.00 Nlocal: 472.000 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2327.00 ave 2327 max 2327 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: 25592.0 ave 25592 max 25592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25592 Ave neighs/atom = 54.220339 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 3 29 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.581 | 4.581 | 4.581 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 -1579.6308 -1579.6308 9.0038464 88.637339 9.8666574 -1298.96 -1298.96 14.813481 -3896.3077 -15.385718 2.5060826 351.08956 Loop time of 1.549e-06 on 1 procs for 0 steps with 472 atoms 193.7% 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 | | 1.549e-06 | | |100.00 Nlocal: 472.000 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2327.00 ave 2327 max 2327 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12796.0 ave 12796 max 12796 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25592.0 ave 25592 max 25592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25592 Ave neighs/atom = 54.220339 Neighbor list builds = 0 Dangerous builds = 0 472 -1579.63075901321 eV 2.50608256699863 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01