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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -44.666822 0.0000000) to (14.888941 44.666822 3.6110985) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3791002 4.3791002 3.6110985 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -44.666822 0.0000000) to (14.888941 44.666822 3.6110985) create_atoms CPU = 0.002 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3791002 4.3791002 3.6110985 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -44.666822 0.0000000) to (14.888941 44.666822 3.6110985) create_atoms CPU = 0.001 seconds 206 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 5 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 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 408 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_343168101490_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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 4.462 | 4.462 | 4.462 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1669.5474 0 -1669.5474 37436.445 52 0 -1723.7248 0 -1723.7248 8424.7403 Loop time of 4.04094 on 1 procs for 52 steps with 408 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 = -1669.54742902415 -1723.72349576479 -1723.72482298532 Force two-norm initial, final = 130.75801 0.10728888 Force max component initial, final = 43.449183 0.023417415 Final line search alpha, max atom move = 1.0000000 0.023417415 Iterations, force evaluations = 52 95 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0184 | 4.0184 | 4.0184 | 0.0 | 99.44 Neigh | 0.0062392 | 0.0062392 | 0.0062392 | 0.0 | 0.15 Comm | 0.0090633 | 0.0090633 | 0.0090633 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007289 | | | 0.18 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3932.00 ave 3932 max 3932 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: 34952.0 ave 34952 max 34952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34952 Ave neighs/atom = 85.666667 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.462 | 4.462 | 4.462 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -1723.7248 0 -1723.7248 8424.7403 4803.0619 60 0 -1723.8205 0 -1723.8205 -60.006607 4826.7848 Loop time of 0.447405 on 1 procs for 8 steps with 408 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 = -1723.72482298532 -1723.81973668257 -1723.82048257305 Force two-norm initial, final = 44.649015 1.1681274 Force max component initial, final = 32.545643 0.75994424 Final line search alpha, max atom move = 0.00028361443 0.00021553116 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44342 | 0.44342 | 0.44342 | 0.0 | 99.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00090179 | 0.00090179 | 0.00090179 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003081 | | | 0.69 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3977.00 ave 3977 max 3977 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: 34976.0 ave 34976 max 34976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34976 Ave neighs/atom = 85.725490 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 4.600 | 4.600 | 4.600 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1723.8205 0 -1723.8205 -60.006607 Loop time of 6.294e-06 on 1 procs for 0 steps with 408 atoms 190.7% 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 | | 6.294e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3977.00 ave 3977 max 3977 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: 35000.0 ave 35000 max 35000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35000 Ave neighs/atom = 85.784314 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 4.600 | 4.600 | 4.600 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 -1723.8205 -1723.8205 14.872422 89.239476 3.6367985 -60.006607 -60.006607 -162.14026 -251.98582 234.10627 2.2976017 186.08029 Loop time of 6.545e-06 on 1 procs for 0 steps with 408 atoms 244.5% 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 | | 6.545e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3977.00 ave 3977 max 3977 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17500.0 ave 17500 max 17500 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 35000.0 ave 35000 max 35000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35000 Ave neighs/atom = 85.784314 Neighbor list builds = 0 Dangerous builds = 0 408 -1723.82048257305 eV 2.29760165566693 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04