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 = 4.2107003 4.2107003 4.2107003 Created orthogonal box = (0.0000000 -44.957977 0.0000000) to (25.956500 44.957977 7.2931469) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8306579 6.3098915 7.2931469 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -44.957977 0.0000000) to (25.956500 44.957977 7.2931469) create_atoms CPU = 0.003 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8306579 6.3098915 7.2931469 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -44.957977 0.0000000) to (25.956500 44.957977 7.2931469) create_atoms CPU = 0.002 seconds 458 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 6 20 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 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 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_878712978062_003#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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 6 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 4.997 | 4.997 | 4.997 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2627.4125 0 -2627.4125 189416.33 134 0 -3394.655 0 -3394.655 2175.3667 Loop time of 6.72508 on 1 procs for 134 steps with 912 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 = -2627.4124746593 -3394.65160326124 -3394.65496045038 Force two-norm initial, final = 4607.6116 0.10608745 Force max component initial, final = 1680.7397 0.017806917 Final line search alpha, max atom move = 1.0000000 0.017806917 Iterations, force evaluations = 134 237 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.529 | 6.529 | 6.529 | 0.0 | 97.08 Neigh | 0.13227 | 0.13227 | 0.13227 | 0.0 | 1.97 Comm | 0.03404 | 0.03404 | 0.03404 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02981 | | | 0.44 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5343.00 ave 5343 max 5343 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: 157008.0 ave 157008 max 157008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157008 Ave neighs/atom = 172.15789 Neighbor list builds = 6 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 6 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 134 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.998 | 4.998 | 4.998 Mbytes Step Temp E_pair E_mol TotEng Press Volume 134 0 -3394.655 0 -3394.655 2175.3667 17021.5 141 0 -3394.7668 0 -3394.7668 137.71198 17107.643 Loop time of 0.213022 on 1 procs for 7 steps with 912 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 = -3394.65496045038 -3394.76428083606 -3394.76684116148 Force two-norm initial, final = 42.831596 2.5962716 Force max component initial, final = 35.523692 1.8233626 Final line search alpha, max atom move = 0.00040910236 0.00074594192 Iterations, force evaluations = 7 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20863 | 0.20863 | 0.20863 | 0.0 | 97.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0008843 | 0.0008843 | 0.0008843 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003506 | | | 1.65 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5317.00 ave 5317 max 5317 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: 157240.0 ave 157240 max 157240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157240 Ave neighs/atom = 172.41228 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 5.136 | 5.136 | 5.136 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3394.7668 0 -3394.7668 137.71198 Loop time of 6.425e-06 on 1 procs for 0 steps with 912 atoms 186.8% 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 | | 6.425e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5343.00 ave 5343 max 5343 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: 156812.0 ave 156812 max 156812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156812 Ave neighs/atom = 171.94298 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 5.136 | 5.136 | 5.136 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 -3394.7668 -3394.7668 25.944072 90.545365 7.282589 137.71198 137.71198 138.08806 171.95812 103.08976 2.7338828 891.89031 Loop time of 7.317e-06 on 1 procs for 0 steps with 912 atoms 246.0% 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 | | 7.317e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5343.00 ave 5343 max 5343 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78406.0 ave 78406 max 78406 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 156812.0 ave 156812 max 156812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156812 Ave neighs/atom = 171.94298 Neighbor list builds = 0 Dangerous builds = 0 912 -3394.76684116147 eV 2.73388280951058 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08