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 = 2.8553246 2.8553246 2.8553246 Created orthogonal box = (0.0000000 -50.435089 0.0000000) to (29.118712 50.435089 4.9455673) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4798018 4.5262259 4.9455673 Created 623 atoms using lattice units in orthogonal box = (0.0000000 -50.435089 0.0000000) to (29.118712 50.435089 4.9455673) create_atoms CPU = 0.005 seconds 623 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4798018 4.5262259 4.9455673 Created 627 atoms using lattice units in orthogonal box = (0.0000000 -50.435089 0.0000000) to (29.118712 50.435089 4.9455673) create_atoms CPU = 0.004 seconds 627 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1248 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_737567242631_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.065 | 5.065 | 5.065 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4115.5454 0 -4115.5454 168478.74 96 0 -5124.283 0 -5124.283 2329.7331 Loop time of 3.40518 on 1 procs for 96 steps with 1248 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 = -4115.54535201173 -5124.27884211386 -5124.28300308467 Force two-norm initial, final = 2550.3918 0.22073162 Force max component initial, final = 672.42178 0.043175164 Final line search alpha, max atom move = 1.0000000 0.043175164 Iterations, force evaluations = 96 174 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3224 | 3.3224 | 3.3224 | 0.0 | 97.57 Neigh | 0.025784 | 0.025784 | 0.025784 | 0.0 | 0.76 Comm | 0.030378 | 0.030378 | 0.030378 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02664 | | | 0.78 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7317.00 ave 7317 max 7317 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: 170990.0 ave 170990 max 170990 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170990 Ave neighs/atom = 137.01122 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 96 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.065 | 5.065 | 5.065 Mbytes Step Temp E_pair E_mol TotEng Press Volume 96 0 -5124.283 0 -5124.283 2329.7331 14526.168 99 0 -5124.3278 0 -5124.3278 -2.414616 14545.569 Loop time of 0.120483 on 1 procs for 3 steps with 1248 atoms 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5124.28300308468 -5124.32761280146 -5124.32779688299 Force two-norm initial, final = 48.638003 0.31425272 Force max component initial, final = 44.855668 0.15271517 Final line search alpha, max atom move = 0.00032243560 4.9240805e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11627 | 0.11627 | 0.11627 | 0.0 | 96.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010109 | 0.0010109 | 0.0010109 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003198 | | | 2.65 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7344.00 ave 7344 max 7344 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: 170714.0 ave 170714 max 170714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170714 Ave neighs/atom = 136.79006 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.203 | 5.203 | 5.203 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5124.3278 0 -5124.3278 -2.414616 Loop time of 6.936e-06 on 1 procs for 0 steps with 1248 atoms 173.0% 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 | | 6.936e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7360.00 ave 7360 max 7360 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: 170620.0 ave 170620 max 170620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170620 Ave neighs/atom = 136.71474 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.203 | 5.203 | 5.203 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 -5124.3278 -5124.3278 29.094238 101.05792 4.9471306 -2.414616 -2.414616 -13.062316 -11.008237 16.826705 2.2572936 539.79349 Loop time of 7.878e-06 on 1 procs for 0 steps with 1248 atoms 253.9% 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 | | 7.878e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7360.00 ave 7360 max 7360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85310.0 ave 85310 max 85310 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 170620.0 ave 170620 max 170620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170620 Ave neighs/atom = 136.71474 Neighbor list builds = 0 Dangerous builds = 0 1248 -5124.32779688299 eV 2.25729357367774 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04