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 = 3.6133157 3.6133157 3.6133157 Created orthogonal box = (0.0000000 -37.896774 0.0000000) to (46.413880 37.896774 8.8507797) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9072211 5.5122581 5.9005198 Created 1317 atoms using lattice units in orthogonal box = (0.0000000 -37.896774 0.0000000) to (46.413880 37.896774 8.8507797) create_atoms CPU = 0.002 seconds 1317 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9072211 5.5122581 5.9005198 Created 1323 atoms using lattice units in orthogonal box = (0.0000000 -37.896774 0.0000000) to (46.413880 37.896774 8.8507797) create_atoms CPU = 0.002 seconds 1323 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 24 3 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2640 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_353393547686_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.572 | 5.572 | 5.572 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8784.4515 0 -8784.4515 56833.971 82 0 -9296.0775 0 -9296.0775 8792.0332 Loop time of 11.4142 on 1 procs for 82 steps with 2640 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8784.45149613239 -9296.06959806743 -9296.07745463718 Force two-norm initial, final = 437.70623 0.34894155 Force max component initial, final = 79.584083 0.16023567 Final line search alpha, max atom move = 0.87037942 0.13946583 Iterations, force evaluations = 82 154 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.36 | 11.36 | 11.36 | 0.0 | 99.52 Neigh | 0.019767 | 0.019767 | 0.019767 | 0.0 | 0.17 Comm | 0.013494 | 0.013494 | 0.013494 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02124 | | | 0.19 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6940.00 ave 6940 max 6940 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: 228314.0 ave 228314 max 228314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 228314 Ave neighs/atom = 86.482576 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.570 | 5.570 | 5.570 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -9296.0775 0 -9296.0775 8792.0332 31135.916 89 0 -9296.9596 0 -9296.9596 -14.845249 31328.73 Loop time of 0.715369 on 1 procs for 7 steps with 2640 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 = -9296.07745463717 -9296.95952140548 -9296.95964691545 Force two-norm initial, final = 325.43583 1.2341078 Force max component initial, final = 261.29648 1.0925796 Final line search alpha, max atom move = 0.00028922679 0.00031600329 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.71036 | 0.71036 | 0.71036 | 0.0 | 99.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061535 | 0.00061535 | 0.00061535 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00439 | | | 0.61 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6929.00 ave 6929 max 6929 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: 228306.0 ave 228306 max 228306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 228306 Ave neighs/atom = 86.479545 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.708 | 5.708 | 5.708 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9296.9596 0 -9296.9596 -14.845249 Loop time of 1.904e-06 on 1 procs for 0 steps with 2640 atoms 210.1% 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 | | 1.904e-06 | | |100.00 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6913.00 ave 6913 max 6913 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: 227906.0 ave 227906 max 227906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227906 Ave neighs/atom = 86.328030 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.708 | 5.708 | 5.708 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 -9296.9596 -9296.9596 46.515276 76.234088 8.8348254 -14.845249 -14.845249 -55.997467 1.406893 10.054827 2.2468844 1584.049 Loop time of 2.171e-06 on 1 procs for 0 steps with 2640 atoms 230.3% 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 | | 2.171e-06 | | |100.00 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6913.00 ave 6913 max 6913 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113953.0 ave 113953 max 113953 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 227906.0 ave 227906 max 227906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227906 Ave neighs/atom = 86.328030 Neighbor list builds = 0 Dangerous builds = 0 2640 -9296.95964691545 eV 2.24688443490461 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12