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 = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -71.683620 0.0000000) to (43.894856 71.683620 8.8681001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0762759 5.1200000 5.9120667 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -71.683620 0.0000000) to (43.894856 71.683620 8.8681001) create_atoms CPU = 0.003 seconds 2358 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0762759 5.1200000 5.9120667 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -71.683620 0.0000000) to (43.894856 71.683620 8.8681001) create_atoms CPU = 0.003 seconds 2358 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 ghost atom cutoff = 6 binsize = 3, bins = 15 48 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 48 atoms, new total = 4668 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_390178379548_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 ghost atom cutoff = 6 binsize = 3, bins = 15 48 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 6.274 | 6.274 | 6.274 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16393.049 0 -16393.049 3450.7773 70 0 -16481.807 0 -16481.807 -5389.5454 Loop time of 8.64263 on 1 procs for 70 steps with 4668 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 = -16393.0485361228 -16481.7912695243 -16481.8069960808 Force two-norm initial, final = 89.821680 0.43292387 Force max component initial, final = 16.309580 0.061445109 Final line search alpha, max atom move = 1.0000000 0.061445109 Iterations, force evaluations = 70 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.5993 | 8.5993 | 8.5993 | 0.0 | 99.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.016281 | 0.016281 | 0.016281 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02706 | | | 0.31 Nlocal: 4668.00 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10843.0 ave 10843 max 10843 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: 360948.0 ave 360948 max 360948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 360948 Ave neighs/atom = 77.323907 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 ghost atom cutoff = 6 binsize = 3, bins = 15 48 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.270 | 6.270 | 6.270 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -16481.807 0 -16481.807 -5389.5454 55807.702 73 0 -16482.129 0 -16482.129 -561.75699 55617.258 Loop time of 0.390308 on 1 procs for 3 steps with 4668 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 = -16481.8069960808 -16482.1292625628 -16482.1293071206 Force two-norm initial, final = 266.37749 0.44455711 Force max component initial, final = 196.86355 0.13163622 Final line search alpha, max atom move = 0.00069758953 9.1828046e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38655 | 0.38655 | 0.38655 | 0.0 | 99.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050279 | 0.00050279 | 0.00050279 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003254 | | | 0.83 Nlocal: 4668.00 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10358.0 ave 10358 max 10358 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: 361488.0 ave 361488 max 361488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 361488 Ave neighs/atom = 77.439589 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 ghost atom cutoff = 6 binsize = 3, bins = 15 48 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 6.409 | 6.409 | 6.409 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16482.129 0 -16482.129 -561.75699 Loop time of 2.256e-06 on 1 procs for 0 steps with 4668 atoms 177.3% 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 | | 2.256e-06 | | |100.00 Nlocal: 4668.00 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10393.0 ave 10393 max 10393 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: 361488.0 ave 361488 max 361488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 361488 Ave neighs/atom = 77.439589 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 ghost atom cutoff = 6 binsize = 3, bins = 15 48 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 6.409 | 6.409 | 6.409 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 -16482.129 -16482.129 43.821595 143.36724 8.8526128 -561.75699 -561.75699 3.7857395 -1689.5371 0.48043735 2.2631145 1883.7238 Loop time of 2.235e-06 on 1 procs for 0 steps with 4668 atoms 179.0% 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 | | 2.235e-06 | | |100.00 Nlocal: 4668.00 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10393.0 ave 10393 max 10393 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 180744.0 ave 180744 max 180744 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 361488.0 ave 361488 max 361488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 361488 Ave neighs/atom = 77.439589 Neighbor list builds = 0 Dangerous builds = 0 4668 -16482.1293071206 eV 2.26311447132975 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09