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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -37.806278 0.0000000) to (46.298631 37.806278 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8925530 5.4985707 5.8858683 Created 1323 atoms using lattice units in orthogonal box = (0.0000000 -37.806278 0.0000000) to (46.298631 37.806278 8.8288024) create_atoms CPU = 0.002 seconds 1323 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8925530 5.4985707 5.8858683 Created 1323 atoms using lattice units in orthogonal box = (0.0000000 -37.806278 0.0000000) to (46.298631 37.806278 8.8288024) 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 16 25 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 56 atoms, new total = 2590 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 16 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.553 | 5.553 | 5.553 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10880.235 0 -10880.235 -7416.8032 291 0 -10963.074 0 -10963.074 -26483.729 Loop time of 46.9822 on 1 procs for 291 steps with 2590 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 = -10880.2349585321 -10963.0631910297 -10963.0735674077 Force two-norm initial, final = 31.856549 0.37142787 Force max component initial, final = 5.8037809 0.13924562 Final line search alpha, max atom move = 0.45763714 0.063723968 Iterations, force evaluations = 291 551 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 46.753 | 46.753 | 46.753 | 0.0 | 99.51 Neigh | 0.1285 | 0.1285 | 0.1285 | 0.0 | 0.27 Comm | 0.0377 | 0.0377 | 0.0377 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06284 | | | 0.13 Nlocal: 2590.00 ave 2590 max 2590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6474.00 ave 6474 max 6474 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: 196958.0 ave 196958 max 196958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 196958 Ave neighs/atom = 76.045560 Neighbor list builds = 8 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 16 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 291 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.553 | 5.553 | 5.553 Mbytes Step Temp E_pair E_mol TotEng Press Volume 291 0 -10963.074 0 -10963.074 -26483.729 30907.499 309 0 -10969.987 0 -10969.987 -2747.3238 30433.771 Loop time of 1.67193 on 1 procs for 18 steps with 2590 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 = -10963.0735674077 -10969.9763437317 -10969.9865870615 Force two-norm initial, final = 841.66864 2.2472685 Force max component initial, final = 804.02439 1.4373351 Final line search alpha, max atom move = 5.3761381e-05 7.7273122e-05 Iterations, force evaluations = 18 19 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6636 | 1.6636 | 1.6636 | 0.0 | 99.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010152 | 0.0010152 | 0.0010152 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007341 | | | 0.44 Nlocal: 2590.00 ave 2590 max 2590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6482.00 ave 6482 max 6482 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: 196988.0 ave 196988 max 196988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 196988 Ave neighs/atom = 76.057143 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 15 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.690 | 5.690 | 5.690 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10969.987 0 -10969.987 -2747.3238 Loop time of 2.059e-06 on 1 procs for 0 steps with 2590 atoms 145.7% 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 | | 2.059e-06 | | |100.00 Nlocal: 2590.00 ave 2590 max 2590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6506.00 ave 6506 max 6506 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: 200050.0 ave 200050 max 200050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200050 Ave neighs/atom = 77.239382 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 15 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.690 | 5.690 | 5.690 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 -10969.987 -10969.987 45.487122 75.612556 8.8485761 -2747.3238 -2747.3238 -74.341778 -8101.1097 -66.520048 2.1823365 7140.2006 Loop time of 2.013e-06 on 1 procs for 0 steps with 2590 atoms 198.7% 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 | | 2.013e-06 | | |100.00 Nlocal: 2590.00 ave 2590 max 2590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6506.00 ave 6506 max 6506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100025.0 ave 100025 max 100025 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 200050.0 ave 200050 max 200050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200050 Ave neighs/atom = 77.239382 Neighbor list builds = 0 Dangerous builds = 0 2590 -10969.9865870615 eV 2.18233649824929 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:49