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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -51.941007 0.0000000) to (25.970503 51.941007 3.5673230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4100855 4.4100855 3.5673230 Created 424 atoms using lattice units in orthogonal box = (0.0000000 -51.941007 0.0000000) to (25.970503 51.941007 3.5673230) create_atoms CPU = 0.001 seconds 424 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4100855 4.4100855 3.5673230 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -51.941007 0.0000000) to (25.970503 51.941007 3.5673230) create_atoms CPU = 0.001 seconds 426 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 38 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 850 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_095610951957_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.546 | 4.546 | 4.546 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3446.7156 0 -3446.7156 48394.821 51 0 -3577.2645 0 -3577.2645 39489.654 Loop time of 2.30822 on 1 procs for 51 steps with 850 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3446.71560937087 -3577.26109287444 -3577.26451984486 Force two-norm initial, final = 225.68118 0.30052435 Force max component initial, final = 84.461922 0.088385810 Final line search alpha, max atom move = 1.0000000 0.088385810 Iterations, force evaluations = 51 93 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2948 | 2.2948 | 2.2948 | 0.0 | 99.42 Neigh | 0.0040366 | 0.0040366 | 0.0040366 | 0.0 | 0.17 Comm | 0.0047921 | 0.0047921 | 0.0047921 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004545 | | | 0.20 Nlocal: 850.000 ave 850 max 850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4530.00 ave 4530 max 4530 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: 49084.0 ave 49084 max 49084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49084 Ave neighs/atom = 57.745882 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.546 | 4.546 | 4.546 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -3577.2645 0 -3577.2645 39489.654 9624.1673 98 0 -3583.3853 0 -3583.3853 278.9654 9932.0743 Loop time of 1.11136 on 1 procs for 47 steps with 850 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3577.26451984486 -3583.3838686957 -3583.38529441154 Force two-norm initial, final = 442.93184 4.7683143 Force max component initial, final = 352.10918 3.0657068 Final line search alpha, max atom move = 0.00035857631 0.0010992898 Iterations, force evaluations = 47 48 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0832 | 1.0832 | 1.0832 | 0.0 | 97.46 Neigh | 0.016243 | 0.016243 | 0.016243 | 0.0 | 1.46 Comm | 0.0023167 | 0.0023167 | 0.0023167 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009623 | | | 0.87 Nlocal: 850.000 ave 850 max 850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4518.00 ave 4518 max 4518 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: 47272.0 ave 47272 max 47272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47272 Ave neighs/atom = 55.614118 Neighbor list builds = 4 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.684 | 4.684 | 4.684 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3583.3853 0 -3583.3853 278.9654 Loop time of 1.492e-06 on 1 procs for 0 steps with 850 atoms 134.0% 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 | | 1.492e-06 | | |100.00 Nlocal: 850.000 ave 850 max 850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4518.00 ave 4518 max 4518 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: 49712.0 ave 49712 max 49712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49712 Ave neighs/atom = 58.484706 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.684 | 4.684 | 4.684 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 -3583.3853 -3583.3853 25.813393 108.71545 3.5391876 278.9654 278.9654 426.88462 -80.627528 490.6391 2.3582235 387.46394 Loop time of 1.68e-06 on 1 procs for 0 steps with 850 atoms 178.6% 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 | | 1.68e-06 | | |100.00 Nlocal: 850.000 ave 850 max 850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4518.00 ave 4518 max 4518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24856.0 ave 24856 max 24856 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 49712.0 ave 49712 max 49712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49712 Ave neighs/atom = 58.484706 Neighbor list builds = 0 Dangerous builds = 0 850 -3583.38529441154 eV 2.35822349765225 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03