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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -49.713793 0.0000000) to (24.855355 49.713793 3.0829274) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2062909 4.2062909 3.0829274 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -49.713793 0.0000000) to (24.855355 49.713793 3.0829274) create_atoms CPU = 0.000 seconds 261 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2062909 4.2062909 3.0829274 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -49.713793 0.0000000) to (24.855355 49.713793 3.0829274) create_atoms CPU = 0.000 seconds 261 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 30 1 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 6 atoms, new total = 516 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.245 | 5.245 | 5.245 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3294.2839 0 -3294.2839 17258.952 69 0 -3349.8389 0 -3349.8389 -10563.419 Loop time of 7.54909 on 1 procs for 69 steps with 516 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 = -3294.28391518132 -3349.83591194661 -3349.83886592652 Force two-norm initial, final = 91.580751 0.23034310 Force max component initial, final = 40.483017 0.055733875 Final line search alpha, max atom move = 0.84978590 0.047361862 Iterations, force evaluations = 69 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.544 | 7.544 | 7.544 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0032663 | 0.0032663 | 0.0032663 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001863 | | | 0.02 Nlocal: 516.000 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3959.00 ave 3959 max 3959 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: 33368.0 ave 33368 max 33368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33368 Ave neighs/atom = 64.666667 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.245 | 5.245 | 5.245 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -3349.8389 0 -3349.8389 -10563.419 7618.863 75 0 -3350.2047 0 -3350.2047 6747.7458 7556.138 Loop time of 0.448272 on 1 procs for 6 steps with 516 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 = -3349.83886592652 -3350.20169856573 -3350.20465150625 Force two-norm initial, final = 127.78041 0.45947795 Force max component initial, final = 98.329573 0.11687693 Final line search alpha, max atom move = 0.00015082900 1.7628432e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44759 | 0.44759 | 0.44759 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001626 | 0.0001626 | 0.0001626 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005169 | | | 0.12 Nlocal: 516.000 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3954.00 ave 3954 max 3954 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: 37068.0 ave 37068 max 37068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37068 Ave neighs/atom = 71.837209 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 30 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.383 | 5.383 | 5.383 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3350.2047 0 -3350.2047 6747.7458 Loop time of 1.9e-06 on 1 procs for 0 steps with 516 atoms 157.9% 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 | | 1.9e-06 | | |100.00 Nlocal: 516.000 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3954.00 ave 3954 max 3954 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: 38048.0 ave 38048 max 38048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38048 Ave neighs/atom = 73.736434 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 30 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.383 | 5.383 | 5.383 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 -3350.2047 -3350.2047 24.776415 99.427586 3.0672877 6747.7458 6747.7458 -6.0690588 20244.3 5.0062013 2.5000023 793.87532 Loop time of 2.2e-06 on 1 procs for 0 steps with 516 atoms 136.4% 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 | | 2.2e-06 | | |100.00 Nlocal: 516.000 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3954.00 ave 3954 max 3954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19024.0 ave 19024 max 19024 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 38048.0 ave 38048 max 38048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38048 Ave neighs/atom = 73.736434 Neighbor list builds = 0 Dangerous builds = 0 516 -3350.20465150625 eV 2.50000225085358 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08