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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -47.511998 0.0000000) to (33.596056 47.511998 4.4499064) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3046405 4.5844911 4.4499064 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -47.511998 0.0000000) to (33.596056 47.511998 4.4499064) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3046405 4.5844911 4.4499064 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -47.511998 0.0000000) to (33.596056 47.511998 4.4499064) create_atoms CPU = 0.001 seconds 458 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 28 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 914 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_486450342170_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.562 | 4.562 | 4.562 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5690.7254 0 -5690.7254 144755.92 47 0 -6186.1274 0 -6186.1274 18247.094 Loop time of 2.31806 on 1 procs for 47 steps with 914 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 = -5690.72535229487 -6186.12269888012 -6186.12742627529 Force two-norm initial, final = 573.63369 0.42952823 Force max component initial, final = 216.80857 0.10470144 Final line search alpha, max atom move = 0.88748898 0.092921373 Iterations, force evaluations = 47 87 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.309 | 2.309 | 2.309 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0045389 | 0.0045389 | 0.0045389 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00449 | | | 0.19 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4950.00 ave 4950 max 4950 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: 59912.0 ave 59912 max 59912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59912 Ave neighs/atom = 65.549234 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.562 | 4.562 | 4.562 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -6186.1274 0 -6186.1274 18247.094 14206.021 58 0 -6187.7146 0 -6187.7146 -169.37688 14304.304 Loop time of 0.372762 on 1 procs for 11 steps with 914 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 = -6186.12742627529 -6187.71425014579 -6187.71458361067 Force two-norm initial, final = 357.73996 4.0549440 Force max component initial, final = 342.93772 3.4199995 Final line search alpha, max atom move = 0.0021605973 0.0073892418 Iterations, force evaluations = 11 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.36943 | 0.36943 | 0.36943 | 0.0 | 99.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00054818 | 0.00054818 | 0.00054818 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002784 | | | 0.75 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4950.00 ave 4950 max 4950 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: 60828.0 ave 60828 max 60828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60828 Ave neighs/atom = 66.551422 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.700 | 4.700 | 4.700 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6187.7146 0 -6187.7146 -169.37688 Loop time of 2.175e-06 on 1 procs for 0 steps with 914 atoms 183.9% 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 | | 2.175e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4938.00 ave 4938 max 4938 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: 60092.0 ave 60092 max 60092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60092 Ave neighs/atom = 65.746171 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.700 | 4.700 | 4.700 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 -6187.7146 -6187.7146 33.554354 95.970693 4.4420068 -169.37688 -169.37688 56.718422 -182.46657 -382.38251 2.3712624 821.3149 Loop time of 2.016e-06 on 1 procs for 0 steps with 914 atoms 198.4% 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 | | 2.016e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4938.00 ave 4938 max 4938 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30046.0 ave 30046 max 30046 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 60092.0 ave 60092 max 60092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60092 Ave neighs/atom = 65.746171 Neighbor list builds = 0 Dangerous builds = 0 914 -6187.71458361067 eV 2.37126242415899 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03