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 = 3.6390875 3.6390875 3.6390875 Created orthogonal box = (0.0000000 -39.194172 0.0000000) to (19.597086 39.194172 3.6390875) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7303311 4.7303311 3.6390875 Created 231 atoms using lattice units in orthogonal box = (0.0000000 -39.194172 0.0000000) to (19.597086 39.194172 3.6390875) create_atoms CPU = 0.001 seconds 231 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7303311 4.7303311 3.6390875 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -39.194172 0.0000000) to (19.597086 39.194172 3.6390875) create_atoms CPU = 0.000 seconds 233 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 5 20 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, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 464 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_945691923444_005#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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.499 | 4.499 | 4.499 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1360.353 0 -1360.353 106032.31 38 0 -1513.9236 0 -1513.9236 8185.3245 Loop time of 0.317088 on 1 procs for 38 steps with 464 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 = -1360.35301957645 -1513.92253106228 -1513.92363573104 Force two-norm initial, final = 442.11580 0.085341145 Force max component initial, final = 103.79859 0.010758440 Final line search alpha, max atom move = 1.0000000 0.010758440 Iterations, force evaluations = 38 62 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30693 | 0.30693 | 0.30693 | 0.0 | 96.80 Neigh | 0.0051522 | 0.0051522 | 0.0051522 | 0.0 | 1.62 Comm | 0.0030785 | 0.0030785 | 0.0030785 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001923 | | | 0.61 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5141.00 ave 5141 max 5141 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: 81576.0 ave 81576 max 81576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81576 Ave neighs/atom = 175.81034 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.499 | 4.499 | 4.499 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -1513.9236 0 -1513.9236 8185.3245 5590.3047 46 0 -1514.0639 0 -1514.0639 -135.72758 5622.4056 Loop time of 0.0560639 on 1 procs for 8 steps with 464 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 = -1513.92363573104 -1514.06371992377 -1514.06394461879 Force two-norm initial, final = 53.676406 0.85354020 Force max component initial, final = 45.119503 0.52744971 Final line search alpha, max atom move = 0.0010665894 0.00056257227 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.053611 | 0.053611 | 0.053611 | 0.0 | 95.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047535 | 0.00047535 | 0.00047535 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001977 | | | 3.53 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5141.00 ave 5141 max 5141 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: 81466.0 ave 81466 max 81466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81466 Ave neighs/atom = 175.57328 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.637 | 4.637 | 4.637 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1514.0639 0 -1514.0639 -135.72758 Loop time of 2.124e-06 on 1 procs for 0 steps with 464 atoms 188.3% 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 | | 2.124e-06 | | |100.00 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5141.00 ave 5141 max 5141 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: 81298.0 ave 81298 max 81298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81298 Ave neighs/atom = 175.21121 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.637 | 4.637 | 4.637 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 -1514.0639 -1514.0639 19.58753 78.92856 3.636707 -135.72758 -135.72758 -110.12044 -151.33938 -145.72293 2.306247 281.12928 Loop time of 3.719e-06 on 1 procs for 0 steps with 464 atoms 161.3% 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 | | 3.719e-06 | | |100.00 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5141.00 ave 5141 max 5141 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40649.0 ave 40649 max 40649 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 81298.0 ave 81298 max 81298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81298 Ave neighs/atom = 175.21121 Neighbor list builds = 0 Dangerous builds = 0 464 -1514.06394461879 eV 2.30624704306104 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00