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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -33.395696 0.0000000) to (16.697848 33.395696 2.8636573) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9289054 3.9289054 2.8636573 Created 136 atoms using lattice units in orthogonal box = (0.0000000 -33.395696 0.0000000) to (16.697848 33.395696 2.8636573) create_atoms CPU = 0.001 seconds 136 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9289054 3.9289054 2.8636573 Created 138 atoms using lattice units in orthogonal box = (0.0000000 -33.395696 0.0000000) to (16.697848 33.395696 2.8636573) create_atoms CPU = 0.000 seconds 138 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 ghost atom cutoff = 6 binsize = 3, bins = 6 23 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 272 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_162036141261_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 ghost atom cutoff = 6 binsize = 3, bins = 6 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.416 | 4.416 | 4.416 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1057.2231 0 -1057.2231 82771.989 41 0 -1159.739 0 -1159.739 8850.2875 Loop time of 0.715992 on 1 procs for 41 steps with 272 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1057.22308267569 -1159.73788551265 -1159.73903686299 Force two-norm initial, final = 246.52975 0.095562201 Force max component initial, final = 71.446724 0.013607351 Final line search alpha, max atom move = 1.0000000 0.013607351 Iterations, force evaluations = 41 75 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.71253 | 0.71253 | 0.71253 | 0.0 | 99.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018191 | 0.0018191 | 0.0018191 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001638 | | | 0.23 Nlocal: 272.000 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2523.00 ave 2523 max 2523 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: 17712.0 ave 17712 max 17712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17712 Ave neighs/atom = 65.117647 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 ghost atom cutoff = 6 binsize = 3, bins = 6 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.416 | 4.416 | 4.416 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -1159.739 0 -1159.739 8850.2875 3193.7583 58 0 -1160.087 0 -1160.087 15.183215 3209.4023 Loop time of 0.186704 on 1 procs for 17 steps with 272 atoms 98.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1159.73903686299 -1160.0862455267 -1160.08701412969 Force two-norm initial, final = 51.605124 0.72602585 Force max component initial, final = 51.340975 0.52256146 Final line search alpha, max atom move = 0.00089567785 0.00046804673 Iterations, force evaluations = 17 20 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18411 | 0.18411 | 0.18411 | 0.0 | 98.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004883 | 0.0004883 | 0.0004883 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002106 | | | 1.13 Nlocal: 272.000 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2493.00 ave 2493 max 2493 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: 17536.0 ave 17536 max 17536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17536 Ave neighs/atom = 64.470588 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 ghost atom cutoff = 6 binsize = 3, bins = 6 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.554 | 4.554 | 4.554 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1160.087 0 -1160.087 15.183215 Loop time of 1.514e-06 on 1 procs for 0 steps with 272 atoms 198.2% 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 | | 1.514e-06 | | |100.00 Nlocal: 272.000 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2478.00 ave 2478 max 2478 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: 17496.0 ave 17496 max 17496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17496 Ave neighs/atom = 64.323529 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 ghost atom cutoff = 6 binsize = 3, bins = 6 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.554 | 4.554 | 4.554 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 -1160.087 -1160.087 16.715232 67.668407 2.8374342 15.183215 15.183215 188.80317 -264.29506 121.04153 2.3733888 156.89735 Loop time of 2.435e-06 on 1 procs for 0 steps with 272 atoms 205.3% 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 | | 2.435e-06 | | |100.00 Nlocal: 272.000 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2478.00 ave 2478 max 2478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8748.00 ave 8748 max 8748 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 17496.0 ave 17496 max 17496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17496 Ave neighs/atom = 64.323529 Neighbor list builds = 0 Dangerous builds = 0 272 -1160.08701412969 eV 2.37338884289324 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01