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 -30.575493 0.0000000) to (21.620139 30.575493 4.0498230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1723075 4.8277095 4.0498230 Created 228 atoms using lattice units in orthogonal box = (0.0000000 -30.575493 0.0000000) to (21.620139 30.575493 4.0498230) create_atoms CPU = 0.002 seconds 228 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1723075 4.8277095 4.0498230 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -30.575493 0.0000000) to (21.620139 30.575493 4.0498230) create_atoms CPU = 0.002 seconds 230 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 = 8 21 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 452 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 = 8 21 2 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) = 4.450 | 4.450 | 4.450 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1744.9832 0 -1744.9832 70107.222 80 0 -1926.8869 0 -1926.8869 -5551.3926 Loop time of 4.49375 on 1 procs for 80 steps with 452 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 = -1744.98316435713 -1926.88516670161 -1926.88691497026 Force two-norm initial, final = 384.84835 0.12739755 Force max component initial, final = 133.41996 0.027847763 Final line search alpha, max atom move = 1.0000000 0.027847763 Iterations, force evaluations = 80 133 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4555 | 4.4555 | 4.4555 | 0.0 | 99.15 Neigh | 0.016632 | 0.016632 | 0.016632 | 0.0 | 0.37 Comm | 0.01075 | 0.01075 | 0.01075 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01084 | | | 0.24 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2900.00 ave 2900 max 2900 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: 29160.0 ave 29160 max 29160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29160 Ave neighs/atom = 64.513274 Neighbor list builds = 3 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 = 8 21 2 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 : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.450 | 4.450 | 4.450 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -1926.8869 0 -1926.8869 -5551.3926 5354.2419 85 0 -1926.9517 0 -1926.9517 3.7566271 5336.6886 Loop time of 0.254224 on 1 procs for 5 steps with 452 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 = -1926.88691497026 -1926.95131992297 -1926.95168827864 Force two-norm initial, final = 37.169558 0.29417571 Force max component initial, final = 32.306640 0.19944303 Final line search alpha, max atom move = 0.00027711563 5.5268779e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25178 | 0.25178 | 0.25178 | 0.0 | 99.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005246 | 0.0005246 | 0.0005246 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001916 | | | 0.75 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2916.00 ave 2916 max 2916 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: 29244.0 ave 29244 max 29244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29244 Ave neighs/atom = 64.699115 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 = 8 21 2 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) = 4.588 | 4.588 | 4.588 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1926.9517 0 -1926.9517 3.7566271 Loop time of 6.826e-06 on 1 procs for 0 steps with 452 atoms 175.8% 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 | | 6.826e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2916.00 ave 2916 max 2916 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: 29256.0 ave 29256 max 29256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29256 Ave neighs/atom = 64.725664 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 = 8 21 2 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) = 4.588 | 4.588 | 4.588 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 -1926.9517 -1926.9517 21.535299 61.118134 4.0546265 3.7566271 3.7566271 -6.4014058 59.844463 -42.173176 2.2543882 425.23311 Loop time of 6.906e-06 on 1 procs for 0 steps with 452 atoms 260.6% 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 | | 6.906e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2916.00 ave 2916 max 2916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14628.0 ave 14628 max 14628 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29256.0 ave 29256 max 29256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29256 Ave neighs/atom = 64.725664 Neighbor list builds = 0 Dangerous builds = 0 452 -1926.95168827864 eV 2.2543881785231 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05