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 = 2.8601955 2.8601955 2.8601955 Created orthogonal box = (0.0000000 -37.401909 0.0000000) to (17.631429 37.401909 4.0449272) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7118798 4.5932169 4.0449272 Created 227 atoms using lattice units in orthogonal box = (0.0000000 -37.401909 0.0000000) to (17.631429 37.401909 4.0449272) create_atoms CPU = 0.001 seconds 227 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7118798 4.5932169 4.0449272 Created 229 atoms using lattice units in orthogonal box = (0.0000000 -37.401909 0.0000000) to (17.631429 37.401909 4.0449272) create_atoms CPU = 0.001 seconds 229 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 7 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 456 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 7 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 4.828 | 4.828 | 4.828 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1861.6645 0 -1861.6645 41580.598 36 0 -1939.1514 0 -1939.1514 6489.4322 Loop time of 1.86501 on 1 procs for 36 steps with 456 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1861.66446426637 -1939.1497610878 -1939.15138931324 Force two-norm initial, final = 136.08197 0.18233416 Force max component initial, final = 56.773261 0.046284768 Final line search alpha, max atom move = 1.0000000 0.046284768 Iterations, force evaluations = 36 62 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.85 | 1.85 | 1.85 | 0.0 | 99.19 Neigh | 0.011453 | 0.011453 | 0.011453 | 0.0 | 0.61 Comm | 0.0017492 | 0.0017492 | 0.0017492 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001816 | | | 0.10 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2459.00 ave 2459 max 2459 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: 26308.0 ave 26308 max 26308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26308 Ave neighs/atom = 57.692982 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 7 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.828 | 4.828 | 4.828 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -1939.1514 0 -1939.1514 6489.4322 5334.8472 40 0 -1939.2358 0 -1939.2358 310.23745 5353.1245 Loop time of 0.178337 on 1 procs for 4 steps with 456 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 = -1939.15138931324 -1939.23457686865 -1939.2358373169 Force two-norm initial, final = 46.302553 2.6701127 Force max component initial, final = 37.843865 2.6308382 Final line search alpha, max atom move = 0.00019776662 0.00052029198 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1777 | 0.1777 | 0.1777 | 0.0 | 99.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001154 | 0.0001154 | 0.0001154 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005182 | | | 0.29 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2466.00 ave 2466 max 2466 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: 26338.0 ave 26338 max 26338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26338 Ave neighs/atom = 57.758772 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 7 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 4.966 | 4.966 | 4.966 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1939.2358 0 -1939.2358 310.23745 Loop time of 1.659e-06 on 1 procs for 0 steps with 456 atoms 180.8% 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 | | 1.659e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2462.00 ave 2462 max 2462 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: 26320.0 ave 26320 max 26320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26320 Ave neighs/atom = 57.719298 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 7 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 4.966 | 4.966 | 4.966 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 -1939.2358 -1939.2358 17.669491 75.014763 4.0386533 310.23745 310.23745 789.10298 48.929991 92.679387 2.2325796 322.95835 Loop time of 1.657e-06 on 1 procs for 0 steps with 456 atoms 181.1% 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 | | 1.657e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2462.00 ave 2462 max 2462 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13160.0 ave 13160 max 13160 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26320.0 ave 26320 max 26320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26320 Ave neighs/atom = 57.719298 Neighbor list builds = 0 Dangerous builds = 0 456 -1939.2358373169 eV 2.23257956072254 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02