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 = 3.5200001 3.5200001 3.5200001 Created orthogonal box = (0.0000000 -43.539996 0.0000000) to (14.513332 43.539996 3.5200001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2686271 4.2686271 3.5200001 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -43.539996 0.0000000) to (14.513332 43.539996 3.5200001) create_atoms CPU = 0.002 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2686271 4.2686271 3.5200001 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -43.539996 0.0000000) to (14.513332 43.539996 3.5200001) create_atoms CPU = 0.001 seconds 206 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 5 26 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 6.85 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 408 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_776437554506_000#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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 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) = 4.469 | 4.469 | 4.469 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1773.0104 0 -1773.0104 19267.619 53 0 -1807.5276 0 -1807.5276 11202.581 Loop time of 0.678736 on 1 procs for 53 steps with 408 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 = -1773.01035759262 -1807.52584983253 -1807.52758355989 Force two-norm initial, final = 59.778095 0.13952855 Force max component initial, final = 19.768861 0.017063877 Final line search alpha, max atom move = 1.0000000 0.017063877 Iterations, force evaluations = 53 102 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.65205 | 0.65205 | 0.65205 | 0.0 | 96.07 Neigh | 0.0068444 | 0.0068444 | 0.0068444 | 0.0 | 1.01 Comm | 0.011509 | 0.011509 | 0.011509 | 0.0 | 1.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008333 | | | 1.23 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4157.00 ave 4157 max 4157 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: 53912.0 ave 53912 max 53912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53912 Ave neighs/atom = 132.13725 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.468 | 4.468 | 4.468 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -1807.5276 0 -1807.5276 11202.581 4448.6495 60 0 -1807.6687 0 -1807.6687 416.63792 4475.6517 Loop time of 0.0537392 on 1 procs for 7 steps with 408 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1807.52758355989 -1807.66811655123 -1807.66867360009 Force two-norm initial, final = 56.310628 2.2817199 Force max component initial, final = 44.455801 1.9097238 Final line search alpha, max atom move = 0.00049524236 0.00094577610 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0504 | 0.0504 | 0.0504 | 0.0 | 93.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00077579 | 0.00077579 | 0.00077579 | 0.0 | 1.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002563 | | | 4.77 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4157.00 ave 4157 max 4157 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: 53916.0 ave 53916 max 53916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53916 Ave neighs/atom = 132.14706 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 5 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 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) = 4.606 | 4.606 | 4.606 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1807.6687 0 -1807.6687 416.63792 Loop time of 6.365e-06 on 1 procs for 0 steps with 408 atoms 188.5% 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 | | 6.365e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4157.00 ave 4157 max 4157 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: 53912.0 ave 53912 max 53912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53912 Ave neighs/atom = 132.13725 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 5 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 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) = 4.606 | 4.606 | 4.606 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 -1807.6687 -1807.6687 14.514967 87.618477 3.5192048 416.63792 416.63792 414.02952 687.86299 148.02124 2.2664131 179.7916 Loop time of 6.865e-06 on 1 procs for 0 steps with 408 atoms 262.2% 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 | | 6.865e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4157.00 ave 4157 max 4157 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26956.0 ave 26956 max 26956 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 53912.0 ave 53912 max 53912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53912 Ave neighs/atom = 132.13725 Neighbor list builds = 0 Dangerous builds = 0 408 -1807.66867360009 eV 2.26641305544591 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01