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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -38.996289 0.0000000) to (9.7490724 38.996289 3.0829274) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8996289 3.8996289 3.0829274 Created 80 atoms using lattice units in orthogonal box = (0.0000000 -38.996289 0.0000000) to (9.7490724 38.996289 3.0829274) create_atoms CPU = 0.001 seconds 80 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8996289 3.8996289 3.0829274 Created 82 atoms using lattice units in orthogonal box = (0.0000000 -38.996289 0.0000000) to (9.7490724 38.996289 3.0829274) create_atoms CPU = 0.000 seconds 82 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 3 24 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 162 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 3 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 4.778 | 4.778 | 4.778 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -520.3107 0 -520.3107 670337.21 69 0 -1048.7 0 -1048.7 39793.15 Loop time of 5.73638 on 1 procs for 69 steps with 162 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 = -520.310698128348 -1048.69895026828 -1048.69996125306 Force two-norm initial, final = 1455.7134 0.15858215 Force max component initial, final = 403.52634 0.031855841 Final line search alpha, max atom move = 1.0000000 0.031855841 Iterations, force evaluations = 69 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.7188 | 5.7188 | 5.7188 | 0.0 | 99.69 Neigh | 0.012015 | 0.012015 | 0.012015 | 0.0 | 0.21 Comm | 0.0031913 | 0.0031913 | 0.0031913 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002328 | | | 0.04 Nlocal: 162.000 ave 162 max 162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2212.00 ave 2212 max 2212 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: 12580.0 ave 12580 max 12580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12580 Ave neighs/atom = 77.654321 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 3 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.777 | 4.777 | 4.777 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -1048.7 0 -1048.7 39793.15 2344.1202 118 0 -1050.2486 0 -1050.2486 9.9158501 2379.348 Loop time of 2.37365 on 1 procs for 49 steps with 162 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 = -1048.69996125306 -1050.2477073376 -1050.24861889737 Force two-norm initial, final = 115.89382 1.4906875 Force max component initial, final = 104.80436 0.75638807 Final line search alpha, max atom move = 0.00095417863 0.00072172934 Iterations, force evaluations = 49 52 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.345 | 2.345 | 2.345 | 0.0 | 98.79 Neigh | 0.023102 | 0.023102 | 0.023102 | 0.0 | 0.97 Comm | 0.0010824 | 0.0010824 | 0.0010824 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004482 | | | 0.19 Nlocal: 162.000 ave 162 max 162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2228.00 ave 2228 max 2228 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: 12020.0 ave 12020 max 12020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12020 Ave neighs/atom = 74.197531 Neighbor list builds = 2 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 3 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 4.916 | 4.916 | 4.916 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1050.2486 0 -1050.2486 9.9158501 Loop time of 1.858e-06 on 1 procs for 0 steps with 162 atoms 161.5% 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 | | 1.858e-06 | | |100.00 Nlocal: 162.000 ave 162 max 162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2263.00 ave 2263 max 2263 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: 12824.0 ave 12824 max 12824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12824 Ave neighs/atom = 79.160494 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 3 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 4.916 | 4.916 | 4.916 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 -1050.2486 -1050.2486 9.8161743 80.887843 2.9966253 9.9158501 9.9158501 481.58974 -528.23484 76.392657 2.5665483 298.16696 Loop time of 1.825e-06 on 1 procs for 0 steps with 162 atoms 164.4% 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 | | 1.825e-06 | | |100.00 Nlocal: 162.000 ave 162 max 162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2263.00 ave 2263 max 2263 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6412.00 ave 6412 max 6412 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 12824.0 ave 12824 max 12824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12824 Ave neighs/atom = 79.160494 Neighbor list builds = 0 Dangerous builds = 0 162 -1050.24861889737 eV 2.56654833599593 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08