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 = 3.5224675 3.5224675 3.5224675 Created orthogonal box = (0.0000000 -41.678397 0.0000000) to (51.045403 41.678397 8.6282479) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8337604 5.3586511 5.7521653 Created 1664 atoms using lattice units in orthogonal box = (0.0000000 -41.678397 0.0000000) to (51.045403 41.678397 8.6282479) create_atoms CPU = 0.003 seconds 1664 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8337604 5.3586511 5.7521653 Created 1688 atoms using lattice units in orthogonal box = (0.0000000 -41.678397 0.0000000) to (51.045403 41.678397 8.6282479) create_atoms CPU = 0.003 seconds 1688 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 15 24 3 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 7.18 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3352 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_763197941039_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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 6.549 | 6.549 | 6.549 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13622.286 0 -13622.286 111192.5 95 0 -14845.726 0 -14845.726 15195.764 Loop time of 3.79984 on 1 procs for 95 steps with 3352 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 = -13622.2862406465 -14845.7114823046 -14845.7260987619 Force two-norm initial, final = 1013.5995 0.53780669 Force max component initial, final = 115.90859 0.15065287 Final line search alpha, max atom move = 0.29966180 0.045144911 Iterations, force evaluations = 95 177 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6208 | 3.6208 | 3.6208 | 0.0 | 95.29 Neigh | 0.12587 | 0.12587 | 0.12587 | 0.0 | 3.31 Comm | 0.021121 | 0.021121 | 0.021121 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03203 | | | 0.84 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9987.00 ave 9987 max 9987 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: 466152.0 ave 466152 max 466152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 466152 Ave neighs/atom = 139.06683 Neighbor list builds = 4 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 95 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.547 | 6.547 | 6.547 Mbytes Step Temp E_pair E_mol TotEng Press Volume 95 0 -14845.726 0 -14845.726 15195.764 36713.032 104 0 -14848.265 0 -14848.265 -223.05622 36995.02 Loop time of 0.229738 on 1 procs for 9 steps with 3352 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 = -14845.7260987619 -14848.2608889207 -14848.2651384632 Force two-norm initial, final = 701.09364 9.2416805 Force max component initial, final = 628.68545 6.3098273 Final line search alpha, max atom move = 5.4871466e-05 0.00034622947 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22256 | 0.22256 | 0.22256 | 0.0 | 96.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00093071 | 0.00093071 | 0.00093071 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00625 | | | 2.72 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9981.00 ave 9981 max 9981 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: 466226.0 ave 466226 max 466226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 466226 Ave neighs/atom = 139.08890 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 6.685 | 6.685 | 6.685 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14848.265 0 -14848.265 -223.05622 Loop time of 2.125e-06 on 1 procs for 0 steps with 3352 atoms 235.3% 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 | | 2.125e-06 | | |100.00 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9981.00 ave 9981 max 9981 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: 465304.0 ave 465304 max 465304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 465304 Ave neighs/atom = 138.81384 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 6.685 | 6.685 | 6.685 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 -14848.265 -14848.265 51.102781 84.056783 8.6124352 -223.05622 -223.05622 -248.93148 -147.47263 -272.76455 2.3248594 1628.6217 Loop time of 2.185e-06 on 1 procs for 0 steps with 3352 atoms 274.6% 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 | | 2.185e-06 | | |100.00 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9981.00 ave 9981 max 9981 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 232652.0 ave 232652 max 232652 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 465304.0 ave 465304 max 465304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 465304 Ave neighs/atom = 138.81384 Neighbor list builds = 0 Dangerous builds = 0 3352 -14848.2651384632 eV 2.32485941047381 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04