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 = 4.0515263 4.0515263 4.0515263 Created orthogonal box = (0.0000000 -80.216128 0.0000000) to (49.122146 80.216128 9.9241721) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6807924 5.7297234 6.6161147 Created 2351 atoms using lattice units in orthogonal box = (0.0000000 -80.216128 0.0000000) to (49.122146 80.216128 9.9241721) create_atoms CPU = 0.004 seconds 2351 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6807924 5.7297234 6.6161147 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -80.216128 0.0000000) to (49.122146 80.216128 9.9241721) create_atoms CPU = 0.004 seconds 2357 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 13 41 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 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 29 atoms, new total = 4679 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_109933561507_005#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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 13 41 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 11.44 | 11.44 | 11.44 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14090.18 0 -14090.18 64503.816 143 0 -15681.665 0 -15681.665 1555.1522 Loop time of 7.70894 on 1 procs for 143 steps with 4679 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14090.1801839025 -15681.6506151866 -15681.6647476677 Force two-norm initial, final = 2252.9060 0.42120373 Force max component initial, final = 417.63786 0.12729575 Final line search alpha, max atom move = 1.0000000 0.12729575 Iterations, force evaluations = 143 236 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.3019 | 7.3019 | 7.3019 | 0.0 | 94.72 Neigh | 0.29518 | 0.29518 | 0.29518 | 0.0 | 3.83 Comm | 0.041766 | 0.041766 | 0.041766 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07008 | | | 0.91 Nlocal: 4679.00 ave 4679 max 4679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12904.0 ave 12904 max 12904 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: 621416.0 ave 621416 max 621416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 621416 Ave neighs/atom = 132.80957 Neighbor list builds = 7 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 13 41 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 143 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.44 | 11.44 | 11.44 Mbytes Step Temp E_pair E_mol TotEng Press Volume 143 0 -15681.665 0 -15681.665 1555.1522 78210.184 146 0 -15681.861 0 -15681.861 185.05479 78318.995 Loop time of 0.154719 on 1 procs for 3 steps with 4679 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 = -15681.6647476676 -15681.8534763612 -15681.8606349145 Force two-norm initial, final = 180.68173 18.544288 Force max component initial, final = 174.92372 16.377215 Final line search alpha, max atom move = 3.8753223e-05 0.00063466987 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15024 | 0.15024 | 0.15024 | 0.0 | 97.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00060498 | 0.00060498 | 0.00060498 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00387 | | | 2.50 Nlocal: 4679.00 ave 4679 max 4679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13048.0 ave 13048 max 13048 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: 621332.0 ave 621332 max 621332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 621332 Ave neighs/atom = 132.79162 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 13 41 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 10.95 | 10.95 | 10.95 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15681.861 0 -15681.861 185.05479 Loop time of 2.296e-06 on 1 procs for 0 steps with 4679 atoms 174.2% 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 | | 2.296e-06 | | |100.00 Nlocal: 4679.00 ave 4679 max 4679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13053.0 ave 13053 max 13053 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: 621218.0 ave 621218 max 621218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 621218 Ave neighs/atom = 132.76726 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 13 41 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 10.95 | 10.95 | 10.95 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 -15681.861 -15681.861 49.109792 160.77904 9.9190389 185.05479 185.05479 48.543477 335.75387 170.86702 2.5901703 2322.1273 Loop time of 2.496e-06 on 1 procs for 0 steps with 4679 atoms 320.5% 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 | | 2.496e-06 | | |100.00 Nlocal: 4679.00 ave 4679 max 4679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13053.0 ave 13053 max 13053 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 310609.0 ave 310609 max 310609 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 621218.0 ave 621218 max 621218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 621218 Ave neighs/atom = 132.76726 Neighbor list builds = 0 Dangerous builds = 0 4679 -15681.8606348713 eV 2.59017033807837 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08