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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -46.273018 0.0000000) to (23.136509 46.273018 3.6133156) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0787459 5.0787459 3.6133156 Created 328 atoms using lattice units in orthogonal box = (0.0000000 -46.273018 0.0000000) to (23.136509 46.273018 3.6133156) create_atoms CPU = 0.001 seconds 328 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0787459 5.0787459 3.6133156 Created 330 atoms using lattice units in orthogonal box = (0.0000000 -46.273018 0.0000000) to (23.136509 46.273018 3.6133156) create_atoms CPU = 0.000 seconds 330 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 27 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 658 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_813575892799_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 7 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.530 | 4.530 | 4.530 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2173.1061 0 -2173.1061 66586.378 58 0 -2322.6315 0 -2322.6315 9435.4263 Loop time of 2.7237 on 1 procs for 58 steps with 658 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 = -2173.10612476679 -2322.62914074861 -2322.63145209752 Force two-norm initial, final = 223.69799 0.14145271 Force max component initial, final = 47.376690 0.024786158 Final line search alpha, max atom move = 1.0000000 0.024786158 Iterations, force evaluations = 58 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.713 | 2.713 | 2.713 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0057721 | 0.0057721 | 0.0057721 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004883 | | | 0.18 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5422.00 ave 5422 max 5422 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: 87736.0 ave 87736 max 87736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87736 Ave neighs/atom = 133.33739 Neighbor list builds = 0 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.530 | 4.530 | 4.530 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -2322.6315 0 -2322.6315 9435.4263 7736.8033 67 0 -2322.9392 0 -2322.9392 171.76482 7786.4693 Loop time of 0.324537 on 1 procs for 9 steps with 658 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2322.63145209752 -2322.93872738137 -2322.93924348714 Force two-norm initial, final = 93.246010 2.1087357 Force max component initial, final = 84.023595 2.0527024 Final line search alpha, max atom move = 0.00024372853 0.00050030214 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32126 | 0.32126 | 0.32126 | 0.0 | 98.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053754 | 0.00053754 | 0.00053754 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002741 | | | 0.84 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5407.00 ave 5407 max 5407 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: 87620.0 ave 87620 max 87620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87620 Ave neighs/atom = 133.16109 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.668 | 4.668 | 4.668 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2322.9392 0 -2322.9392 171.76482 Loop time of 2.005e-06 on 1 procs for 0 steps with 658 atoms 149.6% 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 | | 2.005e-06 | | |100.00 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5412.00 ave 5412 max 5412 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: 87440.0 ave 87440 max 87440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87440 Ave neighs/atom = 132.88754 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.668 | 4.668 | 4.668 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 -2322.9392 -2322.9392 23.113146 93.270418 3.6119156 171.76482 171.76482 421.94613 7.3933825 85.954947 2.3118605 161.24492 Loop time of 2.284e-06 on 1 procs for 0 steps with 658 atoms 218.9% 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 | | 2.284e-06 | | |100.00 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5412.00 ave 5412 max 5412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43720.0 ave 43720 max 43720 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 87440.0 ave 87440 max 87440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87440 Ave neighs/atom = 132.88754 Neighbor list builds = 0 Dangerous builds = 0 658 -2322.93924348714 eV 2.31186049618674 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03