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 -58.709430 0.0000000) to (20.756918 58.709430 5.1100000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6609777 6.2267577 5.1100000 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -58.709430 0.0000000) to (20.756918 58.709430 5.1100000) create_atoms CPU = 0.005 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6609777 6.2267577 5.1100000 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.709430 0.0000000) to (20.756918 58.709430 5.1100000) create_atoms CPU = 0.004 seconds 530 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 8 42 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 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1058 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_849011491644_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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 8 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.618 | 4.618 | 4.618 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3631.6641 0 -3631.6641 31014.99 57 0 -3737.2849 0 -3737.2849 6318.1751 Loop time of 3.88215 on 1 procs for 57 steps with 1058 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 = -3631.66406150898 -3737.28159526927 -3737.28493565256 Force two-norm initial, final = 197.68962 0.17503969 Force max component initial, final = 62.067627 0.042485238 Final line search alpha, max atom move = 1.0000000 0.042485238 Iterations, force evaluations = 57 107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8555 | 3.8555 | 3.8555 | 0.0 | 99.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.01307 | 0.01307 | 0.01307 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01362 | | | 0.35 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4820.00 ave 4820 max 4820 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: 57840.0 ave 57840 max 57840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57840 Ave neighs/atom = 54.669187 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 8 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.614 | 4.614 | 4.614 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -3737.2849 0 -3737.2849 6318.1751 12454.366 62 0 -3737.4652 0 -3737.4652 142.92487 12508.149 Loop time of 0.261383 on 1 procs for 5 steps with 1058 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3737.28493565256 -3737.46460529814 -3737.46521340982 Force two-norm initial, final = 95.311504 2.1401348 Force max component initial, final = 83.972181 1.8058985 Final line search alpha, max atom move = 0.00035551844 0.00064203021 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25791 | 0.25791 | 0.25791 | 0.0 | 98.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00066998 | 0.00066998 | 0.00066998 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002807 | | | 1.07 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4366.00 ave 4366 max 4366 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: 65304.0 ave 65304 max 65304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65304 Ave neighs/atom = 61.724008 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 8 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.752 | 4.752 | 4.752 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3737.4652 0 -3737.4652 142.92487 Loop time of 6.976e-06 on 1 procs for 0 steps with 1058 atoms 172.0% 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 | | 6.976e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4354.00 ave 4354 max 4354 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: 61000.0 ave 61000 max 61000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61000 Ave neighs/atom = 57.655955 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 8 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.752 | 4.752 | 4.752 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 -3737.4652 -3737.4652 20.763039 117.90522 5.1093902 142.92487 142.92487 69.89283 232.27681 126.60496 2.3653051 354.57198 Loop time of 7.297e-06 on 1 procs for 0 steps with 1058 atoms 233.0% 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 | | 7.297e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4354.00 ave 4354 max 4354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30500.0 ave 30500 max 30500 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61000.0 ave 61000 max 61000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61000 Ave neighs/atom = 57.655955 Neighbor list builds = 0 Dangerous builds = 0 1058 -3737.46521340982 eV 2.36530506194955 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04