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 = 3.5162328 3.5162328 3.5162328 Created orthogonal box = (0.0000000 -35.162328 0.0000000) to (4.9727041 35.162328 4.9727041) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9727041 3.5162328 4.9727041 Created 80 atoms using lattice units in orthogonal box = (0.0000000 -35.162328 0.0000000) to (4.9727041 35.162328 4.9727041) create_atoms CPU = 0.000 seconds 80 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9727041 3.5162328 4.9727041 Created 84 atoms using lattice units in orthogonal box = (0.0000000 -35.162328 0.0000000) to (4.9727041 35.162328 4.9727041) create_atoms CPU = 0.000 seconds 84 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 2 16 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 8.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 160 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_047308317761_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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 2 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 4.481 | 4.481 | 4.481 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -780.20993 0 -780.20993 -0.036832448 1 0 -780.20993 0 -780.20993 -0.036832448 Loop time of 0.00790042 on 1 procs for 1 steps with 160 atoms 96.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -780.209930475891 -780.209930475891 -780.209930475863 Force two-norm initial, final = 1.1153325e-07 3.9256348e-08 Force max component initial, final = 3.9281698e-08 1.3601013e-08 Final line search alpha, max atom move = 1.0000000 1.3601013e-08 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0077289 | 0.0077289 | 0.0077289 | 0.0 | 97.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.6887e-05 | 9.6887e-05 | 9.6887e-05 | 0.0 | 1.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 7.461e-05 | | | 0.94 Nlocal: 160.000 ave 160 max 160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4465.00 ave 4465 max 4465 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: 39680.0 ave 39680 max 39680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39680 Ave neighs/atom = 248.00000 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 2 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.481 | 4.481 | 4.481 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -780.20993 0 -780.20993 -0.036832448 1738.973 2 0 -780.20993 0 -780.20993 -1.6398151e-05 1738.973 Loop time of 0.00825101 on 1 procs for 1 steps with 160 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 = -780.209930475863 -780.209930475863 -780.209930475716 Force two-norm initial, final = 6.9242704e-05 7.9993838e-08 Force max component initial, final = 4.0037338e-05 6.8879768e-08 Final line search alpha, max atom move = 1.0000000 6.8879768e-08 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0078033 | 0.0078033 | 0.0078033 | 0.0 | 94.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00010444 | 0.00010444 | 0.00010444 | 0.0 | 1.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003433 | | | 4.16 Nlocal: 160.000 ave 160 max 160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4465.00 ave 4465 max 4465 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: 39680.0 ave 39680 max 39680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39680 Ave neighs/atom = 248.00000 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 2 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 4.619 | 4.619 | 4.619 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -780.20993 0 -780.20993 -1.6398151e-05 Loop time of 1.729e-06 on 1 procs for 0 steps with 160 atoms 173.5% 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 | | 1.729e-06 | | |100.00 Nlocal: 160.000 ave 160 max 160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4465.00 ave 4465 max 4465 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: 39680.0 ave 39680 max 39680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39680 Ave neighs/atom = 248.00000 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 2 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 4.619 | 4.619 | 4.619 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 -780.20993 -780.20993 4.9727041 70.324655 4.9727041 -1.6398151e-05 -1.6398151e-05 7.133435e-06 -6.3461333e-05 7.1334448e-06 2.486352 2.1921507e-16 Loop time of 1.583e-06 on 1 procs for 0 steps with 160 atoms 189.5% 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 | | 1.583e-06 | | |100.00 Nlocal: 160.000 ave 160 max 160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4465.00 ave 4465 max 4465 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19840.0 ave 19840 max 19840 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39680.0 ave 39680 max 39680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39680 Ave neighs/atom = 248.00000 Neighbor list builds = 0 Dangerous builds = 0 160 -780.209930475716 eV 2.48635203233178 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00