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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -48.941910 0.0000000) to (13.320301 48.941910 8.7201838) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7087003 5.4379900 5.8134559 Created 503 atoms using lattice units in orthogonal box = (0.0000000 -48.941910 0.0000000) to (13.320301 48.941910 8.7201838) create_atoms CPU = 0.001 seconds 503 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7087003 5.4379900 5.8134559 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -48.941910 0.0000000) to (13.320301 48.941910 8.7201838) create_atoms CPU = 0.001 seconds 507 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 26 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1008 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.056 | 5.056 | 5.056 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3735.9339 0 -3735.9339 118145.03 52 0 -4417.6534 0 -4417.6534 14133.739 Loop time of 0.908952 on 1 procs for 52 steps with 1008 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3735.93392403956 -4417.64938483181 -4417.65342441099 Force two-norm initial, final = 1253.2459 0.30651605 Force max component initial, final = 270.62429 0.081216731 Final line search alpha, max atom move = 1.0000000 0.081216731 Iterations, force evaluations = 52 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.87264 | 0.87264 | 0.87264 | 0.0 | 96.00 Neigh | 0.024623 | 0.024623 | 0.024623 | 0.0 | 2.71 Comm | 0.0055446 | 0.0055446 | 0.0055446 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006148 | | | 0.68 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5895.00 ave 5895 max 5895 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: 176428.0 ave 176428 max 176428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176428 Ave neighs/atom = 175.02778 Neighbor list builds = 2 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.056 | 5.056 | 5.056 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -4417.6534 0 -4417.6534 14133.739 11369.741 61 0 -4418.3089 0 -4418.3089 153.11412 11440.189 Loop time of 0.108361 on 1 procs for 9 steps with 1008 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 = -4417.65342441104 -4418.30851878607 -4418.30892608179 Force two-norm initial, final = 196.92678 2.8671046 Force max component initial, final = 170.23505 2.7211886 Final line search alpha, max atom move = 0.00027675752 0.00075310939 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10499 | 0.10499 | 0.10499 | 0.0 | 96.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053102 | 0.00053102 | 0.00053102 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002836 | | | 2.62 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5872.00 ave 5872 max 5872 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: 176378.0 ave 176378 max 176378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176378 Ave neighs/atom = 174.97817 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.194 | 5.194 | 5.194 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4418.3089 0 -4418.3089 153.11412 Loop time of 1.776e-06 on 1 procs for 0 steps with 1008 atoms 168.9% 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 | | 1.776e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5862.00 ave 5862 max 5862 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: 176178.0 ave 176178 max 176178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176178 Ave neighs/atom = 174.77976 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 4 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.194 | 5.194 | 5.194 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 -4418.3089 -4418.3089 13.338828 98.663502 8.6927863 153.11412 153.11412 78.501579 384.1328 -3.2920242 2.3473781 401.77637 Loop time of 2.167e-06 on 1 procs for 0 steps with 1008 atoms 230.7% 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 | | 2.167e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5862.00 ave 5862 max 5862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 88089.0 ave 88089 max 88089 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 176178.0 ave 176178 max 176178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176178 Ave neighs/atom = 174.77976 Neighbor list builds = 0 Dangerous builds = 0 1008 -4418.30892608179 eV 2.34737814101141 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01