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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -53.154355 0.0000000) to (37.583316 53.154355 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9342077 6.0610601 4.9780318 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -53.154355 0.0000000) to (37.583316 53.154355 4.9780318) create_atoms CPU = 0.007 seconds 916 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9342077 6.0610601 4.9780318 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -53.154355 0.0000000) to (37.583316 53.154355 4.9780318) create_atoms CPU = 0.006 seconds 916 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 26 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1816 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_103383163946_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.404 | 6.404 | 6.404 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8013.9655 0 -8013.9655 11655.702 38 0 -8061.4786 0 -8061.4786 -2635.2608 Loop time of 2.65964 on 1 procs for 38 steps with 1816 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8013.96553317319 -8061.47075132669 -8061.47863675207 Force two-norm initial, final = 68.349574 0.30948812 Force max component initial, final = 16.459336 0.038141800 Final line search alpha, max atom move = 1.0000000 0.038141800 Iterations, force evaluations = 38 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.574 | 2.574 | 2.574 | 0.0 | 96.78 Neigh | 0.055112 | 0.055112 | 0.055112 | 0.0 | 2.07 Comm | 0.017002 | 0.017002 | 0.017002 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0135 | | | 0.51 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11945.0 ave 11945 max 11945 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: 407744.0 ave 407744 max 407744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 407744 Ave neighs/atom = 224.52863 Neighbor list builds = 1 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.403 | 6.403 | 6.403 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -8061.4786 0 -8061.4786 -2635.2608 19889.396 40 0 -8061.4994 0 -8061.4994 -880.97625 19869.845 Loop time of 0.2137 on 1 procs for 2 steps with 1816 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8061.47863675207 -8061.49776761079 -8061.49940037699 Force two-norm initial, final = 43.470270 0.31579395 Force max component initial, final = 41.396073 0.038957837 Final line search alpha, max atom move = 0.00011578224 4.5106256e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20876 | 0.20876 | 0.20876 | 0.0 | 97.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012916 | 0.0012916 | 0.0012916 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003646 | | | 1.71 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11936.0 ave 11936 max 11936 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: 407456.0 ave 407456 max 407456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 407456 Ave neighs/atom = 224.37004 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.541 | 6.541 | 6.541 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8061.4994 0 -8061.4994 -880.97625 Loop time of 6.696e-06 on 1 procs for 0 steps with 1816 atoms 179.2% 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 | | 6.696e-06 | | |100.00 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11936.0 ave 11936 max 11936 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: 407488.0 ave 407488 max 407488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 407488 Ave neighs/atom = 224.38767 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.541 | 6.541 | 6.541 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 -8061.4994 -8061.4994 37.545339 106.30871 4.9781686 -880.97625 -880.97625 -0.16214137 -2639.6252 -3.1413958 2.2948306 611.61971 Loop time of 6.736e-06 on 1 procs for 0 steps with 1816 atoms 296.9% 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 | | 6.736e-06 | | |100.00 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11936.0 ave 11936 max 11936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 203744.0 ave 203744 max 203744 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 407488.0 ave 407488 max 407488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 407488 Ave neighs/atom = 224.38767 Neighbor list builds = 0 Dangerous builds = 0 1816 -8012.04732979459 eV 2.29483055489654 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03