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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -59.671543 0.0000000) to (29.833813 59.671543 3.9173716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1437609 5.1437609 3.9173716 Created 466 atoms using lattice units in orthogonal box = (0.0000000 -59.671543 0.0000000) to (29.833813 59.671543 3.9173716) create_atoms CPU = 0.003 seconds 466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1437609 5.1437609 3.9173716 Created 466 atoms using lattice units in orthogonal box = (0.0000000 -59.671543 0.0000000) to (29.833813 59.671543 3.9173716) create_atoms CPU = 0.002 seconds 466 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 37 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 916 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_020840179467_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.576 | 4.576 | 4.576 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5241.0938 0 -5241.0938 -1064.423 22 0 -5260.2808 0 -5260.2808 -9626.7644 Loop time of 1.41028 on 1 procs for 22 steps with 916 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 = -5241.09384275471 -5260.27630435942 -5260.28077321097 Force two-norm initial, final = 42.965559 0.20883406 Force max component initial, final = 15.502254 0.058827973 Final line search alpha, max atom move = 1.0000000 0.058827973 Iterations, force evaluations = 22 38 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4003 | 1.4003 | 1.4003 | 0.0 | 99.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0049888 | 0.0049888 | 0.0049888 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004952 | | | 0.35 Nlocal: 916.000 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5638.00 ave 5638 max 5638 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: 70544.0 ave 70544 max 70544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70544 Ave neighs/atom = 77.013100 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.576 | 4.576 | 4.576 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -5260.2808 0 -5260.2808 -9626.7644 13947.642 26 0 -5260.4813 0 -5260.4813 -1413.1435 13880.969 Loop time of 0.258909 on 1 procs for 4 steps with 916 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 = -5260.28077321097 -5260.47791622827 -5260.4813238823 Force two-norm initial, final = 114.86006 0.31482508 Force max component initial, final = 87.066304 0.10110892 Final line search alpha, max atom move = 0.00014286031 1.4444453e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25527 | 0.25527 | 0.25527 | 0.0 | 98.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00080362 | 0.00080362 | 0.00080362 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002831 | | | 1.09 Nlocal: 916.000 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5638.00 ave 5638 max 5638 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: 70736.0 ave 70736 max 70736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70736 Ave neighs/atom = 77.222707 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.714 | 4.714 | 4.714 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5260.4813 0 -5260.4813 -1413.1435 Loop time of 5.934e-06 on 1 procs for 0 steps with 916 atoms 168.5% 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 | | 5.934e-06 | | |100.00 Nlocal: 916.000 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5638.00 ave 5638 max 5638 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: 70736.0 ave 70736 max 70736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70736 Ave neighs/atom = 77.222707 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.714 | 4.714 | 4.714 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 -5260.4813 -5260.4813 29.792146 119.34309 3.9040982 -1413.1435 -1413.1435 -3.0546012 -4237.5385 1.1625927 2.4913818 581.6474 Loop time of 6.826e-06 on 1 procs for 0 steps with 916 atoms 293.0% 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 | | 6.826e-06 | | |100.00 Nlocal: 916.000 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5638.00 ave 5638 max 5638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35368.0 ave 35368 max 35368 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 70736.0 ave 70736 max 70736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70736 Ave neighs/atom = 77.222707 Neighbor list builds = 0 Dangerous builds = 0 916 -5260.4813238823 eV 2.49138176002264 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02