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 = 2.8509989 2.8509989 2.8509989 Created orthogonal box = (0.0000000 -42.190931 0.0000000) to (34.448751 42.190931 6.9834925) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2471063 4.0457057 4.6556617 Created 876 atoms using lattice units in orthogonal box = (0.0000000 -42.190931 0.0000000) to (34.448751 42.190931 6.9834925) create_atoms CPU = 0.001 seconds 876 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2471063 4.0457057 4.6556617 Created 878 atoms using lattice units in orthogonal box = (0.0000000 -42.190931 0.0000000) to (34.448751 42.190931 6.9834925) create_atoms CPU = 0.001 seconds 878 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 ghost atom cutoff = 7 binsize = 3.5, bins = 10 25 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1748 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_262519520678_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 10 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.551 | 5.551 | 5.551 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3941.0481 0 -3941.0481 339749.75 86 0 -7452.1301 0 -7452.1301 3506.7648 Loop time of 13.171 on 1 procs for 86 steps with 1748 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3941.04812586694 -7452.1229901841 -7452.1301393993 Force two-norm initial, final = 5192.0745 0.37569367 Force max component initial, final = 1308.1098 0.083400236 Final line search alpha, max atom move = 1.0000000 0.083400236 Iterations, force evaluations = 86 151 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.112 | 13.112 | 13.112 | 0.0 | 99.55 Neigh | 0.029459 | 0.029459 | 0.029459 | 0.0 | 0.22 Comm | 0.012965 | 0.012965 | 0.012965 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01632 | | | 0.12 Nlocal: 1748.00 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6831.00 ave 6831 max 6831 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: 229064.0 ave 229064 max 229064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229064 Ave neighs/atom = 131.04348 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 ghost atom cutoff = 7 binsize = 3.5, bins = 10 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 86 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.552 | 5.552 | 5.552 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -7452.1301 0 -7452.1301 3506.7648 20299.963 93 0 -7452.7404 0 -7452.7404 -52.364312 20339.641 Loop time of 0.764498 on 1 procs for 7 steps with 1748 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 = -7452.13013939931 -7452.73513831977 -7452.74043739481 Force two-norm initial, final = 178.60500 1.7402569 Force max component initial, final = 174.14968 1.1701752 Final line search alpha, max atom move = 9.4388538e-05 0.00011045113 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.76112 | 0.76112 | 0.76112 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045953 | 0.00045953 | 0.00045953 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002918 | | | 0.38 Nlocal: 1748.00 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6851.00 ave 6851 max 6851 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: 229144.0 ave 229144 max 229144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229144 Ave neighs/atom = 131.08924 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 ghost atom cutoff = 7 binsize = 3.5, bins = 10 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.690 | 5.690 | 5.690 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7452.7404 0 -7452.7404 -52.364312 Loop time of 2.124e-06 on 1 procs for 0 steps with 1748 atoms 188.3% 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 | | 2.124e-06 | | |100.00 Nlocal: 1748.00 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6870.00 ave 6870 max 6870 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: 227680.0 ave 227680 max 227680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227680 Ave neighs/atom = 130.25172 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 ghost atom cutoff = 7 binsize = 3.5, bins = 10 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.690 | 5.690 | 5.690 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 -7452.7404 -7452.7404 34.368273 84.935275 6.9678289 -52.364312 -52.364312 -91.960685 -84.514979 19.382728 2.3181464 1404.8008 Loop time of 1.926e-06 on 1 procs for 0 steps with 1748 atoms 259.6% 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 | | 1.926e-06 | | |100.00 Nlocal: 1748.00 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6870.00 ave 6870 max 6870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113840.0 ave 113840 max 113840 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 227680.0 ave 227680 max 227680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227680 Ave neighs/atom = 130.25172 Neighbor list builds = 0 Dangerous builds = 0 1748 -7452.74043739481 eV 2.31814642085903 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16