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 -45.575586 0.0000000) to (26.313077 45.575586 6.0902938) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6385165 5.4256650 6.0902938 Created 672 atoms using lattice units in orthogonal box = (0.0000000 -45.575586 0.0000000) to (26.313077 45.575586 6.0902938) create_atoms CPU = 0.005 seconds 672 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6385165 5.4256650 6.0902938 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -45.575586 0.0000000) to (26.313077 45.575586 6.0902938) create_atoms CPU = 0.004 seconds 676 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 = 6 21 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 0 atoms, new total = 1348 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 = 6 21 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) = 5.926 | 5.926 | 5.926 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5569.3973 0 -5569.3973 195982.13 74 0 -6544.8761 0 -6544.8761 11524.383 Loop time of 5.6626 on 1 procs for 74 steps with 1348 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 = -5569.39731837775 -6544.87029150256 -6544.8760977298 Force two-norm initial, final = 1106.4941 0.28292114 Force max component initial, final = 218.02387 0.029343960 Final line search alpha, max atom move = 1.0000000 0.029343960 Iterations, force evaluations = 74 124 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.4649 | 5.4649 | 5.4649 | 0.0 | 96.51 Neigh | 0.14612 | 0.14612 | 0.14612 | 0.0 | 2.58 Comm | 0.029277 | 0.029277 | 0.029277 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0223 | | | 0.39 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9413.00 ave 9413 max 9413 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: 344904.0 ave 344904 max 344904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 344904 Ave neighs/atom = 255.86350 Neighbor list builds = 3 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 = 6 21 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 : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.926 | 5.926 | 5.926 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -6544.8761 0 -6544.8761 11524.383 14607.374 81 0 -6545.4146 0 -6545.4146 -6.8571578 14698.608 Loop time of 0.443985 on 1 procs for 7 steps with 1348 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 = -6544.87609772979 -6545.41426101052 -6545.41463092923 Force two-norm initial, final = 201.70542 0.58496462 Force max component initial, final = 172.89383 0.19006064 Final line search alpha, max atom move = 0.00020417470 3.8805575e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43533 | 0.43533 | 0.43533 | 0.0 | 98.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019947 | 0.0019947 | 0.0019947 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006658 | | | 1.50 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9413.00 ave 9413 max 9413 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: 343256.0 ave 343256 max 343256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 343256 Ave neighs/atom = 254.64095 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 = 6 21 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) = 6.063 | 6.063 | 6.063 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6545.4146 0 -6545.4146 -6.8571578 Loop time of 6.204e-06 on 1 procs for 0 steps with 1348 atoms 193.4% 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 | | 6.204e-06 | | |100.00 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9413.00 ave 9413 max 9413 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: 340952.0 ave 340952 max 340952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 340952 Ave neighs/atom = 252.93175 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 = 6 21 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) = 6.063 | 6.063 | 6.063 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 -6545.4146 -6545.4146 26.287119 91.690719 6.0982867 -6.8571578 -6.8571578 -20.696538 -17.117898 17.242962 2.2304805 772.29454 Loop time of 7.146e-06 on 1 procs for 0 steps with 1348 atoms 279.9% 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 | | 7.146e-06 | | |100.00 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9413.00 ave 9413 max 9413 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 170476.0 ave 170476 max 170476 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 340952.0 ave 340952 max 340952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 340952 Ave neighs/atom = 252.93175 Neighbor list builds = 0 Dangerous builds = 0 1348 -6545.41463092923 eV 2.23048053109103 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07