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 -34.448751 0.0000000) to (42.190931 34.448751 6.9834925) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0457057 4.2471063 4.6556617 Created 874 atoms using lattice units in orthogonal box = (0.0000000 -34.448751 0.0000000) to (42.190931 34.448751 6.9834925) create_atoms CPU = 0.001 seconds 874 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0457057 4.2471063 4.6556617 Created 880 atoms using lattice units in orthogonal box = (0.0000000 -34.448751 0.0000000) to (42.190931 34.448751 6.9834925) create_atoms CPU = 0.001 seconds 880 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 = 13 20 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 2 atoms, new total = 1752 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 = 13 20 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) = 5.541 | 5.541 | 5.541 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2221.5748 0 -2221.5748 462648.14 91 0 -7462.5811 0 -7462.5811 9071.4306 Loop time of 14.7593 on 1 procs for 91 steps with 1752 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2221.57484144357 -7462.57425422886 -7462.58111545123 Force two-norm initial, final = 6835.1919 0.31399563 Force max component initial, final = 930.63834 0.076077537 Final line search alpha, max atom move = 1.0000000 0.076077537 Iterations, force evaluations = 91 165 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.685 | 14.685 | 14.685 | 0.0 | 99.50 Neigh | 0.044121 | 0.044121 | 0.044121 | 0.0 | 0.30 Comm | 0.012677 | 0.012677 | 0.012677 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01712 | | | 0.12 Nlocal: 1752.00 ave 1752 max 1752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6660.00 ave 6660 max 6660 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: 228712.0 ave 228712 max 228712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 228712 Ave neighs/atom = 130.54338 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 13 20 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 : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.541 | 5.541 | 5.541 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -7462.5811 0 -7462.5811 9071.4306 20299.963 97 0 -7463.1419 0 -7463.1419 42.432709 20404.986 Loop time of 0.722604 on 1 procs for 6 steps with 1752 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 = -7462.58111545123 -7463.13604550785 -7463.14186643789 Force two-norm initial, final = 227.73433 1.9757554 Force max component initial, final = 199.42254 1.7337767 Final line search alpha, max atom move = 8.1404156e-05 0.00014113663 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.71926 | 0.71926 | 0.71926 | 0.0 | 99.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044346 | 0.00044346 | 0.00044346 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002904 | | | 0.40 Nlocal: 1752.00 ave 1752 max 1752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6660.00 ave 6660 max 6660 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: 230136.0 ave 230136 max 230136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230136 Ave neighs/atom = 131.35616 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 = 13 20 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) = 5.679 | 5.679 | 5.679 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7463.1419 0 -7463.1419 42.432709 Loop time of 2.373e-06 on 1 procs for 0 steps with 1752 atoms 168.6% 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 | | 2.373e-06 | | |100.00 Nlocal: 1752.00 ave 1752 max 1752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6663.00 ave 6663 max 6663 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: 228638.0 ave 228638 max 228638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 228638 Ave neighs/atom = 130.50114 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 = 13 20 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) = 5.679 | 5.679 | 5.679 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 -7463.1419 -7463.1419 42.216327 69.283574 6.9763068 42.432709 42.432709 -46.656287 37.960293 135.99412 2.3272986 1711.027 Loop time of 2.929e-06 on 1 procs for 0 steps with 1752 atoms 273.1% 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 | | 2.929e-06 | | |100.00 Nlocal: 1752.00 ave 1752 max 1752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6663.00 ave 6663 max 6663 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 114319.0 ave 114319 max 114319 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 228638.0 ave 228638 max 228638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 228638 Ave neighs/atom = 130.50114 Neighbor list builds = 0 Dangerous builds = 0 1752 -7463.14186643789 eV 2.3272986300353 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16