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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -56.305250 0.0000000) to (28.150823 56.305250 3.6043435) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0763779 5.0763779 3.6043435 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -56.305250 0.0000000) to (28.150823 56.305250 3.6043435) create_atoms CPU = 0.001 seconds 490 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0763779 5.0763779 3.6043435 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -56.305250 0.0000000) to (28.150823 56.305250 3.6043435) create_atoms CPU = 0.001 seconds 490 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 ghost atom cutoff = 6 binsize = 3, bins = 10 38 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 974 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_492310898779_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 ghost atom cutoff = 6 binsize = 3, bins = 10 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.595 | 4.595 | 4.595 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4086.1291 0 -4086.1291 12161.783 105 0 -4129.0625 0 -4129.0625 -1436.3501 Loop time of 6.98576 on 1 procs for 105 steps with 974 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4086.12910207615 -4129.05869712827 -4129.0625263655 Force two-norm initial, final = 30.130118 0.16527175 Force max component initial, final = 8.4226157 0.027551171 Final line search alpha, max atom move = 1.0000000 0.027551171 Iterations, force evaluations = 105 182 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.9486 | 6.9486 | 6.9486 | 0.0 | 99.47 Neigh | 0.012567 | 0.012567 | 0.012567 | 0.0 | 0.18 Comm | 0.012968 | 0.012968 | 0.012968 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01166 | | | 0.17 Nlocal: 974.000 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5970.00 ave 5970 max 5970 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: 75376.0 ave 75376 max 75376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75376 Ave neighs/atom = 77.388090 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 105 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.598 | 4.598 | 4.598 Mbytes Step Temp E_pair E_mol TotEng Press Volume 105 0 -4129.0625 0 -4129.0625 -1436.3501 11426.051 113 0 -4129.2728 0 -4129.2728 -2774.9719 11435.259 Loop time of 0.39893 on 1 procs for 8 steps with 974 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 = -4129.06252636551 -4129.27094532985 -4129.27279631965 Force two-norm initial, final = 43.075550 0.32227967 Force max component initial, final = 35.916561 0.051719215 Final line search alpha, max atom move = 0.00031505404 1.6294347e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39579 | 0.39579 | 0.39579 | 0.0 | 99.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050352 | 0.00050352 | 0.00050352 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002634 | | | 0.66 Nlocal: 974.000 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5977.00 ave 5977 max 5977 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: 75588.0 ave 75588 max 75588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75588 Ave neighs/atom = 77.605749 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 ghost atom cutoff = 6 binsize = 3, bins = 10 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.736 | 4.736 | 4.736 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4129.2728 0 -4129.2728 -2774.9719 Loop time of 2.031e-06 on 1 procs for 0 steps with 974 atoms 147.7% 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 | | 2.031e-06 | | |100.00 Nlocal: 974.000 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5995.00 ave 5995 max 5995 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: 75608.0 ave 75608 max 75608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75608 Ave neighs/atom = 77.626283 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 ghost atom cutoff = 6 binsize = 3, bins = 10 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.736 | 4.736 | 4.736 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 -4129.2728 -4129.2728 27.967211 112.6105 3.6309307 -2774.9719 -2774.9719 0.75554677 -8323.8311 -1.8402027 2.2962611 160.40076 Loop time of 2.095e-06 on 1 procs for 0 steps with 974 atoms 238.7% 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 | | 2.095e-06 | | |100.00 Nlocal: 974.000 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5995.00 ave 5995 max 5995 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37804.0 ave 37804 max 37804 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75608.0 ave 75608 max 75608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75608 Ave neighs/atom = 77.626283 Neighbor list builds = 0 Dangerous builds = 0 974 -4129.27279631965 eV 2.29626106338669 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07