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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -42.727094 0.0000000) to (52.329789 42.727094 8.8453488) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9805473 5.4934835 5.8968992 Created 1661 atoms using lattice units in orthogonal box = (0.0000000 -42.727094 0.0000000) to (52.329789 42.727094 8.8453488) create_atoms CPU = 0.003 seconds 1661 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9805473 5.4934835 5.8968992 Created 1685 atoms using lattice units in orthogonal box = (0.0000000 -42.727094 0.0000000) to (52.329789 42.727094 8.8453488) create_atoms CPU = 0.002 seconds 1685 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 = 17 27 3 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 0 atoms, new total = 3346 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_179420363944_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 = 17 27 3 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) = 5.681 | 5.681 | 5.681 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13705.543 0 -13705.543 31668.417 332 0 -14173.749 0 -14173.749 -1266.6245 Loop time of 113.033 on 1 procs for 332 steps with 3346 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 = -13705.5427088233 -14173.734646116 -14173.7486341762 Force two-norm initial, final = 439.96290 0.40259156 Force max component initial, final = 84.623169 0.15698375 Final line search alpha, max atom move = 0.87964073 0.13808930 Iterations, force evaluations = 332 639 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 112.67 | 112.67 | 112.67 | 0.0 | 99.68 Neigh | 0.19906 | 0.19906 | 0.19906 | 0.0 | 0.18 Comm | 0.063898 | 0.063898 | 0.063898 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1021 | | | 0.09 Nlocal: 3346.00 ave 3346 max 3346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8456.00 ave 8456 max 8456 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: 304084.0 ave 304084 max 304084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 304084 Ave neighs/atom = 90.879857 Neighbor list builds = 8 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 = 17 27 3 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 : 332 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.070 | 6.070 | 6.070 Mbytes Step Temp E_pair E_mol TotEng Press Volume 332 0 -14173.749 0 -14173.749 -1266.6245 39554.627 342 0 -14176.452 0 -14176.452 -4.1910451 39523.926 Loop time of 2.32237 on 1 procs for 10 steps with 3346 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 = -14173.7486341763 -14176.4424695297 -14176.4524308095 Force two-norm initial, final = 440.17213 2.0684958 Force max component initial, final = 364.00186 1.5228257 Final line search alpha, max atom move = 5.2653819e-05 8.0182591e-05 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.315 | 2.315 | 2.315 | 0.0 | 99.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00084911 | 0.00084911 | 0.00084911 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006554 | | | 0.28 Nlocal: 3346.00 ave 3346 max 3346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8458.00 ave 8458 max 8458 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: 304860.0 ave 304860 max 304860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 304860 Ave neighs/atom = 91.111775 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 = 16 27 3 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) = 6.207 | 6.207 | 6.207 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14176.452 0 -14176.452 -4.1910451 Loop time of 2.256e-06 on 1 procs for 0 steps with 3346 atoms 221.6% 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 | | 2.256e-06 | | |100.00 Nlocal: 3346.00 ave 3346 max 3346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8411.00 ave 8411 max 8411 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: 306338.0 ave 306338 max 306338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306338 Ave neighs/atom = 91.553497 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 = 16 27 3 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) = 6.207 | 6.207 | 6.207 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 -14176.452 -14176.452 51.831424 85.542602 8.9142434 -4.1910451 -4.1910451 26.239751 -61.794467 22.981581 2.330207 11082.413 Loop time of 2.66e-06 on 1 procs for 0 steps with 3346 atoms 263.2% 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 | | 2.66e-06 | | |100.00 Nlocal: 3346.00 ave 3346 max 3346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8411.00 ave 8411 max 8411 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 153169.0 ave 153169 max 153169 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 306338.0 ave 306338 max 306338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306338 Ave neighs/atom = 91.553497 Neighbor list builds = 0 Dangerous builds = 0 3346 -14176.4524308095 eV 2.3302069793336 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:56