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 = 3.5192937 3.5192937 3.5192937 Created orthogonal box = (0.0000000 -46.692226 0.0000000) to (16.506950 46.692226 4.9770328) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0025274 5.3055348 4.9770328 Created 354 atoms using lattice units in orthogonal box = (0.0000000 -46.692226 0.0000000) to (16.506950 46.692226 4.9770328) create_atoms CPU = 0.003 seconds 354 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0025274 5.3055348 4.9770328 Created 354 atoms using lattice units in orthogonal box = (0.0000000 -46.692226 0.0000000) to (16.506950 46.692226 4.9770328) create_atoms CPU = 0.003 seconds 354 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 688 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_715003088863_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.971 | 4.971 | 4.971 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3041.8475 0 -3041.8475 -5861.2546 56 0 -3054.5967 0 -3054.5967 -37371.958 Loop time of 1.48824 on 1 procs for 56 steps with 688 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 = -3041.84752875079 -3054.59369371143 -3054.59665585244 Force two-norm initial, final = 3.3115250 0.20630220 Force max component initial, final = 0.86959515 0.017315663 Final line search alpha, max atom move = 1.0000000 0.017315663 Iterations, force evaluations = 56 105 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4616 | 1.4616 | 1.4616 | 0.0 | 98.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.01496 | 0.01496 | 0.01496 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01166 | | | 0.78 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5870.00 ave 5870 max 5870 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: 118264.0 ave 118264 max 118264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118264 Ave neighs/atom = 171.89535 Neighbor list builds = 0 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.973 | 4.973 | 4.973 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -3054.5967 0 -3054.5967 -37371.958 7672.0588 66 0 -3055.6493 0 -3055.6493 -11856.406 7561.0701 Loop time of 0.201631 on 1 procs for 10 steps with 688 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3054.59665585245 -3055.64901581099 -3055.64929117755 Force two-norm initial, final = 202.21153 0.33885061 Force max component initial, final = 157.31886 0.053297688 Final line search alpha, max atom move = 0.00041967480 2.2367696e-05 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19272 | 0.19272 | 0.19272 | 0.0 | 95.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019134 | 0.0019134 | 0.0019134 | 0.0 | 0.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007 | | | 3.47 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5780.00 ave 5780 max 5780 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: 116932.0 ave 116932 max 116932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116932 Ave neighs/atom = 169.95930 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.111 | 5.111 | 5.111 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3055.6493 0 -3055.6493 -11856.406 Loop time of 6.525e-06 on 1 procs for 0 steps with 688 atoms 183.9% 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 | | 6.525e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5789.00 ave 5789 max 5789 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: 117756.0 ave 117756 max 117756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117756 Ave neighs/atom = 171.15698 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.111 | 5.111 | 5.111 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 -3055.6493 -3055.6493 16.41213 93.384451 4.9333706 -11856.406 -11856.406 -6.4667054 -35567.934 5.1816816 2.3893726 205.17914 Loop time of 6.755e-06 on 1 procs for 0 steps with 688 atoms 296.1% 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 | | 6.755e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5789.00 ave 5789 max 5789 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58878.0 ave 58878 max 58878 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117756.0 ave 117756 max 117756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117756 Ave neighs/atom = 171.15698 Neighbor list builds = 0 Dangerous builds = 0 688 -3055.64929117755 eV 2.38937263472351 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02