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 = 2.8700001 2.8700001 2.8700001 Created orthogonal box = (0.0000000 -49.709860 0.0000000) to (20.293965 49.709860 7.0300358) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8705516 4.3081878 4.6866905 Created 600 atoms using lattice units in orthogonal box = (0.0000000 -49.709860 0.0000000) to (20.293965 49.709860 7.0300358) create_atoms CPU = 0.003 seconds 600 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8705516 4.3081878 4.6866905 Created 602 atoms using lattice units in orthogonal box = (0.0000000 -49.709860 0.0000000) to (20.293965 49.709860 7.0300358) create_atoms CPU = 0.003 seconds 602 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 33 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1196 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.606 | 4.606 | 4.606 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4910.8887 0 -4910.8887 19510.555 115 0 -5095.39 0 -5095.39 2713.2271 Loop time of 1.95252 on 1 procs for 115 steps with 1196 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 = -4910.88869286659 -5095.38521775171 -5095.39001158668 Force two-norm initial, final = 220.15138 0.23755809 Force max component initial, final = 67.053369 0.044609984 Final line search alpha, max atom move = 1.0000000 0.044609984 Iterations, force evaluations = 115 219 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8833 | 1.8833 | 1.8833 | 0.0 | 96.45 Neigh | 0.01567 | 0.01567 | 0.01567 | 0.0 | 0.80 Comm | 0.02354 | 0.02354 | 0.02354 | 0.0 | 1.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03003 | | | 1.54 Nlocal: 1196.00 ave 1196 max 1196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4692.00 ave 4692 max 4692 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: 78588.0 ave 78588 max 78588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78588 Ave neighs/atom = 65.709030 Neighbor list builds = 1 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 115 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.609 | 4.609 | 4.609 Mbytes Step Temp E_pair E_mol TotEng Press Volume 115 0 -5095.39 0 -5095.39 2713.2271 14183.943 117 0 -5095.4149 0 -5095.4149 -0.80793863 14207.012 Loop time of 0.0453878 on 1 procs for 2 steps with 1196 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 = -5095.39001158668 -5095.41293405404 -5095.41487850819 Force two-norm initial, final = 43.763852 0.55036178 Force max component initial, final = 35.084238 0.36121201 Final line search alpha, max atom move = 0.00015976199 5.7707949e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.04287 | 0.04287 | 0.04287 | 0.0 | 94.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049601 | 0.00049601 | 0.00049601 | 0.0 | 1.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002022 | | | 4.45 Nlocal: 1196.00 ave 1196 max 1196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4860.00 ave 4860 max 4860 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: 78308.0 ave 78308 max 78308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78308 Ave neighs/atom = 65.474916 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.747 | 4.747 | 4.747 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5095.4149 0 -5095.4149 -0.80793863 Loop time of 7.037e-06 on 1 procs for 0 steps with 1196 atoms 170.5% 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 | | 7.037e-06 | | |100.00 Nlocal: 1196.00 ave 1196 max 1196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4860.00 ave 4860 max 4860 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: 78260.0 ave 78260 max 78260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78260 Ave neighs/atom = 65.434783 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.747 | 4.747 | 4.747 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 -5095.4149 -5095.4149 20.299431 99.537705 7.0312294 -0.80793863 -0.80793863 40.746165 -5.2206376 -37.949343 2.2689091 752.00571 Loop time of 7.006e-06 on 1 procs for 0 steps with 1196 atoms 256.9% 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 | | 7.006e-06 | | |100.00 Nlocal: 1196.00 ave 1196 max 1196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4860.00 ave 4860 max 4860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39130.0 ave 39130 max 39130 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 78260.0 ave 78260 max 78260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78260 Ave neighs/atom = 65.434783 Neighbor list builds = 0 Dangerous builds = 0 1196 -5095.41475890819 eV 2.26890912782312 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02