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 = 4.0320382 4.0320382 4.0320382 Created orthogonal box = (0.0000000 -41.118883 0.0000000) to (20.559442 41.118883 4.0320382) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7444865 4.7444865 4.0320382 Created 208 atoms using lattice units in orthogonal box = (0.0000000 -41.118883 0.0000000) to (20.559442 41.118883 4.0320382) create_atoms CPU = 0.001 seconds 208 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7444865 4.7444865 4.0320382 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -41.118883 0.0000000) to (20.559442 41.118883 4.0320382) create_atoms CPU = 0.001 seconds 210 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 5 19 1 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 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 416 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_019873715786_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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 4.479 | 4.479 | 4.479 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1355.5309 0 -1355.5309 10106.031 69 0 -1392.1983 0 -1392.1983 5865.5987 Loop time of 1.21388 on 1 procs for 69 steps with 416 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1355.53092105847 -1392.19712529009 -1392.19834842237 Force two-norm initial, final = 29.456916 0.10805387 Force max component initial, final = 6.8027444 0.020030444 Final line search alpha, max atom move = 1.0000000 0.020030444 Iterations, force evaluations = 69 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1812 | 1.1812 | 1.1812 | 0.0 | 97.31 Neigh | 0.0098855 | 0.0098855 | 0.0098855 | 0.0 | 0.81 Comm | 0.013002 | 0.013002 | 0.013002 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009824 | | | 0.81 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4219.00 ave 4219 max 4219 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: 72032.0 ave 72032 max 72032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72032 Ave neighs/atom = 173.15385 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.479 | 4.479 | 4.479 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -1392.1983 0 -1392.1983 5865.5987 6817.2192 73 0 -1392.2868 0 -1392.2868 -1.9562365 6864.4542 Loop time of 0.0637486 on 1 procs for 4 steps with 416 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1392.19834842237 -1392.28576089104 -1392.28675470337 Force two-norm initial, final = 43.383682 0.17065877 Force max component initial, final = 26.862302 0.089582192 Final line search alpha, max atom move = 0.00047800996 4.2821180e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.061193 | 0.061193 | 0.061193 | 0.0 | 95.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00064009 | 0.00064009 | 0.00064009 | 0.0 | 1.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001916 | | | 3.00 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4214.00 ave 4214 max 4214 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: 72080.0 ave 72080 max 72080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72080 Ave neighs/atom = 173.26923 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 4.617 | 4.617 | 4.617 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1392.2868 0 -1392.2868 -1.9562365 Loop time of 6.886e-06 on 1 procs for 0 steps with 416 atoms 159.7% 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 | | 6.886e-06 | | |100.00 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4214.00 ave 4214 max 4214 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: 71924.0 ave 71924 max 71924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71924 Ave neighs/atom = 172.89423 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 4.617 | 4.617 | 4.617 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 -1392.2868 -1392.2868 20.581763 82.489555 4.0431932 -1.9562365 -1.9562365 3.2555406 11.842247 -20.966497 2.6137896 232.75322 Loop time of 7.067e-06 on 1 procs for 0 steps with 416 atoms 212.3% 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 | | 7.067e-06 | | |100.00 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4214.00 ave 4214 max 4214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35962.0 ave 35962 max 35962 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 71924.0 ave 71924 max 71924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71924 Ave neighs/atom = 172.89423 Neighbor list builds = 0 Dangerous builds = 0 416 -1392.28675470337 eV 2.61378956761973 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01