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 = 3.6390851 3.6390851 3.6390851 Created orthogonal box = (0.0000000 -64.279059 0.0000000) to (37.111532 64.279059 6.3030803) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7094664 5.7686335 6.3030803 Created 1245 atoms using lattice units in orthogonal box = (0.0000000 -64.279059 0.0000000) to (37.111532 64.279059 6.3030803) create_atoms CPU = 0.002 seconds 1245 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7094664 5.7686335 6.3030803 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -64.279059 0.0000000) to (37.111532 64.279059 6.3030803) create_atoms CPU = 0.002 seconds 1249 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 27 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 2493 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_120596890176_005#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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 12.01 | 12.01 | 12.01 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7801.4876 0 -7801.4876 44733.246 49 0 -8155.5401 0 -8155.5401 3591.7576 Loop time of 3.49082 on 1 procs for 49 steps with 2493 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 = -7801.48764407905 -8155.53261501234 -8155.54005637943 Force two-norm initial, final = 746.93276 0.20860230 Force max component initial, final = 248.60381 0.018580473 Final line search alpha, max atom move = 1.0000000 0.018580473 Iterations, force evaluations = 49 82 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3822 | 3.3822 | 3.3822 | 0.0 | 96.89 Neigh | 0.081092 | 0.081092 | 0.081092 | 0.0 | 2.32 Comm | 0.015447 | 0.015447 | 0.015447 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01208 | | | 0.35 Nlocal: 2493.00 ave 2493 max 2493 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14855.0 ave 14855 max 14855 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: 792204.0 ave 792204 max 792204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 792204 Ave neighs/atom = 317.77136 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.01 | 12.01 | 12.01 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -8155.5401 0 -8155.5401 3591.7576 30071.925 53 0 -8155.7295 0 -8155.7295 -39.092205 30148.203 Loop time of 0.246215 on 1 procs for 4 steps with 2493 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 = -8155.54005637944 -8155.72830138138 -8155.72952429205 Force two-norm initial, final = 137.51480 2.7451059 Force max component initial, final = 126.44892 2.6891280 Final line search alpha, max atom move = 8.8780608e-05 0.00023874241 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24238 | 0.24238 | 0.24238 | 0.0 | 98.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00071089 | 0.00071089 | 0.00071089 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003122 | | | 1.27 Nlocal: 2493.00 ave 2493 max 2493 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14835.0 ave 14835 max 14835 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: 792392.0 ave 792392 max 792392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 792392 Ave neighs/atom = 317.84677 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 11.52 | 11.52 | 11.52 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8155.7295 0 -8155.7295 -39.092205 Loop time of 1.924e-06 on 1 procs for 0 steps with 2493 atoms 155.9% 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 | | 1.924e-06 | | |100.00 Nlocal: 2493.00 ave 2493 max 2493 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14839.0 ave 14839 max 14839 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: 792146.0 ave 792146 max 792146 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 792146 Ave neighs/atom = 317.74809 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 11.52 | 11.52 | 11.52 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 -8155.7295 -8155.7295 37.087829 128.9644 6.3031869 -39.092205 -39.092205 -142.81799 0.55025595 24.991124 2.1916804 981.13185 Loop time of 2.452e-06 on 1 procs for 0 steps with 2493 atoms 285.5% 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 | | 2.452e-06 | | |100.00 Nlocal: 2493.00 ave 2493 max 2493 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14839.0 ave 14839 max 14839 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 396073.0 ave 396073 max 396073 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 792146.0 ave 792146 max 792146 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 792146 Ave neighs/atom = 317.74809 Neighbor list builds = 0 Dangerous builds = 0 2493 -8155.72952429205 eV 2.19168043087636 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04