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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -74.583721 0.0000000) to (37.289838 74.583721 4.0446508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7031517 5.7031517 4.0446508 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -74.583721 0.0000000) to (37.289838 74.583721 4.0446508) create_atoms CPU = 0.003 seconds 682 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7031517 5.7031517 4.0446508 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -74.583721 0.0000000) to (37.289838 74.583721 4.0446508) create_atoms CPU = 0.002 seconds 682 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 43 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1356 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_478967255435_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.058 | 5.058 | 5.058 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4521.8816 0 -4521.8816 5216.9477 81 0 -4550.1318 0 -4550.1318 -944.48189 Loop time of 20.3522 on 1 procs for 81 steps with 1356 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 = -4521.88158932372 -4550.12730877019 -4550.13177207045 Force two-norm initial, final = 20.375275 0.18142620 Force max component initial, final = 5.2642359 0.037412139 Final line search alpha, max atom move = 1.0000000 0.037412139 Iterations, force evaluations = 81 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.272 | 20.272 | 20.272 | 0.0 | 99.60 Neigh | 0.035773 | 0.035773 | 0.035773 | 0.0 | 0.18 Comm | 0.021943 | 0.021943 | 0.021943 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02279 | | | 0.11 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6804.00 ave 6804 max 6804 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: 107824.0 ave 107824 max 107824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107824 Ave neighs/atom = 79.516224 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.058 | 5.058 | 5.058 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -4550.1318 0 -4550.1318 -944.48189 22498.086 83 0 -4550.1419 0 -4550.1419 -53.196899 22472.651 Loop time of 0.822125 on 1 procs for 2 steps with 1356 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 = -4550.13177207045 -4550.14074986722 -4550.14189453835 Force two-norm initial, final = 20.501780 0.18235532 Force max component initial, final = 17.961431 0.035397605 Final line search alpha, max atom move = 0.00029856854 1.0568611e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.81866 | 0.81866 | 0.81866 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00075488 | 0.00075488 | 0.00075488 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002715 | | | 0.33 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6800.00 ave 6800 max 6800 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: 107856.0 ave 107856 max 107856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107856 Ave neighs/atom = 79.539823 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.196 | 5.196 | 5.196 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4550.1419 0 -4550.1419 -53.196899 Loop time of 6.184e-06 on 1 procs for 0 steps with 1356 atoms 177.9% 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 | | 6.184e-06 | | |100.00 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6800.00 ave 6800 max 6800 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: 108464.0 ave 108464 max 108464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108464 Ave neighs/atom = 79.988201 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.196 | 5.196 | 5.196 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 -4550.1419 -4550.1419 37.289407 149.16744 4.0401249 -53.196899 -53.196899 -1.3532608 -158.4485 0.21106542 2.5555393 173.8238 Loop time of 6.476e-06 on 1 procs for 0 steps with 1356 atoms 324.3% 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 | | 6.476e-06 | | |100.00 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6800.00 ave 6800 max 6800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54232.0 ave 54232 max 54232 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 108464.0 ave 108464 max 108464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108464 Ave neighs/atom = 79.988201 Neighbor list builds = 0 Dangerous builds = 0 1356 -4550.14189453835 eV 2.55553925519342 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22