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 = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -43.898476 0.0000000) to (35.840000 43.898476 8.8681001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1200000 5.0762759 5.9120667 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -43.898476 0.0000000) to (35.840000 43.898476 8.8681001) create_atoms CPU = 0.002 seconds 1184 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1200000 5.0762759 5.9120667 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -43.898476 0.0000000) to (35.840000 43.898476 8.8681001) create_atoms CPU = 0.001 seconds 1184 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 ghost atom cutoff = 6 binsize = 3, bins = 12 30 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 48 atoms, new total = 2320 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_390178379548_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 12 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.130 | 5.130 | 5.130 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8121.969 0 -8121.969 2646.4919 50 0 -8177.1947 0 -8177.1947 -10035.162 Loop time of 3.18713 on 1 procs for 50 steps with 2320 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 = -8121.96902933901 -8177.18806380977 -8177.19472393315 Force two-norm initial, final = 55.029875 0.26964769 Force max component initial, final = 9.2037784 0.035616025 Final line search alpha, max atom move = 1.0000000 0.035616025 Iterations, force evaluations = 50 94 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1723 | 3.1723 | 3.1723 | 0.0 | 99.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0057896 | 0.0057896 | 0.0057896 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009085 | | | 0.29 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6198.00 ave 6198 max 6198 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: 178288.0 ave 178288 max 178288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178288 Ave neighs/atom = 76.848276 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 12 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.128 | 5.128 | 5.128 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -8177.1947 0 -8177.1947 -10035.162 27904.743 54 0 -8177.7364 0 -8177.7364 -1237.8742 27729.159 Loop time of 0.203329 on 1 procs for 4 steps with 2320 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 = -8177.19472393317 -8177.73417990719 -8177.73640996672 Force two-norm initial, final = 242.61322 2.5642871 Force max component initial, final = 176.41438 2.0918013 Final line search alpha, max atom move = 7.7857538e-05 0.00016286250 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20124 | 0.20124 | 0.20124 | 0.0 | 98.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028564 | 0.00028564 | 0.00028564 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001801 | | | 0.89 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5897.00 ave 5897 max 5897 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: 178720.0 ave 178720 max 178720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178720 Ave neighs/atom = 77.034483 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 ghost atom cutoff = 6 binsize = 3, bins = 12 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.266 | 5.266 | 5.266 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8177.7364 0 -8177.7364 -1237.8742 Loop time of 1.649e-06 on 1 procs for 0 steps with 2320 atoms 121.3% 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 | | 1.649e-06 | | |100.00 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5905.00 ave 5905 max 5905 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: 178768.0 ave 178768 max 178768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178768 Ave neighs/atom = 77.055172 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 ghost atom cutoff = 6 binsize = 3, bins = 12 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.266 | 5.266 | 5.266 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 -8177.7364 -8177.7364 35.727187 87.796953 8.8401258 -1237.8742 -1237.8742 -80.665607 -3753.4391 120.48194 2.2779362 1540.8697 Loop time of 1.883e-06 on 1 procs for 0 steps with 2320 atoms 159.3% 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 | | 1.883e-06 | | |100.00 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5905.00 ave 5905 max 5905 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 89384.0 ave 89384 max 89384 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 178768.0 ave 178768 max 178768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178768 Ave neighs/atom = 77.055172 Neighbor list builds = 0 Dangerous builds = 0 2320 -8177.73640996672 eV 2.27793615513924 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03