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 = 3.5181212 3.5181212 3.5181212 Created orthogonal box = (0.0000000 -65.254947 0.0000000) to (23.069864 65.254947 4.9753748) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9015931 6.0699003 4.9753748 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -65.254947 0.0000000) to (23.069864 65.254947 4.9753748) create_atoms CPU = 0.002 seconds 690 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9015931 6.0699003 4.9753748 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -65.254947 0.0000000) to (23.069864 65.254947 4.9753748) create_atoms CPU = 0.002 seconds 690 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 6 31 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 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1368 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_222110751402_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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 6 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 5.949 | 5.949 | 5.949 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5959.0718 0 -5959.0718 8557.7703 75 0 -5987.8264 0 -5987.8264 -6191.8812 Loop time of 2.66791 on 1 procs for 75 steps with 1368 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 = -5959.07181124446 -5987.8213711045 -5987.82640778186 Force two-norm initial, final = 76.742480 0.25689087 Force max component initial, final = 24.371418 0.045804395 Final line search alpha, max atom move = 1.0000000 0.045804395 Iterations, force evaluations = 75 138 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6283 | 2.6283 | 2.6283 | 0.0 | 98.51 Neigh | 0.017849 | 0.017849 | 0.017849 | 0.0 | 0.67 Comm | 0.012676 | 0.012676 | 0.012676 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0091 | | | 0.34 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10836.0 ave 10836 max 10836 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: 337572.0 ave 337572 max 337572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 337572 Ave neighs/atom = 246.76316 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 6 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.951 | 5.951 | 5.951 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -5987.8264 0 -5987.8264 -6191.8812 14980.085 77 0 -5987.8444 0 -5987.8444 -4126.4824 14962.367 Loop time of 0.0983073 on 1 procs for 2 steps with 1368 atoms 98.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5987.82640778182 -5987.84333158789 -5987.8444295429 Force two-norm initial, final = 35.657148 0.25827137 Force max component initial, final = 32.312220 0.045066177 Final line search alpha, max atom move = 0.00018041047 8.1304100e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.096304 | 0.096304 | 0.096304 | 0.0 | 97.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042897 | 0.00042897 | 0.00042897 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001574 | | | 1.60 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10944.0 ave 10944 max 10944 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: 338068.0 ave 338068 max 338068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338068 Ave neighs/atom = 247.12573 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 6 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 6.089 | 6.089 | 6.089 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5987.8444 0 -5987.8444 -4126.4824 Loop time of 1.657e-06 on 1 procs for 0 steps with 1368 atoms 120.7% 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 | | 1.657e-06 | | |100.00 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10944.0 ave 10944 max 10944 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: 338132.0 ave 338132 max 338132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338132 Ave neighs/atom = 247.17251 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 6 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 6.089 | 6.089 | 6.089 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 -5987.8444 -5987.8444 23.066853 130.50989 4.9701388 -4126.4824 -4126.4824 -1.2427093 -12377.917 -0.28765636 2.2804195 355.3652 Loop time of 1.933e-06 on 1 procs for 0 steps with 1368 atoms 206.9% 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 | | 1.933e-06 | | |100.00 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10944.0 ave 10944 max 10944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 169066.0 ave 169066 max 169066 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 338132.0 ave 338132 max 338132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338132 Ave neighs/atom = 247.17251 Neighbor list builds = 0 Dangerous builds = 0 1368 -5987.8444295429 eV 2.28041952701802 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03