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 = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -47.272260 0.0000000) to (22.284357 47.272260 5.1123821) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6914436 5.8053653 5.1123821 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -47.272260 0.0000000) to (22.284357 47.272260 5.1123821) create_atoms CPU = 0.004 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6914436 5.8053653 5.1123821 Created 464 atoms using lattice units in orthogonal box = (0.0000000 -47.272260 0.0000000) to (22.284357 47.272260 5.1123821) create_atoms CPU = 0.003 seconds 464 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 7 30 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 6.4274528135 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 912 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_179025990738_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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 7 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 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) = 4.588 | 4.588 | 4.588 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3166.8553 0 -3166.8553 9665.6184 36 0 -3195.2246 0 -3195.2246 12551 Loop time of 0.686434 on 1 procs for 36 steps with 912 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 = -3166.85529363434 -3195.22160319621 -3195.22457664237 Force two-norm initial, final = 34.389896 0.17629766 Force max component initial, final = 6.2835400 0.028258742 Final line search alpha, max atom move = 1.0000000 0.028258742 Iterations, force evaluations = 36 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.66749 | 0.66749 | 0.66749 | 0.0 | 97.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010244 | 0.010244 | 0.010244 | 0.0 | 1.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008701 | | | 1.27 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4786.00 ave 4786 max 4786 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: 78880.0 ave 78880 max 78880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78880 Ave neighs/atom = 86.491228 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 7 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.590 | 4.590 | 4.590 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -3195.2246 0 -3195.2246 12551 10771.093 45 0 -3195.7992 0 -3195.7992 -201.20634 10857.373 Loop time of 0.106666 on 1 procs for 9 steps with 912 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 = -3195.22457664237 -3195.79872555759 -3195.79921288633 Force two-norm initial, final = 167.48387 3.0435228 Force max component initial, final = 148.23145 2.5994257 Final line search alpha, max atom move = 0.00038467304 0.00099992898 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.099647 | 0.099647 | 0.099647 | 0.0 | 93.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014601 | 0.0014601 | 0.0014601 | 0.0 | 1.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005559 | | | 5.21 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5017.00 ave 5017 max 5017 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: 77984.0 ave 77984 max 77984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77984 Ave neighs/atom = 85.508772 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 7 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 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) = 4.728 | 4.728 | 4.728 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3195.7992 0 -3195.7992 -201.20634 Loop time of 6.334e-06 on 1 procs for 0 steps with 912 atoms 205.2% 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 | | 6.334e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5034.00 ave 5034 max 5034 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: 77952.0 ave 77952 max 77952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77952 Ave neighs/atom = 85.473684 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 7 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 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) = 4.728 | 4.728 | 4.728 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 -3195.7992 -3195.7992 22.303345 95.302468 5.107997 -201.20634 -201.20634 -383.91305 -229.6624 9.9564365 2.3274347 353.03288 Loop time of 9.422e-06 on 1 procs for 0 steps with 912 atoms 180.4% 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 | | 9.422e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5034.00 ave 5034 max 5034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38976.0 ave 38976 max 38976 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 77952.0 ave 77952 max 77952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77952 Ave neighs/atom = 85.473684 Neighbor list builds = 0 Dangerous builds = 0 912 -3195.79921288633 eV 2.32743467782834 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01