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 -38.167047 0.0000000) to (46.744894 38.167047 8.9139016) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9493502 5.5515704 5.9426011 Created 1317 atoms using lattice units in orthogonal box = (0.0000000 -38.167047 0.0000000) to (46.744894 38.167047 8.9139016) create_atoms CPU = 0.002 seconds 1317 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9493502 5.5515704 5.9426011 Created 1323 atoms using lattice units in orthogonal box = (0.0000000 -38.167047 0.0000000) to (46.744894 38.167047 8.9139016) create_atoms CPU = 0.002 seconds 1323 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 = 10 16 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 0 atoms, new total = 2640 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_600021860456_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 = 10 16 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) = 8.144 | 8.144 | 8.144 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7986.2862 0 -7986.2862 82993.394 59 0 -8620.4867 0 -8620.4867 7087.7362 Loop time of 4.32659 on 1 procs for 59 steps with 2640 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7986.28616811111 -8620.47915993837 -8620.4867063671 Force two-norm initial, final = 865.19597 0.22561224 Force max component initial, final = 174.65511 0.013441629 Final line search alpha, max atom move = 1.0000000 0.013441629 Iterations, force evaluations = 59 94 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1898 | 4.1898 | 4.1898 | 0.0 | 96.84 Neigh | 0.096429 | 0.096429 | 0.096429 | 0.0 | 2.23 Comm | 0.021481 | 0.021481 | 0.021481 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01891 | | | 0.44 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11989.0 ave 11989 max 11989 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: 837396.0 ave 837396 max 837396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 837396 Ave neighs/atom = 317.19545 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 = 10 16 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 : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.142 | 8.142 | 8.142 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -8620.4867 0 -8620.4867 7087.7362 31806.843 66 0 -8621.2313 0 -8621.2313 -157.15982 31966.41 Loop time of 0.400745 on 1 procs for 7 steps with 2640 atoms 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8620.48670636701 -8621.23021346575 -8621.2313334025 Force two-norm initial, final = 282.32193 5.9768900 Force max component initial, final = 257.00404 4.3653143 Final line search alpha, max atom move = 0.00011626322 0.00050752547 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39435 | 0.39435 | 0.39435 | 0.0 | 98.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00091346 | 0.00091346 | 0.00091346 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005481 | | | 1.37 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11809.0 ave 11809 max 11809 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: 837636.0 ave 837636 max 837636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 837636 Ave neighs/atom = 317.28636 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 = 10 17 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) = 8.280 | 8.280 | 8.280 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8621.2313 0 -8621.2313 -157.15982 Loop time of 2.157e-06 on 1 procs for 0 steps with 2640 atoms 231.8% 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 | | 2.157e-06 | | |100.00 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11792.0 ave 11792 max 11792 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: 836290.0 ave 836290 max 836290 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 836290 Ave neighs/atom = 316.77652 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 = 10 17 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) = 8.280 | 8.280 | 8.280 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 -8621.2313 -8621.2313 46.726529 76.811185 8.9064756 -157.15982 -157.15982 -195.16647 -57.702968 -218.61001 2.2643378 1442.8966 Loop time of 2.795e-06 on 1 procs for 0 steps with 2640 atoms 322.0% 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 | | 2.795e-06 | | |100.00 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11792.0 ave 11792 max 11792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 418145.0 ave 418145 max 418145 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 836290.0 ave 836290 max 836290 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 836290 Ave neighs/atom = 316.77652 Neighbor list builds = 0 Dangerous builds = 0 2640 -8621.2313334025 eV 2.26433780531985 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05