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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -56.305250 0.0000000) to (28.150823 56.305250 3.6043435) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0763779 5.0763779 3.6043435 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -56.305250 0.0000000) to (28.150823 56.305250 3.6043435) create_atoms CPU = 0.002 seconds 490 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0763779 5.0763779 3.6043435 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -56.305250 0.0000000) to (28.150823 56.305250 3.6043435) create_atoms CPU = 0.002 seconds 490 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 37 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 974 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.598 | 4.598 | 4.598 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4086.2647 0 -4086.2647 12461.795 108 0 -4129.0725 0 -4129.0725 -1374.2869 Loop time of 16.6743 on 1 procs for 108 steps with 974 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 = -4086.26472458204 -4129.06849458515 -4129.07248646126 Force two-norm initial, final = 30.079445 0.17877413 Force max component initial, final = 8.4199967 0.044504101 Final line search alpha, max atom move = 1.0000000 0.044504101 Iterations, force evaluations = 108 189 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.597 | 16.597 | 16.597 | 0.0 | 99.53 Neigh | 0.025155 | 0.025155 | 0.025155 | 0.0 | 0.15 Comm | 0.027603 | 0.027603 | 0.027603 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02479 | | | 0.15 Nlocal: 974.000 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6006.00 ave 6006 max 6006 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: 75760.0 ave 75760 max 75760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75760 Ave neighs/atom = 77.782341 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 108 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.600 | 4.600 | 4.600 Mbytes Step Temp E_pair E_mol TotEng Press Volume 108 0 -4129.0725 0 -4129.0725 -1374.2869 11426.051 116 0 -4129.2781 0 -4129.2781 -2720.502 11435.279 Loop time of 1.00156 on 1 procs for 8 steps with 974 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4129.07248646126 -4129.27658338978 -4129.27805385891 Force two-norm initial, final = 42.513099 0.33502299 Force max component initial, final = 35.329764 0.067958699 Final line search alpha, max atom move = 0.00035472865 2.4106898e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.99506 | 0.99506 | 0.99506 | 0.0 | 99.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013339 | 0.0013339 | 0.0013339 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005163 | | | 0.52 Nlocal: 974.000 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6003.00 ave 6003 max 6003 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: 75916.0 ave 75916 max 75916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75916 Ave neighs/atom = 77.942505 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.738 | 4.738 | 4.738 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4129.2781 0 -4129.2781 -2720.502 Loop time of 7.106e-06 on 1 procs for 0 steps with 974 atoms 197.0% 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 | | 7.106e-06 | | |100.00 Nlocal: 974.000 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6013.00 ave 6013 max 6013 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: 75868.0 ave 75868 max 75868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75868 Ave neighs/atom = 77.893224 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.738 | 4.738 | 4.738 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 -4129.2781 -4129.2781 27.969228 112.6105 3.6306751 -2720.502 -2720.502 2.6868152 -8163.1659 -1.0269559 2.2919958 160.41303 Loop time of 9.592e-06 on 1 procs for 0 steps with 974 atoms 260.6% 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 | | 9.592e-06 | | |100.00 Nlocal: 974.000 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6013.00 ave 6013 max 6013 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37934.0 ave 37934 max 37934 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75868.0 ave 75868 max 75868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75868 Ave neighs/atom = 77.893224 Neighbor list builds = 0 Dangerous builds = 0 974 -4129.27805385891 eV 2.29199584831004 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18