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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -39.953426 0.0000000) to (34.597289 39.953426 6.7850866) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2097698 6.1460782 6.7850866 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -39.953426 0.0000000) to (34.597289 39.953426 6.7850866) create_atoms CPU = 0.004 seconds 629 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2097698 6.1460782 6.7850866 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -39.953426 0.0000000) to (34.597289 39.953426 6.7850866) create_atoms CPU = 0.004 seconds 629 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 25 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 27 atoms, new total = 1231 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_020840179467_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.602 | 4.602 | 4.602 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6998.2845 0 -6998.2845 7259.5677 26 0 -7048.0553 0 -7048.0553 -5245.6587 Loop time of 2.19519 on 1 procs for 26 steps with 1231 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 = -6998.28448535852 -7048.04958002456 -7048.05532740654 Force two-norm initial, final = 65.811708 0.32472040 Force max component initial, final = 16.636375 0.067871880 Final line search alpha, max atom move = 1.0000000 0.067871880 Iterations, force evaluations = 26 46 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1841 | 2.1841 | 2.1841 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0044925 | 0.0044925 | 0.0044925 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006606 | | | 0.30 Nlocal: 1231.00 ave 1231 max 1231 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3964.00 ave 3964 max 3964 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: 94496.0 ave 94496 max 94496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94496 Ave neighs/atom = 76.763607 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.602 | 4.602 | 4.602 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -7048.0553 0 -7048.0553 -5245.6587 18757.782 29 0 -7048.1167 0 -7048.1167 -1974.4737 18722.15 Loop time of 0.276736 on 1 procs for 3 steps with 1231 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7048.05532740652 -7048.11600527378 -7048.11669608248 Force two-norm initial, final = 73.669336 0.34676772 Force max component initial, final = 69.045639 0.068585166 Final line search alpha, max atom move = 0.00015149947 1.0390617e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27405 | 0.27405 | 0.27405 | 0.0 | 99.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049851 | 0.00049851 | 0.00049851 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002184 | | | 0.79 Nlocal: 1231.00 ave 1231 max 1231 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3982.00 ave 3982 max 3982 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: 94640.0 ave 94640 max 94640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94640 Ave neighs/atom = 76.880585 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.740 | 4.740 | 4.740 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7048.1167 0 -7048.1167 -1974.4737 Loop time of 6.495e-06 on 1 procs for 0 steps with 1231 atoms 184.8% 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 | | 6.495e-06 | | |100.00 Nlocal: 1231.00 ave 1231 max 1231 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3982.00 ave 3982 max 3982 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: 94658.0 ave 94658 max 94658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94658 Ave neighs/atom = 76.895207 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.740 | 4.740 | 4.740 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 -7048.1167 -7048.1167 34.590281 79.906851 6.7735697 -1974.4737 -1974.4737 -4.8136964 -5915.9713 -2.6362689 2.497581 1103.2615 Loop time of 7.087e-06 on 1 procs for 0 steps with 1231 atoms 268.1% 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 | | 7.087e-06 | | |100.00 Nlocal: 1231.00 ave 1231 max 1231 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3982.00 ave 3982 max 3982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47329.0 ave 47329 max 47329 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 94658.0 ave 94658 max 94658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94658 Ave neighs/atom = 76.895207 Neighbor list builds = 0 Dangerous builds = 0 1231 -7048.11669608248 eV 2.49758103710818 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03