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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -53.472188 0.0000000) to (43.659859 53.472188 8.8507796) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3827223 5.1274701 5.9005197 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -53.472188 0.0000000) to (43.659859 53.472188 8.8507796) create_atoms CPU = 0.003 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3827223 5.1274701 5.9005197 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -53.472188 0.0000000) to (43.659859 53.472188 8.8507796) create_atoms CPU = 0.002 seconds 1758 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 16 38 4 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 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3508 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_849011491644_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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 16 38 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 5.226 | 5.226 | 5.226 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11611.814 0 -11611.814 59890.729 100 0 -12369.964 0 -12369.964 8860.6623 Loop time of 19.9136 on 1 procs for 100 steps with 3508 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 = -11611.8142792036 -12369.9541099903 -12369.9640443637 Force two-norm initial, final = 530.68774 0.38973694 Force max component initial, final = 78.806819 0.11992283 Final line search alpha, max atom move = 1.0000000 0.11992283 Iterations, force evaluations = 100 181 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.742 | 19.742 | 19.742 | 0.0 | 99.14 Neigh | 0.080304 | 0.080304 | 0.080304 | 0.0 | 0.40 Comm | 0.032322 | 0.032322 | 0.032322 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0586 | | | 0.29 Nlocal: 3508.00 ave 3508 max 3508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7519.00 ave 7519 max 7519 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: 225624.0 ave 225624 max 225624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225624 Ave neighs/atom = 64.316990 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 16 38 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 100 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.607 | 5.607 | 5.607 Mbytes Step Temp E_pair E_mol TotEng Press Volume 100 0 -12369.964 0 -12369.964 8860.6623 41325.851 109 0 -12371.411 0 -12371.411 28.997477 41580.821 Loop time of 1.30133 on 1 procs for 9 steps with 3508 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 = -12369.9640443637 -12371.4105533081 -12371.4109107189 Force two-norm initial, final = 450.13660 2.8525399 Force max component initial, final = 403.18762 2.6853948 Final line search alpha, max atom move = 0.00013292354 0.00035695219 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2876 | 1.2876 | 1.2876 | 0.0 | 98.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014919 | 0.0014919 | 0.0014919 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01223 | | | 0.94 Nlocal: 3508.00 ave 3508 max 3508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7561.00 ave 7561 max 7561 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: 221816.0 ave 221816 max 221816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 221816 Ave neighs/atom = 63.231471 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 16 38 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 5.745 | 5.745 | 5.745 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12371.411 0 -12371.411 28.997477 Loop time of 4.076e-06 on 1 procs for 0 steps with 3508 atoms 147.2% 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 | | 4.076e-06 | | |100.00 Nlocal: 3508.00 ave 3508 max 3508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7566.00 ave 7566 max 7566 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: 203910.0 ave 203910 max 203910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203910 Ave neighs/atom = 58.127138 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 16 38 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 5.745 | 5.745 | 5.745 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 -12371.411 -12371.411 43.602488 107.79087 8.8470774 28.997477 28.997477 -16.258724 -0.1781799 103.42934 2.2652937 1799.3607 Loop time of 4.418e-06 on 1 procs for 0 steps with 3508 atoms 226.3% 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 | | 4.418e-06 | | |100.00 Nlocal: 3508.00 ave 3508 max 3508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7566.00 ave 7566 max 7566 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101955.0 ave 101955 max 101955 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 203910.0 ave 203910 max 203910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203910 Ave neighs/atom = 58.127138 Neighbor list builds = 0 Dangerous builds = 0 3508 -12371.4109107189 eV 2.26529366525179 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22