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 = 3.4301372 3.4301372 3.4301372 Created orthogonal box = (0.0000000 -47.156590 0.0000000) to (12.834398 47.156590 8.4020859) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5004564 5.2396211 5.6013906 Created 503 atoms using lattice units in orthogonal box = (0.0000000 -47.156590 0.0000000) to (12.834398 47.156590 8.4020859) create_atoms CPU = 0.002 seconds 503 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5004564 5.2396211 5.6013906 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -47.156590 0.0000000) to (12.834398 47.156590 8.4020859) create_atoms CPU = 0.001 seconds 507 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 24 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 1003 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_044341472608_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.490 | 5.490 | 5.490 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3774.3701 0 -3774.3701 88037.533 79 0 -3995.4157 0 -3995.4157 30481.848 Loop time of 1.47304 on 1 procs for 79 steps with 1003 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3774.37009374615 -3995.4118679521 -3995.41574018839 Force two-norm initial, final = 589.46752 0.27360102 Force max component initial, final = 128.47557 0.072853855 Final line search alpha, max atom move = 1.0000000 0.072853855 Iterations, force evaluations = 79 149 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4471 | 1.4471 | 1.4471 | 0.0 | 98.24 Neigh | 0.01125 | 0.01125 | 0.01125 | 0.0 | 0.76 Comm | 0.0077216 | 0.0077216 | 0.0077216 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006988 | | | 0.47 Nlocal: 1003.00 ave 1003 max 1003 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6668.00 ave 6668 max 6668 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: 202834.0 ave 202834 max 202834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202834 Ave neighs/atom = 202.22732 Neighbor list builds = 1 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.488 | 5.488 | 5.488 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -3995.4157 0 -3995.4157 30481.848 10170.329 87 0 -3996.5082 0 -3996.5082 -14.717539 10243.973 Loop time of 0.109508 on 1 procs for 8 steps with 1003 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 = -3995.41574018839 -3996.50805533591 -3996.50820463284 Force two-norm initial, final = 363.86779 0.86855887 Force max component initial, final = 308.78585 0.12579089 Final line search alpha, max atom move = 0.00028219772 3.5497902e-05 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10652 | 0.10652 | 0.10652 | 0.0 | 97.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00051754 | 0.00051754 | 0.00051754 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002467 | | | 2.25 Nlocal: 1003.00 ave 1003 max 1003 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6531.00 ave 6531 max 6531 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: 201190.0 ave 201190 max 201190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201190 Ave neighs/atom = 200.58824 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.626 | 5.626 | 5.626 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3996.5082 0 -3996.5082 -14.717539 Loop time of 2.203e-06 on 1 procs for 0 steps with 1003 atoms 181.6% 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 | | 2.203e-06 | | |100.00 Nlocal: 1003.00 ave 1003 max 1003 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6528.00 ave 6528 max 6528 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: 199894.0 ave 199894 max 199894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199894 Ave neighs/atom = 199.29611 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.626 | 5.626 | 5.626 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 -3996.5082 -3996.5082 12.839932 94.964829 8.4012304 -14.717539 -14.717539 -19.682413 -18.40355 -6.0666541 2.1796834 620.18334 Loop time of 2.356e-06 on 1 procs for 0 steps with 1003 atoms 169.8% 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 | | 2.356e-06 | | |100.00 Nlocal: 1003.00 ave 1003 max 1003 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6528.00 ave 6528 max 6528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 99947.0 ave 99947 max 99947 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 199894.0 ave 199894 max 199894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199894 Ave neighs/atom = 199.29611 Neighbor list builds = 0 Dangerous builds = 0 1003 -3996.50820463284 eV 2.17968338260463 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01