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 = 3.6284291 3.6284291 3.6284291 Created orthogonal box = (0.0000000 -41.050989 0.0000000) to (5.1313736 41.050989 3.6284291) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1313736 5.1313736 3.6284291 Created 64 atoms using lattice units in orthogonal box = (0.0000000 -41.050989 0.0000000) to (5.1313736 41.050989 3.6284291) create_atoms CPU = 0.002 seconds 64 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1313736 5.1313736 3.6284291 Created 66 atoms using lattice units in orthogonal box = (0.0000000 -41.050989 0.0000000) to (5.1313736 41.050989 3.6284291) create_atoms CPU = 0.001 seconds 66 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 2 22 1 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 7.549891471862793 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 130 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_650279905230_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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 2 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 4.422 | 4.422 | 4.422 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -188.5348 0 -188.5348 508269.59 133 0 -545.81071 0 -545.81071 6364.5273 Loop time of 0.66378 on 1 procs for 133 steps with 130 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 = -188.534796728624 -545.810231650599 -545.810714788703 Force two-norm initial, final = 1415.2229 0.070127739 Force max component initial, final = 697.59784 0.011827141 Final line search alpha, max atom move = 1.0000000 0.011827141 Iterations, force evaluations = 133 253 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.63675 | 0.63675 | 0.63675 | 0.0 | 95.93 Neigh | 0.0031125 | 0.0031125 | 0.0031125 | 0.0 | 0.47 Comm | 0.015017 | 0.015017 | 0.015017 | 0.0 | 2.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008903 | | | 1.34 Nlocal: 130.000 ave 130 max 130 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3012.00 ave 3012 max 3012 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: 19668.0 ave 19668 max 19668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19668 Ave neighs/atom = 151.29231 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 2 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 133 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.424 | 4.424 | 4.424 Mbytes Step Temp E_pair E_mol TotEng Press Volume 133 0 -545.81071 0 -545.81071 6364.5273 1528.6423 577 0 -554.29427 0 -554.29427 335.49877 1528.7096 Loop time of 1.62773 on 1 procs for 444 steps with 130 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 = -545.810714788703 -554.293722903094 -554.294266774806 Force two-norm initial, final = 81.030822 0.96359871 Force max component initial, final = 71.671307 0.66464467 Final line search alpha, max atom move = 0.0011086522 0.00073685978 Iterations, force evaluations = 444 503 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.472 | 1.472 | 1.472 | 0.0 | 90.43 Neigh | 0.015247 | 0.015247 | 0.015247 | 0.0 | 0.94 Comm | 0.033103 | 0.033103 | 0.033103 | 0.0 | 2.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1074 | | | 6.60 Nlocal: 130.000 ave 130 max 130 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2848.00 ave 2848 max 2848 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: 20688.0 ave 20688 max 20688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20688 Ave neighs/atom = 159.13846 Neighbor list builds = 5 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 2 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 4.550 | 4.550 | 4.550 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -554.29427 0 -554.29427 335.49877 Loop time of 6.475e-06 on 1 procs for 0 steps with 130 atoms 169.9% 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 | | 6.475e-06 | | |100.00 Nlocal: 130.000 ave 130 max 130 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2844.00 ave 2844 max 2844 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: 20688.0 ave 20688 max 20688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20688 Ave neighs/atom = 159.13846 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 2 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 4.550 | 4.550 | 4.550 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 -554.29427 -554.29427 4.9444253 77.107577 4.0097021 335.49877 335.49877 671.20794 41.878729 293.40963 2.4264973 89.67572 Loop time of 6.374e-06 on 1 procs for 0 steps with 130 atoms 251.0% 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 | | 6.374e-06 | | |100.00 Nlocal: 130.000 ave 130 max 130 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2844.00 ave 2844 max 2844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 10344.0 ave 10344 max 10344 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 20688.0 ave 20688 max 20688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20688 Ave neighs/atom = 159.13846 Neighbor list builds = 0 Dangerous builds = 0 130 -554.294235780391 eV 2.42649730677924 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02