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 = 3.5184747 3.5184747 3.5184747 Created orthogonal box = (0.0000000 -49.758746 0.0000000) to (24.879373 49.758746 3.5184747) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9806997 3.9806997 3.5184747 Created 400 atoms using lattice units in orthogonal box = (0.0000000 -49.758746 0.0000000) to (24.879373 49.758746 3.5184747) create_atoms CPU = 0.001 seconds 400 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9806997 3.9806997 3.5184747 Created 402 atoms using lattice units in orthogonal box = (0.0000000 -49.758746 0.0000000) to (24.879373 49.758746 3.5184747) create_atoms CPU = 0.000 seconds 402 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 = 7 25 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 800 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_922363340570_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 = 7 25 1 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) = 4.996 | 4.996 | 4.996 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2843.8447 0 -2843.8447 185620.38 50 0 -3463.7763 0 -3463.7763 5139.0342 Loop time of 0.966048 on 1 procs for 50 steps with 800 atoms 78.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2843.84470992583 -3463.77326272398 -3463.77634944988 Force two-norm initial, final = 1465.8452 0.20562935 Force max component initial, final = 434.42136 0.025171184 Final line search alpha, max atom move = 1.0000000 0.025171184 Iterations, force evaluations = 50 94 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.95442 | 0.95442 | 0.95442 | 0.0 | 98.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.007026 | 0.007026 | 0.007026 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004604 | | | 0.48 Nlocal: 800.000 ave 800 max 800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7650.00 ave 7650 max 7650 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: 159864.0 ave 159864 max 159864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159864 Ave neighs/atom = 199.83000 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 7 25 1 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 : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.001 | 5.001 | 5.001 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -3463.7763 0 -3463.7763 5139.0342 8711.5067 52 0 -3463.8179 0 -3463.8179 -594.35903 8738.0147 Loop time of 0.0341298 on 1 procs for 2 steps with 800 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 = -3463.77634944986 -3463.81575227149 -3463.81791793661 Force two-norm initial, final = 48.979229 6.6344970 Force max component initial, final = 33.514855 5.6706317 Final line search alpha, max atom move = 0.00014436523 0.00081864204 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.032886 | 0.032886 | 0.032886 | 0.0 | 96.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025591 | 0.00025591 | 0.00025591 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009875 | | | 2.89 Nlocal: 800.000 ave 800 max 800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8314.00 ave 8314 max 8314 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: 158760.0 ave 158760 max 158760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158760 Ave neighs/atom = 198.45000 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 = 7 25 1 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) = 5.139 | 5.139 | 5.139 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3463.8179 0 -3463.8179 -594.35903 Loop time of 1.819e-06 on 1 procs for 0 steps with 800 atoms 164.9% 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 | | 1.819e-06 | | |100.00 Nlocal: 800.000 ave 800 max 800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8302.00 ave 8302 max 8302 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: 158680.0 ave 158680 max 158680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158680 Ave neighs/atom = 198.35000 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 = 7 25 1 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) = 5.139 | 5.139 | 5.139 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 -3463.8179 -3463.8179 24.90343 99.670891 3.5203453 -594.35903 -594.35903 -618.35826 -124.41579 -1040.303 2.2237999 187.87318 Loop time of 2.145e-06 on 1 procs for 0 steps with 800 atoms 186.5% 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 | | 2.145e-06 | | |100.00 Nlocal: 800.000 ave 800 max 800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8302.00 ave 8302 max 8302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79340.0 ave 79340 max 79340 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 158680.0 ave 158680 max 158680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158680 Ave neighs/atom = 198.35000 Neighbor list builds = 0 Dangerous builds = 0 800 -3463.81791793661 eV 2.2237999177148 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01