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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -40.787212 0.0000000) to (23.546691 40.787212 5.4500000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0457195 4.8552459 5.4500000 Created 340 atoms using lattice units in orthogonal box = (0.0000000 -40.787212 0.0000000) to (23.546691 40.787212 5.4500000) create_atoms CPU = 0.003 seconds 340 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0457195 4.8552459 5.4500000 Created 339 atoms using lattice units in orthogonal box = (0.0000000 -40.787212 0.0000000) to (23.546691 40.787212 5.4500000) create_atoms CPU = 0.002 seconds 339 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 29 2 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 672 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.502 | 4.502 | 4.502 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4503.2999 0 -4503.2999 25095.96 31 0 -4548.8163 0 -4548.8163 9810.2361 Loop time of 2.38736 on 1 procs for 31 steps with 672 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 = -4503.29985014418 -4548.81356378395 -4548.81632392106 Force two-norm initial, final = 36.825690 0.85824317 Force max component initial, final = 6.7001419 0.19418259 Final line search alpha, max atom move = 0.53735839 0.10434565 Iterations, force evaluations = 31 57 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.371 | 2.371 | 2.371 | 0.0 | 99.31 Neigh | 0.005993 | 0.005993 | 0.005993 | 0.0 | 0.25 Comm | 0.0049583 | 0.0049583 | 0.0049583 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005438 | | | 0.23 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2946.00 ave 2946 max 2946 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: 38656.0 ave 38656 max 38656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38656 Ave neighs/atom = 57.523810 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 31 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.502 | 4.502 | 4.502 Mbytes Step Temp E_pair E_mol TotEng Press Volume 31 0 -4548.8163 0 -4548.8163 9810.2361 10468.402 34 0 -4548.9306 0 -4548.9306 1145.2001 10502.388 Loop time of 0.203376 on 1 procs for 3 steps with 672 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 = -4548.81632392106 -4548.92818732573 -4548.93057010609 Force two-norm initial, final = 93.076255 1.3532862 Force max component initial, final = 75.273908 0.73535499 Final line search alpha, max atom move = 0.00016548744 0.00012169202 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2017 | 0.2017 | 0.2017 | 0.0 | 99.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032653 | 0.00032653 | 0.00032653 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001349 | | | 0.66 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2946.00 ave 2946 max 2946 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: 38702.0 ave 38702 max 38702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38702 Ave neighs/atom = 57.592262 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.640 | 4.640 | 4.640 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4548.9306 0 -4548.9306 1145.2001 Loop time of 6.274e-06 on 1 procs for 0 steps with 672 atoms 175.3% 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 | | 6.274e-06 | | |100.00 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2946.00 ave 2946 max 2946 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: 38692.0 ave 38692 max 38692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38692 Ave neighs/atom = 57.577381 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.640 | 4.640 | 4.640 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 -4548.9306 -4548.9306 23.56689 81.574424 5.4630073 1145.2001 1145.2001 112.27724 3219.9568 103.36635 2.415718 537.50005 Loop time of 6.435e-06 on 1 procs for 0 steps with 672 atoms 233.1% 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 | | 6.435e-06 | | |100.00 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2946.00 ave 2946 max 2946 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19346.0 ave 19346 max 19346 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 38692.0 ave 38692 max 38692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38692 Ave neighs/atom = 57.577381 Neighbor list builds = 0 Dangerous builds = 0 672 -4548.93057010609 eV 2.41571801627708 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03