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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -63.360000 0.0000000) to (44.802286 63.360000 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0842611 5.8666667 4.9780318 Created 1294 atoms using lattice units in orthogonal box = (0.0000000 -63.360000 0.0000000) to (44.802286 63.360000 4.9780318) create_atoms CPU = 0.011 seconds 1294 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0842611 5.8666667 4.9780318 Created 1298 atoms using lattice units in orthogonal box = (0.0000000 -63.360000 0.0000000) to (44.802286 63.360000 4.9780318) create_atoms CPU = 0.010 seconds 1298 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 11 30 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 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 2586 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_826591359508_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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 10.84 | 10.84 | 10.84 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11355.5 0 -11355.5 10381.518 134 0 -11476.943 0 -11476.943 1613.7594 Loop time of 16.1652 on 1 procs for 134 steps with 2586 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11355.4995066198 -11476.9319051342 -11476.9433743949 Force two-norm initial, final = 227.33806 0.36886549 Force max component initial, final = 38.341387 0.090609068 Final line search alpha, max atom move = 1.0000000 0.090609068 Iterations, force evaluations = 134 256 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.769 | 15.769 | 15.769 | 0.0 | 97.55 Neigh | 0.23463 | 0.23463 | 0.23463 | 0.0 | 1.45 Comm | 0.092582 | 0.092582 | 0.092582 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06859 | | | 0.42 Nlocal: 2586.00 ave 2586 max 2586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15536.0 ave 15536 max 15536 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: 581564.0 ave 581564 max 581564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 581564 Ave neighs/atom = 224.88940 Neighbor list builds = 3 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 134 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.83 | 10.83 | 10.83 Mbytes Step Temp E_pair E_mol TotEng Press Volume 134 0 -11476.943 0 -11476.943 1613.7594 28262.007 136 0 -11476.96 0 -11476.96 -3.060231 28287.587 Loop time of 0.311865 on 1 procs for 2 steps with 2586 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11476.943374395 -11476.958895078 -11476.9600485397 Force two-norm initial, final = 52.396424 1.0037392 Force max component initial, final = 41.006961 0.81013821 Final line search alpha, max atom move = 0.00012784988 0.00010357607 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30561 | 0.30561 | 0.30561 | 0.0 | 97.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015367 | 0.0015367 | 0.0015367 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004721 | | | 1.51 Nlocal: 2586.00 ave 2586 max 2586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14605.0 ave 14605 max 14605 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: 580696.0 ave 580696 max 580696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 580696 Ave neighs/atom = 224.55375 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 10.35 | 10.35 | 10.35 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11476.96 0 -11476.96 -3.060231 Loop time of 6.525e-06 on 1 procs for 0 steps with 2586 atoms 214.6% 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 | | 6.525e-06 | | |100.00 Nlocal: 2586.00 ave 2586 max 2586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14605.0 ave 14605 max 14605 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: 580624.0 ave 580624 max 580624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 580624 Ave neighs/atom = 224.52591 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 10.35 | 10.35 | 10.35 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 -11476.96 -11476.96 44.802292 126.75707 4.9810794 -3.060231 -3.060231 21.037435 -45.898723 15.680595 2.2674095 1149.226 Loop time of 6.775e-06 on 1 procs for 0 steps with 2586 atoms 280.4% 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 | | 6.775e-06 | | |100.00 Nlocal: 2586.00 ave 2586 max 2586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14605.0 ave 14605 max 14605 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 290312.0 ave 290312 max 290312 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 580624.0 ave 580624 max 580624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 580624 Ave neighs/atom = 224.52591 Neighbor list builds = 0 Dangerous builds = 0 2586 -11476.9600485397 eV 2.26740952075664 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18