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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -52.094774 0.0000000) to (42.532331 52.094774 8.6222058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2437121 4.9950518 5.7481372 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -52.094774 0.0000000) to (42.532331 52.094774 8.6222058) create_atoms CPU = 0.007 seconds 1755 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2437121 4.9950518 5.7481372 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -52.094774 0.0000000) to (42.532331 52.094774 8.6222058) create_atoms CPU = 0.006 seconds 1755 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 27 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 38 atoms, new total = 3472 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_820335782779_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.404 | 7.404 | 7.404 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15317.287 0 -15317.287 -726.43982 62 0 -15379.481 0 -15379.481 -7141.3568 Loop time of 7.20456 on 1 procs for 62 steps with 3472 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 = -15317.2872996733 -15379.4680228301 -15379.4811529478 Force two-norm initial, final = 41.623391 0.48574852 Force max component initial, final = 5.6293066 0.089515888 Final line search alpha, max atom move = 0.69186686 0.061933076 Iterations, force evaluations = 62 111 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.9602 | 6.9602 | 6.9602 | 0.0 | 96.61 Neigh | 0.17517 | 0.17517 | 0.17517 | 0.0 | 2.43 Comm | 0.030536 | 0.030536 | 0.030536 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03867 | | | 0.54 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11687.0 ave 11687 max 11687 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: 609684.0 ave 609684 max 609684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 609684 Ave neighs/atom = 175.60023 Neighbor list builds = 2 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.406 | 7.406 | 7.406 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -15379.481 0 -15379.481 -7141.3568 38208.653 65 0 -15379.71 0 -15379.71 -1585.694 38095.593 Loop time of 0.435871 on 1 procs for 3 steps with 3472 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 = -15379.4811529478 -15379.7097068675 -15379.7100026475 Force two-norm initial, final = 218.66234 0.53794757 Force max component initial, final = 156.95452 0.074436616 Final line search alpha, max atom move = 0.00026178108 1.9486098e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.42665 | 0.42665 | 0.42665 | 0.0 | 97.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016237 | 0.0016237 | 0.0016237 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007601 | | | 1.74 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11692.0 ave 11692 max 11692 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: 609588.0 ave 609588 max 609588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 609588 Ave neighs/atom = 175.57258 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.544 | 7.544 | 7.544 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15379.71 0 -15379.71 -1585.694 Loop time of 6.104e-06 on 1 procs for 0 steps with 3472 atoms 213.0% 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 | | 6.104e-06 | | |100.00 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11735.0 ave 11735 max 11735 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: 609930.0 ave 609930 max 609930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 609930 Ave neighs/atom = 175.67108 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.544 | 7.544 | 7.544 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 -15379.71 -15379.71 42.465563 104.18955 8.610209 -1585.694 -1585.694 0.51807363 -4755.0196 -2.5803017 2.267032 1627.7536 Loop time of 1.0915e-05 on 1 procs for 0 steps with 3472 atoms 650.5% 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 | | 1.091e-05 | | |100.00 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11735.0 ave 11735 max 11735 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 304965.0 ave 304965 max 304965 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 609930.0 ave 609930 max 609930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 609930 Ave neighs/atom = 175.67108 Neighbor list builds = 0 Dangerous builds = 0 3472 -15379.7100026475 eV 2.26703200323716 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09