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 = 2.8603420 2.8603420 2.8603420 Created orthogonal box = (0.0000000 -33.359894 0.0000000) to (11.793492 33.359894 4.0451344) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8561438 4.9054461 4.0451344 Created 138 atoms using lattice units in orthogonal box = (0.0000000 -33.359894 0.0000000) to (11.793492 33.359894 4.0451344) create_atoms CPU = 0.001 seconds 138 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8561438 4.9054461 4.0451344 Created 138 atoms using lattice units in orthogonal box = (0.0000000 -33.359894 0.0000000) to (11.793492 33.359894 4.0451344) create_atoms CPU = 0.000 seconds 138 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 = 4 18 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 270 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_657255834688_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 = 4 18 2 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) = 4.440 | 4.440 | 4.440 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1133.5607 0 -1133.5607 4368.8321 324 0 -1180.4861 0 -1180.4861 -10435.599 Loop time of 1.43097 on 1 procs for 324 steps with 270 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 = -1133.56071432725 -1180.48503745019 -1180.48613534619 Force two-norm initial, final = 29.222994 0.15585692 Force max component initial, final = 10.313606 0.055583782 Final line search alpha, max atom move = 1.0000000 0.055583782 Iterations, force evaluations = 324 617 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3829 | 1.3829 | 1.3829 | 0.0 | 96.64 Neigh | 0.022996 | 0.022996 | 0.022996 | 0.0 | 1.61 Comm | 0.016083 | 0.016083 | 0.016083 | 0.0 | 1.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009028 | | | 0.63 Nlocal: 270.000 ave 270 max 270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3595.00 ave 3595 max 3595 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: 43340.0 ave 43340 max 43340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43340 Ave neighs/atom = 160.51852 Neighbor list builds = 9 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 = 4 18 2 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 : 324 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.440 | 4.440 | 4.440 Mbytes Step Temp E_pair E_mol TotEng Press Volume 324 0 -1180.4861 0 -1180.4861 -10435.599 3182.9516 352 0 -1181.4754 0 -1181.4754 12436.219 3139.7341 Loop time of 0.0772972 on 1 procs for 28 steps with 270 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 = -1180.48613534619 -1181.47499043977 -1181.47536135658 Force two-norm initial, final = 94.202414 1.7604787 Force max component initial, final = 94.155660 1.2271966 Final line search alpha, max atom move = 0.00059036148 0.00072448959 Iterations, force evaluations = 28 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.073063 | 0.073063 | 0.073063 | 0.0 | 94.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00079249 | 0.00079249 | 0.00079249 | 0.0 | 1.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003441 | | | 4.45 Nlocal: 270.000 ave 270 max 270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3605.00 ave 3605 max 3605 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: 43052.0 ave 43052 max 43052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43052 Ave neighs/atom = 159.45185 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 = 3 18 2 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) = 4.578 | 4.578 | 4.578 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1181.4754 0 -1181.4754 12436.219 Loop time of 1.613e-06 on 1 procs for 0 steps with 270 atoms 124.0% 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 | | 1.613e-06 | | |100.00 Nlocal: 270.000 ave 270 max 270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3660.00 ave 3660 max 3660 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: 43702.0 ave 43702 max 43702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43702 Ave neighs/atom = 161.85926 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 = 3 18 2 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) = 4.578 | 4.578 | 4.578 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 -1181.4754 -1181.4754 11.534954 66.719787 4.079645 12436.219 12436.219 -5.135653 37945.361 -631.56933 2.3481495 1640.764 Loop time of 1.407e-06 on 1 procs for 0 steps with 270 atoms 142.1% 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 | | 1.407e-06 | | |100.00 Nlocal: 270.000 ave 270 max 270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3660.00 ave 3660 max 3660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21851.0 ave 21851 max 21851 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 43702.0 ave 43702 max 43702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43702 Ave neighs/atom = 161.85926 Neighbor list builds = 0 Dangerous builds = 0 270 -1181.47536135658 eV 2.34814954581271 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01