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 4.9780317) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0842610 5.8666667 4.9780317 Created 1296 atoms using lattice units in orthogonal box = (0.0000000 -63.360000 0.0000000) to (44.802286 63.360000 4.9780317) create_atoms CPU = 0.010 seconds 1296 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0842610 5.8666667 4.9780317 Created 1300 atoms using lattice units in orthogonal box = (0.0000000 -63.360000 0.0000000) to (44.802286 63.360000 4.9780317) create_atoms CPU = 0.009 seconds 1300 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 15 43 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2596 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_444394830472_001#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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 15 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.710 | 5.710 | 5.710 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11343.587 0 -11343.587 25070.714 31 0 -11513.197 0 -11513.197 10169.395 Loop time of 5.65531 on 1 procs for 31 steps with 2596 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 = -11343.5870467898 -11513.1913844033 -11513.1972264076 Force two-norm initial, final = 188.93294 1.8892126 Force max component initial, final = 31.529929 0.34950742 Final line search alpha, max atom move = 0.33741442 0.11792884 Iterations, force evaluations = 31 58 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6252 | 5.6252 | 5.6252 | 0.0 | 99.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.014669 | 0.014669 | 0.014669 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01544 | | | 0.27 Nlocal: 2596.00 ave 2596 max 2596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10018.0 ave 10018 max 10018 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: 203208.0 ave 203208 max 203208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203208 Ave neighs/atom = 78.277350 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 15 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.710 | 5.710 | 5.710 Mbytes Step Temp E_pair E_mol TotEng Press Volume 31 0 -11513.197 0 -11513.197 10169.395 28262.007 36 0 -11513.855 0 -11513.855 147.23891 28419.183 Loop time of 0.67185 on 1 procs for 5 steps with 2596 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11513.1972264076 -11513.8520163212 -11513.8552618844 Force two-norm initial, final = 330.18900 6.6522187 Force max component initial, final = 270.59540 5.3895260 Final line search alpha, max atom move = 5.2977386e-05 0.00028552300 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.664 | 0.664 | 0.664 | 0.0 | 98.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016276 | 0.0016276 | 0.0016276 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006224 | | | 0.93 Nlocal: 2596.00 ave 2596 max 2596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9997.00 ave 9997 max 9997 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: 202728.0 ave 202728 max 202728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202728 Ave neighs/atom = 78.092450 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 15 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.848 | 5.848 | 5.848 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11513.855 0 -11513.855 147.23891 Loop time of 6.285e-06 on 1 procs for 0 steps with 2596 atoms 206.8% 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 | | 6.285e-06 | | |100.00 Nlocal: 2596.00 ave 2596 max 2596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9997.00 ave 9997 max 9997 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: 202584.0 ave 202584 max 202584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202584 Ave neighs/atom = 78.036980 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 15 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.848 | 5.848 | 5.848 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 -11513.855 -11513.855 44.845822 127.23194 4.980735 147.23891 147.23891 179.98092 305.07059 -43.334772 2.2940654 1102.916 Loop time of 6.996e-06 on 1 procs for 0 steps with 2596 atoms 271.6% 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 | | 6.996e-06 | | |100.00 Nlocal: 2596.00 ave 2596 max 2596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9997.00 ave 9997 max 9997 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101292.0 ave 101292 max 101292 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 202584.0 ave 202584 max 202584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202584 Ave neighs/atom = 78.036980 Neighbor list builds = 0 Dangerous builds = 0 2596 -11513.8552618844 eV 2.29406535931678 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07