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 = 3.6056636 3.6056636 3.6056636 Created orthogonal box = (0.0000000 -36.056636 0.0000000) to (18.028318 36.056636 3.6056636) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0479290 5.0479290 3.6056636 Created 200 atoms using lattice units in orthogonal box = (0.0000000 -36.056636 0.0000000) to (18.028318 36.056636 3.6056636) create_atoms CPU = 0.002 seconds 200 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0479290 5.0479290 3.6056636 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -36.056636 0.0000000) to (18.028318 36.056636 3.6056636) create_atoms CPU = 0.001 seconds 202 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 5 19 1 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 7.673367000244601 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 400 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_960699513424_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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 4.478 | 4.478 | 4.478 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 121017.54 0 121017.54 1.4021586e+08 67 0 -1667.7861 0 -1667.7861 7703.055 Loop time of 0.981966 on 1 procs for 67 steps with 400 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 = 121017.543036704 -1667.78462677419 -1667.78613417319 Force two-norm initial, final = 792097.13 0.15196439 Force max component initial, final = 276238.73 0.042349255 Final line search alpha, max atom move = 1.0000000 0.042349255 Iterations, force evaluations = 67 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.94877 | 0.94877 | 0.94877 | 0.0 | 96.62 Neigh | 0.0098232 | 0.0098232 | 0.0098232 | 0.0 | 1.00 Comm | 0.014057 | 0.014057 | 0.014057 | 0.0 | 1.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009317 | | | 0.95 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4560.00 ave 4560 max 4560 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: 66432.0 ave 66432 max 66432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66432 Ave neighs/atom = 166.08000 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.478 | 4.478 | 4.478 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -1667.7861 0 -1667.7861 7703.055 4687.6546 133 0 -1669.8979 0 -1669.8979 -614.83753 4717.9977 Loop time of 0.612334 on 1 procs for 66 steps with 400 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 = -1667.78613417319 -1669.8967019879 -1669.89785067424 Force two-norm initial, final = 82.457798 3.8040116 Force max component initial, final = 81.560195 2.8422002 Final line search alpha, max atom move = 0.00097211103 0.0027629341 Iterations, force evaluations = 66 74 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.57124 | 0.57124 | 0.57124 | 0.0 | 93.29 Neigh | 0.0097017 | 0.0097017 | 0.0097017 | 0.0 | 1.58 Comm | 0.0075028 | 0.0075028 | 0.0075028 | 0.0 | 1.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02389 | | | 3.90 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4572.00 ave 4572 max 4572 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: 63476.0 ave 63476 max 63476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63476 Ave neighs/atom = 158.69000 Neighbor list builds = 1 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 5 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 4.616 | 4.616 | 4.616 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1669.8979 0 -1669.8979 -614.83753 Loop time of 6.194e-06 on 1 procs for 0 steps with 400 atoms 177.6% 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 | | 6.194e-06 | | |100.00 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4572.00 ave 4572 max 4572 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: 63744.0 ave 63744 max 63744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63744 Ave neighs/atom = 159.36000 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 5 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 4.616 | 4.616 | 4.616 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 -1669.8979 -1669.8979 17.737145 70.668619 3.7639809 -614.83753 -614.83753 -949.58928 -352.89964 -542.02368 2.3261508 162.97136 Loop time of 6.455e-06 on 1 procs for 0 steps with 400 atoms 232.4% 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 | | 6.455e-06 | | |100.00 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4572.00 ave 4572 max 4572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31872.0 ave 31872 max 31872 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 63744.0 ave 63744 max 63744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63744 Ave neighs/atom = 159.36000 Neighbor list builds = 0 Dangerous builds = 0 400 -1669.89785067423 eV 2.32615076511562 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02