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 -70.579316 0.0000000) to (40.746955 70.579316 6.0968202) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4734715 5.6179738 6.0968202 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -70.579316 0.0000000) to (40.746955 70.579316 6.0968202) create_atoms CPU = 0.010 seconds 1610 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4734715 5.6179738 6.0968202 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -70.579316 0.0000000) to (40.746955 70.579316 6.0968202) create_atoms CPU = 0.010 seconds 1610 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 37 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 28 atoms, new total = 3192 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 37 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) = 10.94 | 10.94 | 10.94 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14118.564 0 -14118.564 -2228.6244 32 0 -14156.387 0 -14156.387 -6778.1747 Loop time of 3.55248 on 1 procs for 32 steps with 3192 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 = -14118.564293341 -14156.3732453846 -14156.3865899129 Force two-norm initial, final = 27.253918 0.48301530 Force max component initial, final = 3.7124066 0.11365653 Final line search alpha, max atom move = 0.93248441 0.10598294 Iterations, force evaluations = 32 57 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4396 | 3.4396 | 3.4396 | 0.0 | 96.82 Neigh | 0.073584 | 0.073584 | 0.073584 | 0.0 | 2.07 Comm | 0.02036 | 0.02036 | 0.02036 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01895 | | | 0.53 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13132.0 ave 13132 max 13132 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: 561172.0 ave 561172 max 561172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 561172 Ave neighs/atom = 175.80576 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 37 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 : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.94 | 10.94 | 10.94 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -14156.387 0 -14156.387 -6778.1747 35067.595 35 0 -14156.541 0 -14156.541 -2255.785 34981.94 Loop time of 0.362281 on 1 procs for 3 steps with 3192 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14156.3865899129 -14156.5407919221 -14156.5411165044 Force two-norm initial, final = 172.06147 0.51143937 Force max component initial, final = 141.78423 0.13314581 Final line search alpha, max atom move = 0.00020232248 2.6938391e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35437 | 0.35437 | 0.35437 | 0.0 | 97.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017896 | 0.0017896 | 0.0017896 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006124 | | | 1.69 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13132.0 ave 13132 max 13132 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: 561276.0 ave 561276 max 561276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 561276 Ave neighs/atom = 175.83835 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 37 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) = 10.45 | 10.45 | 10.45 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14156.541 0 -14156.541 -2255.785 Loop time of 6.465e-06 on 1 procs for 0 steps with 3192 atoms 185.6% 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 | | 6.465e-06 | | |100.00 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13132.0 ave 13132 max 13132 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: 561488.0 ave 561488 max 561488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 561488 Ave neighs/atom = 175.90476 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 37 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) = 10.45 | 10.45 | 10.45 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 -14156.541 -14156.541 40.711616 141.15863 6.0872076 -2255.785 -2255.785 -6.0928033 -6758.2193 -3.0427332 2.253654 1027.006 Loop time of 7.047e-06 on 1 procs for 0 steps with 3192 atoms 283.8% 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 | | 7.047e-06 | | |100.00 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13132.0 ave 13132 max 13132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 280744.0 ave 280744 max 280744 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 561488.0 ave 561488 max 561488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 561488 Ave neighs/atom = 175.90476 Neighbor list builds = 0 Dangerous builds = 0 3192 -14156.5411165044 eV 2.25365401661458 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05