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 = 4.0310361 4.0310361 4.0310361 Created orthogonal box = (0.0000000 -65.990905 0.0000000) to (46.662617 65.990905 5.7007459) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9645696 6.4021027 5.7007459 Created 1071 atoms using lattice units in orthogonal box = (0.0000000 -65.990905 0.0000000) to (46.662617 65.990905 5.7007459) create_atoms CPU = 0.009 seconds 1071 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9645696 6.4021027 5.7007459 Created 1079 atoms using lattice units in orthogonal box = (0.0000000 -65.990905 0.0000000) to (46.662617 65.990905 5.7007459) create_atoms CPU = 0.008 seconds 1079 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 35 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 2144 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_699137396381_005#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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.633 | 5.633 | 5.633 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7057.6983 0 -7057.6983 6935.1345 149 0 -7192.5945 0 -7192.5945 1666.8014 Loop time of 7.61468 on 1 procs for 149 steps with 2144 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 = -7057.69829960855 -7192.5881395701 -7192.59452328471 Force two-norm initial, final = 47.665052 0.20587240 Force max component initial, final = 7.6064946 0.046738573 Final line search alpha, max atom move = 1.0000000 0.046738573 Iterations, force evaluations = 149 281 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.4124 | 7.4124 | 7.4124 | 0.0 | 97.34 Neigh | 0.072787 | 0.072787 | 0.072787 | 0.0 | 0.96 Comm | 0.066548 | 0.066548 | 0.066548 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06296 | | | 0.83 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9118.00 ave 9118 max 9118 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: 283164.0 ave 283164 max 283164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 283164 Ave neighs/atom = 132.07276 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 149 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.627 | 5.627 | 5.627 Mbytes Step Temp E_pair E_mol TotEng Press Volume 149 0 -7192.5945 0 -7192.5945 1666.8014 35108.709 151 0 -7192.6429 0 -7192.6429 1.1366136 35187.085 Loop time of 0.13057 on 1 procs for 2 steps with 2144 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 = -7192.59452328471 -7192.63911688243 -7192.6428711905 Force two-norm initial, final = 64.980428 0.28482861 Force max component initial, final = 43.813075 0.15052536 Final line search alpha, max atom move = 0.00011047577 1.6629405e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12623 | 0.12623 | 0.12623 | 0.0 | 96.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010411 | 0.0010411 | 0.0010411 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003302 | | | 2.53 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8958.00 ave 8958 max 8958 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: 283132.0 ave 283132 max 283132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 283132 Ave neighs/atom = 132.05784 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.765 | 5.765 | 5.765 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7192.6429 0 -7192.6429 1.1366136 Loop time of 6.285e-06 on 1 procs for 0 steps with 2144 atoms 222.8% 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: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8958.00 ave 8958 max 8958 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: 283068.0 ave 283068 max 283068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 283068 Ave neighs/atom = 132.02799 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.765 | 5.765 | 5.765 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 -7192.6429 -7192.6429 46.658534 132.14899 5.7067436 1.1366136 1.1366136 1.9299103 6.8625654 -5.3826349 2.677466 1007.3915 Loop time of 6.716e-06 on 1 procs for 0 steps with 2144 atoms 312.7% 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 | | 6.716e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8958.00 ave 8958 max 8958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 141534.0 ave 141534 max 141534 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 283068.0 ave 283068 max 283068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 283068 Ave neighs/atom = 132.02799 Neighbor list builds = 0 Dangerous builds = 0 2144 -7192.6428711905 eV 2.67746603856295 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08