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 = 4.0709491 4.0709491 4.0709491 Created orthogonal box = (0.0000000 -51.497957 0.0000000) to (12.873471 51.497957 4.0709491) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1493886 5.1493886 4.0709491 Created 161 atoms using lattice units in orthogonal box = (0.0000000 -51.497957 0.0000000) to (12.873471 51.497957 4.0709491) create_atoms CPU = 0.001 seconds 161 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1493886 5.1493886 4.0709491 Created 161 atoms using lattice units in orthogonal box = (0.0000000 -51.497957 0.0000000) to (12.873471 51.497957 4.0709491) create_atoms CPU = 0.000 seconds 161 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 34 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 316 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.427 | 4.427 | 4.427 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1057.7237 0 -1057.7237 -624.69359 48 0 -1060.9561 0 -1060.9561 -7833.3173 Loop time of 1.08346 on 1 procs for 48 steps with 316 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 = -1057.72371339743 -1060.95507065176 -1060.95606538806 Force two-norm initial, final = 5.8687098 0.072832481 Force max component initial, final = 2.0209528 0.0080912764 Final line search alpha, max atom move = 1.0000000 0.0080912764 Iterations, force evaluations = 48 89 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0783 | 1.0783 | 1.0783 | 0.0 | 99.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026456 | 0.0026456 | 0.0026456 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002485 | | | 0.23 Nlocal: 316.000 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2428.00 ave 2428 max 2428 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: 16858.0 ave 16858 max 16858 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16858 Ave neighs/atom = 53.348101 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.426 | 4.426 | 4.426 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -1060.9561 0 -1060.9561 -7833.3173 5397.7323 53 0 -1061.0199 0 -1061.0199 -2411.3975 5369.3202 Loop time of 0.0830219 on 1 procs for 5 steps with 316 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 = -1060.95606538806 -1061.01980708012 -1061.01988501735 Force two-norm initial, final = 32.458393 0.13258231 Force max component initial, final = 28.576962 0.034783599 Final line search alpha, max atom move = 0.0010734782 3.7339436e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.082123 | 0.082123 | 0.082123 | 0.0 | 98.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015935 | 0.00015935 | 0.00015935 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007392 | | | 0.89 Nlocal: 316.000 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2394.00 ave 2394 max 2394 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: 16912.0 ave 16912 max 16912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16912 Ave neighs/atom = 53.518987 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.565 | 4.565 | 4.565 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1061.0199 0 -1061.0199 -2411.3975 Loop time of 2.002e-06 on 1 procs for 0 steps with 316 atoms 149.9% 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 | | 2.002e-06 | | |100.00 Nlocal: 316.000 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2440.00 ave 2440 max 2440 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: 16912.0 ave 16912 max 16912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16912 Ave neighs/atom = 53.518987 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.565 | 4.565 | 4.565 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 -1061.0199 -1061.0199 12.82402 102.99591 4.0651366 -2411.3975 -2411.3975 6.7948803 -7246.3847 5.3973777 2.5892639 212.4059 Loop time of 1.686e-06 on 1 procs for 0 steps with 316 atoms 177.9% 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 | | 1.686e-06 | | |100.00 Nlocal: 316.000 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2440.00 ave 2440 max 2440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8456.00 ave 8456 max 8456 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 16912.0 ave 16912 max 16912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16912 Ave neighs/atom = 53.518987 Neighbor list builds = 0 Dangerous builds = 0 316 -1061.01988501735 eV 2.58926388037118 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01