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 = 3.8693370 3.8693370 3.8693370 Created orthogonal box = (0.0000000 -39.459650 0.0000000) to (19.729825 39.459650 3.8693370) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5530365 4.5530365 3.8693370 Created 208 atoms using lattice units in orthogonal box = (0.0000000 -39.459650 0.0000000) to (19.729825 39.459650 3.8693370) create_atoms CPU = 0.001 seconds 208 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5530365 4.5530365 3.8693370 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -39.459650 0.0000000) to (19.729825 39.459650 3.8693370) create_atoms CPU = 0.000 seconds 210 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 = 8.1953264 ghost atom cutoff = 8.1953264 binsize = 4.0976632, bins = 5 20 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 8.19532644834285 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 412 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_042691367780_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 = 8.1953264 ghost atom cutoff = 8.1953264 binsize = 4.0976632, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19532644834285 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) = 4.482 | 4.482 | 4.482 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1247.5762 0 -1247.5762 30778.038 51 0 -1313.5525 0 -1313.5525 -4087.7883 Loop time of 0.3848 on 1 procs for 51 steps with 412 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 = -1247.57619399119 -1313.55148910699 -1313.5524810411 Force two-norm initial, final = 170.11392 0.10447574 Force max component initial, final = 58.454047 0.023992541 Final line search alpha, max atom move = 1.0000000 0.023992541 Iterations, force evaluations = 51 95 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37381 | 0.37381 | 0.37381 | 0.0 | 97.14 Neigh | 0.0044551 | 0.0044551 | 0.0044551 | 0.0 | 1.16 Comm | 0.0040049 | 0.0040049 | 0.0040049 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002533 | | | 0.66 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4609.00 ave 4609 max 4609 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: 60960.0 ave 60960 max 60960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60960 Ave neighs/atom = 147.96117 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 = 8.1953264 ghost atom cutoff = 8.1953264 binsize = 4.0976632, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19532644834285 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.481 | 4.481 | 4.481 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -1313.5525 0 -1313.5525 -4087.7883 6024.8052 53 0 -1313.5744 0 -1313.5744 -0.67074318 6007.8063 Loop time of 0.0210441 on 1 procs for 2 steps with 412 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 = -1313.5524810411 -1313.57428504033 -1313.57441586742 Force two-norm initial, final = 26.638150 0.11082514 Force max component initial, final = 15.771698 0.023942459 Final line search alpha, max atom move = 0.0016395380 3.9254571e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.020085 | 0.020085 | 0.020085 | 0.0 | 95.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019138 | 0.00019138 | 0.00019138 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007679 | | | 3.65 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4580.00 ave 4580 max 4580 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: 59608.0 ave 59608 max 59608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59608 Ave neighs/atom = 144.67961 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 = 8.1953264 ghost atom cutoff = 8.1953264 binsize = 4.0976632, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19532644834285 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) = 4.619 | 4.619 | 4.619 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1313.5744 0 -1313.5744 -0.67074318 Loop time of 2.011e-06 on 1 procs for 0 steps with 412 atoms 149.2% 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 | | 2.011e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4580.00 ave 4580 max 4580 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: 60136.0 ave 60136 max 60136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60136 Ave neighs/atom = 145.96117 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 = 8.1953264 ghost atom cutoff = 8.1953264 binsize = 4.0976632, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19532644834285 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) = 4.619 | 4.619 | 4.619 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 -1313.5744 -1313.5744 19.708961 78.829312 3.8669134 -0.67074318 -0.67074318 0.36251561 1.3056421 -3.6803872 2.517237 228.03477 Loop time of 2.178e-06 on 1 procs for 0 steps with 412 atoms 321.4% 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 | | 2.178e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4580.00 ave 4580 max 4580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30068.0 ave 30068 max 30068 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 60136.0 ave 60136 max 60136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60136 Ave neighs/atom = 145.96117 Neighbor list builds = 0 Dangerous builds = 0 412 -1313.57441586742 eV 2.51723697489874 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01