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 -44.599084 0.0000000) to (9.1029190 44.599084 9.9717481) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4617514 5.9460018 6.6478321 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -44.599084 0.0000000) to (9.1029190 44.599084 9.9717481) create_atoms CPU = 0.001 seconds 242 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4617514 5.9460018 6.6478321 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -44.599084 0.0000000) to (9.1029190 44.599084 9.9717481) create_atoms CPU = 0.000 seconds 242 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 = 3 30 4 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 8 atoms, new total = 476 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 = 3 30 4 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) = 4.436 | 4.436 | 4.436 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1585.6968 0 -1585.6968 3900.6004 49 0 -1596.9314 0 -1596.9314 -2769.1114 Loop time of 1.22624 on 1 procs for 49 steps with 476 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 = -1585.69681545337 -1596.92992113985 -1596.93135241112 Force two-norm initial, final = 18.736980 0.10032317 Force max component initial, final = 5.6345768 0.016590181 Final line search alpha, max atom move = 1.0000000 0.016590181 Iterations, force evaluations = 49 94 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2225 | 1.2225 | 1.2225 | 0.0 | 99.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018407 | 0.0018407 | 0.0018407 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00191 | | | 0.16 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2439.00 ave 2439 max 2439 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: 25456.0 ave 25456 max 25456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25456 Ave neighs/atom = 53.478992 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 = 3 30 4 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 : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.435 | 4.435 | 4.435 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -1596.9314 0 -1596.9314 -2769.1114 8096.6975 52 0 -1596.9572 0 -1596.9572 98.185696 8072.2597 Loop time of 0.0779558 on 1 procs for 3 steps with 476 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 = -1596.93135241112 -1596.95710358972 -1596.95723096396 Force two-norm initial, final = 24.330728 0.14316595 Force max component initial, final = 18.188506 0.053829771 Final line search alpha, max atom move = 0.0012778834 6.8788172e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.077371 | 0.077371 | 0.077371 | 0.0 | 99.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00010846 | 0.00010846 | 0.00010846 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004767 | | | 0.61 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2334.00 ave 2334 max 2334 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: 25556.0 ave 25556 max 25556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25556 Ave neighs/atom = 53.689076 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 = 3 30 4 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) = 4.573 | 4.573 | 4.573 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1596.9572 0 -1596.9572 98.185696 Loop time of 1.559e-06 on 1 procs for 0 steps with 476 atoms 128.3% 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 | | 1.559e-06 | | |100.00 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2334.00 ave 2334 max 2334 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: 25560.0 ave 25560 max 25560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25560 Ave neighs/atom = 53.697479 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 = 3 30 4 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) = 4.573 | 4.573 | 4.573 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 -1596.9572 -1596.9572 9.0920663 89.198168 9.9535178 98.185696 98.185696 6.741282 277.15124 10.664563 2.490598 351.71551 Loop time of 1.376e-06 on 1 procs for 0 steps with 476 atoms 145.3% 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 | | 1.376e-06 | | |100.00 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2334.00 ave 2334 max 2334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12780.0 ave 12780 max 12780 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25560.0 ave 25560 max 25560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25560 Ave neighs/atom = 53.697479 Neighbor list builds = 0 Dangerous builds = 0 476 -1596.95723096396 eV 2.49059795176518 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01