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 = 3.6149390 3.6149390 3.6149390 Created orthogonal box = (0.0000000 -39.599673 0.0000000) to (8.0832494 39.599673 8.8547561) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8499496 5.2799564 5.9031707 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -39.599673 0.0000000) to (8.0832494 39.599673 8.8547561) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8499496 5.2799564 5.9031707 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -39.599673 0.0000000) to (8.0832494 39.599673 8.8547561) create_atoms CPU = 0.001 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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 2 19 3 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 8.395337104797363 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 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_547744193826_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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 2 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337104797363 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) = 4.592 | 4.592 | 4.592 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1614.2585 0 -1614.2585 26278.062 121 0 -1678.6588 0 -1678.6588 1159.3459 Loop time of 1.25798 on 1 procs for 121 steps with 476 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1614.258486278 -1678.65752957935 -1678.65877259263 Force two-norm initial, final = 156.26391 0.10817050 Force max component initial, final = 54.912795 0.028740668 Final line search alpha, max atom move = 1.0000000 0.028740668 Iterations, force evaluations = 121 229 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2218 | 1.2218 | 1.2218 | 0.0 | 97.12 Neigh | 0.019987 | 0.019987 | 0.019987 | 0.0 | 1.59 Comm | 0.0092579 | 0.0092579 | 0.0092579 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006934 | | | 0.55 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4738.00 ave 4738 max 4738 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: 95156.0 ave 95156 max 95156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95156 Ave neighs/atom = 199.90756 Neighbor list builds = 3 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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 2 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337104797363 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 121 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.590 | 4.590 | 4.590 Mbytes Step Temp E_pair E_mol TotEng Press Volume 121 0 -1678.6588 0 -1678.6588 1159.3459 5668.7092 127 0 -1678.7338 0 -1678.7338 36.073459 5673.6813 Loop time of 0.0454953 on 1 procs for 6 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 = -1678.65877259263 -1678.73222133201 -1678.73383302511 Force two-norm initial, final = 23.344808 0.40821550 Force max component initial, final = 22.029481 0.29489735 Final line search alpha, max atom move = 0.00040686682 0.00011998395 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.043994 | 0.043994 | 0.043994 | 0.0 | 96.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026334 | 0.00026334 | 0.00026334 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001238 | | | 2.72 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4420.00 ave 4420 max 4420 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: 95112.0 ave 95112 max 95112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95112 Ave neighs/atom = 199.81513 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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 2 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337104797363 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) = 4.728 | 4.728 | 4.728 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1678.7338 0 -1678.7338 36.073459 Loop time of 1.968e-06 on 1 procs for 0 steps with 476 atoms 152.4% 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 | | 1.968e-06 | | |100.00 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4444.00 ave 4444 max 4444 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: 95040.0 ave 95040 max 95040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95040 Ave neighs/atom = 199.66387 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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 2 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337104797363 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) = 4.728 | 4.728 | 4.728 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 -1678.7338 -1678.7338 8.0637224 79.66077 8.8325249 36.073459 36.073459 5.0831119 20.071025 83.06624 2.2907583 315.23934 Loop time of 2.389e-06 on 1 procs for 0 steps with 476 atoms 251.2% 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 | | 2.389e-06 | | |100.00 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4444.00 ave 4444 max 4444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47520.0 ave 47520 max 47520 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 95040.0 ave 95040 max 95040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95040 Ave neighs/atom = 199.66387 Neighbor list builds = 0 Dangerous builds = 0 476 -1678.73383302511 eV 2.29075827253038 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01