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 = 2.8601955 2.8601955 2.8601955 Created orthogonal box = (0.0000000 -30.000843 0.0000000) to (36.739876 30.000843 7.0060194) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6759842 4.3633430 4.6706796 Created 663 atoms using lattice units in orthogonal box = (0.0000000 -30.000843 0.0000000) to (36.739876 30.000843 7.0060194) create_atoms CPU = 0.001 seconds 663 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6759842 4.3633430 4.6706796 Created 663 atoms using lattice units in orthogonal box = (0.0000000 -30.000843 0.0000000) to (36.739876 30.000843 7.0060194) create_atoms CPU = 0.001 seconds 663 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 14 23 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 9 atoms, new total = 1317 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.323 | 5.323 | 5.323 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5434.7237 0 -5434.7237 33401.751 59 0 -5591.8921 0 -5591.8921 3964.2493 Loop time of 12.1419 on 1 procs for 59 steps with 1317 atoms 71.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5434.72369027617 -5591.88670147486 -5591.89210741542 Force two-norm initial, final = 143.66550 0.33489854 Force max component initial, final = 31.577600 0.076941884 Final line search alpha, max atom move = 0.88979453 0.068462468 Iterations, force evaluations = 59 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.111 | 12.111 | 12.111 | 0.0 | 99.75 Neigh | 0.020992 | 0.020992 | 0.020992 | 0.0 | 0.17 Comm | 0.0037859 | 0.0037859 | 0.0037859 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005906 | | | 0.05 Nlocal: 1317.00 ave 1317 max 1317 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3686.00 ave 3686 max 3686 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: 75746.0 ave 75746 max 75746 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75746 Ave neighs/atom = 57.514047 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.323 | 5.323 | 5.323 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -5591.8921 0 -5591.8921 3964.2493 15444.451 61 0 -5591.9232 0 -5591.9232 3689.9304 15446.791 Loop time of 0.310476 on 1 procs for 2 steps with 1317 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 = -5591.89210741543 -5591.92065358971 -5591.92324815246 Force two-norm initial, final = 37.283105 1.9853005 Force max component initial, final = 30.775898 1.6734965 Final line search alpha, max atom move = 0.00010743082 0.00017978510 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30978 | 0.30978 | 0.30978 | 0.0 | 99.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011013 | 0.00011013 | 0.00011013 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005904 | | | 0.19 Nlocal: 1317.00 ave 1317 max 1317 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3693.00 ave 3693 max 3693 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: 75714.0 ave 75714 max 75714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75714 Ave neighs/atom = 57.489749 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.461 | 5.461 | 5.461 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5591.9232 0 -5591.9232 3689.9304 Loop time of 1.628e-06 on 1 procs for 0 steps with 1317 atoms 122.9% 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 | | 1.628e-06 | | |100.00 Nlocal: 1317.00 ave 1317 max 1317 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3686.00 ave 3686 max 3686 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: 75724.0 ave 75724 max 75724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75724 Ave neighs/atom = 57.497342 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.461 | 5.461 | 5.461 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 -5591.9232 -5591.9232 36.785632 60.001686 6.9983653 3689.9304 3689.9304 173.79506 10791.982 104.01364 2.2316459 1439.0161 Loop time of 1.599e-06 on 1 procs for 0 steps with 1317 atoms 187.6% 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 | | 1.599e-06 | | |100.00 Nlocal: 1317.00 ave 1317 max 1317 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3686.00 ave 3686 max 3686 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37862.0 ave 37862 max 37862 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75724.0 ave 75724 max 75724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75724 Ave neighs/atom = 57.497342 Neighbor list builds = 0 Dangerous builds = 0 1317 -5591.92324815246 eV 2.23164589029817 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13