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 = 3.6385685 3.6385685 3.6385685 Created orthogonal box = (0.0000000 -67.485392 0.0000000) to (23.859689 67.485392 5.1457129) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1036414 6.2777108 5.1457129 Created 688 atoms using lattice units in orthogonal box = (0.0000000 -67.485392 0.0000000) to (23.859689 67.485392 5.1457129) create_atoms CPU = 0.003 seconds 688 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1036414 6.2777108 5.1457129 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -67.485392 0.0000000) to (23.859689 67.485392 5.1457129) create_atoms CPU = 0.002 seconds 690 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 29 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1378 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_097471813275_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.366 | 6.366 | 6.366 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4415.838 0 -4415.838 58859.041 67 0 -4686.4079 0 -4686.4079 2929.5682 Loop time of 2.93815 on 1 procs for 67 steps with 1378 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 = -4415.83798758081 -4686.40335245939 -4686.40792230869 Force two-norm initial, final = 759.44970 0.16848769 Force max component initial, final = 303.27589 0.022304546 Final line search alpha, max atom move = 1.0000000 0.022304546 Iterations, force evaluations = 67 124 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8896 | 2.8896 | 2.8896 | 0.0 | 98.35 Neigh | 0.023945 | 0.023945 | 0.023945 | 0.0 | 0.81 Comm | 0.014584 | 0.014584 | 0.014584 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01002 | | | 0.34 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12163.0 ave 12163 max 12163 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: 439012.0 ave 439012 max 439012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 439012 Ave neighs/atom = 318.58636 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.365 | 6.365 | 6.365 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -4686.4079 0 -4686.4079 2929.5682 16571.053 70 0 -4686.4701 0 -4686.4701 -28.112856 16605.165 Loop time of 0.139604 on 1 procs for 3 steps with 1378 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 = -4686.40792230869 -4686.47009242118 -4686.4701392591 Force two-norm initial, final = 62.014256 0.80658915 Force max component initial, final = 43.980185 0.73062891 Final line search alpha, max atom move = 0.00061680709 0.00045065709 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13688 | 0.13688 | 0.13688 | 0.0 | 98.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00054293 | 0.00054293 | 0.00054293 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002182 | | | 1.56 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12169.0 ave 12169 max 12169 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: 438940.0 ave 438940 max 438940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 438940 Ave neighs/atom = 318.53411 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.503 | 6.503 | 6.503 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4686.4701 0 -4686.4701 -28.112856 Loop time of 1.773e-06 on 1 procs for 0 steps with 1378 atoms 169.2% 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 | | 1.773e-06 | | |100.00 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12165.0 ave 12165 max 12165 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: 438860.0 ave 438860 max 438860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 438860 Ave neighs/atom = 318.47605 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.503 | 6.503 | 6.503 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 -4686.4701 -4686.4701 23.893771 134.85385 5.1534154 -28.112856 -28.112856 -70.596623 -25.575792 11.833846 2.3832188 581.16003 Loop time of 1.943e-06 on 1 procs for 0 steps with 1378 atoms 257.3% 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 | | 1.943e-06 | | |100.00 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12165.0 ave 12165 max 12165 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 219430.0 ave 219430 max 219430 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 438860.0 ave 438860 max 438860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 438860 Ave neighs/atom = 318.47605 Neighbor list builds = 0 Dangerous builds = 0 1378 -4686.4701392591 eV 2.38321880020163 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03