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 = 3.6584048 3.6584048 3.6584048 Created orthogonal box = (0.0000000 -47.979530 0.0000000) to (33.926651 47.979530 5.1737657) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3119350 6.1369166 5.1737657 Created 686 atoms using lattice units in orthogonal box = (0.0000000 -47.979530 0.0000000) to (33.926651 47.979530 5.1737657) create_atoms CPU = 0.004 seconds 686 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3119350 6.1369166 5.1737657 Created 694 atoms using lattice units in orthogonal box = (0.0000000 -47.979530 0.0000000) to (33.926651 47.979530 5.1737657) create_atoms CPU = 0.003 seconds 694 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 27 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1380 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_884343146310_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.081 | 5.081 | 5.081 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4844.239 0 -4844.239 108011.66 721 0 -5454.6315 0 -5454.6315 -60299.957 Loop time of 20.8416 on 1 procs for 721 steps with 1380 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4844.23900890474 -5454.627007113 -5454.63148008623 Force two-norm initial, final = 770.38680 0.22498564 Force max component initial, final = 112.46971 0.050455009 Final line search alpha, max atom move = 1.0000000 0.050455009 Iterations, force evaluations = 721 1412 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.29 | 20.29 | 20.29 | 0.0 | 97.35 Neigh | 0.26209 | 0.26209 | 0.26209 | 0.0 | 1.26 Comm | 0.15409 | 0.15409 | 0.15409 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1351 | | | 0.65 Nlocal: 1380.00 ave 1380 max 1380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7338.00 ave 7338 max 7338 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: 186996.0 ave 186996 max 186996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186996 Ave neighs/atom = 135.50435 Neighbor list builds = 15 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 721 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.083 | 5.083 | 5.083 Mbytes Step Temp E_pair E_mol TotEng Press Volume 721 0 -5454.6315 0 -5454.6315 -60299.957 16843.554 766 0 -5482.9824 0 -5482.9824 79.234981 16126.82 Loop time of 0.847664 on 1 procs for 45 steps with 1380 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5454.63148008625 -5482.98164314944 -5482.98241197693 Force two-norm initial, final = 1253.0084 3.6385080 Force max component initial, final = 1111.0480 2.4358247 Final line search alpha, max atom move = 0.00035823885 0.00087260703 Iterations, force evaluations = 45 47 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.81435 | 0.81435 | 0.81435 | 0.0 | 96.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.004926 | 0.004926 | 0.004926 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02838 | | | 3.35 Nlocal: 1380.00 ave 1380 max 1380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7323.00 ave 7323 max 7323 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: 186792.0 ave 186792 max 186792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186792 Ave neighs/atom = 135.35652 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.226 | 5.226 | 5.226 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5482.9824 0 -5482.9824 79.234981 Loop time of 2.161e-06 on 1 procs for 0 steps with 1380 atoms 185.1% 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 | | 2.161e-06 | | |100.00 Nlocal: 1380.00 ave 1380 max 1380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7576.00 ave 7576 max 7576 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: 193308.0 ave 193308 max 193308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193308 Ave neighs/atom = 140.07826 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.226 | 5.226 | 5.226 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 -5482.9824 -5482.9824 33.748904 96.577937 4.9477886 79.234981 79.234981 240.72785 -39.474305 36.451399 2.2724386 4719.1463 Loop time of 2.677e-06 on 1 procs for 0 steps with 1380 atoms 224.1% 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 | | 2.677e-06 | | |100.00 Nlocal: 1380.00 ave 1380 max 1380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7576.00 ave 7576 max 7576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96654.0 ave 96654 max 96654 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 193308.0 ave 193308 max 193308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193308 Ave neighs/atom = 140.07826 Neighbor list builds = 0 Dangerous builds = 0 1380 -5482.98241197693 eV 2.27243861595937 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22