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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -41.665669 0.0000000) to (51.029814 41.665669 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8319788 5.3570146 5.7504086 Created 1669 atoms using lattice units in orthogonal box = (0.0000000 -41.665669 0.0000000) to (51.029814 41.665669 8.6256130) create_atoms CPU = 0.003 seconds 1669 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8319788 5.3570146 5.7504086 Created 1693 atoms using lattice units in orthogonal box = (0.0000000 -41.665669 0.0000000) to (51.029814 41.665669 8.6256130) create_atoms CPU = 0.002 seconds 1693 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 ghost atom cutoff = 7 binsize = 3.5, bins = 15 24 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 3356 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_663355627503_001#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 ghost atom cutoff = 7 binsize = 3.5, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.539 | 6.539 | 6.539 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14205.841 0 -14205.841 53833.668 59 0 -14864.551 0 -14864.551 7801.3548 Loop time of 21.3289 on 1 procs for 59 steps with 3356 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14205.8408753326 -14864.5384776672 -14864.5506579165 Force two-norm initial, final = 456.62684 0.39818854 Force max component initial, final = 43.130224 0.086483838 Final line search alpha, max atom move = 1.0000000 0.086483838 Iterations, force evaluations = 59 100 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.256 | 21.256 | 21.256 | 0.0 | 99.66 Neigh | 0.033258 | 0.033258 | 0.033258 | 0.0 | 0.16 Comm | 0.016319 | 0.016319 | 0.016319 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02306 | | | 0.11 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9900.00 ave 9900 max 9900 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: 448362.0 ave 448362 max 448362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 448362 Ave neighs/atom = 133.60012 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/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) = 6.536 | 6.536 | 6.536 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -14864.551 0 -14864.551 7801.3548 36679.407 66 0 -14865.611 0 -14865.611 -3.7917902 36833.004 Loop time of 2.12072 on 1 procs for 7 steps with 3356 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 = -14864.5506579165 -14865.610478916 -14865.6105909415 Force two-norm initial, final = 393.12671 0.77626647 Force max component initial, final = 374.12207 0.28389824 Final line search alpha, max atom move = 0.00028725143 8.1550176e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.114 | 2.114 | 2.114 | 0.0 | 99.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00090684 | 0.00090684 | 0.00090684 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005773 | | | 0.27 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9512.00 ave 9512 max 9512 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: 448378.0 ave 448378 max 448378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 448378 Ave neighs/atom = 133.60489 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 ghost atom cutoff = 7 binsize = 3.5, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.674 | 6.674 | 6.674 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14865.611 0 -14865.611 -3.7917902 Loop time of 2.061e-06 on 1 procs for 0 steps with 3356 atoms 194.1% 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 | | 2.061e-06 | | |100.00 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9512.00 ave 9512 max 9512 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: 447248.0 ave 447248 max 447248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 447248 Ave neighs/atom = 133.26818 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 ghost atom cutoff = 7 binsize = 3.5, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.674 | 6.674 | 6.674 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 -14865.611 -14865.611 51.019146 83.832322 8.6117707 -3.7917902 -3.7917902 7.2098653 -6.2559359 -12.3293 2.2622247 1605.8789 Loop time of 2.476e-06 on 1 procs for 0 steps with 3356 atoms 282.7% 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 | | 2.476e-06 | | |100.00 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9512.00 ave 9512 max 9512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 223624.0 ave 223624 max 223624 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 447248.0 ave 447248 max 447248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 447248 Ave neighs/atom = 133.26818 Neighbor list builds = 0 Dangerous builds = 0 3356 -14865.6105909415 eV 2.26222471956968 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:24