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 = 4.0709491 4.0709491 4.0709491 Created orthogonal box = (0.0000000 -77.885913 0.0000000) to (44.965103 77.885913 7.0510907) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6341955 5.9581737 7.0510907 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -77.885913 0.0000000) to (44.965103 77.885913 7.0510907) create_atoms CPU = 0.003 seconds 1466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6341955 5.9581737 7.0510907 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -77.885913 0.0000000) to (44.965103 77.885913 7.0510907) create_atoms CPU = 0.003 seconds 1466 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 15 52 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 2904 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 15 52 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.268 | 5.268 | 5.268 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9737.5518 0 -9737.5518 91.090007 40 0 -9757.2213 0 -9757.2213 -5075.5325 Loop time of 5.28476 on 1 procs for 40 steps with 2904 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9737.55177635531 -9757.2158484299 -9757.22125579696 Force two-norm initial, final = 19.598410 0.43530359 Force max component initial, final = 3.3999499 0.10283571 Final line search alpha, max atom move = 1.0000000 0.10283571 Iterations, force evaluations = 40 67 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2388 | 5.2388 | 5.2388 | 0.0 | 99.13 Neigh | 0.027366 | 0.027366 | 0.027366 | 0.0 | 0.52 Comm | 0.0072235 | 0.0072235 | 0.0072235 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01136 | | | 0.21 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7754.00 ave 7754 max 7754 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: 156348.0 ave 156348 max 156348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156348 Ave neighs/atom = 53.838843 Neighbor list builds = 2 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 15 52 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.268 | 5.268 | 5.268 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -9757.2213 0 -9757.2213 -5075.5325 49387.928 43 0 -9757.474 0 -9757.474 -1025.1758 49191.258 Loop time of 0.373295 on 1 procs for 3 steps with 2904 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 = -9757.22125579695 -9757.46510459531 -9757.4739774435 Force two-norm initial, final = 183.95728 16.184607 Force max component initial, final = 145.67238 16.060129 Final line search alpha, max atom move = 3.9670897e-05 0.00063711973 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37117 | 0.37117 | 0.37117 | 0.0 | 99.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029406 | 0.00029406 | 0.00029406 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00183 | | | 0.49 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7747.00 ave 7747 max 7747 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: 156372.0 ave 156372 max 156372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156372 Ave neighs/atom = 53.847107 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 15 52 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.406 | 5.406 | 5.406 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9757.474 0 -9757.474 -1025.1758 Loop time of 3.379e-06 on 1 procs for 0 steps with 2904 atoms 177.6% 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 | | 3.379e-06 | | |100.00 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7756.00 ave 7756 max 7756 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: 156400.0 ave 156400 max 156400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156400 Ave neighs/atom = 53.856749 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 15 52 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.406 | 5.406 | 5.406 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 -9757.474 -9757.474 44.9071 155.77183 7.0320833 -1025.1758 -1025.1758 522.40927 -3660.8046 62.867967 2.5246151 1384.1146 Loop time of 2.013e-06 on 1 procs for 0 steps with 2904 atoms 198.7% 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 | | 2.013e-06 | | |100.00 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7756.00 ave 7756 max 7756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78200.0 ave 78200 max 78200 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 156400.0 ave 156400 max 156400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156400 Ave neighs/atom = 53.856749 Neighbor list builds = 0 Dangerous builds = 0 2904 -9757.4739774435 eV 2.52461513704707 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06