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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -32.919740 0.0000000) to (23.275591 32.919740 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3084682 5.1973669 4.3599177 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -32.919740 0.0000000) to (23.275591 32.919740 4.3599177) create_atoms CPU = 0.001 seconds 230 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3084682 5.1973669 4.3599177 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -32.919740 0.0000000) to (23.275591 32.919740 4.3599177) create_atoms CPU = 0.000 seconds 230 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 20 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 5 atoms, new total = 455 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 4.834 | 4.834 | 4.834 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2774.0029 0 -2774.0029 95570.775 98 0 -2947.052 0 -2947.052 2688.7221 Loop time of 20.9798 on 1 procs for 98 steps with 455 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 = -2774.00286326788 -2947.04959436893 -2947.05201234468 Force two-norm initial, final = 374.87831 0.28245594 Force max component initial, final = 132.00742 0.11484466 Final line search alpha, max atom move = 0.86980957 0.099892981 Iterations, force evaluations = 98 175 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.94 | 20.94 | 20.94 | 0.0 | 99.81 Neigh | 0.03154 | 0.03154 | 0.03154 | 0.0 | 0.15 Comm | 0.0045541 | 0.0045541 | 0.0045541 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004138 | | | 0.02 Nlocal: 455.000 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2985.00 ave 2985 max 2985 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: 33854.0 ave 33854 max 33854 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33854 Ave neighs/atom = 74.404396 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 98 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.215 | 5.215 | 5.215 Mbytes Step Temp E_pair E_mol TotEng Press Volume 98 0 -2947.052 0 -2947.052 2688.7221 6681.3682 103 0 -2947.2537 0 -2947.2537 2366.4497 6682.1376 Loop time of 0.834438 on 1 procs for 5 steps with 455 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 = -2947.05201234468 -2947.25219421404 -2947.2537217052 Force two-norm initial, final = 70.466689 0.82822587 Force max component initial, final = 55.978528 0.20958498 Final line search alpha, max atom move = 0.00021428406 4.4910720e-05 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.83356 | 0.83356 | 0.83356 | 0.0 | 99.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016449 | 0.00016449 | 0.00016449 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007112 | | | 0.09 Nlocal: 455.000 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2973.00 ave 2973 max 2973 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: 34224.0 ave 34224 max 34224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34224 Ave neighs/atom = 75.217582 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.353 | 5.353 | 5.353 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2947.2537 0 -2947.2537 2366.4497 Loop time of 1.917e-06 on 1 procs for 0 steps with 455 atoms 156.5% 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 | | 1.917e-06 | | |100.00 Nlocal: 455.000 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2973.00 ave 2973 max 2973 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: 34206.0 ave 34206 max 34206 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34206 Ave neighs/atom = 75.178022 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.353 | 5.353 | 5.353 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 -2947.2537 -2947.2537 23.372625 65.83948 4.3423171 2366.4497 2366.4497 23.786687 7025.5131 50.049338 2.452786 1002.4575 Loop time of 1.544e-06 on 1 procs for 0 steps with 455 atoms 194.3% 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 | | 1.544e-06 | | |100.00 Nlocal: 455.000 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2973.00 ave 2973 max 2973 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17103.0 ave 17103 max 17103 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 34206.0 ave 34206 max 34206 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34206 Ave neighs/atom = 75.178022 Neighbor list builds = 0 Dangerous builds = 0 455 -2947.2537217052 eV 2.45278601879138 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22