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 = 2.8601955 2.8601955 2.8601955 Created orthogonal box = (0.0000000 -53.966060 0.0000000) to (26.983030 53.966060 2.8601955) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9413414 3.9413414 2.8601955 Created 356 atoms using lattice units in orthogonal box = (0.0000000 -53.966060 0.0000000) to (26.983030 53.966060 2.8601955) create_atoms CPU = 0.002 seconds 356 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9413414 3.9413414 2.8601955 Created 357 atoms using lattice units in orthogonal box = (0.0000000 -53.966060 0.0000000) to (26.983030 53.966060 2.8601955) create_atoms CPU = 0.001 seconds 357 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 41 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 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 713 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 5.275 | 5.275 | 5.275 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2967.0966 0 -2967.0966 26878.089 27 0 -3039.4068 0 -3039.4068 7736.7511 Loop time of 6.17305 on 1 procs for 27 steps with 713 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 = -2967.09655072476 -3039.40394429917 -3039.40676777095 Force two-norm initial, final = 115.42674 0.19714756 Force max component initial, final = 44.331046 0.026967750 Final line search alpha, max atom move = 1.0000000 0.026967750 Iterations, force evaluations = 27 45 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.1629 | 6.1629 | 6.1629 | 0.0 | 99.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0049878 | 0.0049878 | 0.0049878 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005117 | | | 0.08 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4226.00 ave 4226 max 4226 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: 41248.0 ave 41248 max 41248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41248 Ave neighs/atom = 57.851332 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 27 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.275 | 5.275 | 5.275 Mbytes Step Temp E_pair E_mol TotEng Press Volume 27 0 -3039.4068 0 -3039.4068 7736.7511 8329.8491 37 0 -3039.7887 0 -3039.7887 -80.657432 8364.4272 Loop time of 1.58672 on 1 procs for 10 steps with 713 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 = -3039.40676777095 -3039.78864238089 -3039.78874328403 Force two-norm initial, final = 101.18576 1.1775432 Force max component initial, final = 100.11683 0.97381634 Final line search alpha, max atom move = 0.00062776072 0.00061132365 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5806 | 1.5806 | 1.5806 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011575 | 0.0011575 | 0.0011575 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005008 | | | 0.32 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4207.00 ave 4207 max 4207 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: 41158.0 ave 41158 max 41158 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41158 Ave neighs/atom = 57.725105 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 5.413 | 5.413 | 5.413 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3039.7887 0 -3039.7887 -80.657432 Loop time of 6.315e-06 on 1 procs for 0 steps with 713 atoms 190.0% 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 | | 6.315e-06 | | |100.00 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4207.00 ave 4207 max 4207 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: 41138.0 ave 41138 max 41138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41138 Ave neighs/atom = 57.697055 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 5.413 | 5.413 | 5.413 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 -3039.7887 -3039.7887 26.993651 108.80501 2.8479061 -80.657432 -80.657432 -52.216633 -4.0260485 -185.72962 2.2898652 321.73536 Loop time of 6.736e-06 on 1 procs for 0 steps with 713 atoms 267.2% 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 | | 6.736e-06 | | |100.00 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4207.00 ave 4207 max 4207 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20569.0 ave 20569 max 20569 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 41138.0 ave 41138 max 41138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41138 Ave neighs/atom = 57.697055 Neighbor list builds = 0 Dangerous builds = 0 713 -3039.78874328403 eV 2.28986516352885 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08