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 -44.891183 0.0000000) to (22.444050 44.891183 3.0829274) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8112538 3.8112538 3.0829274 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -44.891183 0.0000000) to (22.444050 44.891183 3.0829274) create_atoms CPU = 0.000 seconds 213 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8112538 3.8112538 3.0829274 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -44.891183 0.0000000) to (22.444050 44.891183 3.0829274) create_atoms CPU = 0.000 seconds 213 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 27 1 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 6 atoms, new total = 420 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_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 27 1 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) = 5.223 | 5.223 | 5.223 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2654.9101 0 -2654.9101 28018.085 73 0 -2723.629 0 -2723.629 -11361.885 Loop time of 7.58392 on 1 procs for 73 steps with 420 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 = -2654.91009710259 -2723.62634264158 -2723.62904383138 Force two-norm initial, final = 174.53193 0.23912510 Force max component initial, final = 75.261715 0.043477352 Final line search alpha, max atom move = 1.0000000 0.043477352 Iterations, force evaluations = 73 134 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.5567 | 7.5567 | 7.5567 | 0.0 | 99.64 Neigh | 0.021631 | 0.021631 | 0.021631 | 0.0 | 0.29 Comm | 0.0036786 | 0.0036786 | 0.0036786 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001919 | | | 0.03 Nlocal: 420.000 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3678.00 ave 3678 max 3678 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: 30776.0 ave 30776 max 30776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30776 Ave neighs/atom = 73.276190 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 27 1 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 : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.220 | 5.220 | 5.220 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -2723.629 0 -2723.629 -11361.885 6212.3451 80 0 -2723.8771 0 -2723.8771 4588.9102 6164.6445 Loop time of 0.494772 on 1 procs for 7 steps with 420 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 = -2723.62904383137 -2723.87589395375 -2723.8771298657 Force two-norm initial, final = 90.353535 0.81272570 Force max component initial, final = 64.601057 0.69174651 Final line search alpha, max atom move = 0.00013857966 9.5861996e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49401 | 0.49401 | 0.49401 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001653 | 0.0001653 | 0.0001653 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006011 | | | 0.12 Nlocal: 420.000 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3420.00 ave 3420 max 3420 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: 30550.0 ave 30550 max 30550 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30550 Ave neighs/atom = 72.738095 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 27 1 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) = 5.358 | 5.358 | 5.358 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2723.8771 0 -2723.8771 4588.9102 Loop time of 2.4e-06 on 1 procs for 0 steps with 420 atoms 125.0% 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 | | 2.4e-06 | | |100.00 Nlocal: 420.000 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3420.00 ave 3420 max 3420 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: 31452.0 ave 31452 max 31452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31452 Ave neighs/atom = 74.885714 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 27 1 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) = 5.358 | 5.358 | 5.358 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 -2723.8771 -2723.8771 22.413365 89.782366 3.0634439 4588.9102 4588.9102 179.53748 13544.244 42.948886 2.5477212 639.54419 Loop time of 2e-06 on 1 procs for 0 steps with 420 atoms 0.0% 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 | | 2e-06 | | |100.00 Nlocal: 420.000 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3420.00 ave 3420 max 3420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15726.0 ave 15726 max 15726 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 31452.0 ave 31452 max 31452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31452 Ave neighs/atom = 74.885714 Neighbor list builds = 0 Dangerous builds = 0 420 -2723.8771298657 eV 2.54772116440996 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08