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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -45.990000 0.0000000) to (10.839947 45.990000 5.1100000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0221927 5.1100000 5.1100000 Created 216 atoms using lattice units in orthogonal box = (0.0000000 -45.990000 0.0000000) to (10.839947 45.990000 5.1100000) create_atoms CPU = 0.002 seconds 216 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0221927 5.1100000 5.1100000 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -45.990000 0.0000000) to (10.839947 45.990000 5.1100000) create_atoms CPU = 0.001 seconds 218 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 4 33 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, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 434 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_849011491644_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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 4 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.466 | 4.466 | 4.466 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1368.0137 0 -1368.0137 96389.074 62 0 -1531.4707 0 -1531.4707 12338.217 Loop time of 1.86053 on 1 procs for 62 steps with 434 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1368.01370508306 -1531.46933502377 -1531.47072346847 Force two-norm initial, final = 303.51175 0.097927718 Force max component initial, final = 78.778660 0.014615503 Final line search alpha, max atom move = 1.0000000 0.014615503 Iterations, force evaluations = 62 111 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8387 | 1.8387 | 1.8387 | 0.0 | 98.83 Neigh | 0.0052601 | 0.0052601 | 0.0052601 | 0.0 | 0.28 Comm | 0.0084859 | 0.0084859 | 0.0084859 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008068 | | | 0.43 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2785.00 ave 2785 max 2785 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: 26788.0 ave 26788 max 26788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26788 Ave neighs/atom = 61.723502 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 4 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.466 | 4.466 | 4.466 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -1531.4707 0 -1531.4707 12338.217 5094.968 71 0 -1531.7138 0 -1531.7138 260.63144 5137.7747 Loop time of 0.183573 on 1 procs for 9 steps with 434 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 = -1531.47072346847 -1531.71234033396 -1531.71377003251 Force two-norm initial, final = 71.219668 1.4704765 Force max component initial, final = 56.493258 0.98159499 Final line search alpha, max atom move = 0.00047171774 0.00046303577 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18024 | 0.18024 | 0.18024 | 0.0 | 98.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00070137 | 0.00070137 | 0.00070137 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002636 | | | 1.44 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2816.00 ave 2816 max 2816 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: 27812.0 ave 27812 max 27812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27812 Ave neighs/atom = 64.082949 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 4 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.604 | 4.604 | 4.604 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1531.7138 0 -1531.7138 260.63144 Loop time of 6.384e-06 on 1 procs for 0 steps with 434 atoms 172.3% 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 | | 6.384e-06 | | |100.00 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2816.00 ave 2816 max 2816 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: 26460.0 ave 26460 max 26460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26460 Ave neighs/atom = 60.967742 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 4 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.604 | 4.604 | 4.604 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 -1531.7138 -1531.7138 10.83712 92.781255 5.1097649 260.63144 260.63144 237.60539 308.76956 235.51938 2.3731229 269.97721 Loop time of 6.947e-06 on 1 procs for 0 steps with 434 atoms 244.7% 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 | | 6.947e-06 | | |100.00 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2816.00 ave 2816 max 2816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13230.0 ave 13230 max 13230 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26460.0 ave 26460 max 26460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26460 Ave neighs/atom = 60.967742 Neighbor list builds = 0 Dangerous builds = 0 434 -1531.71377003251 eV 2.37312285447234 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02