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 -37.072370 0.0000000) to (21.403743 37.072370 4.9540038) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5865163 4.4133774 4.9540038 Created 334 atoms using lattice units in orthogonal box = (0.0000000 -37.072370 0.0000000) to (21.403743 37.072370 4.9540038) create_atoms CPU = 0.001 seconds 334 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5865163 4.4133774 4.9540038 Created 339 atoms using lattice units in orthogonal box = (0.0000000 -37.072370 0.0000000) to (21.403743 37.072370 4.9540038) create_atoms CPU = 0.001 seconds 339 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 = 9 28 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 = 673 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 = 9 28 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) = 4.883 | 4.883 | 4.883 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2670.07 0 -2670.07 58005.528 41 0 -2862.9218 0 -2862.9218 7720.1346 Loop time of 3.0318 on 1 procs for 41 steps with 673 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 = -2670.06995909256 -2862.91902771111 -2862.92179715619 Force two-norm initial, final = 357.83534 0.20899497 Force max component initial, final = 126.62538 0.050397818 Final line search alpha, max atom move = 1.0000000 0.050397818 Iterations, force evaluations = 41 67 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0137 | 3.0137 | 3.0137 | 0.0 | 99.40 Neigh | 0.013178 | 0.013178 | 0.013178 | 0.0 | 0.43 Comm | 0.002085 | 0.002085 | 0.002085 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002824 | | | 0.09 Nlocal: 673.000 ave 673 max 673 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2997.00 ave 2997 max 2997 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: 38818.0 ave 38818 max 38818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38818 Ave neighs/atom = 57.679049 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 28 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 : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.883 | 4.883 | 4.883 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -2862.9218 0 -2862.9218 7720.1346 7861.88 45 0 -2863.0268 0 -2863.0268 6.7934112 7895.2395 Loop time of 0.322093 on 1 procs for 4 steps with 673 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 = -2862.9217971562 -2863.02537453808 -2863.02684836286 Force two-norm initial, final = 69.625079 0.74528120 Force max component initial, final = 56.892576 0.51131743 Final line search alpha, max atom move = 0.00016864983 8.6233595e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32085 | 0.32085 | 0.32085 | 0.0 | 99.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00018706 | 0.00018706 | 0.00018706 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001051 | | | 0.33 Nlocal: 673.000 ave 673 max 673 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2980.00 ave 2980 max 2980 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: 38800.0 ave 38800 max 38800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38800 Ave neighs/atom = 57.652303 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 = 9 28 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) = 5.021 | 5.021 | 5.021 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2863.0268 0 -2863.0268 6.7934112 Loop time of 1.945e-06 on 1 procs for 0 steps with 673 atoms 154.2% 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 | | 1.945e-06 | | |100.00 Nlocal: 673.000 ave 673 max 673 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2980.00 ave 2980 max 2980 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: 38782.0 ave 38782 max 38782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38782 Ave neighs/atom = 57.625557 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 = 9 28 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) = 5.021 | 5.021 | 5.021 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 -2863.0268 -2863.0268 21.413993 74.379041 4.956979 6.7934112 6.7934112 -78.063856 -5.3795821 103.82367 2.1623159 529.68436 Loop time of 1.873e-06 on 1 procs for 0 steps with 673 atoms 160.2% 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 | | 1.873e-06 | | |100.00 Nlocal: 673.000 ave 673 max 673 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2980.00 ave 2980 max 2980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19391.0 ave 19391 max 19391 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 38782.0 ave 38782 max 38782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38782 Ave neighs/atom = 57.625557 Neighbor list builds = 0 Dangerous builds = 0 673 -2863.02684836286 eV 2.16231591096848 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03