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 = 6.4001079 6.4001079 6.4001079 Created orthogonal box = (0.0000000 -103.19864 0.0000000) to (51.599319 103.19864 6.4001079) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 8.7321925 8.7321925 6.4001079 Created 520 atoms using lattice units in orthogonal box = (0.0000000 -103.19864 0.0000000) to (51.599319 103.19864 6.4001079) create_atoms CPU = 0.002 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 8.7321925 8.7321925 6.4001079 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -103.19864 0.0000000) to (51.599319 103.19864 6.4001079) create_atoms CPU = 0.002 seconds 522 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 12 45 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 9.2864 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1034 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_128037485276_003#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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 12 45 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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) = 4.584 | 4.584 | 4.584 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4200.0574 0 -4200.0574 326200.79 1 0 -4200.0574 0 -4200.0574 326200.79 Loop time of 0.266671 on 1 procs for 1 steps with 1034 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -4200.05735714334 -4200.05735714334 -4200.05735714334 Force two-norm initial, final = 27.491235 27.491235 Force max component initial, final = 5.4569619 5.4569619 Final line search alpha, max atom move = 8.5333432e-12 4.6566129e-11 Iterations, force evaluations = 1 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26056 | 0.26056 | 0.26056 | 0.0 | 97.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0032257 | 0.0032257 | 0.0032257 | 0.0 | 1.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002883 | | | 1.08 Nlocal: 1034.00 ave 1034 max 1034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4327.00 ave 4327 max 4327 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: 55380.0 ave 55380 max 55380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55380 Ave neighs/atom = 53.558994 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 12 45 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.584 | 4.584 | 4.584 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -4200.0574 0 -4200.0574 326200.79 68160.887 2 0 -4200.0574 0 -4200.0574 326200.79 68160.887 Loop time of 0.288882 on 1 procs for 1 steps with 1034 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -4200.05735714334 -4200.05735714334 -4200.05735714334 Force two-norm initial, final = 24037.014 24037.014 Force max component initial, final = 13975.466 13975.466 Final line search alpha, max atom move = 1.6659956e-17 2.3283064e-13 Iterations, force evaluations = 1 33 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27391 | 0.27391 | 0.27391 | 0.0 | 94.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0032016 | 0.0032016 | 0.0032016 | 0.0 | 1.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01177 | | | 4.08 Nlocal: 1034.00 ave 1034 max 1034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4327.00 ave 4327 max 4327 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: 55380.0 ave 55380 max 55380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55380 Ave neighs/atom = 53.558994 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 12 45 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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) = 4.722 | 4.722 | 4.722 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4200.0574 0 -4200.0574 326200.79 Loop time of 6.194e-06 on 1 procs for 0 steps with 1034 atoms 177.6% 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 | | 6.194e-06 | | |100.00 Nlocal: 1034.00 ave 1034 max 1034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4327.00 ave 4327 max 4327 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: 55380.0 ave 55380 max 55380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55380 Ave neighs/atom = 53.558994 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 12 45 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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) = 4.722 | 4.722 | 4.722 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 -4200.0574 -4200.0574 51.599319 206.39728 6.4001079 326200.79 326200.79 328504.57 323270.92 326826.89 2.3841018 1441.6495 Loop time of 7.116e-06 on 1 procs for 0 steps with 1034 atoms 210.8% 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 | | 7.116e-06 | | |100.00 Nlocal: 1034.00 ave 1034 max 1034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4327.00 ave 4327 max 4327 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27690.0 ave 27690 max 27690 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 55380.0 ave 55380 max 55380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55380 Ave neighs/atom = 53.558994 Neighbor list builds = 0 Dangerous builds = 0 1034 -428.345790710411 eV 2.38410179564156 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02