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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -81.202250 0.0000000) to (46.882141 81.202250 7.0148060) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2976010 6.4638607 7.0148060 Created 1607 atoms using lattice units in orthogonal box = (0.0000000 -81.202250 0.0000000) to (46.882141 81.202250 7.0148060) create_atoms CPU = 0.004 seconds 1607 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2976010 6.4638607 7.0148060 Created 1609 atoms using lattice units in orthogonal box = (0.0000000 -81.202250 0.0000000) to (46.882141 81.202250 7.0148060) create_atoms CPU = 0.003 seconds 1609 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 12 39 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 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 3213 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_678952612413_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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 6.665 | 6.665 | 6.665 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10690.499 0 -10690.499 2075.0598 137 0 -10774.317 0 -10774.317 1750.127 Loop time of 6.9315 on 1 procs for 137 steps with 3213 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10690.4986748292 -10774.3061830492 -10774.3167766918 Force two-norm initial, final = 38.402959 0.26607877 Force max component initial, final = 7.6290830 0.079908812 Final line search alpha, max atom move = 1.0000000 0.079908812 Iterations, force evaluations = 137 247 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.7348 | 6.7348 | 6.7348 | 0.0 | 97.16 Neigh | 0.11504 | 0.11504 | 0.11504 | 0.0 | 1.66 Comm | 0.03983 | 0.03983 | 0.03983 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04187 | | | 0.60 Nlocal: 3213.00 ave 3213 max 3213 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12877.0 ave 12877 max 12877 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: 452648.0 ave 452648 max 452648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 452648 Ave neighs/atom = 140.88017 Neighbor list builds = 4 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 137 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.665 | 6.665 | 6.665 Mbytes Step Temp E_pair E_mol TotEng Press Volume 137 0 -10774.317 0 -10774.317 1750.127 53409.826 142 0 -10774.65 0 -10774.65 -148.51931 53537.671 Loop time of 0.196213 on 1 procs for 5 steps with 3213 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 = -10774.3167766916 -10774.6425369783 -10774.6495071961 Force two-norm initial, final = 146.62807 8.7990826 Force max component initial, final = 140.41064 5.8738498 Final line search alpha, max atom move = 6.2644723e-05 0.00036796569 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19129 | 0.19129 | 0.19129 | 0.0 | 97.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00071866 | 0.00071866 | 0.00071866 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004201 | | | 2.14 Nlocal: 3213.00 ave 3213 max 3213 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12874.0 ave 12874 max 12874 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: 452578.0 ave 452578 max 452578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 452578 Ave neighs/atom = 140.85839 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 12 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 6.803 | 6.803 | 6.803 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10774.65 0 -10774.65 -148.51931 Loop time of 2.182e-06 on 1 procs for 0 steps with 3213 atoms 183.3% 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 | | 2.182e-06 | | |100.00 Nlocal: 3213.00 ave 3213 max 3213 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12862.0 ave 12862 max 12862 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: 452162.0 ave 452162 max 452162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 452162 Ave neighs/atom = 140.72891 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 12 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 6.803 | 6.803 | 6.803 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 -10774.65 -10774.65 46.877999 163.16727 6.9993446 -148.51931 -148.51931 -175.76619 -103.88801 -165.90374 2.5685254 1333.7128 Loop time of 2.435e-06 on 1 procs for 0 steps with 3213 atoms 246.4% 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 | | 2.435e-06 | | |100.00 Nlocal: 3213.00 ave 3213 max 3213 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12862.0 ave 12862 max 12862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 226081.0 ave 226081 max 226081 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 452162.0 ave 452162 max 452162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 452162 Ave neighs/atom = 140.72891 Neighbor list builds = 0 Dangerous builds = 0 3213 -10774.6495071961 eV 2.56852541038384 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07