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 = 2.8665000 2.8665000 2.8665000 Created orthogonal box = (0.0000000 -29.232678 0.0000000) to (25.316242 29.232678 4.9649236) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5439409 4.4973351 4.9649236 Created 309 atoms using lattice units in orthogonal box = (0.0000000 -29.232678 0.0000000) to (25.316242 29.232678 4.9649236) create_atoms CPU = 0.003 seconds 309 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5439409 4.4973351 4.9649236 Created 317 atoms using lattice units in orthogonal box = (0.0000000 -29.232678 0.0000000) to (25.316242 29.232678 4.9649236) create_atoms CPU = 0.002 seconds 317 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 9 21 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 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 624 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_142799717516_005#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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 9 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.489 | 4.489 | 4.489 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2554.0844 0 -2554.0844 33314.345 66 0 -2671.4633 0 -2671.4633 12885.269 Loop time of 0.505429 on 1 procs for 66 steps with 624 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 = -2554.08438779686 -2671.46122739749 -2671.46331511268 Force two-norm initial, final = 101.94828 0.17620993 Force max component initial, final = 40.309597 0.032540206 Final line search alpha, max atom move = 1.0000000 0.032540206 Iterations, force evaluations = 66 102 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.45563 | 0.45563 | 0.45563 | 0.0 | 90.15 Neigh | 0.026132 | 0.026132 | 0.026132 | 0.0 | 5.17 Comm | 0.01163 | 0.01163 | 0.01163 | 0.0 | 2.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01204 | | | 2.38 Nlocal: 624.000 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2981.00 ave 2981 max 2981 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: 38298.0 ave 38298 max 38298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38298 Ave neighs/atom = 61.375000 Neighbor list builds = 3 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 9 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.489 | 4.489 | 4.489 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -2671.4633 0 -2671.4633 12885.269 7348.6982 70 0 -2671.675 0 -2671.675 -3.6575561 7401.1535 Loop time of 0.0285872 on 1 procs for 4 steps with 624 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 = -2671.46331511268 -2671.67460698019 -2671.67497290955 Force two-norm initial, final = 102.55577 0.26812939 Force max component initial, final = 62.651964 0.11632548 Final line search alpha, max atom move = 0.00050856397 5.9158945e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.026075 | 0.026075 | 0.026075 | 0.0 | 91.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055482 | 0.00055482 | 0.00055482 | 0.0 | 1.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001958 | | | 6.85 Nlocal: 624.000 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2974.00 ave 2974 max 2974 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: 38178.0 ave 38178 max 38178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38178 Ave neighs/atom = 61.182692 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 9 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.627 | 4.627 | 4.627 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2671.675 0 -2671.675 -3.6575561 Loop time of 6.435e-06 on 1 procs for 0 steps with 624 atoms 202.0% 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 | | 6.435e-06 | | |100.00 Nlocal: 624.000 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2974.00 ave 2974 max 2974 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: 37622.0 ave 37622 max 37622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37622 Ave neighs/atom = 60.291667 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 9 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.627 | 4.627 | 4.627 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 -2671.675 -2671.675 25.364047 58.604723 4.9790701 -3.6575561 -3.6575561 -17.863851 25.241769 -18.350587 2.3230939 661.53343 Loop time of 6.846e-06 on 1 procs for 0 steps with 624 atoms 219.1% 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 | | 6.846e-06 | | |100.00 Nlocal: 624.000 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2974.00 ave 2974 max 2974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18811.0 ave 18811 max 18811 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 37622.0 ave 37622 max 37622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37622 Ave neighs/atom = 60.291667 Neighbor list builds = 0 Dangerous builds = 0 624 -2671.67497290955 eV 2.3230939226383 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01