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 = 3.5213918 3.5213918 3.5213918 Created orthogonal box = (0.0000000 -55.454933 0.0000000) to (33.959072 55.454933 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4772697 5.3666064 5.7504087 Created 1487 atoms using lattice units in orthogonal box = (0.0000000 -55.454933 0.0000000) to (33.959072 55.454933 8.6256130) create_atoms CPU = 0.003 seconds 1487 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4772697 5.3666064 5.7504087 Created 1493 atoms using lattice units in orthogonal box = (0.0000000 -55.454933 0.0000000) to (33.959072 55.454933 8.6256130) create_atoms CPU = 0.002 seconds 1493 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 35 3 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2976 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_500937681860_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 35 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.654 | 5.654 | 5.654 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11571.359 0 -11571.359 103104.14 83 0 -13197.626 0 -13197.626 7913.3214 Loop time of 20.0319 on 1 procs for 83 steps with 2976 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 = -11571.3587432265 -13197.6155967666 -13197.6264455836 Force two-norm initial, final = 1342.9741 0.37715998 Force max component initial, final = 217.54495 0.063192700 Final line search alpha, max atom move = 1.0000000 0.063192700 Iterations, force evaluations = 83 150 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.952 | 19.952 | 19.952 | 0.0 | 99.60 Neigh | 0.042938 | 0.042938 | 0.042938 | 0.0 | 0.21 Comm | 0.014662 | 0.014662 | 0.014662 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02204 | | | 0.11 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8501.00 ave 8501 max 8501 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: 262910.0 ave 262910 max 262910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 262910 Ave neighs/atom = 88.343414 Neighbor list builds = 2 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 35 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.667 | 5.667 | 5.667 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -13197.626 0 -13197.626 7913.3214 32487.476 89 0 -13198.384 0 -13198.384 -16.682305 32624.557 Loop time of 1.24615 on 1 procs for 6 steps with 2976 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 = -13197.6264455836 -13198.3835235689 -13198.384169774 Force two-norm initial, final = 333.95764 2.0019674 Force max component initial, final = 305.47355 1.7312433 Final line search alpha, max atom move = 0.00010274327 0.00017787359 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.241 | 1.241 | 1.241 | 0.0 | 99.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069112 | 0.00069112 | 0.00069112 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004462 | | | 0.36 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8579.00 ave 8579 max 8579 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: 261920.0 ave 261920 max 261920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261920 Ave neighs/atom = 88.010753 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 35 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.805 | 5.805 | 5.805 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13198.384 0 -13198.384 -16.682305 Loop time of 2.074e-06 on 1 procs for 0 steps with 2976 atoms 192.9% 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 | | 2.074e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8604.00 ave 8604 max 8604 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: 260890.0 ave 260890 max 260890 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 260890 Ave neighs/atom = 87.664651 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 35 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.805 | 5.805 | 5.805 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 -13198.384 -13198.384 33.969629 111.4726 8.6156031 -16.682305 -16.682305 -85.046967 -5.7626797 40.762731 2.2420735 920.15669 Loop time of 2.363e-06 on 1 procs for 0 steps with 2976 atoms 211.6% 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 | | 2.363e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8604.00 ave 8604 max 8604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130445.0 ave 130445 max 130445 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 260890.0 ave 260890 max 260890 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 260890 Ave neighs/atom = 87.664651 Neighbor list builds = 0 Dangerous builds = 0 2976 -13198.384169774 eV 2.24207346751554 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22