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 = 3.6150017 3.6150017 3.6150017 Created orthogonal box = (0.0000000 -42.157802 0.0000000) to (21.078901 42.157802 3.6150017) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9597414 4.9597414 3.6150017 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -42.157802 0.0000000) to (21.078901 42.157802 3.6150017) create_atoms CPU = 0.003 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9597414 4.9597414 3.6150017 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.157802 0.0000000) to (21.078901 42.157802 3.6150017) create_atoms CPU = 0.002 seconds 274 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 5 20 1 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 544 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_592013496703_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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 4.918 | 4.918 | 4.918 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1786.3034 0 -1786.3034 41848.452 58 0 -1917.6337 0 -1917.6337 7361.022 Loop time of 1.50819 on 1 procs for 58 steps with 544 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 = -1786.30344703529 -1917.63208801143 -1917.63371312347 Force two-norm initial, final = 201.39737 0.10559881 Force max component initial, final = 55.096268 0.015250866 Final line search alpha, max atom move = 1.0000000 0.015250866 Iterations, force evaluations = 58 107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4652 | 1.4652 | 1.4652 | 0.0 | 97.15 Neigh | 0.01665 | 0.01665 | 0.01665 | 0.0 | 1.10 Comm | 0.016044 | 0.016044 | 0.016044 | 0.0 | 1.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01033 | | | 0.68 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6182.00 ave 6182 max 6182 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: 113480.0 ave 113480 max 113480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113480 Ave neighs/atom = 208.60294 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.922 | 4.922 | 4.922 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -1917.6337 0 -1917.6337 7361.022 6424.8711 64 0 -1917.782 0 -1917.782 -68.78271 6459.0707 Loop time of 0.111695 on 1 procs for 6 steps with 544 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 = -1917.63371312347 -1917.78042843011 -1917.78199052545 Force two-norm initial, final = 58.178308 0.71099170 Force max component initial, final = 49.849917 0.67517757 Final line search alpha, max atom move = 0.00030946431 0.00020894336 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10733 | 0.10733 | 0.10733 | 0.0 | 96.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010844 | 0.0010844 | 0.0010844 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003278 | | | 2.94 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6518.00 ave 6518 max 6518 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: 112216.0 ave 112216 max 112216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112216 Ave neighs/atom = 206.27941 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 5 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.060 | 5.060 | 5.060 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1917.782 0 -1917.782 -68.78271 Loop time of 6.816e-06 on 1 procs for 0 steps with 544 atoms 176.1% 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 | | 6.816e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6470.00 ave 6470 max 6470 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: 109736.0 ave 109736 max 109736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109736 Ave neighs/atom = 201.72059 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 5 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.060 | 5.060 | 5.060 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 -1917.782 -1917.782 21.043992 84.789692 3.6199191 -68.78271 -68.78271 -8.3586787 -30.283419 -167.70603 2.3102468 247.90228 Loop time of 6.906e-06 on 1 procs for 0 steps with 544 atoms 217.2% 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 | | 6.906e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6470.00 ave 6470 max 6470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54868.0 ave 54868 max 54868 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 109736.0 ave 109736 max 109736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109736 Ave neighs/atom = 201.72059 Neighbor list builds = 0 Dangerous builds = 0 544 -1917.78199052545 eV 2.31024684594314 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02