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 = 2.8548760 2.8548760 2.8548760 Created orthogonal box = (0.0000000 -46.036347 0.0000000) to (23.016746 46.036347 2.8548760) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.1869341 3.1869341 2.8548760 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -46.036347 0.0000000) to (23.016746 46.036347 2.8548760) create_atoms CPU = 0.001 seconds 261 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.1869341 3.1869341 2.8548760 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -46.036347 0.0000000) to (23.016746 46.036347 2.8548760) create_atoms CPU = 0.001 seconds 261 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 26 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 518 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.501 | 4.501 | 4.501 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2035.9573 0 -2035.9573 23942.25 67 0 -2072.7859 0 -2072.7859 -2279.355 Loop time of 1.17075 on 1 procs for 67 steps with 518 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 = -2035.95727877187 -2072.78439203838 -2072.78591407494 Force two-norm initial, final = 92.612344 0.11521496 Force max component initial, final = 29.984668 0.014802667 Final line search alpha, max atom move = 1.0000000 0.014802667 Iterations, force evaluations = 67 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1338 | 1.1338 | 1.1338 | 0.0 | 96.85 Neigh | 0.0099141 | 0.0099141 | 0.0099141 | 0.0 | 0.85 Comm | 0.01588 | 0.01588 | 0.01588 | 0.0 | 1.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01112 | | | 0.95 Nlocal: 518.000 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5473.00 ave 5473 max 5473 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: 70870.0 ave 70870 max 70870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70870 Ave neighs/atom = 136.81467 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.505 | 4.505 | 4.505 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -2072.7859 0 -2072.7859 -2279.355 6050.0927 70 0 -2072.7966 0 -2072.7966 -231.68215 6042.9808 Loop time of 0.0582349 on 1 procs for 3 steps with 518 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 = -2072.78591407494 -2072.79656548857 -2072.79663802173 Force two-norm initial, final = 13.830806 0.12244560 Force max component initial, final = 13.258342 0.015780477 Final line search alpha, max atom move = 0.00068526537 1.0813814e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.055326 | 0.055326 | 0.055326 | 0.0 | 95.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00080927 | 0.00080927 | 0.00080927 | 0.0 | 1.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0021 | | | 3.61 Nlocal: 518.000 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5858.00 ave 5858 max 5858 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: 70822.0 ave 70822 max 70822 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70822 Ave neighs/atom = 136.72201 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.643 | 4.643 | 4.643 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2072.7966 0 -2072.7966 -231.68215 Loop time of 6.425e-06 on 1 procs for 0 steps with 518 atoms 171.2% 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 | | 6.425e-06 | | |100.00 Nlocal: 518.000 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5864.00 ave 5864 max 5864 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: 70874.0 ave 70874 max 70874 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70874 Ave neighs/atom = 136.82239 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.643 | 4.643 | 4.643 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 -2072.7966 -2072.7966 22.975133 92.072694 2.8566848 -231.68215 -231.68215 2.8258682 -698.09763 0.22529456 2.3208193 117.4738 Loop time of 6.947e-06 on 1 procs for 0 steps with 518 atoms 244.7% 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 | | 6.947e-06 | | |100.00 Nlocal: 518.000 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5864.00 ave 5864 max 5864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35437.0 ave 35437 max 35437 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 70874.0 ave 70874 max 70874 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70874 Ave neighs/atom = 136.82239 Neighbor list builds = 0 Dangerous builds = 0 518 -1999.54023683467 eV 2.32081933162442 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01