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 = 3.6110509 3.6110509 3.6110509 Created orthogonal box = (0.0000000 -71.495160 0.0000000) to (43.781665 71.495160 8.8452321) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0631858 5.1067972 5.8968214 Created 2351 atoms using lattice units in orthogonal box = (0.0000000 -71.495160 0.0000000) to (43.781665 71.495160 8.8452321) create_atoms CPU = 0.003 seconds 2351 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0631858 5.1067972 5.8968214 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -71.495160 0.0000000) to (43.781665 71.495160 8.8452321) create_atoms CPU = 0.003 seconds 2357 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 28 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 4680 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_984358344196_004#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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 16.43 | 16.43 | 16.43 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -18798.373 0 -18798.373 18519.72 104 0 -19361.793 0 -19361.793 -2568.2743 Loop time of 13.2564 on 1 procs for 104 steps with 4680 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -18798.3726349072 -19361.7754515308 -19361.7931075508 Force two-norm initial, final = 528.13672 0.59488802 Force max component initial, final = 94.481805 0.10558847 Final line search alpha, max atom move = 1.0000000 0.10558847 Iterations, force evaluations = 104 195 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.032 | 13.032 | 13.032 | 0.0 | 98.31 Neigh | 0.098314 | 0.098314 | 0.098314 | 0.0 | 0.74 Comm | 0.069639 | 0.069639 | 0.069639 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05616 | | | 0.42 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21482.0 ave 21482 max 21482 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: 1.77295e+06 ave 1.77295e+06 max 1.77295e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1772952 Ave neighs/atom = 378.83590 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 104 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 16.43 | 16.43 | 16.43 Mbytes Step Temp E_pair E_mol TotEng Press Volume 104 0 -19361.793 0 -19361.793 -2568.2743 55374.288 106 0 -19361.903 0 -19361.903 -15.123378 55291.525 Loop time of 0.338311 on 1 procs for 2 steps with 4680 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 = -19361.793107551 -19361.8870901357 -19361.9030778498 Force two-norm initial, final = 171.13314 11.628213 Force max component initial, final = 133.50986 9.2933322 Final line search alpha, max atom move = 2.2421872e-05 0.00020837391 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33292 | 0.33292 | 0.33292 | 0.0 | 98.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00095313 | 0.00095313 | 0.00095313 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004443 | | | 1.31 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21492.0 ave 21492 max 21492 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: 1.77367e+06 ave 1.77367e+06 max 1.77367e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1773666 Ave neighs/atom = 378.98846 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 15.94 | 15.94 | 15.94 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19361.903 0 -19361.903 -15.123378 Loop time of 2.439e-06 on 1 procs for 0 steps with 4680 atoms 164.0% 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 | | 2.439e-06 | | |100.00 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21506.0 ave 21506 max 21506 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: 1.77385e+06 ave 1.77385e+06 max 1.77385e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1773850 Ave neighs/atom = 379.02778 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 15.94 | 15.94 | 15.94 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 -19361.903 -19361.903 43.746644 143.05205 8.8352682 -15.123378 -15.123378 -269.07647 23.605166 200.10117 2.2589896 1783.7293 Loop time of 2.646e-06 on 1 procs for 0 steps with 4680 atoms 302.3% 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 | | 2.646e-06 | | |100.00 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21506.0 ave 21506 max 21506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 886925.0 ave 886925 max 886925 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.77385e+06 ave 1.77385e+06 max 1.77385e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1773850 Ave neighs/atom = 379.02778 Neighbor list builds = 0 Dangerous builds = 0 4680 -19361.9030778498 eV 2.25898955852818 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14