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 = 2.8688302 2.8688302 2.8688302 Created orthogonal box = (0.0000000 -42.454810 0.0000000) to (34.664208 42.454810 7.0271702) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2736694 4.0710092 4.6847802 Created 876 atoms using lattice units in orthogonal box = (0.0000000 -42.454810 0.0000000) to (34.664208 42.454810 7.0271702) create_atoms CPU = 0.002 seconds 876 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2736694 4.0710092 4.6847802 Created 878 atoms using lattice units in orthogonal box = (0.0000000 -42.454810 0.0000000) to (34.664208 42.454810 7.0271702) create_atoms CPU = 0.001 seconds 878 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 = 7 17 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 10 atoms, new total = 1744 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 = 7 17 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) = 7.219 | 7.219 | 7.219 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6188.7626 0 -6188.7626 75314.951 82 0 -7165.9845 0 -7165.9845 -919.99956 Loop time of 3.588 on 1 procs for 82 steps with 1744 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 = -6188.76255788945 -7165.97738276097 -7165.98450270735 Force two-norm initial, final = 1044.5833 0.34160971 Force max component initial, final = 204.04093 0.022820868 Final line search alpha, max atom move = 1.0000000 0.022820868 Iterations, force evaluations = 82 139 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4417 | 3.4417 | 3.4417 | 0.0 | 95.92 Neigh | 0.1104 | 0.1104 | 0.1104 | 0.0 | 3.08 Comm | 0.020547 | 0.020547 | 0.020547 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01539 | | | 0.43 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12071.0 ave 12071 max 12071 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: 672084.0 ave 672084 max 672084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 672084 Ave neighs/atom = 385.36927 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 7 17 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 : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.219 | 7.219 | 7.219 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -7165.9845 0 -7165.9845 -919.99956 20683.244 91 0 -7167.0779 0 -7167.0779 -30.089278 20670.931 Loop time of 0.289458 on 1 procs for 9 steps with 1744 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 = -7165.98450270736 -7167.07777083089 -7167.07785938303 Force two-norm initial, final = 224.36932 1.9661953 Force max component initial, final = 170.43703 1.5437534 Final line search alpha, max atom move = 0.0011788385 0.0018198359 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28283 | 0.28283 | 0.28283 | 0.0 | 97.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011559 | 0.0011559 | 0.0011559 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005475 | | | 1.89 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12020.0 ave 12020 max 12020 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: 674680.0 ave 674680 max 674680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 674680 Ave neighs/atom = 386.85780 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 = 7 17 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) = 7.357 | 7.357 | 7.357 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7167.0779 0 -7167.0779 -30.089278 Loop time of 1.965e-06 on 1 procs for 0 steps with 1744 atoms 152.7% 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 | | 1.965e-06 | | |100.00 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12064.0 ave 12064 max 12064 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: 676752.0 ave 676752 max 676752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 676752 Ave neighs/atom = 388.04587 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 = 7 17 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) = 7.357 | 7.357 | 7.357 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 -7167.0779 -7167.0779 34.465332 85.571046 7.008914 -30.089278 -30.089278 8.4019464 20.673642 -119.34342 2.3283851 1667.1813 Loop time of 2.89e-06 on 1 procs for 0 steps with 1744 atoms 276.8% 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 | | 2.89e-06 | | |100.00 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12064.0 ave 12064 max 12064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 338376.0 ave 338376 max 338376 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 676752.0 ave 676752 max 676752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 676752 Ave neighs/atom = 388.04587 Neighbor list builds = 0 Dangerous builds = 0 1744 -7167.07785938303 eV 2.328385116093 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04