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 = 3.6390851 3.6390851 3.6390851 Created orthogonal box = (0.0000000 -58.678484 0.0000000) to (29.339242 58.678484 3.6390851) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9651025 4.9651025 3.6390851 Created 520 atoms using lattice units in orthogonal box = (0.0000000 -58.678484 0.0000000) to (29.339242 58.678484 3.6390851) create_atoms CPU = 0.002 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9651025 4.9651025 3.6390851 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.678484 0.0000000) to (29.339242 58.678484 3.6390851) create_atoms CPU = 0.002 seconds 522 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 25 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1040 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_120596890176_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.862 | 5.862 | 5.862 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2711.9197 0 -2711.9197 141699.78 63 0 -3401.6378 0 -3401.6378 5054.6047 Loop time of 4.81152 on 1 procs for 63 steps with 1040 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 = -2711.91966499442 -3401.6344329431 -3401.63778552579 Force two-norm initial, final = 1534.2032 0.14859193 Force max component initial, final = 455.57064 0.0088050055 Final line search alpha, max atom move = 1.0000000 0.0088050055 Iterations, force evaluations = 63 115 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7268 | 4.7268 | 4.7268 | 0.0 | 98.24 Neigh | 0.036044 | 0.036044 | 0.036044 | 0.0 | 0.75 Comm | 0.031226 | 0.031226 | 0.031226 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0175 | | | 0.36 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11382.0 ave 11382 max 11382 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: 330688.0 ave 330688 max 330688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 330688 Ave neighs/atom = 317.96923 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.855 | 5.855 | 5.855 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -3401.6378 0 -3401.6378 5054.6047 12529.969 69 0 -3401.8083 0 -3401.8083 245.09668 12571.794 Loop time of 0.372568 on 1 procs for 6 steps with 1040 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 = -3401.63778552579 -3401.80761197707 -3401.80831371503 Force two-norm initial, final = 82.439182 4.1461350 Force max component initial, final = 75.204947 3.8721281 Final line search alpha, max atom move = 0.00021067939 0.00081577758 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.36448 | 0.36448 | 0.36448 | 0.0 | 97.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020687 | 0.0020687 | 0.0020687 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006017 | | | 1.62 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10996.0 ave 10996 max 10996 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: 330704.0 ave 330704 max 330704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 330704 Ave neighs/atom = 317.98462 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.992 | 5.992 | 5.992 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3401.8083 0 -3401.8083 245.09668 Loop time of 6.775e-06 on 1 procs for 0 steps with 1040 atoms 191.9% 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 | | 6.775e-06 | | |100.00 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10948.0 ave 10948 max 10948 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: 330448.0 ave 330448 max 330448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 330448 Ave neighs/atom = 317.73846 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.992 | 5.992 | 5.992 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 -3401.8083 -3401.8083 29.306362 117.93368 3.6374538 245.09668 245.09668 492.91933 175.45331 66.917404 2.2475928 379.50497 Loop time of 6.966e-06 on 1 procs for 0 steps with 1040 atoms 258.4% 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 | | 6.966e-06 | | |100.00 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10948.0 ave 10948 max 10948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 165224.0 ave 165224 max 165224 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 330448.0 ave 330448 max 330448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 330448 Ave neighs/atom = 317.73846 Neighbor list builds = 0 Dangerous builds = 0 1040 -3401.80831371503 eV 2.24759276890247 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06