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 = 3.6800447 3.6800447 3.6800447 Created orthogonal box = (0.0000000 -43.542876 0.0000000) to (53.328914 43.542876 9.0142317) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0947330 5.5983698 6.0094878 Created 1666 atoms using lattice units in orthogonal box = (0.0000000 -43.542876 0.0000000) to (53.328914 43.542876 9.0142317) create_atoms CPU = 0.003 seconds 1666 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0947330 5.5983698 6.0094878 Created 1690 atoms using lattice units in orthogonal box = (0.0000000 -43.542876 0.0000000) to (53.328914 43.542876 9.0142317) create_atoms CPU = 0.002 seconds 1690 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 19 31 4 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 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3356 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_142799717516_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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 19 31 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 5.226 | 5.226 | 5.226 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13839.986 0 -13839.986 16610.484 114 0 -14241.51 0 -14241.51 -8336.0306 Loop time of 1.54646 on 1 procs for 114 steps with 3356 atoms 96.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13839.9855901736 -14241.4974266163 -14241.5100529631 Force two-norm initial, final = 210.57603 0.38310951 Force max component initial, final = 29.781291 0.067260439 Final line search alpha, max atom move = 1.0000000 0.067260439 Iterations, force evaluations = 114 167 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3853 | 1.3853 | 1.3853 | 0.0 | 89.58 Neigh | 0.11822 | 0.11822 | 0.11822 | 0.0 | 7.64 Comm | 0.013493 | 0.013493 | 0.013493 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02941 | | | 1.90 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7108.00 ave 7108 max 7108 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: 188086.0 ave 188086 max 188086 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188086 Ave neighs/atom = 56.044696 Neighbor list builds = 6 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 19 31 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 114 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.224 | 5.224 | 5.224 Mbytes Step Temp E_pair E_mol TotEng Press Volume 114 0 -14241.51 0 -14241.51 -8336.0306 41863.792 121 0 -14242.749 0 -14242.749 25.650883 41617.07 Loop time of 0.0806261 on 1 procs for 7 steps with 3356 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14241.5100529631 -14242.7489307321 -14242.7493947994 Force two-norm initial, final = 444.03800 1.4109444 Force max component initial, final = 408.85199 0.96016952 Final line search alpha, max atom move = 0.00019843750 0.00019053364 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.075203 | 0.075203 | 0.075203 | 0.0 | 93.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005552 | 0.0005552 | 0.0005552 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004868 | | | 6.04 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7074.00 ave 7074 max 7074 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: 188456.0 ave 188456 max 188456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188456 Ave neighs/atom = 56.154946 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 19 31 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 5.362 | 5.362 | 5.362 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14242.749 0 -14242.749 25.650883 Loop time of 2.127e-06 on 1 procs for 0 steps with 3356 atoms 188.1% 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 | | 2.127e-06 | | |100.00 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7085.00 ave 7085 max 7085 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: 189064.0 ave 189064 max 189064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189064 Ave neighs/atom = 56.336114 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.863225, bins = 19 31 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 5.362 | 5.362 | 5.362 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 -14242.749 -14242.749 53.002979 87.122251 9.0124349 25.650883 25.650883 30.773964 36.980157 9.1985281 2.3590922 2464.043 Loop time of 2.484e-06 on 1 procs for 0 steps with 3356 atoms 241.5% 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 | | 2.484e-06 | | |100.00 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7085.00 ave 7085 max 7085 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 94532.0 ave 94532 max 94532 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 189064.0 ave 189064 max 189064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189064 Ave neighs/atom = 56.336114 Neighbor list builds = 0 Dangerous builds = 0 3356 -14242.7493947994 eV 2.35909221586841 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02