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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -50.582069 0.0000000) to (29.203571 50.582069 4.9599800) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4928571 4.5394165 4.9599800 Created 622 atoms using lattice units in orthogonal box = (0.0000000 -50.582069 0.0000000) to (29.203571 50.582069 4.9599800) create_atoms CPU = 0.002 seconds 622 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4928571 4.5394165 4.9599800 Created 627 atoms using lattice units in orthogonal box = (0.0000000 -50.582069 0.0000000) to (29.203571 50.582069 4.9599800) create_atoms CPU = 0.001 seconds 627 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 30 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 1248 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_110119204723_001#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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.047 | 5.047 | 5.047 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4940.7171 0 -4940.7171 65397.205 56 0 -5334.1159 0 -5334.1159 5502.5067 Loop time of 12.5803 on 1 procs for 56 steps with 1248 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4940.71708392639 -5334.11160180088 -5334.11592989795 Force two-norm initial, final = 519.09204 0.21508661 Force max component initial, final = 89.736126 0.047297459 Final line search alpha, max atom move = 1.0000000 0.047297459 Iterations, force evaluations = 56 94 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.552 | 12.552 | 12.552 | 0.0 | 99.77 Neigh | 0.0092509 | 0.0092509 | 0.0092509 | 0.0 | 0.07 Comm | 0.010065 | 0.010065 | 0.010065 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00947 | | | 0.08 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6666.00 ave 6666 max 6666 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: 139974.0 ave 139974 max 139974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139974 Ave neighs/atom = 112.15865 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.047 | 5.047 | 5.047 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -5334.1159 0 -5334.1159 5502.5067 14653.537 59 0 -5334.2136 0 -5334.2136 -1.8082839 14700.195 Loop time of 0.861996 on 1 procs for 3 steps with 1248 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 = -5334.11592989795 -5334.21038482254 -5334.21363102965 Force two-norm initial, final = 90.707486 0.28701149 Force max component initial, final = 67.264794 0.15779252 Final line search alpha, max atom move = 9.1379139e-05 1.4418944e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.8593 | 0.8593 | 0.8593 | 0.0 | 99.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00043095 | 0.00043095 | 0.00043095 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002269 | | | 0.26 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6648.00 ave 6648 max 6648 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: 139902.0 ave 139902 max 139902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139902 Ave neighs/atom = 112.10096 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.184 | 5.184 | 5.184 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5334.2136 0 -5334.2136 -1.8082839 Loop time of 2.44e-06 on 1 procs for 0 steps with 1248 atoms 163.9% 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 | | 2.44e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6648.00 ave 6648 max 6648 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: 139830.0 ave 139830 max 139830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139830 Ave neighs/atom = 112.04327 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.184 | 5.184 | 5.184 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 -5334.2136 -5334.2136 29.204071 101.37002 4.9655821 -1.8082839 -1.8082839 5.0380551 6.7543478 -17.217255 2.3263625 745.71059 Loop time of 2.62e-06 on 1 procs for 0 steps with 1248 atoms 190.8% 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 | | 2.62e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6648.00 ave 6648 max 6648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69915.0 ave 69915 max 69915 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 139830.0 ave 139830 max 139830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139830 Ave neighs/atom = 112.04327 Neighbor list builds = 0 Dangerous builds = 0 1248 -5334.21363102965 eV 2.3263624725999 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14