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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -77.382771 0.0000000) to (44.674629 77.382771 7.0055407) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5913386 5.9196840 7.0055407 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -77.382771 0.0000000) to (44.674629 77.382771 7.0055407) create_atoms CPU = 0.009 seconds 1466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5913386 5.9196840 7.0055407 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -77.382771 0.0000000) to (44.674629 77.382771 7.0055407) create_atoms CPU = 0.008 seconds 1466 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 13 45 3 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 2906 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_058537087384_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 13 45 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.784 | 5.784 | 5.784 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9710.544 0 -9710.544 1131.4422 81 0 -9740.1607 0 -9740.1607 -2721.7928 Loop time of 45.0863 on 1 procs for 81 steps with 2906 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 = -9710.54402993121 -9740.15108622977 -9740.16069143979 Force two-norm initial, final = 32.200011 0.24188003 Force max component initial, final = 6.1499178 0.029655466 Final line search alpha, max atom move = 1.0000000 0.029655466 Iterations, force evaluations = 81 148 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 44.893 | 44.893 | 44.893 | 0.0 | 99.57 Neigh | 0.11625 | 0.11625 | 0.11625 | 0.0 | 0.26 Comm | 0.033283 | 0.033283 | 0.033283 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04334 | | | 0.10 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9541.00 ave 9541 max 9541 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: 229292.0 ave 229292 max 229292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229292 Ave neighs/atom = 78.902959 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 13 45 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.784 | 5.784 | 5.784 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -9740.1607 0 -9740.1607 -2721.7928 48436.961 84 0 -9740.261 0 -9740.261 -594.29097 48305.236 Loop time of 1.82119 on 1 procs for 3 steps with 2906 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 = -9740.16069143979 -9740.26058095822 -9740.26097244009 Force two-norm initial, final = 102.76170 0.25442232 Force max component initial, final = 77.322669 0.048398238 Final line search alpha, max atom move = 0.00034755894 1.6821240e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8149 | 1.8149 | 1.8149 | 0.0 | 99.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012418 | 0.0012418 | 0.0012418 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005091 | | | 0.28 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9544.00 ave 9544 max 9544 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: 228684.0 ave 228684 max 228684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 228684 Ave neighs/atom = 78.693737 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 13 45 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.927 | 5.927 | 5.927 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9740.261 0 -9740.261 -594.29097 Loop time of 7.056e-06 on 1 procs for 0 steps with 2906 atoms 184.2% 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 | | 7.056e-06 | | |100.00 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9550.00 ave 9550 max 9550 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: 238804.0 ave 238804 max 238804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238804 Ave neighs/atom = 82.176187 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 13 45 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.927 | 5.927 | 5.927 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 -9740.261 -9740.261 44.601262 154.76554 6.9979813 -594.29097 -594.29097 -1.2431178 -1780.0263 -1.603529 2.5645423 1521.0508 Loop time of 6.405e-06 on 1 procs for 0 steps with 2906 atoms 327.9% 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 | | 6.405e-06 | | |100.00 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9550.00 ave 9550 max 9550 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 119402.0 ave 119402 max 119402 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 238804.0 ave 238804 max 238804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238804 Ave neighs/atom = 82.176187 Neighbor list builds = 0 Dangerous builds = 0 2906 -9740.26097244011 eV 2.56454226052266 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:48