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 = 3.6133157 3.6133157 3.6133157 Created orthogonal box = (0.0000000 -62.584463 0.0000000) to (25.550000 62.584463 8.8507797) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1320000 5.4239868 5.9005198 Created 1195 atoms using lattice units in orthogonal box = (0.0000000 -62.584463 0.0000000) to (25.550000 62.584463 8.8507797) create_atoms CPU = 0.002 seconds 1195 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1320000 5.4239868 5.9005198 Created 1203 atoms using lattice units in orthogonal box = (0.0000000 -62.584463 0.0000000) to (25.550000 62.584463 8.8507797) create_atoms CPU = 0.002 seconds 1203 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 39 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2398 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_353393547686_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 39 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.552 | 5.552 | 5.552 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8116.1327 0 -8116.1327 39890.453 114 0 -8465.7648 0 -8465.7648 2873.6635 Loop time of 12.3101 on 1 procs for 114 steps with 2398 atoms 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8116.13270502847 -8465.75879494322 -8465.76484034434 Force two-norm initial, final = 365.68916 0.26991642 Force max component initial, final = 58.630003 0.081806664 Final line search alpha, max atom move = 1.0000000 0.081806664 Iterations, force evaluations = 114 194 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.229 | 12.229 | 12.229 | 0.0 | 99.34 Neigh | 0.035639 | 0.035639 | 0.035639 | 0.0 | 0.29 Comm | 0.018269 | 0.018269 | 0.018269 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02675 | | | 0.22 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7577.00 ave 7577 max 7577 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: 207082.0 ave 207082 max 207082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207082 Ave neighs/atom = 86.356130 Neighbor list builds = 2 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 39 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.554 | 5.554 | 5.554 Mbytes Step Temp E_pair E_mol TotEng Press Volume 114 0 -8465.7648 0 -8465.7648 2873.6635 28305.378 118 0 -8465.9695 0 -8465.9695 -46.052544 28363.141 Loop time of 0.400927 on 1 procs for 4 steps with 2398 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 = -8465.76484034435 -8465.96248611896 -8465.9695258365 Force two-norm initial, final = 122.27840 1.6355172 Force max component initial, final = 119.90300 1.2690030 Final line search alpha, max atom move = 6.9101575e-05 8.7690108e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39801 | 0.39801 | 0.39801 | 0.0 | 99.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039983 | 0.00039983 | 0.00039983 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002516 | | | 0.63 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7581.00 ave 7581 max 7581 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: 207132.0 ave 207132 max 207132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207132 Ave neighs/atom = 86.376981 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 39 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.692 | 5.692 | 5.692 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8465.9695 0 -8465.9695 -46.052544 Loop time of 2.673e-06 on 1 procs for 0 steps with 2398 atoms 187.1% 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 | | 2.673e-06 | | |100.00 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7581.00 ave 7581 max 7581 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: 206980.0 ave 206980 max 206980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206980 Ave neighs/atom = 86.313595 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 39 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.692 | 5.692 | 5.692 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 -8465.9695 -8465.9695 25.538821 125.62516 8.8405006 -46.052544 -46.052544 -12.106927 -54.450538 -71.600166 2.3186621 834.67242 Loop time of 2.758e-06 on 1 procs for 0 steps with 2398 atoms 253.8% 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 | | 2.758e-06 | | |100.00 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7581.00 ave 7581 max 7581 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103490.0 ave 103490 max 103490 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 206980.0 ave 206980 max 206980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206980 Ave neighs/atom = 86.313595 Neighbor list builds = 0 Dangerous builds = 0 2398 -8465.9695258365 eV 2.31866206402589 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13