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 = 3.6110509 3.6110509 3.6110509 Created orthogonal box = (0.0000000 -37.873021 0.0000000) to (46.384789 37.873021 8.8452321) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9035186 5.5088031 5.8968214 Created 1318 atoms using lattice units in orthogonal box = (0.0000000 -37.873021 0.0000000) to (46.384789 37.873021 8.8452321) create_atoms CPU = 0.002 seconds 1318 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9035186 5.5088031 5.8968214 Created 1324 atoms using lattice units in orthogonal box = (0.0000000 -37.873021 0.0000000) to (46.384789 37.873021 8.8452321) create_atoms CPU = 0.002 seconds 1324 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 15 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 2616 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_984358344196_004#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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 15 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 8.940 | 8.940 | 8.940 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9999.5694 0 -9999.5694 43773.105 71 0 -10799.719 0 -10799.719 -7762.1589 Loop time of 4.76233 on 1 procs for 71 steps with 2616 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9999.56943241659 -10799.7088546827 -10799.7186127773 Force two-norm initial, final = 706.20218 0.42108744 Force max component initial, final = 127.64895 0.020777862 Final line search alpha, max atom move = 1.0000000 0.020777862 Iterations, force evaluations = 71 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6051 | 4.6051 | 4.6051 | 0.0 | 96.70 Neigh | 0.11339 | 0.11339 | 0.11339 | 0.0 | 2.38 Comm | 0.024407 | 0.024407 | 0.024407 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01947 | | | 0.41 Nlocal: 2616.00 ave 2616 max 2616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13409.0 ave 13409 max 13409 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: 990286.0 ave 990286 max 990286 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 990286 Ave neighs/atom = 378.54969 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 15 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.941 | 8.941 | 8.941 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -10799.719 0 -10799.719 -7762.1589 31077.406 77 0 -10800.774 0 -10800.774 -184.96232 30936.521 Loop time of 0.302017 on 1 procs for 6 steps with 2616 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10799.7186127773 -10800.7693185674 -10800.7740400079 Force two-norm initial, final = 373.08495 6.8859891 Force max component initial, final = 341.81818 5.6667704 Final line search alpha, max atom move = 4.7102889e-05 0.00026692126 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2965 | 0.2965 | 0.2965 | 0.0 | 98.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00090487 | 0.00090487 | 0.00090487 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004613 | | | 1.53 Nlocal: 2616.00 ave 2616 max 2616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13414.0 ave 13414 max 13414 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: 991418.0 ave 991418 max 991418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 991418 Ave neighs/atom = 378.98242 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 15 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 9.079 | 9.079 | 9.079 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10800.774 0 -10800.774 -184.96232 Loop time of 2.103e-06 on 1 procs for 0 steps with 2616 atoms 190.2% 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 | | 2.103e-06 | | |100.00 Nlocal: 2616.00 ave 2616 max 2616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13444.0 ave 13444 max 13444 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: 992670.0 ave 992670 max 992670 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 992670 Ave neighs/atom = 379.46101 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 9 15 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 9.079 | 9.079 | 9.079 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 -10800.774 -10800.774 46.14629 75.621108 8.8652634 -184.96232 -184.96232 -182.82343 -292.99323 -79.070307 2.370031 2178.8305 Loop time of 2.598e-06 on 1 procs for 0 steps with 2616 atoms 230.9% 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 | | 2.598e-06 | | |100.00 Nlocal: 2616.00 ave 2616 max 2616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13444.0 ave 13444 max 13444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 496335.0 ave 496335 max 496335 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 992670.0 ave 992670 max 992670 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 992670 Ave neighs/atom = 379.46101 Neighbor list builds = 0 Dangerous builds = 0 2616 -10800.7740400079 eV 2.37003095920038 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05