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 = 2.8603420 2.8603420 2.8603420 Created orthogonal box = (0.0000000 -56.634743 0.0000000) to (34.679804 56.634743 7.0063784) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0105895 4.0451344 4.6709189 Created 1182 atoms using lattice units in orthogonal box = (0.0000000 -56.634743 0.0000000) to (34.679804 56.634743 7.0063784) create_atoms CPU = 0.002 seconds 1182 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0105895 4.0451344 4.6709189 Created 1182 atoms using lattice units in orthogonal box = (0.0000000 -56.634743 0.0000000) to (34.679804 56.634743 7.0063784) create_atoms CPU = 0.001 seconds 1182 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2364 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_657255834688_000#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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.498 | 6.498 | 6.498 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9783.4542 0 -9783.4542 37890.757 1269 0 -10321.177 0 -10321.177 11729.106 Loop time of 44.6178 on 1 procs for 1269 steps with 2364 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 = -9783.45417871041 -10321.1667942884 -10321.1765687867 Force two-norm initial, final = 156.84683 0.52414837 Force max component initial, final = 21.712902 0.15371831 Final line search alpha, max atom move = 0.30484320 0.046859983 Iterations, force evaluations = 1269 2500 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 43.388 | 43.388 | 43.388 | 0.0 | 97.24 Neigh | 0.76399 | 0.76399 | 0.76399 | 0.0 | 1.71 Comm | 0.23988 | 0.23988 | 0.23988 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2254 | | | 0.51 Nlocal: 2364.00 ave 2364 max 2364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10160.0 ave 10160 max 10160 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: 389762.0 ave 389762 max 389762 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 389762 Ave neighs/atom = 164.87394 Neighbor list builds = 32 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1269 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.118 | 6.118 | 6.118 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1269 0 -10321.177 0 -10321.177 11729.106 27522.2 1291 0 -10331.861 0 -10331.861 4777.2058 27494.491 Loop time of 0.428922 on 1 procs for 22 steps with 2364 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 = -10321.1765687868 -10331.8590640894 -10331.8609338241 Force two-norm initial, final = 821.04006 6.1507449 Force max component initial, final = 692.84639 2.6998112 Final line search alpha, max atom move = 0.00021946979 0.00059252699 Iterations, force evaluations = 22 23 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41712 | 0.41712 | 0.41712 | 0.0 | 97.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018075 | 0.0018075 | 0.0018075 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009993 | | | 2.33 Nlocal: 2364.00 ave 2364 max 2364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10187.0 ave 10187 max 10187 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: 389478.0 ave 389478 max 389478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 389478 Ave neighs/atom = 164.75381 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.258 | 6.258 | 6.258 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10331.861 0 -10331.861 4777.2058 Loop time of 1.681e-06 on 1 procs for 0 steps with 2364 atoms 119.0% 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 | | 1.681e-06 | | |100.00 Nlocal: 2364.00 ave 2364 max 2364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10320.0 ave 10320 max 10320 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: 386442.0 ave 386442 max 386442 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 386442 Ave neighs/atom = 163.46954 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.258 | 6.258 | 6.258 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 -10331.861 -10331.861 35.349581 113.26949 6.8667065 4777.2058 4777.2058 -158.13455 14335.563 154.18885 2.3011551 10361.765 Loop time of 1.697e-06 on 1 procs for 0 steps with 2364 atoms 235.7% 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 | | 1.697e-06 | | |100.00 Nlocal: 2364.00 ave 2364 max 2364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10320.0 ave 10320 max 10320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 193221.0 ave 193221 max 193221 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 386442.0 ave 386442 max 386442 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 386442 Ave neighs/atom = 163.46954 Neighbor list builds = 0 Dangerous builds = 0 2364 -10331.8609338241 eV 2.30115506805054 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:45