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 = 2.8659524 2.8659524 2.8659524 Created orthogonal box = (0.0000000 -29.227095 0.0000000) to (14.613547 29.227095 2.8659524) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.3723571 3.3723571 2.8659524 Created 104 atoms using lattice units in orthogonal box = (0.0000000 -29.227095 0.0000000) to (14.613547 29.227095 2.8659524) create_atoms CPU = 0.001 seconds 104 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.3723571 3.3723571 2.8659524 Created 106 atoms using lattice units in orthogonal box = (0.0000000 -29.227095 0.0000000) to (14.613547 29.227095 2.8659524) create_atoms CPU = 0.000 seconds 106 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 4 16 1 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 7.549891651270771 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 208 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_681088298208_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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 4 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 4.412 | 4.412 | 4.412 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -860.17381 0 -860.17381 53105.041 26 0 -886.54052 0 -886.54052 10943.274 Loop time of 0.177696 on 1 procs for 26 steps with 208 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 = -860.17381326282 -886.539844599051 -886.540524074495 Force two-norm initial, final = 79.415995 0.078678129 Force max component initial, final = 28.343026 0.012294711 Final line search alpha, max atom move = 1.0000000 0.012294711 Iterations, force evaluations = 26 48 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17389 | 0.17389 | 0.17389 | 0.0 | 97.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0023405 | 0.0023405 | 0.0023405 | 0.0 | 1.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001466 | | | 0.82 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2996.00 ave 2996 max 2996 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: 34536.0 ave 34536 max 34536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34536 Ave neighs/atom = 166.03846 Neighbor list builds = 0 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 4 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.412 | 4.412 | 4.412 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -886.54052 0 -886.54052 10943.274 2448.1626 38 0 -886.6921 0 -886.6921 -39.945804 2464.8662 Loop time of 0.054264 on 1 procs for 12 steps with 208 atoms 97.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -886.540524074495 -886.691886834528 -886.692096962708 Force two-norm initial, final = 33.701635 0.43535506 Force max component initial, final = 30.785610 0.24082147 Final line search alpha, max atom move = 0.0022813542 0.00054939908 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.051097 | 0.051097 | 0.051097 | 0.0 | 94.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00066355 | 0.00066355 | 0.00066355 | 0.0 | 1.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002504 | | | 4.61 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2996.00 ave 2996 max 2996 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: 34208.0 ave 34208 max 34208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34208 Ave neighs/atom = 164.46154 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 4 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 4.550 | 4.550 | 4.550 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -886.6921 0 -886.6921 -39.945804 Loop time of 3.183e-06 on 1 procs for 0 steps with 208 atoms 125.7% 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 | | 3.183e-06 | | |100.00 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2996.00 ave 2996 max 2996 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: 34168.0 ave 34168 max 34168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34168 Ave neighs/atom = 164.26923 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 4 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 4.550 | 4.550 | 4.550 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 -886.6921 -886.6921 14.586281 59.121327 2.8582789 -39.945804 -39.945804 3.5978745 -158.3218 34.886519 2.3799622 132.38036 Loop time of 2.966e-06 on 1 procs for 0 steps with 208 atoms 134.9% 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 | | 2.966e-06 | | |100.00 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2996.00 ave 2996 max 2996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17084.0 ave 17084 max 17084 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 34168.0 ave 34168 max 34168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34168 Ave neighs/atom = 164.26923 Neighbor list builds = 0 Dangerous builds = 0 208 -886.692096962708 eV 2.37996224623469 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00