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 = 2.8601955 2.8601955 2.8601955 Created orthogonal box = (0.0000000 -29.168385 0.0000000) to (14.584192 29.168385 2.8601955) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.3655829 3.3655829 2.8601955 Created 104 atoms using lattice units in orthogonal box = (0.0000000 -29.168385 0.0000000) to (14.584192 29.168385 2.8601955) create_atoms CPU = 0.001 seconds 104 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.3655829 3.3655829 2.8601955 Created 106 atoms using lattice units in orthogonal box = (0.0000000 -29.168385 0.0000000) to (14.584192 29.168385 2.8601955) create_atoms CPU = 0.001 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 22 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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_137964310702_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.381 | 4.381 | 4.381 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -864.51967 0 -864.51967 32218.42 34 0 -884.32828 0 -884.32828 8043.79 Loop time of 2.2707 on 1 procs for 34 steps with 208 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 = -864.519671598141 -884.327493941294 -884.328282687749 Force two-norm initial, final = 48.310088 0.10027099 Force max component initial, final = 17.061695 0.023717599 Final line search alpha, max atom move = 1.0000000 0.023717599 Iterations, force evaluations = 34 64 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2657 | 2.2657 | 2.2657 | 0.0 | 99.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0028158 | 0.0028158 | 0.0028158 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00219 | | | 0.10 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1917.00 ave 1917 max 1917 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: 11992.0 ave 11992 max 11992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11992 Ave neighs/atom = 57.653846 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 34 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.381 | 4.381 | 4.381 Mbytes Step Temp E_pair E_mol TotEng Press Volume 34 0 -884.32828 0 -884.32828 8043.79 2433.4391 47 0 -884.49477 0 -884.49477 -478.40182 2445.3015 Loop time of 0.563081 on 1 procs for 13 steps with 208 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 = -884.328282687748 -884.494481873075 -884.494773370659 Force two-norm initial, final = 30.715249 1.4712352 Force max component initial, final = 30.129588 1.1152188 Final line search alpha, max atom move = 0.0033639325 0.0037515208 Iterations, force evaluations = 13 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.56002 | 0.56002 | 0.56002 | 0.0 | 99.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00070067 | 0.00070067 | 0.00070067 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002365 | | | 0.42 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1917.00 ave 1917 max 1917 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: 11960.0 ave 11960 max 11960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11960 Ave neighs/atom = 57.500000 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.520 | 4.520 | 4.520 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -884.49477 0 -884.49477 -478.40182 Loop time of 6.395e-06 on 1 procs for 0 steps with 208 atoms 187.6% 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 | | 6.395e-06 | | |100.00 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1917.00 ave 1917 max 1917 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: 11952.0 ave 11952 max 11952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11952 Ave neighs/atom = 57.461538 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.520 | 4.520 | 4.520 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 -884.49477 -884.49477 14.529874 59.03317 2.8508506 -478.40182 -478.40182 -727.97672 -487.15074 -220.07799 2.3515472 102.73361 Loop time of 7.528e-06 on 1 procs for 0 steps with 208 atoms 252.4% 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 | | 7.528e-06 | | |100.00 Nlocal: 208.000 ave 208 max 208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1917.00 ave 1917 max 1917 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5976.00 ave 5976 max 5976 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 11952.0 ave 11952 max 11952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11952 Ave neighs/atom = 57.461538 Neighbor list builds = 0 Dangerous builds = 0 208 -884.494773370659 eV 2.35154718644278 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03