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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -32.916657 0.0000000) to (23.275591 32.916657 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3084682 5.1973669 4.3599177 Created 228 atoms using lattice units in orthogonal box = (0.0000000 -32.916657 0.0000000) to (23.275591 32.916657 4.3599177) create_atoms CPU = 0.001 seconds 228 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3084682 5.1973669 4.3599177 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -32.916657 0.0000000) to (23.275591 32.916657 4.3599177) create_atoms CPU = 0.001 seconds 230 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 20 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 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 2 atoms, new total = 456 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 4.833 | 4.833 | 4.833 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2201.3066 0 -2201.3066 308830.47 97 0 -2951.741 0 -2951.741 10519.868 Loop time of 28.4562 on 1 procs for 97 steps with 456 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 = -2201.30658414018 -2951.73840597378 -2951.74096122303 Force two-norm initial, final = 2036.4975 0.24284333 Force max component initial, final = 706.12312 0.043525098 Final line search alpha, max atom move = 1.0000000 0.043525098 Iterations, force evaluations = 97 181 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.407 | 28.407 | 28.407 | 0.0 | 99.83 Neigh | 0.036836 | 0.036836 | 0.036836 | 0.0 | 0.13 Comm | 0.0063102 | 0.0063102 | 0.0063102 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005679 | | | 0.02 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2992.00 ave 2992 max 2992 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: 33876.0 ave 33876 max 33876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33876 Ave neighs/atom = 74.289474 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 97 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.215 | 5.215 | 5.215 Mbytes Step Temp E_pair E_mol TotEng Press Volume 97 0 -2951.741 0 -2951.741 10519.868 6680.7425 103 0 -2952.021 0 -2952.021 -142.09392 6712.729 Loop time of 1.21435 on 1 procs for 6 steps with 456 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 = -2951.74096122303 -2952.0208523969 -2952.02102780426 Force two-norm initial, final = 100.10833 1.2456301 Force max component initial, final = 70.737613 0.92960786 Final line search alpha, max atom move = 0.00054299100 0.00050476870 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.213 | 1.213 | 1.213 | 0.0 | 99.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002341 | 0.0002341 | 0.0002341 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00114 | | | 0.09 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2992.00 ave 2992 max 2992 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: 33936.0 ave 33936 max 33936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33936 Ave neighs/atom = 74.421053 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.353 | 5.353 | 5.353 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2952.021 0 -2952.021 -142.09392 Loop time of 1.786e-06 on 1 procs for 0 steps with 456 atoms 168.0% 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 | | 1.786e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2992.00 ave 2992 max 2992 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: 33804.0 ave 33804 max 33804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33804 Ave neighs/atom = 74.131579 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.353 | 5.353 | 5.353 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 -2952.021 -2952.021 23.209402 66.0523 4.3787205 -142.09392 -142.09392 -95.174491 -222.6144 -108.49287 2.4674518 835.67877 Loop time of 1.828e-06 on 1 procs for 0 steps with 456 atoms 164.1% 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 | | 1.828e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2992.00 ave 2992 max 2992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16902.0 ave 16902 max 16902 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 33804.0 ave 33804 max 33804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33804 Ave neighs/atom = 74.131579 Neighbor list builds = 0 Dangerous builds = 0 456 -2952.02102780426 eV 2.46745177137471 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:30