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 = 4.0333018 4.0333018 4.0333018 Created orthogonal box = (0.0000000 -68.921092 0.0000000) to (34.460546 68.921092 4.0333018) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1926850 5.1926850 4.0333018 Created 584 atoms using lattice units in orthogonal box = (0.0000000 -68.921092 0.0000000) to (34.460546 68.921092 4.0333018) create_atoms CPU = 0.001 seconds 584 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1926850 5.1926850 4.0333018 Created 586 atoms using lattice units in orthogonal box = (0.0000000 -68.921092 0.0000000) to (34.460546 68.921092 4.0333018) create_atoms CPU = 0.001 seconds 586 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 33 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1168 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_577453891941_005#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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 33 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.071 | 5.071 | 5.071 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3855.36 0 -3855.36 12323.579 25 0 -3926.0489 0 -3926.0489 4352.4856 Loop time of 0.486771 on 1 procs for 25 steps with 1168 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 = -3855.35996603163 -3926.04513353668 -3926.04891672053 Force two-norm initial, final = 122.94134 0.12589820 Force max component initial, final = 41.607075 0.012573553 Final line search alpha, max atom move = 1.0000000 0.012573553 Iterations, force evaluations = 25 44 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48002 | 0.48002 | 0.48002 | 0.0 | 98.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0037195 | 0.0037195 | 0.0037195 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003032 | | | 0.62 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8642.00 ave 8642 max 8642 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: 164656.0 ave 164656 max 164656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164656 Ave neighs/atom = 140.97260 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 33 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.071 | 5.071 | 5.071 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -3926.0489 0 -3926.0489 4352.4856 19158.655 33 0 -3926.3842 0 -3926.3842 -20.062897 19259.93 Loop time of 0.121491 on 1 procs for 8 steps with 1168 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 = -3926.04891672053 -3926.38069202067 -3926.38419325201 Force two-norm initial, final = 105.82931 0.56900346 Force max component initial, final = 97.305319 0.41410078 Final line search alpha, max atom move = 0.00017268551 7.1509203e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10648 | 0.10648 | 0.10648 | 0.0 | 87.65 Neigh | 0.010654 | 0.010654 | 0.010654 | 0.0 | 8.77 Comm | 0.00089852 | 0.00089852 | 0.00089852 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003458 | | | 2.85 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8612.00 ave 8612 max 8612 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: 165056.0 ave 165056 max 165056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165056 Ave neighs/atom = 141.31507 Neighbor list builds = 1 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 33 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.209 | 5.209 | 5.209 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3926.3842 0 -3926.3842 -20.062897 Loop time of 2.225e-06 on 1 procs for 0 steps with 1168 atoms 179.8% 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 | | 2.225e-06 | | |100.00 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8612.00 ave 8612 max 8612 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: 165064.0 ave 165064 max 165064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165064 Ave neighs/atom = 141.32192 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 33 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.209 | 5.209 | 5.209 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 -3926.3842 -3926.3842 34.42555 138.92162 4.0272072 -20.062897 -20.062897 -3.0373364 -22.755591 -34.395764 2.5630677 616.09292 Loop time of 2.973e-06 on 1 procs for 0 steps with 1168 atoms 201.8% 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 | | 2.973e-06 | | |100.00 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8612.00 ave 8612 max 8612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 82532.0 ave 82532 max 82532 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 165064.0 ave 165064 max 165064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165064 Ave neighs/atom = 141.32192 Neighbor list builds = 0 Dangerous builds = 0 1168 -3926.38419325201 eV 2.56306767115802 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01