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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -46.164368 0.0000000) to (32.643137 46.164368 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0731418 5.9047447 4.9780318 Created 686 atoms using lattice units in orthogonal box = (0.0000000 -46.164368 0.0000000) to (32.643137 46.164368 4.9780318) create_atoms CPU = 0.005 seconds 686 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0731418 5.9047447 4.9780318 Created 694 atoms using lattice units in orthogonal box = (0.0000000 -46.164368 0.0000000) to (32.643137 46.164368 4.9780318) create_atoms CPU = 0.005 seconds 694 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 8 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, cut 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1376 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_826591359508_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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 5.902 | 5.902 | 5.902 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6034.7235 0 -6034.7235 5031.4281 57 0 -6101.7066 0 -6101.7066 5703.4173 Loop time of 3.88352 on 1 procs for 57 steps with 1376 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 = -6034.72354712787 -6101.70131101468 -6101.70664553124 Force two-norm initial, final = 27.680250 0.25335117 Force max component initial, final = 4.4902766 0.035417291 Final line search alpha, max atom move = 1.0000000 0.035417291 Iterations, force evaluations = 57 107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7976 | 3.7976 | 3.7976 | 0.0 | 97.79 Neigh | 0.042785 | 0.042785 | 0.042785 | 0.0 | 1.10 Comm | 0.024441 | 0.024441 | 0.024441 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01865 | | | 0.48 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9721.00 ave 9721 max 9721 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: 308664.0 ave 308664 max 308664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 308664 Ave neighs/atom = 224.31977 Neighbor list builds = 1 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.906 | 5.906 | 5.906 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -6101.7066 0 -6101.7066 5703.4173 15003.288 60 0 -6101.8074 0 -6101.8074 1.3168181 15051.601 Loop time of 0.20235 on 1 procs for 3 steps with 1376 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 = -6101.70664553123 -6101.8052173092 -6101.80740991181 Force two-norm initial, final = 95.916328 0.94210321 Force max component initial, final = 73.713421 0.64938213 Final line search alpha, max atom move = 0.00014048217 9.1226612e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19722 | 0.19722 | 0.19722 | 0.0 | 97.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001296 | 0.001296 | 0.001296 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003838 | | | 1.90 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9721.00 ave 9721 max 9721 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: 309576.0 ave 309576 max 309576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 309576 Ave neighs/atom = 224.98256 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 6.044 | 6.044 | 6.044 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6101.8074 0 -6101.8074 1.3168181 Loop time of 6.165e-06 on 1 procs for 0 steps with 1376 atoms 178.4% 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 | | 6.165e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9721.00 ave 9721 max 9721 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: 309424.0 ave 309424 max 309424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 309424 Ave neighs/atom = 224.87209 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 6.044 | 6.044 | 6.044 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 -6101.8074 -6101.8074 32.658913 92.517099 4.9814867 1.3168181 1.3168181 66.552034 6.5702564 -69.171836 2.2917541 929.86659 Loop time of 7.317e-06 on 1 procs for 0 steps with 1376 atoms 259.7% 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 | | 7.317e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9721.00 ave 9721 max 9721 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 154712.0 ave 154712 max 154712 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 309424.0 ave 309424 max 309424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 309424 Ave neighs/atom = 224.87209 Neighbor list builds = 0 Dangerous builds = 0 1376 -6101.80740991181 eV 2.29175411673168 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05