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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -65.804713 0.0000000) to (13.432331 65.804713 9.9204338) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1056049 5.9822467 6.6136225 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -65.804713 0.0000000) to (13.432331 65.804713 9.9204338) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1056049 5.9822467 6.6136225 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -65.804713 0.0000000) to (13.432331 65.804713 9.9204338) create_atoms CPU = 0.001 seconds 530 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 = 4 31 3 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 2 atoms, new total = 1056 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_678952612413_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 = 4 31 3 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) = 5.043 | 5.043 | 5.043 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3488.2445 0 -3488.2445 4189.0884 125 0 -3539.7368 0 -3539.7368 2716.995 Loop time of 2.30084 on 1 procs for 125 steps with 1056 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3488.24446984994 -3539.73322994874 -3539.73676234817 Force two-norm initial, final = 42.287260 0.16388256 Force max component initial, final = 10.901781 0.042341918 Final line search alpha, max atom move = 1.0000000 0.042341918 Iterations, force evaluations = 125 226 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2382 | 2.2382 | 2.2382 | 0.0 | 97.28 Neigh | 0.034072 | 0.034072 | 0.034072 | 0.0 | 1.48 Comm | 0.013978 | 0.013978 | 0.013978 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01458 | | | 0.63 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6144.00 ave 6144 max 6144 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: 149300.0 ave 149300 max 149300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149300 Ave neighs/atom = 141.38258 Neighbor list builds = 3 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 = 4 31 3 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 : 125 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.045 | 5.045 | 5.045 Mbytes Step Temp E_pair E_mol TotEng Press Volume 125 0 -3539.7368 0 -3539.7368 2716.995 17537.555 132 0 -3539.9265 0 -3539.9265 44.409731 17596.525 Loop time of 0.0912598 on 1 procs for 7 steps with 1056 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 = -3539.73676234819 -3539.92540207476 -3539.92652412868 Force two-norm initial, final = 67.019415 0.88673585 Force max component initial, final = 64.745522 0.55802857 Final line search alpha, max atom move = 0.00034179614 0.00019073201 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.088116 | 0.088116 | 0.088116 | 0.0 | 96.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047888 | 0.00047888 | 0.00047888 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002665 | | | 2.92 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6118.00 ave 6118 max 6118 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: 149180.0 ave 149180 max 149180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149180 Ave neighs/atom = 141.26894 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 = 4 32 3 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) = 5.183 | 5.183 | 5.183 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3539.9265 0 -3539.9265 44.409731 Loop time of 2.749e-06 on 1 procs for 0 steps with 1056 atoms 145.5% 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 | | 2.749e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6136.00 ave 6136 max 6136 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: 149052.0 ave 149052 max 149052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149052 Ave neighs/atom = 141.14773 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 = 4 32 3 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) = 5.183 | 5.183 | 5.183 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 -3539.9265 -3539.9265 13.409347 132.45824 9.9069573 44.409731 44.409731 35.601734 46.88757 50.739889 2.5609828 532.67709 Loop time of 2.838e-06 on 1 procs for 0 steps with 1056 atoms 246.7% 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 | | 2.838e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6136.00 ave 6136 max 6136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 74526.0 ave 74526 max 74526 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 149052.0 ave 149052 max 149052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149052 Ave neighs/atom = 141.14773 Neighbor list builds = 0 Dangerous builds = 0 1056 -3539.92652412868 eV 2.5609827597775 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02