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 = 2.8700001 2.8700001 2.8700001 Created orthogonal box = (0.0000000 -34.681213 0.0000000) to (42.472123 34.681213 7.0300358) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0726693 4.2754121 4.6866905 Created 879 atoms using lattice units in orthogonal box = (0.0000000 -34.681213 0.0000000) to (42.472123 34.681213 7.0300358) create_atoms CPU = 0.002 seconds 879 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0726693 4.2754121 4.6866905 Created 879 atoms using lattice units in orthogonal box = (0.0000000 -34.681213 0.0000000) to (42.472123 34.681213 7.0300358) create_atoms CPU = 0.002 seconds 879 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 14 23 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 33 atoms, new total = 1725 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.057 | 5.057 | 5.057 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7260.7339 0 -7260.7339 3849.1063 129 0 -7333.2858 0 -7333.2858 -11061.722 Loop time of 2.56555 on 1 procs for 129 steps with 1725 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7260.73393182106 -7333.2787364715 -7333.2857904956 Force two-norm initial, final = 73.727512 0.29373153 Force max component initial, final = 14.668050 0.039777596 Final line search alpha, max atom move = 1.0000000 0.039777596 Iterations, force evaluations = 129 240 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4958 | 2.4958 | 2.4958 | 0.0 | 97.28 Neigh | 0.021284 | 0.021284 | 0.021284 | 0.0 | 0.83 Comm | 0.019835 | 0.019835 | 0.019835 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02867 | | | 1.12 Nlocal: 1725.00 ave 1725 max 1725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5288.00 ave 5288 max 5288 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: 112692.0 ave 112692 max 112692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112692 Ave neighs/atom = 65.328696 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 129 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.069 | 5.069 | 5.069 Mbytes Step Temp E_pair E_mol TotEng Press Volume 129 0 -7333.2858 0 -7333.2858 -11061.722 20710.271 133 0 -7333.7003 0 -7333.7003 -1547.2519 20589.351 Loop time of 0.0648216 on 1 procs for 4 steps with 1725 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 = -7333.28579049561 -7333.69887017663 -7333.70032636142 Force two-norm initial, final = 200.53176 3.4540050 Force max component initial, final = 148.22250 3.4167166 Final line search alpha, max atom move = 9.5319623e-05 0.00032568013 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.061566 | 0.061566 | 0.061566 | 0.0 | 94.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048128 | 0.00048128 | 0.00048128 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002775 | | | 4.28 Nlocal: 1725.00 ave 1725 max 1725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5684.00 ave 5684 max 5684 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: 112264.0 ave 112264 max 112264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112264 Ave neighs/atom = 65.080580 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.207 | 5.207 | 5.207 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7333.7003 0 -7333.7003 -1547.2519 Loop time of 5.898e-06 on 1 procs for 0 steps with 1725 atoms 169.5% 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 | | 5.898e-06 | | |100.00 Nlocal: 1725.00 ave 1725 max 1725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5690.00 ave 5690 max 5690 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: 112504.0 ave 112504 max 112504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112504 Ave neighs/atom = 65.219710 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.207 | 5.207 | 5.207 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 -7333.7003 -7333.7003 42.333055 69.362426 7.0119493 -1547.2519 -1547.2519 -24.183656 -4882.7624 265.19046 2.281247 1643.6902 Loop time of 2.824e-06 on 1 procs for 0 steps with 1725 atoms 177.1% 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 | | 2.824e-06 | | |100.00 Nlocal: 1725.00 ave 1725 max 1725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5690.00 ave 5690 max 5690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56252.0 ave 56252 max 56252 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 112504.0 ave 112504 max 112504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112504 Ave neighs/atom = 65.219710 Neighbor list builds = 0 Dangerous builds = 0 1725 -7333.70015386142 eV 2.28124699923404 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03