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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -73.916736 0.0000000) to (36.956409 73.916736 3.9173716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3981272 5.3981272 3.9173716 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -73.916736 0.0000000) to (36.956409 73.916736 3.9173716) create_atoms CPU = 0.003 seconds 714 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3981272 5.3981272 3.9173716 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -73.916736 0.0000000) to (36.956409 73.916736 3.9173716) create_atoms CPU = 0.004 seconds 714 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 46 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1412 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_020840179467_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 46 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.083 | 5.083 | 5.083 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8064.447 0 -8064.447 6772.0426 69 0 -8120.8591 0 -8120.8591 -6850.651 Loop time of 7.02035 on 1 procs for 69 steps with 1412 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8064.44702125131 -8120.8521350469 -8120.85910613735 Force two-norm initial, final = 64.651081 0.32495603 Force max component initial, final = 15.158624 0.086434902 Final line search alpha, max atom move = 1.0000000 0.086434902 Iterations, force evaluations = 69 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.9768 | 6.9768 | 6.9768 | 0.0 | 99.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.022814 | 0.022814 | 0.022814 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02074 | | | 0.30 Nlocal: 1412.00 ave 1412 max 1412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7921.00 ave 7921 max 7921 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: 109152.0 ave 109152 max 109152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109152 Ave neighs/atom = 77.303116 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 46 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.083 | 5.083 | 5.083 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -8120.8591 0 -8120.8591 -6850.651 21402.146 72 0 -8120.9788 0 -8120.9788 -1747.672 21339.143 Loop time of 0.338878 on 1 procs for 3 steps with 1412 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 = -8120.85910613735 -8120.97514598905 -8120.97878479971 Force two-norm initial, final = 110.68307 0.33892042 Force max component initial, final = 84.373185 0.067323021 Final line search alpha, max atom move = 0.00011231393 7.5613129e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3346 | 0.3346 | 0.3346 | 0.0 | 98.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00095863 | 0.00095863 | 0.00095863 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003316 | | | 0.98 Nlocal: 1412.00 ave 1412 max 1412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7885.00 ave 7885 max 7885 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: 109216.0 ave 109216 max 109216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109216 Ave neighs/atom = 77.348442 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 46 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.221 | 5.221 | 5.221 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8120.9788 0 -8120.9788 -1747.672 Loop time of 6.566e-06 on 1 procs for 0 steps with 1412 atoms 198.0% 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 | | 6.566e-06 | | |100.00 Nlocal: 1412.00 ave 1412 max 1412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7885.00 ave 7885 max 7885 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: 109216.0 ave 109216 max 109216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109216 Ave neighs/atom = 77.348442 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 46 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.221 | 5.221 | 5.221 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 -8120.9788 -8120.9788 36.92816 147.83347 3.9088276 -1747.672 -1747.672 -4.5001578 -5238.8187 0.30300826 2.4735469 565.47106 Loop time of 7.056e-06 on 1 procs for 0 steps with 1412 atoms 297.6% 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 | | 7.056e-06 | | |100.00 Nlocal: 1412.00 ave 1412 max 1412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7885.00 ave 7885 max 7885 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54608.0 ave 54608 max 54608 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 109216.0 ave 109216 max 109216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109216 Ave neighs/atom = 77.348442 Neighbor list builds = 0 Dangerous builds = 0 1412 -8120.97878479971 eV 2.47354692247047 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07