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 = 3.5181212 3.5181212 3.5181212 Created orthogonal box = (0.0000000 -63.326182 0.0000000) to (44.778373 63.326182 4.9753748) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0810136 5.8635354 4.9753748 Created 1294 atoms using lattice units in orthogonal box = (0.0000000 -63.326182 0.0000000) to (44.778373 63.326182 4.9753748) create_atoms CPU = 0.004 seconds 1294 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0810136 5.8635354 4.9753748 Created 1298 atoms using lattice units in orthogonal box = (0.0000000 -63.326182 0.0000000) to (44.778373 63.326182 4.9753748) create_atoms CPU = 0.003 seconds 1298 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 11 30 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 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2592 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_222110751402_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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 11.23 | 11.23 | 11.23 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10512.784 0 -10512.784 87276.021 69 0 -11335.896 0 -11335.896 3239.3927 Loop time of 4.6251 on 1 procs for 69 steps with 2592 atoms 97.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10512.7841401042 -11335.8865730404 -11335.8963104647 Force two-norm initial, final = 1068.7061 0.32633573 Force max component initial, final = 223.41699 0.064794520 Final line search alpha, max atom move = 0.52779330 0.034198114 Iterations, force evaluations = 69 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5217 | 4.5217 | 4.5217 | 0.0 | 97.77 Neigh | 0.066373 | 0.066373 | 0.066373 | 0.0 | 1.44 Comm | 0.019804 | 0.019804 | 0.019804 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01719 | | | 0.37 Nlocal: 2592.00 ave 2592 max 2592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15804.0 ave 15804 max 15804 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: 642608.0 ave 642608 max 642608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 642608 Ave neighs/atom = 247.91975 Neighbor list builds = 2 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 11.23 | 11.23 | 11.23 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -11335.896 0 -11335.896 3239.3927 28216.777 71 0 -11335.973 0 -11335.973 1.1209798 28269.557 Loop time of 0.182966 on 1 procs for 2 steps with 2592 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 = -11335.8963104647 -11335.9645635667 -11335.9725882113 Force two-norm initial, final = 106.92449 1.8843311 Force max component initial, final = 76.813346 1.3785710 Final line search alpha, max atom move = 4.2750536e-05 5.8934651e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18005 | 0.18005 | 0.18005 | 0.0 | 98.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057131 | 0.00057131 | 0.00057131 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002349 | | | 1.28 Nlocal: 2592.00 ave 2592 max 2592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15804.0 ave 15804 max 15804 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: 642792.0 ave 642792 max 642792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 642792 Ave neighs/atom = 247.99074 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 10.74 | 10.74 | 10.74 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11335.973 0 -11335.973 1.1209798 Loop time of 1.556e-06 on 1 procs for 0 steps with 2592 atoms 192.8% 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 | | 1.556e-06 | | |100.00 Nlocal: 2592.00 ave 2592 max 2592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15786.0 ave 15786 max 15786 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: 642520.0 ave 642520 max 642520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 642520 Ave neighs/atom = 247.88580 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 10.74 | 10.74 | 10.74 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 -11335.973 -11335.973 44.829425 126.78219 4.9739062 1.1209798 1.1209798 -70.202083 78.21057 -4.6455476 2.2463581 1154.1472 Loop time of 2.171e-06 on 1 procs for 0 steps with 2592 atoms 230.3% 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 | | 2.171e-06 | | |100.00 Nlocal: 2592.00 ave 2592 max 2592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15786.0 ave 15786 max 15786 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 321260.0 ave 321260 max 321260 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 642520.0 ave 642520 max 642520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 642520 Ave neighs/atom = 247.88580 Neighbor list builds = 0 Dangerous builds = 0 2592 -11335.9725882113 eV 2.24635805975862 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05