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 = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -40.899057 0.0000000) to (17.709811 40.899057 6.2613638) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9032704 5.1123821 6.2613638 Created 384 atoms using lattice units in orthogonal box = (0.0000000 -40.899057 0.0000000) to (17.709811 40.899057 6.2613638) create_atoms CPU = 0.001 seconds 384 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9032704 5.1123821 6.2613638 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -40.899057 0.0000000) to (17.709811 40.899057 6.2613638) create_atoms CPU = 0.001 seconds 396 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 5 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 7.506786 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 776 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_346334655118_005#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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 5 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 4.975 | 4.975 | 4.975 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2385.2977 0 -2385.2977 142609.18 91 0 -2733.6472 0 -2733.6472 20654.738 Loop time of 0.920447 on 1 procs for 91 steps with 776 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2385.29774802154 -2733.64514976938 -2733.64723150681 Force two-norm initial, final = 386.56391 0.13405868 Force max component initial, final = 75.773554 0.013524615 Final line search alpha, max atom move = 1.0000000 0.013524615 Iterations, force evaluations = 91 173 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.90119 | 0.90119 | 0.90119 | 0.0 | 97.91 Neigh | 0.0067698 | 0.0067698 | 0.0067698 | 0.0 | 0.74 Comm | 0.0067595 | 0.0067595 | 0.0067595 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005725 | | | 0.62 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4862.00 ave 4862 max 4862 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: 110560.0 ave 110560 max 110560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110560 Ave neighs/atom = 142.47423 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 5 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.975 | 4.975 | 4.975 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -2733.6472 0 -2733.6472 20654.738 9070.3942 104 0 -2734.7764 0 -2734.7764 8.7590696 9202.3391 Loop time of 0.0868229 on 1 procs for 13 steps with 776 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 = -2733.64723150681 -2734.77637964265 -2734.77643558137 Force two-norm initial, final = 212.39290 0.39026660 Force max component initial, final = 164.79288 0.082550518 Final line search alpha, max atom move = 0.00085700581 7.0746274e-05 Iterations, force evaluations = 13 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.083444 | 0.083444 | 0.083444 | 0.0 | 96.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057487 | 0.00057487 | 0.00057487 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002804 | | | 3.23 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4880.00 ave 4880 max 4880 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: 110864.0 ave 110864 max 110864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110864 Ave neighs/atom = 142.86598 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 5 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 5.113 | 5.113 | 5.113 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2734.7764 0 -2734.7764 8.7590696 Loop time of 1.785e-06 on 1 procs for 0 steps with 776 atoms 168.1% 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 | | 1.785e-06 | | |100.00 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4880.00 ave 4880 max 4880 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: 110368.0 ave 110368 max 110368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110368 Ave neighs/atom = 142.22680 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 5 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 5.113 | 5.113 | 5.113 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 -2734.7764 -2734.7764 17.686771 82.761549 6.2866759 8.7590696 8.7590696 14.353789 5.1609506 6.7624696 2.3799916 495.99858 Loop time of 1.648e-06 on 1 procs for 0 steps with 776 atoms 182.0% 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 | | 1.648e-06 | | |100.00 Nlocal: 776.000 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4880.00 ave 4880 max 4880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 55184.0 ave 55184 max 55184 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 110368.0 ave 110368 max 110368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110368 Ave neighs/atom = 142.22680 Neighbor list builds = 0 Dangerous builds = 0 776 -2734.77627967619 eV 2.37999159770749 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01