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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -53.472189 0.0000000) to (43.659859 53.472189 8.8507796) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3827224 5.1274701 5.9005197 Created 1747 atoms using lattice units in orthogonal box = (0.0000000 -53.472189 0.0000000) to (43.659859 53.472189 8.8507796) create_atoms CPU = 0.002 seconds 1747 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3827224 5.1274701 5.9005197 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -53.472189 0.0000000) to (43.659859 53.472189 8.8507796) create_atoms CPU = 0.002 seconds 1755 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 ghost atom cutoff = 7 binsize = 3.5, bins = 13 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3502 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_407917731909_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 13 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 6.540 | 6.540 | 6.540 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11655.918 0 -11655.918 53643.816 84 0 -12349.147 0 -12349.147 6404.9602 Loop time of 15.565 on 1 procs for 84 steps with 3502 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11655.9180003444 -12349.1384446948 -12349.1474413525 Force two-norm initial, final = 519.48206 0.36820778 Force max component initial, final = 84.792173 0.11872642 Final line search alpha, max atom move = 1.0000000 0.11872642 Iterations, force evaluations = 84 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.459 | 15.459 | 15.459 | 0.0 | 99.32 Neigh | 0.060516 | 0.060516 | 0.060516 | 0.0 | 0.39 Comm | 0.019181 | 0.019181 | 0.019181 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02589 | | | 0.17 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10008.0 ave 10008 max 10008 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: 463726.0 ave 463726 max 463726 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 463726 Ave neighs/atom = 132.41748 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 13 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.540 | 6.540 | 6.540 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -12349.147 0 -12349.147 6404.9602 41325.852 91 0 -12350.082 0 -12350.082 -164.27611 41516.221 Loop time of 0.929699 on 1 procs for 7 steps with 3502 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 = -12349.1474413525 -12350.0737156933 -12350.0817765174 Force two-norm initial, final = 341.28236 7.6356591 Force max component initial, final = 316.78421 5.5907839 Final line search alpha, max atom move = 6.0060565e-05 0.00033578564 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.92437 | 0.92437 | 0.92437 | 0.0 | 99.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00071122 | 0.00071122 | 0.00071122 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004619 | | | 0.50 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9998.00 ave 9998 max 9998 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: 463830.0 ave 463830 max 463830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 463830 Ave neighs/atom = 132.44717 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 ghost atom cutoff = 7 binsize = 3.5, bins = 13 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 6.677 | 6.677 | 6.677 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12350.082 0 -12350.082 -164.27611 Loop time of 1.916e-06 on 1 procs for 0 steps with 3502 atoms 208.8% 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 | | 1.916e-06 | | |100.00 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9975.00 ave 9975 max 9975 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: 463502.0 ave 463502 max 463502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 463502 Ave neighs/atom = 132.35351 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 ghost atom cutoff = 7 binsize = 3.5, bins = 13 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 6.677 | 6.677 | 6.677 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 -12350.082 -12350.082 43.5991 107.65268 8.8453585 -164.27611 -164.27611 -215.45692 -164.83258 -112.53882 2.2722479 1782.3698 Loop time of 2.122e-06 on 1 procs for 0 steps with 3502 atoms 282.8% 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 | | 2.122e-06 | | |100.00 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9975.00 ave 9975 max 9975 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 231751.0 ave 231751 max 231751 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 463502.0 ave 463502 max 463502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 463502 Ave neighs/atom = 132.35351 Neighbor list builds = 0 Dangerous builds = 0 3502 -12350.0817765174 eV 2.27224794839632 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17