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 = 3.6149602 3.6149602 3.6149602 Created orthogonal box = (0.0000000 -43.679730 0.0000000) to (53.496525 43.679730 8.8548078) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1298038 5.3851722 5.9032052 Created 1748 atoms using lattice units in orthogonal box = (0.0000000 -43.679730 0.0000000) to (53.496525 43.679730 8.8548078) create_atoms CPU = 0.003 seconds 1748 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1298038 5.3851722 5.9032052 Created 1754 atoms using lattice units in orthogonal box = (0.0000000 -43.679730 0.0000000) to (53.496525 43.679730 8.8548078) create_atoms CPU = 0.002 seconds 1754 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 = 8.4662927 ghost atom cutoff = 8.4662927 binsize = 4.2331463, bins = 13 21 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 8.466292682285578 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 3494 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_318213562153_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 = 8.4662927 ghost atom cutoff = 8.4662927 binsize = 4.2331463, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.466292682285578 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) = 7.818 | 7.818 | 7.818 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11606.737 0 -11606.737 39304.392 78 0 -12335.414 0 -12335.414 6147.3777 Loop time of 4.42956 on 1 procs for 78 steps with 3494 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11606.7370435255 -12335.4012602197 -12335.4135838818 Force two-norm initial, final = 735.62208 0.33174625 Force max component initial, final = 139.93547 0.049980160 Final line search alpha, max atom move = 1.0000000 0.049980160 Iterations, force evaluations = 78 119 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1549 | 4.1549 | 4.1549 | 0.0 | 93.80 Neigh | 0.22564 | 0.22564 | 0.22564 | 0.0 | 5.09 Comm | 0.020866 | 0.020866 | 0.020866 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0282 | | | 0.64 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12297.0 ave 12297 max 12297 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: 738764.0 ave 738764 max 738764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 738764 Ave neighs/atom = 211.43789 Neighbor list builds = 5 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 = 8.4662927 ghost atom cutoff = 8.4662927 binsize = 4.2331463, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.466292682285578 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.820 | 7.820 | 7.820 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -12335.414 0 -12335.414 6147.3777 41382.303 87 0 -12336.645 0 -12336.645 31.395935 41564.055 Loop time of 0.390355 on 1 procs for 9 steps with 3494 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12335.4135838817 -12336.640468981 -12336.6446301864 Force two-norm initial, final = 348.27943 1.6024547 Force max component initial, final = 332.18232 0.90710527 Final line search alpha, max atom move = 9.3252377e-05 8.4589723e-05 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38115 | 0.38115 | 0.38115 | 0.0 | 97.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012294 | 0.0012294 | 0.0012294 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007975 | | | 2.04 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12286.0 ave 12286 max 12286 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: 738822.0 ave 738822 max 738822 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 738822 Ave neighs/atom = 211.45449 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 = 8.4662927 ghost atom cutoff = 8.4662927 binsize = 4.2331463, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.466292682285578 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) = 7.978 | 7.978 | 7.978 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12336.645 0 -12336.645 31.395935 Loop time of 2.441e-06 on 1 procs for 0 steps with 3494 atoms 204.8% 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 | | 2.441e-06 | | |100.00 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12424.0 ave 12424 max 12424 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: 729556.0 ave 729556 max 729556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 729556 Ave neighs/atom = 208.80252 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 = 8.4662927 ghost atom cutoff = 8.4662927 binsize = 4.2331463, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.466292682285578 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) = 7.978 | 7.978 | 7.978 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 -12336.645 -12336.645 53.386638 88.099545 8.8371388 31.395935 31.395935 29.74522 29.546022 34.896564 2.2975986 1613.0669 Loop time of 2.717e-06 on 1 procs for 0 steps with 3494 atoms 331.2% 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 | | 2.717e-06 | | |100.00 Nlocal: 3494.00 ave 3494 max 3494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12424.0 ave 12424 max 12424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 364778.0 ave 364778 max 364778 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 729556.0 ave 729556 max 729556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 729556 Ave neighs/atom = 208.80252 Neighbor list builds = 0 Dangerous builds = 0 3494 -12336.6446301864 eV 2.29759855529636 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05