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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -43.633723 0.0000000) to (53.440179 43.633723 8.8454813) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1244007 5.3795001 5.8969875 Created 1748 atoms using lattice units in orthogonal box = (0.0000000 -43.633723 0.0000000) to (53.440179 43.633723 8.8454813) create_atoms CPU = 0.003 seconds 1748 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1244007 5.3795001 5.8969875 Created 1754 atoms using lattice units in orthogonal box = (0.0000000 -43.633723 0.0000000) to (53.440179 43.633723 8.8454813) 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 20 33 4 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 24 atoms, new total = 3478 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 20 33 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 6.353 | 6.353 | 6.353 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13595.762 0 -13595.762 42361.938 131 0 -14723.75 0 -14723.75 -8314.6686 Loop time of 39.6094 on 1 procs for 131 steps with 3478 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 = -13595.7623597435 -14723.7370363932 -14723.7498966479 Force two-norm initial, final = 964.97651 0.41367897 Force max component initial, final = 176.23584 0.059735483 Final line search alpha, max atom move = 1.0000000 0.059735483 Iterations, force evaluations = 131 224 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 39.374 | 39.374 | 39.374 | 0.0 | 99.41 Neigh | 0.17456 | 0.17456 | 0.17456 | 0.0 | 0.44 Comm | 0.020493 | 0.020493 | 0.020493 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04043 | | | 0.10 Nlocal: 3478.00 ave 3478 max 3478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6720.00 ave 6720 max 6720 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: 187850.0 ave 187850 max 187850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187850 Ave neighs/atom = 54.010926 Neighbor list builds = 4 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 20 33 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 131 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.351 | 6.351 | 6.351 Mbytes Step Temp E_pair E_mol TotEng Press Volume 131 0 -14723.75 0 -14723.75 -8314.6686 41251.68 136 0 -14724.533 0 -14724.533 4.437188 41044.433 Loop time of 1.39723 on 1 procs for 5 steps with 3478 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 = -14723.7498966479 -14724.5271264865 -14724.53283446 Force two-norm initial, final = 397.19548 4.2628513 Force max component initial, final = 290.70078 3.5309044 Final line search alpha, max atom move = 3.0055023e-05 0.00010612141 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3934 | 1.3934 | 1.3934 | 0.0 | 99.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00043892 | 0.00043892 | 0.00043892 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003374 | | | 0.24 Nlocal: 3478.00 ave 3478 max 3478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6728.00 ave 6728 max 6728 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: 187732.0 ave 187732 max 187732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187732 Ave neighs/atom = 53.976998 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 20 33 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 6.489 | 6.489 | 6.489 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14724.533 0 -14724.533 4.437188 Loop time of 2.358e-06 on 1 procs for 0 steps with 3478 atoms 169.6% 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 | | 2.358e-06 | | |100.00 Nlocal: 3478.00 ave 3478 max 3478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6737.00 ave 6737 max 6737 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: 187852.0 ave 187852 max 187852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187852 Ave neighs/atom = 54.011501 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 20 33 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 6.489 | 6.489 | 6.489 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 -14724.533 -14724.533 53.31366 86.946781 8.8544637 4.437188 4.437188 137.50315 -74.652451 -49.539135 2.3221383 1473.0521 Loop time of 2.278e-06 on 1 procs for 0 steps with 3478 atoms 219.5% 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 | | 2.278e-06 | | |100.00 Nlocal: 3478.00 ave 3478 max 3478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6737.00 ave 6737 max 6737 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 93926.0 ave 93926 max 93926 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 187852.0 ave 187852 max 187852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187852 Ave neighs/atom = 54.011501 Neighbor list builds = 0 Dangerous builds = 0 3478 -14724.53283446 eV 2.32213827118835 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:42