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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -51.865307 0.0000000) to (36.674310 51.865307 5.7275650) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2614676 6.9575412 5.7275650 Created 655 atoms using lattice units in orthogonal box = (0.0000000 -51.865307 0.0000000) to (36.674310 51.865307 5.7275650) create_atoms CPU = 0.005 seconds 655 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2614676 6.9575412 5.7275650 Created 659 atoms using lattice units in orthogonal box = (0.0000000 -51.865307 0.0000000) to (36.674310 51.865307 5.7275650) create_atoms CPU = 0.005 seconds 659 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 28 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 1311 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_418978237058_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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.059 | 5.059 | 5.059 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4262.0064 0 -4262.0064 13677.573 94 0 -4399.0987 0 -4399.0987 3974.6823 Loop time of 2.87292 on 1 procs for 94 steps with 1311 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 = -4262.00640840344 -4399.09444368734 -4399.09870590559 Force two-norm initial, final = 116.36157 0.15333326 Force max component initial, final = 27.046319 0.054072764 Final line search alpha, max atom move = 1.0000000 0.054072764 Iterations, force evaluations = 94 176 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7692 | 2.7692 | 2.7692 | 0.0 | 96.39 Neigh | 0.046032 | 0.046032 | 0.046032 | 0.0 | 1.60 Comm | 0.029494 | 0.029494 | 0.029494 | 0.0 | 1.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02814 | | | 0.98 Nlocal: 1311.00 ave 1311 max 1311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6653.00 ave 6653 max 6653 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: 171380.0 ave 171380 max 171380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171380 Ave neighs/atom = 130.72464 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 94 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.059 | 5.059 | 5.059 Mbytes Step Temp E_pair E_mol TotEng Press Volume 94 0 -4399.0987 0 -4399.0987 3974.6823 21789.082 102 0 -4399.4256 0 -4399.4256 77.60651 21897.99 Loop time of 0.163543 on 1 procs for 8 steps with 1311 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4399.09870590558 -4399.42512349734 -4399.42559652966 Force two-norm initial, final = 109.36739 1.9056005 Force max component initial, final = 100.13890 1.4204947 Final line search alpha, max atom move = 0.00051034526 0.00072494272 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15624 | 0.15624 | 0.15624 | 0.0 | 95.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016091 | 0.0016091 | 0.0016091 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00569 | | | 3.48 Nlocal: 1311.00 ave 1311 max 1311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6645.00 ave 6645 max 6645 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: 171486.0 ave 171486 max 171486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171486 Ave neighs/atom = 130.80549 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.197 | 5.197 | 5.197 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4399.4256 0 -4399.4256 77.60651 Loop time of 6.896e-06 on 1 procs for 0 steps with 1311 atoms 174.0% 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 | | 6.896e-06 | | |100.00 Nlocal: 1311.00 ave 1311 max 1311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6645.00 ave 6645 max 6645 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: 171054.0 ave 171054 max 171054 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171054 Ave neighs/atom = 130.47597 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.197 | 5.197 | 5.197 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 -4399.4256 -4399.4256 36.64091 104.47764 5.720245 77.60651 77.60651 58.060041 104.67962 70.079871 2.5867127 834.40328 Loop time of 6.435e-06 on 1 procs for 0 steps with 1311 atoms 295.3% 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 | | 6.435e-06 | | |100.00 Nlocal: 1311.00 ave 1311 max 1311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6645.00 ave 6645 max 6645 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85527.0 ave 85527 max 85527 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 171054.0 ave 171054 max 171054 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171054 Ave neighs/atom = 130.47597 Neighbor list builds = 0 Dangerous builds = 0 1311 -4399.42559652966 eV 2.5867126675448 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03