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 -36.826675 0.0000000) to (18.413338 36.826675 3.6111526) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2492318 4.2492318 3.6111526 Created 208 atoms using lattice units in orthogonal box = (0.0000000 -36.826675 0.0000000) to (18.413338 36.826675 3.6111526) create_atoms CPU = 0.002 seconds 208 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2492318 4.2492318 3.6111526 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -36.826675 0.0000000) to (18.413338 36.826675 3.6111526) create_atoms CPU = 0.001 seconds 210 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 = 7 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 2 atoms, new total = 416 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 = 7 28 2 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) = 4.819 | 4.819 | 4.819 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1624.8513 0 -1624.8513 62364.154 81 0 -1757.8437 0 -1757.8437 8311.3657 Loop time of 8.28627 on 1 procs for 81 steps with 416 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 = -1624.85127216492 -1757.84244364097 -1757.84373060483 Force two-norm initial, final = 260.55860 0.11917572 Force max component initial, final = 71.158608 0.016447169 Final line search alpha, max atom move = 1.0000000 0.016447169 Iterations, force evaluations = 81 152 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.266 | 8.266 | 8.266 | 0.0 | 99.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010252 | 0.010252 | 0.010252 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01007 | | | 0.12 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2636.00 ave 2636 max 2636 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: 22424.0 ave 22424 max 22424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22424 Ave neighs/atom = 53.903846 Neighbor list builds = 0 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 = 7 28 2 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 : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.819 | 4.819 | 4.819 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -1757.8437 0 -1757.8437 8311.3657 4897.4597 86 0 -1757.9261 0 -1757.9261 -476.3522 4923.5415 Loop time of 0.380414 on 1 procs for 5 steps with 416 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 = -1757.84373060483 -1757.92473247328 -1757.92608573566 Force two-norm initial, final = 44.921516 2.9733290 Force max component initial, final = 32.726840 2.1397880 Final line search alpha, max atom move = 0.00020666014 0.00044220889 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37832 | 0.37832 | 0.37832 | 0.0 | 99.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044316 | 0.00044316 | 0.00044316 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001655 | | | 0.43 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2596.00 ave 2596 max 2596 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: 22360.0 ave 22360 max 22360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22360 Ave neighs/atom = 53.750000 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 = 7 28 2 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) = 4.957 | 4.957 | 4.957 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1757.9261 0 -1757.9261 -476.3522 Loop time of 2.7473e-05 on 1 procs for 0 steps with 416 atoms 0.0% 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 | | 2.747e-05 | | |100.00 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2596.00 ave 2596 max 2596 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: 22360.0 ave 22360 max 22360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22360 Ave neighs/atom = 53.750000 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 = 7 28 2 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) = 4.957 | 4.957 | 4.957 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 -1757.9261 -1757.9261 18.416171 73.688454 3.6280964 -476.3522 -476.3522 -696.41855 -665.35595 -67.282093 2.3044085 121.27461 Loop time of 7.267e-06 on 1 procs for 0 steps with 416 atoms 206.4% 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 | | 7.267e-06 | | |100.00 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2596.00 ave 2596 max 2596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11180.0 ave 11180 max 11180 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 22360.0 ave 22360 max 22360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22360 Ave neighs/atom = 53.750000 Neighbor list builds = 0 Dangerous builds = 0 416 -1757.92608573566 eV 2.304408507232 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09