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 = 4.0452705 4.0452705 4.0452705 Created orthogonal box = (0.0000000 -46.476619 0.0000000) to (32.863933 46.476619 5.7208764) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9711372 6.3377208 5.7208764 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -46.476619 0.0000000) to (32.863933 46.476619 5.7208764) create_atoms CPU = 0.004 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9711372 6.3377208 5.7208764 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -46.476619 0.0000000) to (32.863933 46.476619 5.7208764) create_atoms CPU = 0.003 seconds 532 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 20 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 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1056 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_658278549784_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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 5.423 | 5.423 | 5.423 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3368.2369 0 -3368.2369 31605.271 65 0 -3592.5318 0 -3592.5318 4268.5313 Loop time of 3.0603 on 1 procs for 65 steps with 1056 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 = -3368.23690151203 -3592.52823393577 -3592.5317713337 Force two-norm initial, final = 342.54636 0.13273889 Force max component initial, final = 73.847485 0.017380880 Final line search alpha, max atom move = 1.0000000 0.017380880 Iterations, force evaluations = 65 111 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9604 | 2.9604 | 2.9604 | 0.0 | 96.74 Neigh | 0.062758 | 0.062758 | 0.062758 | 0.0 | 2.05 Comm | 0.020642 | 0.020642 | 0.020642 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01646 | | | 0.54 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7487.00 ave 7487 max 7487 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: 231304.0 ave 231304 max 231304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231304 Ave neighs/atom = 219.03788 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.427 | 5.427 | 5.427 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -3592.5318 0 -3592.5318 4268.5313 17476.184 72 0 -3592.7638 0 -3592.7638 10.369197 17567.195 Loop time of 0.239908 on 1 procs for 7 steps with 1056 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 = -3592.5317713337 -3592.76351578177 -3592.76376109856 Force two-norm initial, final = 89.728079 0.46780203 Force max component initial, final = 75.359022 0.42168605 Final line search alpha, max atom move = 0.00034362286 0.00014490097 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23339 | 0.23339 | 0.23339 | 0.0 | 97.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015055 | 0.0015055 | 0.0015055 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005009 | | | 2.09 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7935.00 ave 7935 max 7935 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: 230136.0 ave 230136 max 230136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230136 Ave neighs/atom = 217.93182 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 5.565 | 5.565 | 5.565 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3592.7638 0 -3592.7638 10.369197 Loop time of 6.345e-06 on 1 procs for 0 steps with 1056 atoms 204.9% 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 | | 6.345e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7935.00 ave 7935 max 7935 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: 227312.0 ave 227312 max 227312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227312 Ave neighs/atom = 215.25758 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 5.565 | 5.565 | 5.565 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 -3592.7638 -3592.7638 32.912391 93.503134 5.708432 10.369197 10.369197 0.42340189 38.686443 -8.0022542 2.6560158 681.72397 Loop time of 6.816e-06 on 1 procs for 0 steps with 1056 atoms 278.8% 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 | | 6.816e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7935.00 ave 7935 max 7935 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113656.0 ave 113656 max 113656 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 227312.0 ave 227312 max 227312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227312 Ave neighs/atom = 215.25758 Neighbor list builds = 0 Dangerous builds = 0 1056 -3592.76376109856 eV 2.65601581385977 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04