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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -34.178917 0.0000000) to (41.860453 34.178917 7.0757080) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7840518 4.3944321 4.7171386 Created 835 atoms using lattice units in orthogonal box = (0.0000000 -34.178917 0.0000000) to (41.860453 34.178917 7.0757080) create_atoms CPU = 0.002 seconds 835 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7840518 4.3944321 4.7171386 Created 841 atoms using lattice units in orthogonal box = (0.0000000 -34.178917 0.0000000) to (41.860453 34.178917 7.0757080) create_atoms CPU = 0.001 seconds 841 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 = 16 26 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 1676 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 16 26 3 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) = 5.791 | 5.791 | 5.791 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6661.4673 0 -6661.4673 42212.113 77 0 -6951.329 0 -6951.329 3341.0187 Loop time of 17.0969 on 1 procs for 77 steps with 1676 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 = -6661.46727995575 -6951.32217183476 -6951.32899696072 Force two-norm initial, final = 356.74341 0.35358869 Force max component initial, final = 148.06062 0.054338557 Final line search alpha, max atom move = 1.0000000 0.054338557 Iterations, force evaluations = 77 141 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.049 | 17.049 | 17.049 | 0.0 | 99.72 Neigh | 0.025669 | 0.025669 | 0.025669 | 0.0 | 0.15 Comm | 0.0087384 | 0.0087384 | 0.0087384 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01361 | | | 0.08 Nlocal: 1676.00 ave 1676 max 1676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4411.00 ave 4411 max 4411 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: 96152.0 ave 96152 max 96152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96152 Ave neighs/atom = 57.369928 Neighbor list builds = 1 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 = 16 26 3 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 : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.407 | 5.407 | 5.407 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -6951.329 0 -6951.329 3341.0187 20247.067 81 0 -6951.5241 0 -6951.5241 -70.808123 20283.783 Loop time of 0.718196 on 1 procs for 4 steps with 1676 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 = -6951.32899696072 -6951.52313765117 -6951.52409048536 Force two-norm initial, final = 116.29193 1.6739233 Force max component initial, final = 109.89514 0.96195677 Final line search alpha, max atom move = 0.00016905922 0.00016262766 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.71619 | 0.71619 | 0.71619 | 0.0 | 99.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028333 | 0.00028333 | 0.00028333 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001719 | | | 0.24 Nlocal: 1676.00 ave 1676 max 1676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4393.00 ave 4393 max 4393 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: 96142.0 ave 96142 max 96142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96142 Ave neighs/atom = 57.363962 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 = 16 26 3 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) = 5.545 | 5.545 | 5.545 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6951.5241 0 -6951.5241 -70.808123 Loop time of 3.207e-06 on 1 procs for 0 steps with 1676 atoms 155.9% 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 | | 3.207e-06 | | |100.00 Nlocal: 1676.00 ave 1676 max 1676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4391.00 ave 4391 max 4391 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: 96120.0 ave 96120 max 96120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96120 Ave neighs/atom = 57.350835 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 = 16 26 3 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) = 5.545 | 5.545 | 5.545 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 -6951.5241 -6951.5241 41.871151 68.57838 7.0639372 -70.808123 -70.808123 -74.554615 -62.013062 -75.856691 2.2720821 1720.4107 Loop time of 2.669e-06 on 1 procs for 0 steps with 1676 atoms 299.7% 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 | | 2.669e-06 | | |100.00 Nlocal: 1676.00 ave 1676 max 1676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4391.00 ave 4391 max 4391 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 48060.0 ave 48060 max 48060 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 96120.0 ave 96120 max 96120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96120 Ave neighs/atom = 57.350835 Neighbor list builds = 0 Dangerous builds = 0 1676 -6951.52409048536 eV 2.27208205471698 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18