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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -51.757199 0.0000000) to (18.297688 51.757199 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7438451 5.7504086 4.9800000 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -51.757199 0.0000000) to (18.297688 51.757199 4.9800000) create_atoms CPU = 0.001 seconds 434 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7438451 5.7504086 4.9800000 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -51.757199 0.0000000) to (18.297688 51.757199 4.9800000) create_atoms CPU = 0.001 seconds 434 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 6 34 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 856 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 6 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.589 | 4.589 | 4.589 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3765.5202 0 -3765.5202 8535.955 43 0 -3795.0655 0 -3795.0655 -5175.859 Loop time of 2.10469 on 1 procs for 43 steps with 856 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3765.52015241021 -3795.06292057254 -3795.06553425703 Force two-norm initial, final = 52.410717 0.17035267 Force max component initial, final = 19.042634 0.023465981 Final line search alpha, max atom move = 1.0000000 0.023465981 Iterations, force evaluations = 43 73 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0914 | 2.0914 | 2.0914 | 0.0 | 99.37 Neigh | 0.0059129 | 0.0059129 | 0.0059129 | 0.0 | 0.28 Comm | 0.0039405 | 0.0039405 | 0.0039405 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003459 | | | 0.16 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5157.00 ave 5157 max 5157 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: 73272.0 ave 73272 max 73272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73272 Ave neighs/atom = 85.598131 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 6 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.590 | 4.590 | 4.590 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -3795.0655 0 -3795.0655 -5175.859 9432.4894 45 0 -3795.0887 0 -3795.0887 -1718.7065 9414.7559 Loop time of 0.143213 on 1 procs for 2 steps with 856 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 = -3795.06553425703 -3795.08823028228 -3795.08870470132 Force two-norm initial, final = 34.448505 0.17730228 Force max component initial, final = 25.288911 0.021349726 Final line search alpha, max atom move = 0.00044299814 9.4578890e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14222 | 0.14222 | 0.14222 | 0.0 | 99.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020085 | 0.00020085 | 0.00020085 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007877 | | | 0.55 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5270.00 ave 5270 max 5270 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: 73348.0 ave 73348 max 73348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73348 Ave neighs/atom = 85.686916 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 6 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.728 | 4.728 | 4.728 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3795.0887 0 -3795.0887 -1718.7065 Loop time of 1.547e-06 on 1 procs for 0 steps with 856 atoms 129.3% 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 | | 1.547e-06 | | |100.00 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5270.00 ave 5270 max 5270 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: 73356.0 ave 73356 max 73356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73356 Ave neighs/atom = 85.696262 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 6 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.728 | 4.728 | 4.728 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 -3795.0887 -3795.0887 18.275762 103.5144 4.9766007 -1718.7065 -1718.7065 1.9650023 -5155.3885 -2.6960964 2.2889828 486.29648 Loop time of 1.64e-06 on 1 procs for 0 steps with 856 atoms 182.9% 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 | | 1.64e-06 | | |100.00 Nlocal: 856.000 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5270.00 ave 5270 max 5270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36678.0 ave 36678 max 36678 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 73356.0 ave 73356 max 73356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73356 Ave neighs/atom = 85.696262 Neighbor list builds = 0 Dangerous builds = 0 856 -3795.08870470132 eV 2.28898281386575 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02