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 = 3.1666864 3.1666864 3.1666864 Created orthogonal box = (0.0000000 -59.748920 0.0000000) to (29.874460 59.748920 3.1666864) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3636851 4.3636851 3.1666864 Created 356 atoms using lattice units in orthogonal box = (0.0000000 -59.748920 0.0000000) to (29.874460 59.748920 3.1666864) create_atoms CPU = 0.001 seconds 356 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3636851 4.3636851 3.1666864 Created 357 atoms using lattice units in orthogonal box = (0.0000000 -59.748920 0.0000000) to (29.874460 59.748920 3.1666864) create_atoms CPU = 0.001 seconds 357 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 = 6.7012 ghost atom cutoff = 6.7012 binsize = 3.3506, bins = 9 36 1 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 6.7012 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 709 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_560387080449_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 = 6.7012 ghost atom cutoff = 6.7012 binsize = 3.3506, bins = 9 36 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7012 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) = 4.540 | 4.540 | 4.540 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 78.676987 0 78.676987 2253.3569 262 0 21.443165 0 21.443165 -2295.556 Loop time of 118.045 on 1 procs for 262 steps with 709 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 = 78.6769868613865 21.4431824614646 21.4431651651026 Force two-norm initial, final = 50.155119 0.014521933 Force max component initial, final = 18.041642 0.0024748277 Final line search alpha, max atom move = 1.0000000 0.0024748277 Iterations, force evaluations = 262 487 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 117.99 | 117.99 | 117.99 | 0.0 | 99.95 Neigh | 0.012583 | 0.012583 | 0.012583 | 0.0 | 0.01 Comm | 0.025644 | 0.025644 | 0.025644 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01912 | | | 0.02 Nlocal: 709.000 ave 709 max 709 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5094.00 ave 5094 max 5094 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: 45844.0 ave 45844 max 45844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45844 Ave neighs/atom = 64.660085 Neighbor list builds = 3 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 = 6.7012 ghost atom cutoff = 6.7012 binsize = 3.3506, bins = 9 36 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7012 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 262 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.537 | 4.537 | 4.537 Mbytes Step Temp E_pair E_mol TotEng Press Volume 262 0 21.443165 0 21.443165 -2295.556 11304.859 265 0 21.432693 0 21.432693 4.4394171 11294.706 Loop time of 1.91787 on 1 procs for 3 steps with 709 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 = 21.4431651651027 21.4326926903809 21.432692502209 Force two-norm initial, final = 30.045723 0.070616027 Force max component initial, final = 24.978992 0.056625769 Final line search alpha, max atom move = 0.012422875 0.00070345483 Iterations, force evaluations = 3 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9163 | 1.9163 | 1.9163 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027463 | 0.00027463 | 0.00027463 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001319 | | | 0.07 Nlocal: 709.000 ave 709 max 709 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5111.00 ave 5111 max 5111 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: 45838.0 ave 45838 max 45838 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45838 Ave neighs/atom = 64.651622 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 = 6.7012 ghost atom cutoff = 6.7012 binsize = 3.3506, bins = 9 36 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7012 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) = 4.675 | 4.675 | 4.675 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 21.432693 0 21.432693 4.4394171 Loop time of 1.863e-06 on 1 procs for 0 steps with 709 atoms 161.0% 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 | | 1.863e-06 | | |100.00 Nlocal: 709.000 ave 709 max 709 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5132.00 ave 5132 max 5132 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: 45848.0 ave 45848 max 45848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45848 Ave neighs/atom = 64.665726 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 = 6.7012 ghost atom cutoff = 6.7012 binsize = 3.3506, bins = 9 36 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.7012 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) = 4.675 | 4.675 | 4.675 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 21.432693 21.432693 29.872718 119.49139 3.1641974 4.4394171 4.4394171 0.24438051 8.0320446 5.0418262 2.4325082 276.40644 Loop time of 1.84e-06 on 1 procs for 0 steps with 709 atoms 108.7% 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 | | 1.84e-06 | | |100.00 Nlocal: 709.000 ave 709 max 709 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5132.00 ave 5132 max 5132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22924.0 ave 22924 max 22924 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 45848.0 ave 45848 max 45848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45848 Ave neighs/atom = 64.665726 Neighbor list builds = 0 Dangerous builds = 0 709 -4854.39399848774 eV 2.43250817978041 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:02:02