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 = 3.5181212 3.5181212 3.5181212 Created orthogonal box = (0.0000000 -44.781891 0.0000000) to (31.663091 44.781891 4.9753748) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8635354 6.0810136 4.9753748 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -44.781891 0.0000000) to (31.663091 44.781891 4.9753748) create_atoms CPU = 0.002 seconds 650 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8635354 6.0810136 4.9753748 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -44.781891 0.0000000) to (31.663091 44.781891 4.9753748) create_atoms CPU = 0.001 seconds 650 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 8 21 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 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1288 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_222110751402_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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 5.885 | 5.885 | 5.885 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5579.6241 0 -5579.6241 22852.743 56 0 -5635.0064 0 -5635.0064 -5653.657 Loop time of 1.7939 on 1 procs for 56 steps with 1288 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 = -5579.62409637521 -5635.00189863875 -5635.00635591455 Force two-norm initial, final = 123.51092 0.20477656 Force max component initial, final = 37.231224 0.028854389 Final line search alpha, max atom move = 1.0000000 0.028854389 Iterations, force evaluations = 56 99 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7641 | 1.7641 | 1.7641 | 0.0 | 98.34 Neigh | 0.016194 | 0.016194 | 0.016194 | 0.0 | 0.90 Comm | 0.007555 | 0.007555 | 0.007555 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006062 | | | 0.34 Nlocal: 1288.00 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8860.00 ave 8860 max 8860 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: 317144.0 ave 317144 max 317144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 317144 Ave neighs/atom = 246.22981 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.886 | 5.886 | 5.886 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -5635.0064 0 -5635.0064 -5653.657 14109.497 58 0 -5635.0199 0 -5635.0199 -4173.5744 14097.396 Loop time of 0.0899405 on 1 procs for 2 steps with 1288 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 = -5635.00635591453 -5635.01837361592 -5635.01993722746 Force two-norm initial, final = 27.341657 0.20580606 Force max component initial, final = 26.849633 0.028302797 Final line search alpha, max atom move = 0.00013222483 3.7423326e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.08836 | 0.08836 | 0.08836 | 0.0 | 98.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033981 | 0.00033981 | 0.00033981 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001241 | | | 1.38 Nlocal: 1288.00 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8858.00 ave 8858 max 8858 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: 317392.0 ave 317392 max 317392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 317392 Ave neighs/atom = 246.42236 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 6.040 | 6.040 | 6.040 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5635.0199 0 -5635.0199 -4173.5744 Loop time of 1.548e-06 on 1 procs for 0 steps with 1288 atoms 129.2% 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 | | 1.548e-06 | | |100.00 Nlocal: 1288.00 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10058.0 ave 10058 max 10058 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: 317464.0 ave 317464 max 317464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 317464 Ave neighs/atom = 246.47826 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 6.040 | 6.040 | 6.040 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 -5635.0199 -5635.0199 31.669062 89.563782 4.9701704 -4173.5744 -4173.5744 -1.3050179 -12519.556 0.13759947 2.2752068 456.82028 Loop time of 2.095e-06 on 1 procs for 0 steps with 1288 atoms 190.9% 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 | | 2.095e-06 | | |100.00 Nlocal: 1288.00 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10058.0 ave 10058 max 10058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 158732.0 ave 158732 max 158732 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 317464.0 ave 317464 max 317464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 317464 Ave neighs/atom = 246.47826 Neighbor list builds = 0 Dangerous builds = 0 1288 -5635.01993722746 eV 2.27520680598078 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02