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 -35.881456 0.0000000) to (31.071206 35.881456 6.0935647) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5768830 5.5196827 6.0935647 Created 628 atoms using lattice units in orthogonal box = (0.0000000 -35.881456 0.0000000) to (31.071206 35.881456 6.0935647) create_atoms CPU = 0.001 seconds 628 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5768830 5.5196827 6.0935647 Created 630 atoms using lattice units in orthogonal box = (0.0000000 -35.881456 0.0000000) to (31.071206 35.881456 6.0935647) create_atoms CPU = 0.001 seconds 630 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 17 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 24 atoms, new total = 1234 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 17 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) = 5.882 | 5.882 | 5.882 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5316.2369 0 -5316.2369 30593.773 59 0 -5378.2743 0 -5378.2743 -7167.646 Loop time of 1.79492 on 1 procs for 59 steps with 1234 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 = -5316.23687204972 -5378.26922773504 -5378.27432377749 Force two-norm initial, final = 132.32755 0.21082432 Force max component initial, final = 23.189250 0.039427983 Final line search alpha, max atom move = 0.73196345 0.028859842 Iterations, force evaluations = 59 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7627 | 1.7627 | 1.7627 | 0.0 | 98.21 Neigh | 0.01641 | 0.01641 | 0.01641 | 0.0 | 0.91 Comm | 0.009209 | 0.009209 | 0.009209 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006551 | | | 0.36 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8322.00 ave 8322 max 8322 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: 302752.0 ave 302752 max 302752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 302752 Ave neighs/atom = 245.34198 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 17 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 : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.882 | 5.882 | 5.882 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -5378.2743 0 -5378.2743 -7167.646 13587.188 61 0 -5378.3033 0 -5378.3033 -4101.1383 13562.169 Loop time of 0.0851596 on 1 procs for 2 steps with 1234 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 = -5378.27432377747 -5378.30325789068 -5378.30330163981 Force two-norm initial, final = 44.403310 0.21792839 Force max component initial, final = 31.557919 0.035857899 Final line search alpha, max atom move = 0.0010917066 3.9146306e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.083632 | 0.083632 | 0.083632 | 0.0 | 98.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030418 | 0.00030418 | 0.00030418 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001224 | | | 1.44 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8346.00 ave 8346 max 8346 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: 302948.0 ave 302948 max 302948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 302948 Ave neighs/atom = 245.50081 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 17 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) = 6.020 | 6.020 | 6.020 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5378.3033 0 -5378.3033 -4101.1383 Loop time of 1.868e-06 on 1 procs for 0 steps with 1234 atoms 107.1% 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 | | 1.868e-06 | | |100.00 Nlocal: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8346.00 ave 8346 max 8346 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: 303064.0 ave 303064 max 303064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 303064 Ave neighs/atom = 245.59481 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 17 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) = 6.020 | 6.020 | 6.020 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 -5378.3033 -5378.3033 31.041247 71.762912 6.0882147 -4101.1383 -4101.1383 1.5189541 -12300.702 -4.2323792 2.1649554 774.19229 Loop time of 1.84e-06 on 1 procs for 0 steps with 1234 atoms 217.4% 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: 1234.00 ave 1234 max 1234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8346.00 ave 8346 max 8346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 151532.0 ave 151532 max 151532 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 303064.0 ave 303064 max 303064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 303064 Ave neighs/atom = 245.59481 Neighbor list builds = 0 Dangerous builds = 0 1234 -5378.30330163981 eV 2.16495542109401 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02