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 = 3.1435003 3.1435003 3.1435003 Created orthogonal box = (0.0000000 -47.880370 0.0000000) to (23.940185 47.880370 3.1435003) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1276181 4.1276181 3.1435003 Created 231 atoms using lattice units in orthogonal box = (0.0000000 -47.880370 0.0000000) to (23.940185 47.880370 3.1435003) create_atoms CPU = 0.001 seconds 231 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1276181 4.1276181 3.1435003 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -47.880370 0.0000000) to (23.940185 47.880370 3.1435003) create_atoms CPU = 0.000 seconds 233 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 20 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 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 464 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_534363225491_004#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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.920 | 4.920 | 4.920 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2140.9685 0 -2140.9685 271543.02 66 0 -3082.7283 0 -3082.7283 16606.403 Loop time of 0.725047 on 1 procs for 66 steps with 464 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2140.96847394843 -3082.72561989858 -3082.72829745224 Force two-norm initial, final = 1930.2871 0.30060679 Force max component initial, final = 579.16336 0.075688684 Final line search alpha, max atom move = 1.0000000 0.075688684 Iterations, force evaluations = 66 119 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.70451 | 0.70451 | 0.70451 | 0.0 | 97.17 Neigh | 0.0073409 | 0.0073409 | 0.0073409 | 0.0 | 1.01 Comm | 0.0087936 | 0.0087936 | 0.0087936 | 0.0 | 1.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004406 | | | 0.61 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7245.00 ave 7245 max 7245 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: 128888.0 ave 128888 max 128888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128888 Ave neighs/atom = 277.77586 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.920 | 4.920 | 4.920 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -3082.7283 0 -3082.7283 16606.403 7206.5681 249 0 -3097.369 0 -3097.369 697.40773 7229.1067 Loop time of 1.43982 on 1 procs for 183 steps with 464 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3082.72829745223 -3097.36748298645 -3097.36896125113 Force two-norm initial, final = 240.23017 7.6934912 Force max component initial, final = 163.17779 4.1023139 Final line search alpha, max atom move = 0.00029060901 0.0011921694 Iterations, force evaluations = 183 229 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3494 | 1.3494 | 1.3494 | 0.0 | 93.72 Neigh | 0.021778 | 0.021778 | 0.021778 | 0.0 | 1.51 Comm | 0.013608 | 0.013608 | 0.013608 | 0.0 | 0.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05501 | | | 3.82 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7140.00 ave 7140 max 7140 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: 126262.0 ave 126262 max 126262 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126262 Ave neighs/atom = 272.11638 Neighbor list builds = 3 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.057 | 5.057 | 5.057 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3097.369 0 -3097.369 697.40773 Loop time of 1.548e-06 on 1 procs for 0 steps with 464 atoms 193.8% 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: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7102.00 ave 7102 max 7102 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: 127100.0 ave 127100 max 127100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127100 Ave neighs/atom = 273.92241 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.057 | 5.057 | 5.057 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 -3097.369 -3097.369 24.725917 99.398808 2.9413795 697.40773 697.40773 633.38324 608.10914 850.73083 2.6434855 717.88708 Loop time of 2.034e-06 on 1 procs for 0 steps with 464 atoms 196.7% 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 | | 2.034e-06 | | |100.00 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7102.00 ave 7102 max 7102 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63550.0 ave 63550 max 63550 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 127100.0 ave 127100 max 127100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127100 Ave neighs/atom = 273.92241 Neighbor list builds = 0 Dangerous builds = 0 464 -3097.36896125113 eV 2.64348550443229 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02