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 = 3.6584030 3.6584030 3.6584030 Created orthogonal box = (0.0000000 -42.663944 0.0000000) to (21.331972 42.663944 3.6584030) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0192876 5.0192876 3.6584030 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -42.663944 0.0000000) to (21.331972 42.663944 3.6584030) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0192876 5.0192876 3.6584030 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.663944 0.0000000) to (21.331972 42.663944 3.6584030) create_atoms CPU = 0.000 seconds 274 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 21 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 546 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_577453891941_005#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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.917 | 4.917 | 4.917 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1586.5281 0 -1586.5281 215224.65 186 0 -2121.3946 0 -2121.3946 1288.7694 Loop time of 2.23321 on 1 procs for 186 steps with 546 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1586.52812303282 -2121.39270997584 -2121.39464897269 Force two-norm initial, final = 1347.9512 0.14273956 Force max component initial, final = 536.34885 0.026464110 Final line search alpha, max atom move = 1.0000000 0.026464110 Iterations, force evaluations = 186 355 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1882 | 2.1882 | 2.1882 | 0.0 | 97.98 Neigh | 0.012923 | 0.012923 | 0.012923 | 0.0 | 0.58 Comm | 0.021308 | 0.021308 | 0.021308 | 0.0 | 0.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01081 | | | 0.48 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6618.00 ave 6618 max 6618 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: 113268.0 ave 113268 max 113268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113268 Ave neighs/atom = 207.45055 Neighbor list builds = 2 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 186 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.922 | 4.922 | 4.922 Mbytes Step Temp E_pair E_mol TotEng Press Volume 186 0 -2121.3946 0 -2121.3946 1288.7694 6659.0696 254 0 -2129.571 0 -2129.571 -382.71445 6663.2486 Loop time of 0.512754 on 1 procs for 68 steps with 546 atoms 96.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2121.39464897269 -2129.569160263 -2129.57095097154 Force two-norm initial, final = 223.63740 3.8274914 Force max component initial, final = 166.28002 1.9881920 Final line search alpha, max atom move = 0.00026361345 0.00052411416 Iterations, force evaluations = 68 72 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47102 | 0.47102 | 0.47102 | 0.0 | 91.86 Neigh | 0.023702 | 0.023702 | 0.023702 | 0.0 | 4.62 Comm | 0.0037231 | 0.0037231 | 0.0037231 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01431 | | | 2.79 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5399.00 ave 5399 max 5399 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: 113816.0 ave 113816 max 113816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113816 Ave neighs/atom = 208.45421 Neighbor list builds = 4 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.051 | 5.051 | 5.051 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2129.571 0 -2129.571 -382.71445 Loop time of 1.68e-06 on 1 procs for 0 steps with 546 atoms 178.6% 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 | | 1.68e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5399.00 ave 5399 max 5399 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: 113780.0 ave 113780 max 113780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113780 Ave neighs/atom = 208.38828 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.051 | 5.051 | 5.051 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 -2129.571 -2129.571 21.412519 81.208631 3.8319167 -382.71445 -382.71445 -340.24457 -454.98163 -352.91715 2.2096776 290.85343 Loop time of 1.44e-06 on 1 procs for 0 steps with 546 atoms 138.9% 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 | | 1.44e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5399.00 ave 5399 max 5399 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56890.0 ave 56890 max 56890 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 113780.0 ave 113780 max 113780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113780 Ave neighs/atom = 208.38828 Neighbor list builds = 0 Dangerous builds = 0 546 -2129.57095097154 eV 2.20967760737024 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03