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 = 4.0397985 4.0397985 4.0397985 Created orthogonal box = (0.0000000 -57.131378 0.0000000) to (28.565689 57.131378 4.0397985) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5705102 4.5705102 4.0397985 Created 400 atoms using lattice units in orthogonal box = (0.0000000 -57.131378 0.0000000) to (28.565689 57.131378 4.0397985) create_atoms CPU = 0.002 seconds 400 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5705102 4.5705102 4.0397985 Created 402 atoms using lattice units in orthogonal box = (0.0000000 -57.131378 0.0000000) to (28.565689 57.131378 4.0397985) create_atoms CPU = 0.001 seconds 402 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, 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 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 796 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_279544746097_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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 5.814 | 5.814 | 5.814 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2156.0597 0 -2156.0597 15040.825 66 0 -2287.4903 0 -2287.4903 -1182.7314 Loop time of 5.41016 on 1 procs for 66 steps with 796 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 = -2156.05967931084 -2287.4887156076 -2287.49029846623 Force two-norm initial, final = 204.02422 0.11573866 Force max component initial, final = 68.289779 0.012072665 Final line search alpha, max atom move = 1.0000000 0.012072665 Iterations, force evaluations = 66 119 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.3245 | 5.3245 | 5.3245 | 0.0 | 98.42 Neigh | 0.040237 | 0.040237 | 0.040237 | 0.0 | 0.74 Comm | 0.030416 | 0.030416 | 0.030416 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01505 | | | 0.28 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10595.0 ave 10595 max 10595 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: 323100.0 ave 323100 max 323100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 323100 Ave neighs/atom = 405.90452 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 5.816 | 5.816 | 5.816 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -2287.4903 0 -2287.4903 -1182.7314 13185.879 72 0 -2287.5532 0 -2287.5532 127.0692 13162.698 Loop time of 0.352263 on 1 procs for 6 steps with 796 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 = -2287.49029846625 -2287.55265918091 -2287.55316906326 Force two-norm initial, final = 23.510177 2.5117340 Force max component initial, final = 19.274662 2.4390637 Final line search alpha, max atom move = 0.00040232405 0.00098129398 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34547 | 0.34547 | 0.34547 | 0.0 | 98.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018117 | 0.0018117 | 0.0018117 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004986 | | | 1.42 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10630.0 ave 10630 max 10630 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: 315324.0 ave 315324 max 315324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 315324 Ave neighs/atom = 396.13568 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 5.954 | 5.954 | 5.954 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2287.5532 0 -2287.5532 127.0692 Loop time of 4.1927e-05 on 1 procs for 0 steps with 796 atoms 33.4% 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 | | 4.193e-05 | | |100.00 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10630.0 ave 10630 max 10630 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: 320084.0 ave 320084 max 320084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320084 Ave neighs/atom = 402.11558 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 5.954 | 5.954 | 5.954 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 -2287.5532 -2287.5532 28.508694 113.80949 4.0568514 127.0692 127.0692 63.30459 19.76457 298.13845 2.5594896 272.58904 Loop time of 6.665e-06 on 1 procs for 0 steps with 796 atoms 255.1% 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 | | 6.665e-06 | | |100.00 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10630.0 ave 10630 max 10630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 160042.0 ave 160042 max 160042 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 320084.0 ave 320084 max 320084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320084 Ave neighs/atom = 402.11558 Neighbor list builds = 0 Dangerous builds = 0 796 -2287.55316906326 eV 2.55948957072648 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06