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 = 3.6073527 3.6073527 3.6073527 Created orthogonal box = (0.0000000 -36.073527 0.0000000) to (18.036764 36.073527 3.6073527) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0502938 5.0502938 3.6073527 Created 200 atoms using lattice units in orthogonal box = (0.0000000 -36.073527 0.0000000) to (18.036764 36.073527 3.6073527) create_atoms CPU = 0.001 seconds 200 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0502938 5.0502938 3.6073527 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -36.073527 0.0000000) to (18.036764 36.073527 3.6073527) create_atoms CPU = 0.000 seconds 202 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 12 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 400 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_151002396060_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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 12 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 5.341 | 5.341 | 5.341 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1262.5337 0 -1262.5337 53859.799 108 0 -1404.9911 0 -1404.9911 5811.4178 Loop time of 2.36449 on 1 procs for 108 steps with 400 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 = -1262.53371421789 -1404.98983396687 -1404.9911416239 Force two-norm initial, final = 287.68598 0.14029861 Force max component initial, final = 99.785595 0.016568433 Final line search alpha, max atom move = 1.0000000 0.016568433 Iterations, force evaluations = 108 202 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3187 | 2.3187 | 2.3187 | 0.0 | 98.07 Neigh | 0.026029 | 0.026029 | 0.026029 | 0.0 | 1.10 Comm | 0.013735 | 0.013735 | 0.013735 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005983 | | | 0.25 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8989.00 ave 8989 max 8989 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: 253800.0 ave 253800 max 253800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 253800 Ave neighs/atom = 634.50000 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 12 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 108 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.340 | 5.340 | 5.340 Mbytes Step Temp E_pair E_mol TotEng Press Volume 108 0 -1404.9911 0 -1404.9911 5811.4178 4694.2457 118 0 -1405.1351 0 -1405.1351 -20.90677 4713.6267 Loop time of 0.15092 on 1 procs for 10 steps with 400 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 = -1404.9911416239 -1405.13501682463 -1405.13510483084 Force two-norm initial, final = 39.629250 0.38788135 Force max component initial, final = 29.410952 0.11088507 Final line search alpha, max atom move = 0.00069487664 7.7051447e-05 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14695 | 0.14695 | 0.14695 | 0.0 | 97.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00083882 | 0.00083882 | 0.00083882 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003134 | | | 2.08 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8968.00 ave 8968 max 8968 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: 252320.0 ave 252320 max 252320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 252320 Ave neighs/atom = 630.80000 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 12 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 5.479 | 5.479 | 5.479 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1405.1351 0 -1405.1351 -20.90677 Loop time of 1.528e-06 on 1 procs for 0 steps with 400 atoms 196.3% 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 | | 1.528e-06 | | |100.00 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9013.00 ave 9013 max 9013 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: 252496.0 ave 252496 max 252496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 252496 Ave neighs/atom = 631.24000 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 12 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 5.479 | 5.479 | 5.479 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 -1405.1351 -1405.1351 17.949796 72.141308 3.6400862 -20.90677 -20.90677 -8.3307466 -16.357375 -38.032188 2.2658135 127.05609 Loop time of 1.769e-06 on 1 procs for 0 steps with 400 atoms 226.1% 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 | | 1.769e-06 | | |100.00 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9013.00 ave 9013 max 9013 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 126248.0 ave 126248 max 126248 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 252496.0 ave 252496 max 252496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 252496 Ave neighs/atom = 631.24000 Neighbor list builds = 0 Dangerous builds = 0 400 -1405.13510483084 eV 2.26581347085969 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02