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 = 3.1582519 3.1582519 3.1582519 Created orthogonal box = (0.0000000 -34.015414 0.0000000) to (17.007707 34.015414 3.1582519) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1053086 4.1053086 3.1582519 Created 116 atoms using lattice units in orthogonal box = (0.0000000 -34.015414 0.0000000) to (17.007707 34.015414 3.1582519) create_atoms CPU = 0.001 seconds 116 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1053086 4.1053086 3.1582519 Created 117 atoms using lattice units in orthogonal box = (0.0000000 -34.015414 0.0000000) to (17.007707 34.015414 3.1582519) create_atoms CPU = 0.001 seconds 117 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 5 17 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 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 233 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_228581001644_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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 5 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.423 | 4.423 | 4.423 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1230.1822 0 -1230.1822 193822.88 47 0 -1470.495 0 -1470.495 37324.911 Loop time of 0.396552 on 1 procs for 47 steps with 233 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 = -1230.18216249058 -1470.49361279427 -1470.49498237224 Force two-norm initial, final = 569.74348 0.19586221 Force max component initial, final = 227.79919 0.046292168 Final line search alpha, max atom move = 1.0000000 0.046292168 Iterations, force evaluations = 47 85 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38402 | 0.38402 | 0.38402 | 0.0 | 96.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0075432 | 0.0075432 | 0.0075432 | 0.0 | 1.90 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004994 | | | 1.26 Nlocal: 233.000 ave 233 max 233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3535.00 ave 3535 max 3535 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: 39162.0 ave 39162 max 39162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39162 Ave neighs/atom = 168.07725 Neighbor list builds = 0 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 5 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.421 | 4.421 | 4.421 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -1470.495 0 -1470.495 37324.911 3654.2504 694 0 -1486.0434 0 -1486.0434 602.34138 3680.3878 Loop time of 3.72771 on 1 procs for 647 steps with 233 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 = -1470.49498237224 -1486.04260269273 -1486.04339805215 Force two-norm initial, final = 179.84145 4.1269161 Force max component initial, final = 161.04090 3.1059854 Final line search alpha, max atom move = 0.00050888195 0.0015805799 Iterations, force evaluations = 647 839 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4483 | 3.4483 | 3.4483 | 0.0 | 92.50 Neigh | 0.024526 | 0.024526 | 0.024526 | 0.0 | 0.66 Comm | 0.062191 | 0.062191 | 0.062191 | 0.0 | 1.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1927 | | | 5.17 Nlocal: 233.000 ave 233 max 233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3687.00 ave 3687 max 3687 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: 36516.0 ave 36516 max 36516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36516 Ave neighs/atom = 156.72103 Neighbor list builds = 5 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 5 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.563 | 4.563 | 4.563 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1486.0434 0 -1486.0434 602.34138 Loop time of 6.375e-06 on 1 procs for 0 steps with 233 atoms 172.5% 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 | | 6.375e-06 | | |100.00 Nlocal: 233.000 ave 233 max 233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3687.00 ave 3687 max 3687 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: 36404.0 ave 36404 max 36404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36404 Ave neighs/atom = 156.24034 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 5 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.563 | 4.563 | 4.563 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 -1486.0434 -1486.0434 17.516594 73.263006 2.8678682 602.34138 602.34138 679.47353 -100.25215 1227.8028 2.6752475 776.03878 Loop time of 7.307e-06 on 1 procs for 0 steps with 233 atoms 232.7% 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 | | 7.307e-06 | | |100.00 Nlocal: 233.000 ave 233 max 233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3687.00 ave 3687 max 3687 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18202.0 ave 18202 max 18202 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 36404.0 ave 36404 max 36404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36404 Ave neighs/atom = 156.24034 Neighbor list builds = 0 Dangerous builds = 0 233 -1486.04339805215 eV 2.67524751228012 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04