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 = 2.8638485 2.8638485 2.8638485 Created orthogonal box = (0.0000000 -28.638485 0.0000000) to (2.8638485 28.638485 2.8638485) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 2.8638485 2.8638485 2.8638485 Created 20 atoms using lattice units in orthogonal box = (0.0000000 -28.638485 0.0000000) to (2.8638485 28.638485 2.8638485) create_atoms CPU = 0.001 seconds 20 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 2.8638485 2.8638485 2.8638485 Created 21 atoms using lattice units in orthogonal box = (0.0000000 -28.638485 0.0000000) to (2.8638485 28.638485 2.8638485) create_atoms CPU = 0.000 seconds 21 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 1 10 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 41 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_147603128437_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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 1 10 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 4.489 | 4.489 | 4.489 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -33.067259 0 -33.067259 363127.95 44 0 -169.32123 0 -169.32123 59483.317 Loop time of 0.308356 on 1 procs for 44 steps with 41 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 = -33.0672594633483 -169.321085501067 -169.321231957941 Force two-norm initial, final = 562.73171 0.051754556 Force max component initial, final = 397.80786 0.014079642 Final line search alpha, max atom move = 1.0000000 0.014079642 Iterations, force evaluations = 44 72 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29335 | 0.29335 | 0.29335 | 0.0 | 95.13 Neigh | 0.0028964 | 0.0028964 | 0.0028964 | 0.0 | 0.94 Comm | 0.0087644 | 0.0087644 | 0.0087644 | 0.0 | 2.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003347 | | | 1.09 Nlocal: 41.0000 ave 41 max 41 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5125.00 ave 5125 max 5125 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: 25352.0 ave 25352 max 25352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25352 Ave neighs/atom = 618.34146 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 1 10 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.489 | 4.489 | 4.489 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -169.32123 0 -169.32123 59483.317 469.76442 373 0 -171.59184 0 -171.59184 409.8579 482.46392 Loop time of 1.58026 on 1 procs for 329 steps with 41 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 = -169.321231957941 -171.591668382073 -171.591836274902 Force two-norm initial, final = 30.773415 0.34919912 Force max component initial, final = 21.613608 0.17840468 Final line search alpha, max atom move = 0.0020170705 0.00035985481 Iterations, force evaluations = 329 337 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3901 | 1.3901 | 1.3901 | 0.0 | 87.97 Neigh | 0.046924 | 0.046924 | 0.046924 | 0.0 | 2.97 Comm | 0.043387 | 0.043387 | 0.043387 | 0.0 | 2.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0998 | | | 6.32 Nlocal: 41.0000 ave 41 max 41 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5859.00 ave 5859 max 5859 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: 25208.0 ave 25208 max 25208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25208 Ave neighs/atom = 614.82927 Neighbor list builds = 17 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 1 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 4.634 | 4.634 | 4.634 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -171.59184 0 -171.59184 409.8579 Loop time of 6.846e-06 on 1 procs for 0 steps with 41 atoms 160.7% 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 | | 6.846e-06 | | |100.00 Nlocal: 41.0000 ave 41 max 41 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5859.00 ave 5859 max 5859 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: 25212.0 ave 25212 max 25212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25212 Ave neighs/atom = 614.92683 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 1 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 4.634 | 4.634 | 4.634 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 -171.59184 -171.59184 2.539629 74.651943 2.5447988 409.8579 409.8579 440.03325 772.16983 17.370614 2.4831565 32.983917 Loop time of 6.675e-06 on 1 procs for 0 steps with 41 atoms 239.7% 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 | | 6.675e-06 | | |100.00 Nlocal: 41.0000 ave 41 max 41 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5859.00 ave 5859 max 5859 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12606.0 ave 12606 max 12606 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25212.0 ave 25212 max 25212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25212 Ave neighs/atom = 614.92683 Neighbor list builds = 0 Dangerous builds = 0 41 -171.591836274902 eV 2.48315645981292 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02