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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -81.099040 0.0000000) to (46.820218 81.099040 7.0055406) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2892830 6.4553230 7.0055406 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -81.099040 0.0000000) to (46.820218 81.099040 7.0055406) create_atoms CPU = 0.013 seconds 1610 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2892830 6.4553230 7.0055406 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -81.099040 0.0000000) to (46.820218 81.099040 7.0055406) create_atoms CPU = 0.012 seconds 1610 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 50 3 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 32 atoms, new total = 3188 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_876687166519_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 50 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.831 | 5.831 | 5.831 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10669.148 0 -10669.148 -644.75435 40 0 -10687.061 0 -10687.061 -3791.2783 Loop time of 16.5449 on 1 procs for 40 steps with 3188 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 = -10669.1478419594 -10687.0527632438 -10687.0607506423 Force two-norm initial, final = 19.885547 0.21305878 Force max component initial, final = 4.4962116 0.040753488 Final line search alpha, max atom move = 0.80674119 0.032877517 Iterations, force evaluations = 40 64 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.43 | 16.43 | 16.43 | 0.0 | 99.31 Neigh | 0.075739 | 0.075739 | 0.075739 | 0.0 | 0.46 Comm | 0.016274 | 0.016274 | 0.016274 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02278 | | | 0.14 Nlocal: 3188.00 ave 3188 max 3188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10009.0 ave 10009 max 10009 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: 245048.0 ave 245048 max 245048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 245048 Ave neighs/atom = 76.865747 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 50 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.831 | 5.831 | 5.831 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -10687.061 0 -10687.061 -3791.2783 53201.122 43 0 -10687.269 0 -10687.269 -815.77949 52998.602 Loop time of 1.21369 on 1 procs for 3 steps with 3188 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 = -10687.0607506422 -10687.2685984581 -10687.2691784756 Force two-norm initial, final = 155.61751 3.1366729 Force max component initial, final = 117.10355 2.9631350 Final line search alpha, max atom move = 0.00018469334 0.00054727130 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2081 | 1.2081 | 1.2081 | 0.0 | 99.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010325 | 0.0010325 | 0.0010325 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00453 | | | 0.37 Nlocal: 3188.00 ave 3188 max 3188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10009.0 ave 10009 max 10009 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: 245084.0 ave 245084 max 245084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 245084 Ave neighs/atom = 76.877039 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 50 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.969 | 5.969 | 5.969 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10687.269 0 -10687.269 -815.77949 Loop time of 6.295e-06 on 1 procs for 0 steps with 3188 atoms 190.6% 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 | | 6.295e-06 | | |100.00 Nlocal: 3188.00 ave 3188 max 3188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10012.0 ave 10012 max 10012 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: 245208.0 ave 245208 max 245208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 245208 Ave neighs/atom = 76.915935 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 50 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.969 | 5.969 | 5.969 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 -10687.269 -10687.269 46.744416 162.19808 6.9901897 -815.77949 -815.77949 89.432155 -2567.0271 30.256448 2.5193117 1199.2384 Loop time of 6.535e-06 on 1 procs for 0 steps with 3188 atoms 306.0% 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 | | 6.535e-06 | | |100.00 Nlocal: 3188.00 ave 3188 max 3188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10012.0 ave 10012 max 10012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 122604.0 ave 122604 max 122604 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 245208.0 ave 245208 max 245208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 245208 Ave neighs/atom = 76.915935 Neighbor list builds = 0 Dangerous builds = 0 3188 -10687.2691784756 eV 2.51931165801966 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19