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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -72.584397 0.0000000) to (41.904531 72.584397 6.2700241) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6289669 5.7775743 6.2700241 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -72.584397 0.0000000) to (41.904531 72.584397 6.2700241) create_atoms CPU = 0.004 seconds 1610 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6289669 5.7775743 6.2700241 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -72.584397 0.0000000) to (41.904531 72.584397 6.2700241) create_atoms CPU = 0.004 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 38 2 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 3192 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_657255834688_000#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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 10.95 | 10.95 | 10.95 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11240.253 0 -11240.253 -450.34705 30 0 -11273.772 0 -11273.772 -4844.3197 Loop time of 1.48075 on 1 procs for 30 steps with 3192 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11240.2528167864 -11273.7613384618 -11273.7724703007 Force two-norm initial, final = 30.039685 0.34962224 Force max component initial, final = 4.7324528 0.065142410 Final line search alpha, max atom move = 0.86242464 0.056180419 Iterations, force evaluations = 30 51 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.43 | 1.43 | 1.43 | 0.0 | 96.57 Neigh | 0.033206 | 0.033206 | 0.033206 | 0.0 | 2.24 Comm | 0.0089606 | 0.0089606 | 0.0089606 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008577 | | | 0.58 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14519.0 ave 14519 max 14519 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: 556088.0 ave 556088 max 556088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556088 Ave neighs/atom = 174.21303 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 30 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.95 | 10.95 | 10.95 Mbytes Step Temp E_pair E_mol TotEng Press Volume 30 0 -11273.772 0 -11273.772 -4844.3197 38142 33 0 -11273.912 0 -11273.912 -1188.1029 38038.607 Loop time of 0.169727 on 1 procs for 3 steps with 3192 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 = -11273.7724703007 -11273.912174406 -11273.9123430892 Force two-norm initial, final = 143.70547 0.36130128 Force max component initial, final = 112.09059 0.068106702 Final line search alpha, max atom move = 0.00038328680 2.6104400e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16559 | 0.16559 | 0.16559 | 0.0 | 97.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00067552 | 0.00067552 | 0.00067552 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003459 | | | 2.04 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14534.0 ave 14534 max 14534 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: 556604.0 ave 556604 max 556604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556604 Ave neighs/atom = 174.37469 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 10.46 | 10.46 | 10.46 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11273.912 0 -11273.912 -1188.1029 Loop time of 2.311e-06 on 1 procs for 0 steps with 3192 atoms 173.1% 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 | | 2.311e-06 | | |100.00 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14545.0 ave 14545 max 14545 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: 556732.0 ave 556732 max 556732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556732 Ave neighs/atom = 174.41479 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 10.46 | 10.46 | 10.46 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 -11273.912 -11273.912 41.858193 145.16879 6.25995 -1188.1029 -1188.1029 -0.75501612 -3565.5838 2.0300781 2.322968 1064.3663 Loop time of 2.486e-06 on 1 procs for 0 steps with 3192 atoms 281.6% 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 | | 2.486e-06 | | |100.00 Nlocal: 3192.00 ave 3192 max 3192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14545.0 ave 14545 max 14545 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 278366.0 ave 278366 max 278366 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 556732.0 ave 556732 max 556732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556732 Ave neighs/atom = 174.41479 Neighbor list builds = 0 Dangerous builds = 0 3192 -11273.9123430892 eV 2.32296799115182 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02