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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -47.920248 0.0000000) to (58.690078 47.920248 9.9204338) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7074375 6.1611747 6.6136225 Created 1670 atoms using lattice units in orthogonal box = (0.0000000 -47.920248 0.0000000) to (58.690078 47.920248 9.9204338) create_atoms CPU = 0.003 seconds 1670 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7074375 6.1611747 6.6136225 Created 1694 atoms using lattice units in orthogonal box = (0.0000000 -47.920248 0.0000000) to (58.690078 47.920248 9.9204338) create_atoms CPU = 0.003 seconds 1694 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 14 23 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 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 3358 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_678952612413_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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 6.554 | 6.554 | 6.554 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11107.719 0 -11107.719 3074.5161 71 0 -11248.568 0 -11248.568 2901.2636 Loop time of 3.53366 on 1 procs for 71 steps with 3358 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11107.718549214 -11248.5581458961 -11248.5682144075 Force two-norm initial, final = 36.239393 0.24708540 Force max component initial, final = 3.0384218 0.024126392 Final line search alpha, max atom move = 1.0000000 0.024126392 Iterations, force evaluations = 71 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4596 | 3.4596 | 3.4596 | 0.0 | 97.90 Neigh | 0.034701 | 0.034701 | 0.034701 | 0.0 | 0.98 Comm | 0.015675 | 0.015675 | 0.015675 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02373 | | | 0.67 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10375.0 ave 10375 max 10375 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: 475938.0 ave 475938 max 475938 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 475938 Ave neighs/atom = 141.73258 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.557 | 6.557 | 6.557 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -11248.568 0 -11248.568 2901.2636 55801.311 78 0 -11249.23 0 -11249.23 -1.0191162 56007.897 Loop time of 0.249763 on 1 procs for 7 steps with 3358 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 = -11248.5682144075 -11249.2235790053 -11249.230173389 Force two-norm initial, final = 224.74630 0.50862628 Force max component initial, final = 213.31742 0.14928699 Final line search alpha, max atom move = 7.5666301e-05 1.1295995e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24321 | 0.24321 | 0.24321 | 0.0 | 97.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0008089 | 0.0008089 | 0.0008089 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005747 | | | 2.30 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10693.0 ave 10693 max 10693 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: 475136.0 ave 475136 max 475136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 475136 Ave neighs/atom = 141.49375 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 6.695 | 6.695 | 6.695 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11249.23 0 -11249.23 -1.0191162 Loop time of 2.147e-06 on 1 procs for 0 steps with 3358 atoms 186.3% 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 | | 2.147e-06 | | |100.00 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10693.0 ave 10693 max 10693 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: 474542.0 ave 474542 max 474542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 474542 Ave neighs/atom = 141.31686 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 6.695 | 6.695 | 6.695 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 -11249.23 -11249.23 58.666911 96.477246 9.8953497 -1.0191162 -1.0191162 -4.2688569 -0.65617952 1.8676877 2.6544192 2091.3824 Loop time of 2.776e-06 on 1 procs for 0 steps with 3358 atoms 288.2% 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 | | 2.776e-06 | | |100.00 Nlocal: 3358.00 ave 3358 max 3358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10693.0 ave 10693 max 10693 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 237271.0 ave 237271 max 237271 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 474542.0 ave 474542 max 474542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 474542 Ave neighs/atom = 141.31686 Neighbor list builds = 0 Dangerous builds = 0 3358 -11249.230173389 eV 2.65441918614319 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04