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 = 2.8688302 2.8688302 2.8688302 Created orthogonal box = (0.0000000 -50.673645 0.0000000) to (29.256443 50.673645 4.9689597) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5009912 4.5476348 4.9689597 Created 623 atoms using lattice units in orthogonal box = (0.0000000 -50.673645 0.0000000) to (29.256443 50.673645 4.9689597) create_atoms CPU = 0.002 seconds 623 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5009912 4.5476348 4.9689597 Created 626 atoms using lattice units in orthogonal box = (0.0000000 -50.673645 0.0000000) to (29.256443 50.673645 4.9689597) create_atoms CPU = 0.002 seconds 626 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 20 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1249 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_984358344196_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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.329 | 6.329 | 6.329 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4310.469 0 -4310.469 89312.283 388 0 -5149.3931 0 -5149.3931 5220.061 Loop time of 15.5878 on 1 procs for 388 steps with 1249 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4310.46895824099 -5149.38809553043 -5149.39306449924 Force two-norm initial, final = 1038.7429 0.33584021 Force max component initial, final = 246.41236 0.12464135 Final line search alpha, max atom move = 0.53324001 0.066463757 Iterations, force evaluations = 388 756 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.148 | 15.148 | 15.148 | 0.0 | 97.18 Neigh | 0.29181 | 0.29181 | 0.29181 | 0.0 | 1.87 Comm | 0.090962 | 0.090962 | 0.090962 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05697 | | | 0.37 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11765.0 ave 11765 max 11765 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: 481674.0 ave 481674 max 481674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 481674 Ave neighs/atom = 385.64772 Neighbor list builds = 11 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 388 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.328 | 6.328 | 6.328 Mbytes Step Temp E_pair E_mol TotEng Press Volume 388 0 -5149.3931 0 -5149.3931 5220.061 14733.27 414 0 -5159.8804 0 -5159.8804 -20.296951 14761.174 Loop time of 0.641489 on 1 procs for 26 steps with 1249 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5149.39306449925 -5159.87750201861 -5159.88036700446 Force two-norm initial, final = 664.80773 4.5090258 Force max component initial, final = 470.03151 1.3295979 Final line search alpha, max atom move = 0.00015556930 0.00020684461 Iterations, force evaluations = 26 27 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.57443 | 0.57443 | 0.57443 | 0.0 | 89.55 Neigh | 0.051246 | 0.051246 | 0.051246 | 0.0 | 7.99 Comm | 0.0030695 | 0.0030695 | 0.0030695 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01274 | | | 1.99 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11691.0 ave 11691 max 11691 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: 482388.0 ave 482388 max 482388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 482388 Ave neighs/atom = 386.21938 Neighbor list builds = 2 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.465 | 6.465 | 6.465 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5159.8804 0 -5159.8804 -20.296951 Loop time of 2.266e-06 on 1 procs for 0 steps with 1249 atoms 132.4% 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 | | 2.266e-06 | | |100.00 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11676.0 ave 11676 max 11676 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: 483142.0 ave 483142 max 483142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 483142 Ave neighs/atom = 386.82306 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.465 | 6.465 | 6.465 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 -5159.8804 -5159.8804 29.584771 98.771272 5.0515195 -20.296951 -20.296951 -138.87373 140.64629 -62.663415 2.1801858 4990.8872 Loop time of 2.349e-06 on 1 procs for 0 steps with 1249 atoms 212.9% 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 | | 2.349e-06 | | |100.00 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11676.0 ave 11676 max 11676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 241571.0 ave 241571 max 241571 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 483142.0 ave 483142 max 483142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 483142 Ave neighs/atom = 386.82306 Neighbor list builds = 0 Dangerous builds = 0 1249 -5159.88036700446 eV 2.18018581376586 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16