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 = 3.6110509 3.6110509 3.6110509 Created orthogonal box = (0.0000000 -52.577695 0.0000000) to (26.288847 52.577695 3.6110509) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4641439 4.4641439 3.6110509 Created 424 atoms using lattice units in orthogonal box = (0.0000000 -52.577695 0.0000000) to (26.288847 52.577695 3.6110509) create_atoms CPU = 0.001 seconds 424 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4641439 4.4641439 3.6110509 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -52.577695 0.0000000) to (26.288847 52.577695 3.6110509) create_atoms CPU = 0.001 seconds 426 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 21 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 2 atoms, new total = 848 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 21 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) = 5.824 | 5.824 | 5.824 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3186.7719 0 -3186.7719 61960.462 47 0 -3501.9475 0 -3501.9475 8555.8865 Loop time of 1.13614 on 1 procs for 47 steps with 848 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 = -3186.77191672875 -3501.94456202384 -3501.94749603748 Force two-norm initial, final = 496.87090 0.23396486 Force max component initial, final = 141.95484 0.042494294 Final line search alpha, max atom move = 1.0000000 0.042494294 Iterations, force evaluations = 47 79 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1071 | 1.1071 | 1.1071 | 0.0 | 97.44 Neigh | 0.01579 | 0.01579 | 0.01579 | 0.0 | 1.39 Comm | 0.008393 | 0.008393 | 0.008393 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004885 | | | 0.43 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10895.0 ave 10895 max 10895 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: 322640.0 ave 322640 max 322640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 322640 Ave neighs/atom = 380.47170 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 21 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 : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.826 | 5.826 | 5.826 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -3501.9475 0 -3501.9475 8555.8865 9982.4396 53 0 -3502.1872 0 -3502.1872 -367.68453 10034.094 Loop time of 0.120824 on 1 procs for 6 steps with 848 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3501.94749603748 -3502.18575418115 -3502.18716813684 Force two-norm initial, final = 101.59089 4.8432799 Force max component initial, final = 84.659352 3.5591216 Final line search alpha, max atom move = 0.00015414688 0.00054862747 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11709 | 0.11709 | 0.11709 | 0.0 | 96.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00073067 | 0.00073067 | 0.00073067 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003002 | | | 2.48 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10904.0 ave 10904 max 10904 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: 321608.0 ave 321608 max 321608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 321608 Ave neighs/atom = 379.25472 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 21 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) = 5.964 | 5.964 | 5.964 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3502.1872 0 -3502.1872 -367.68453 Loop time of 2.222e-06 on 1 procs for 0 steps with 848 atoms 135.0% 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 | | 2.222e-06 | | |100.00 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10885.0 ave 10885 max 10885 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: 321432.0 ave 321432 max 321432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 321432 Ave neighs/atom = 379.04717 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 21 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) = 5.964 | 5.964 | 5.964 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 -3502.1872 -3502.1872 26.251573 105.7208 3.6154503 -367.68453 -367.68453 -567.49077 -14.652775 -520.91004 2.2931001 377.10681 Loop time of 4.183e-06 on 1 procs for 0 steps with 848 atoms 215.2% 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 | | 4.183e-06 | | |100.00 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10885.0 ave 10885 max 10885 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 160716.0 ave 160716 max 160716 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 321432.0 ave 321432 max 321432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 321432 Ave neighs/atom = 379.04717 Neighbor list builds = 0 Dangerous builds = 0 848 -3502.18716813685 eV 2.29310008199638 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01