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 -65.398913 0.0000000) to (23.122008 65.398913 5.1067972) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2034654 5.5828341 5.1067972 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -65.398913 0.0000000) to (23.122008 65.398913 5.1067972) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2034654 5.5828341 5.1067972 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -65.398913 0.0000000) to (23.122008 65.398913 5.1067972) create_atoms CPU = 0.002 seconds 658 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 = 5 26 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 = 1312 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 = 5 26 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) = 6.771 | 6.771 | 6.771 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5265.5493 0 -5265.5493 26989.588 82 0 -5442.0476 0 -5442.0476 2781.6783 Loop time of 3.55225 on 1 procs for 82 steps with 1312 atoms 97.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5265.54933983914 -5442.04246083586 -5442.04756860702 Force two-norm initial, final = 283.83986 0.31514039 Force max component initial, final = 93.382316 0.028658825 Final line search alpha, max atom move = 1.0000000 0.028658825 Iterations, force evaluations = 82 156 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4832 | 3.4832 | 3.4832 | 0.0 | 98.06 Neigh | 0.028268 | 0.028268 | 0.028268 | 0.0 | 0.80 Comm | 0.026107 | 0.026107 | 0.026107 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01466 | | | 0.41 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13485.0 ave 13485 max 13485 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: 498584.0 ave 498584 max 498584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 498584 Ave neighs/atom = 380.01829 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 = 5 26 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 : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.766 | 6.766 | 6.766 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -5442.0476 0 -5442.0476 2781.6783 15444.529 86 0 -5442.1858 0 -5442.1858 -86.802772 15470.058 Loop time of 0.15817 on 1 procs for 4 steps with 1312 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 = -5442.04756860702 -5442.18529000541 -5442.1857901258 Force two-norm initial, final = 91.829360 2.1520168 Force max component initial, final = 77.693619 2.0463743 Final line search alpha, max atom move = 0.00016714837 0.00034204814 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15412 | 0.15412 | 0.15412 | 0.0 | 97.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00074894 | 0.00074894 | 0.00074894 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003299 | | | 2.09 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12998.0 ave 12998 max 12998 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: 499040.0 ave 499040 max 499040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 499040 Ave neighs/atom = 380.36585 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 = 5 26 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) = 6.904 | 6.904 | 6.904 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5442.1858 0 -5442.1858 -86.802772 Loop time of 2.088e-06 on 1 procs for 0 steps with 1312 atoms 191.6% 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 | | 2.088e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12998.0 ave 12998 max 12998 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: 498680.0 ave 498680 max 498680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 498680 Ave neighs/atom = 380.09146 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 = 5 26 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) = 6.904 | 6.904 | 6.904 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 -5442.1858 -5442.1858 23.172674 130.97123 5.0972964 -86.802772 -86.802772 -212.3998 10.0987 -58.107215 2.4067004 457.69507 Loop time of 3.036e-06 on 1 procs for 0 steps with 1312 atoms 296.4% 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 | | 3.036e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12998.0 ave 12998 max 12998 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 249340.0 ave 249340 max 249340 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 498680.0 ave 498680 max 498680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 498680 Ave neighs/atom = 380.09146 Neighbor list builds = 0 Dangerous builds = 0 1312 -5442.1857901258 eV 2.40670040748015 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04