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 = 3.7004755 3.7004755 3.7004755 Created orthogonal box = (0.0000000 -48.531282 0.0000000) to (34.316798 48.531282 5.2332627) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3845207 6.2074895 5.2332627 Created 686 atoms using lattice units in orthogonal box = (0.0000000 -48.531282 0.0000000) to (34.316798 48.531282 5.2332627) create_atoms CPU = 0.002 seconds 686 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3845207 6.2074895 5.2332627 Created 694 atoms using lattice units in orthogonal box = (0.0000000 -48.531282 0.0000000) to (34.316798 48.531282 5.2332627) create_atoms CPU = 0.002 seconds 694 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 9 25 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 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1380 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_466808877130_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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 5.102 | 5.102 | 5.102 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4469.2266 0 -4469.2266 139457.93 534 0 -5566.2878 0 -5566.2878 -83742.434 Loop time of 14.5509 on 1 procs for 534 steps with 1380 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 = -4469.22660789197 -5566.28240090405 -5566.2877631462 Force two-norm initial, final = 1267.5422 0.23697946 Force max component initial, final = 231.65797 0.062227320 Final line search alpha, max atom move = 1.0000000 0.062227320 Iterations, force evaluations = 534 1030 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.191 | 14.191 | 14.191 | 0.0 | 97.53 Neigh | 0.17021 | 0.17021 | 0.17021 | 0.0 | 1.17 Comm | 0.1066 | 0.1066 | 0.1066 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08329 | | | 0.57 Nlocal: 1380.00 ave 1380 max 1380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7940.00 ave 7940 max 7940 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: 218112.0 ave 218112 max 218112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 218112 Ave neighs/atom = 158.05217 Neighbor list builds = 12 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 534 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.484 | 5.484 | 5.484 Mbytes Step Temp E_pair E_mol TotEng Press Volume 534 0 -5566.2878 0 -5566.2878 -83742.434 17431.351 575 0 -5594.9103 0 -5594.9103 464.17916 16446.253 Loop time of 0.621183 on 1 procs for 41 steps with 1380 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 = -5566.28776314624 -5594.9061494646 -5594.91034657367 Force two-norm initial, final = 1591.3789 10.226283 Force max component initial, final = 1074.3137 6.0388970 Final line search alpha, max atom move = 0.00011727564 0.00070821550 Iterations, force evaluations = 41 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.589 | 0.589 | 0.589 | 0.0 | 94.82 Neigh | 0.013553 | 0.013553 | 0.013553 | 0.0 | 2.18 Comm | 0.0031107 | 0.0031107 | 0.0031107 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01552 | | | 2.50 Nlocal: 1380.00 ave 1380 max 1380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8102.00 ave 8102 max 8102 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: 224734.0 ave 224734 max 224734 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224734 Ave neighs/atom = 162.85072 Neighbor list builds = 1 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 5.625 | 5.625 | 5.625 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5594.9103 0 -5594.9103 464.17916 Loop time of 2.117e-06 on 1 procs for 0 steps with 1380 atoms 188.9% 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 | | 2.117e-06 | | |100.00 Nlocal: 1380.00 ave 1380 max 1380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8363.00 ave 8363 max 8363 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: 227772.0 ave 227772 max 227772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227772 Ave neighs/atom = 165.05217 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 5.625 | 5.625 | 5.625 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 -5594.9103 -5594.9103 33.9796 95.496326 5.0682967 464.17916 464.17916 429.64527 578.80987 384.08234 2.2909266 5099.9182 Loop time of 2.321e-06 on 1 procs for 0 steps with 1380 atoms 258.5% 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 | | 2.321e-06 | | |100.00 Nlocal: 1380.00 ave 1380 max 1380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8363.00 ave 8363 max 8363 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113886.0 ave 113886 max 113886 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 227772.0 ave 227772 max 227772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227772 Ave neighs/atom = 165.05217 Neighbor list builds = 0 Dangerous builds = 0 1380 -5594.91034657367 eV 2.29092659177453 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16