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 = 3.6131481 3.6131481 3.6131481 Created orthogonal box = (0.0000000 -46.270873 0.0000000) to (32.718448 46.270873 5.1097631) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5860765 6.2070683 5.1097631 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -46.270873 0.0000000) to (32.718448 46.270873 5.1097631) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5860765 6.2070683 5.1097631 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -46.270873 0.0000000) to (32.718448 46.270873 5.1097631) create_atoms CPU = 0.002 seconds 660 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 7 18 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 10.45965 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1304 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_173787283511_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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 7 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 6.730 | 6.730 | 6.730 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4256.5265 0 -4256.5265 31200.957 68 0 -4536.3855 0 -4536.3855 -4870.1745 Loop time of 2.94167 on 1 procs for 68 steps with 1304 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4256.52648641739 -4536.38127315625 -4536.38547332037 Force two-norm initial, final = 372.84389 0.25686854 Force max component initial, final = 91.538968 0.021534305 Final line search alpha, max atom move = 1.0000000 0.021534305 Iterations, force evaluations = 68 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.881 | 2.881 | 2.881 | 0.0 | 97.94 Neigh | 0.028797 | 0.028797 | 0.028797 | 0.0 | 0.98 Comm | 0.019618 | 0.019618 | 0.019618 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01222 | | | 0.42 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12405.0 ave 12405 max 12405 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: 502456.0 ave 502456 max 502456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 502456 Ave neighs/atom = 385.31902 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 7 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.730 | 6.730 | 6.730 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -4536.3855 0 -4536.3855 -4870.1745 15471.455 80 0 -4537.9451 0 -4537.9451 34.919452 15411.247 Loop time of 0.358424 on 1 procs for 12 steps with 1304 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 = -4536.3854733204 -4537.94391697506 -4537.94514666569 Force two-norm initial, final = 238.16326 1.0750901 Force max component initial, final = 201.82788 0.63573555 Final line search alpha, max atom move = 0.00021152501 0.00013447397 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35006 | 0.35006 | 0.35006 | 0.0 | 97.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001422 | 0.001422 | 0.001422 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006938 | | | 1.94 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12424.0 ave 12424 max 12424 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: 507624.0 ave 507624 max 507624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 507624 Ave neighs/atom = 389.28221 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 7 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 6.869 | 6.869 | 6.869 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4537.9451 0 -4537.9451 34.919452 Loop time of 2.435e-06 on 1 procs for 0 steps with 1304 atoms 164.3% 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 | | 2.435e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12487.0 ave 12487 max 12487 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: 511016.0 ave 511016 max 511016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 511016 Ave neighs/atom = 391.88344 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 7 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 6.869 | 6.869 | 6.869 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 -4537.9451 -4537.9451 32.348085 93.195009 5.1120671 34.919452 34.919452 31.029598 66.55858 7.1701782 2.3443054 1059.7323 Loop time of 2.795e-06 on 1 procs for 0 steps with 1304 atoms 286.2% 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 | | 2.795e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12487.0 ave 12487 max 12487 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 255508.0 ave 255508 max 255508 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 511016.0 ave 511016 max 511016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 511016 Ave neighs/atom = 391.88344 Neighbor list builds = 0 Dangerous builds = 0 1304 -4537.94514666569 eV 2.34430535212678 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03