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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -66.940075 0.0000000) to (33.470037 66.940075 3.9173716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0434303 5.0434303 3.9173716 Created 584 atoms using lattice units in orthogonal box = (0.0000000 -66.940075 0.0000000) to (33.470037 66.940075 3.9173716) create_atoms CPU = 0.002 seconds 584 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0434303 5.0434303 3.9173716 Created 586 atoms using lattice units in orthogonal box = (0.0000000 -66.940075 0.0000000) to (33.470037 66.940075 3.9173716) create_atoms CPU = 0.002 seconds 586 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 42 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1168 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_020840179467_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.640 | 4.640 | 4.640 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6484.9309 0 -6484.9309 37989.506 27 0 -6711.3143 0 -6711.3143 10313.275 Loop time of 2.14716 on 1 procs for 27 steps with 1168 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 = -6484.93087154838 -6711.30909331808 -6711.31434314666 Force two-norm initial, final = 342.45158 0.25882034 Force max component initial, final = 114.87238 0.051050971 Final line search alpha, max atom move = 1.0000000 0.051050971 Iterations, force evaluations = 27 45 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.133 | 2.133 | 2.133 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0073444 | 0.0073444 | 0.0073444 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006851 | | | 0.32 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6856.00 ave 6856 max 6856 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: 90976.0 ave 90976 max 90976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90976 Ave neighs/atom = 77.890411 Neighbor list builds = 0 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 27 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.639 | 4.639 | 4.639 Mbytes Step Temp E_pair E_mol TotEng Press Volume 27 0 -6711.3143 0 -6711.3143 10313.275 17553.639 35 0 -6711.9844 0 -6711.9844 -35.362297 17655.975 Loop time of 0.490219 on 1 procs for 8 steps with 1168 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 = -6711.31434314666 -6711.98217478923 -6711.98437103562 Force two-norm initial, final = 223.34997 0.99064515 Force max component initial, final = 200.65485 0.65452920 Final line search alpha, max atom move = 0.00017871918 0.00011697692 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4678 | 0.4678 | 0.4678 | 0.0 | 95.43 Neigh | 0.014811 | 0.014811 | 0.014811 | 0.0 | 3.02 Comm | 0.0018689 | 0.0018689 | 0.0018689 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005737 | | | 1.17 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6829.00 ave 6829 max 6829 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: 90420.0 ave 90420 max 90420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90420 Ave neighs/atom = 77.414384 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.779 | 4.779 | 4.779 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6711.9844 0 -6711.9844 -35.362297 Loop time of 6.365e-06 on 1 procs for 0 steps with 1168 atoms 188.5% 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 | | 6.365e-06 | | |100.00 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6829.00 ave 6829 max 6829 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: 90420.0 ave 90420 max 90420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90420 Ave neighs/atom = 77.414384 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.779 | 4.779 | 4.779 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 -6711.9844 -6711.9844 33.46705 134.85799 3.9119885 -35.362297 -35.362297 -11.936191 -59.82851 -34.322191 2.4985835 590.3333 Loop time of 7.217e-06 on 1 procs for 0 steps with 1168 atoms 277.1% 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 | | 7.217e-06 | | |100.00 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6829.00 ave 6829 max 6829 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45210.0 ave 45210 max 45210 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 90420.0 ave 90420 max 90420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90420 Ave neighs/atom = 77.414384 Neighbor list builds = 0 Dangerous builds = 0 1168 -6711.98437103562 eV 2.49858345409672 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03