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 = 4.0452705 4.0452705 4.0452705 Created orthogonal box = (0.0000000 -59.453091 0.0000000) to (21.019842 59.453091 5.7208764) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4495887 6.6058990 5.7208764 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -59.453091 0.0000000) to (21.019842 59.453091 5.7208764) create_atoms CPU = 0.004 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4495887 6.6058990 5.7208764 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -59.453091 0.0000000) to (21.019842 59.453091 5.7208764) create_atoms CPU = 0.003 seconds 434 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 5 26 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 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 862 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_658278549784_005#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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 5.033 | 5.033 | 5.033 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2724.2565 0 -2724.2565 34417.293 75 0 -2932.206 0 -2932.206 3484.155 Loop time of 2.74361 on 1 procs for 75 steps with 862 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2724.25652117905 -2932.2035313408 -2932.20601003715 Force two-norm initial, final = 436.11531 0.10486167 Force max component initial, final = 117.15703 0.023761499 Final line search alpha, max atom move = 1.0000000 0.023761499 Iterations, force evaluations = 75 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6291 | 2.6291 | 2.6291 | 0.0 | 95.83 Neigh | 0.075097 | 0.075097 | 0.075097 | 0.0 | 2.74 Comm | 0.023097 | 0.023097 | 0.023097 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01633 | | | 0.60 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7748.00 ave 7748 max 7748 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: 188876.0 ave 188876 max 188876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188876 Ave neighs/atom = 219.11369 Neighbor list builds = 3 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.032 | 5.032 | 5.032 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -2932.206 0 -2932.206 3484.155 14298.696 82 0 -2932.3819 0 -2932.3819 -54.87379 14360.004 Loop time of 0.194767 on 1 procs for 7 steps with 862 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 = -2932.20601003716 -2932.3811108413 -2932.38194861767 Force two-norm initial, final = 65.204942 0.92494976 Force max component initial, final = 61.085108 0.69348988 Final line search alpha, max atom move = 0.00040856492 0.00028333564 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18873 | 0.18873 | 0.18873 | 0.0 | 96.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014226 | 0.0014226 | 0.0014226 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004618 | | | 2.37 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7616.00 ave 7616 max 7616 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: 189188.0 ave 189188 max 189188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189188 Ave neighs/atom = 219.47564 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 5 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 5.170 | 5.170 | 5.170 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2932.3819 0 -2932.3819 -54.87379 Loop time of 6.314e-06 on 1 procs for 0 steps with 862 atoms 158.4% 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 | | 6.314e-06 | | |100.00 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7616.00 ave 7616 max 7616 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: 187976.0 ave 187976 max 187976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187976 Ave neighs/atom = 218.06961 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 5 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 5.170 | 5.170 | 5.170 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 -2932.3819 -2932.3819 20.986069 119.67268 5.7177932 -54.87379 -54.87379 -77.249837 -59.963726 -27.407808 2.5402971 552.43587 Loop time of 6.826e-06 on 1 procs for 0 steps with 862 atoms 278.3% 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 | | 6.826e-06 | | |100.00 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7616.00 ave 7616 max 7616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 93988.0 ave 93988 max 93988 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 187976.0 ave 187976 max 187976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187976 Ave neighs/atom = 218.06961 Neighbor list builds = 0 Dangerous builds = 0 862 -2932.38194861767 eV 2.54029709659398 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03