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 = 2.8688302 2.8688302 2.8688302 Created orthogonal box = (0.0000000 -40.571386 0.0000000) to (20.285693 40.571386 2.8688302) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.2457109 3.2457109 2.8688302 Created 200 atoms using lattice units in orthogonal box = (0.0000000 -40.571386 0.0000000) to (20.285693 40.571386 2.8688302) create_atoms CPU = 0.002 seconds 200 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.2457109 3.2457109 2.8688302 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -40.571386 0.0000000) to (20.285693 40.571386 2.8688302) create_atoms CPU = 0.001 seconds 202 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 = 4 16 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 0 atoms, new total = 402 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 = 4 16 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) = 4.908 | 4.908 | 4.908 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1466.329 0 -1466.329 82004.022 98 0 -1652.7606 0 -1652.7606 14515.104 Loop time of 3.65851 on 1 procs for 98 steps with 402 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 = -1466.32899838292 -1652.75898188769 -1652.76061996156 Force two-norm initial, final = 365.96201 0.18290313 Force max component initial, final = 119.19181 0.023280468 Final line search alpha, max atom move = 1.0000000 0.023280468 Iterations, force evaluations = 98 185 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5872 | 3.5872 | 3.5872 | 0.0 | 98.05 Neigh | 0.020272 | 0.020272 | 0.020272 | 0.0 | 0.55 Comm | 0.035065 | 0.035065 | 0.035065 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01597 | | | 0.44 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8239.00 ave 8239 max 8239 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: 157856.0 ave 157856 max 157856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157856 Ave neighs/atom = 392.67662 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 = 4 16 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 : 98 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.912 | 4.912 | 4.912 Mbytes Step Temp E_pair E_mol TotEng Press Volume 98 0 -1652.7606 0 -1652.7606 14515.104 4722.2018 150 0 -1654.1075 0 -1654.1075 -254.71841 4758.9396 Loop time of 1.21618 on 1 procs for 52 steps with 402 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1652.76061996156 -1654.107124677 -1654.10745222787 Force two-norm initial, final = 86.551128 2.0082888 Force max component initial, final = 65.137084 1.2112410 Final line search alpha, max atom move = 0.00074090654 0.00089741638 Iterations, force evaluations = 52 58 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1568 | 1.1568 | 1.1568 | 0.0 | 95.12 Neigh | 0.019785 | 0.019785 | 0.019785 | 0.0 | 1.63 Comm | 0.010449 | 0.010449 | 0.010449 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02912 | | | 2.39 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8217.00 ave 8217 max 8217 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: 153772.0 ave 153772 max 153772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 153772 Ave neighs/atom = 382.51741 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 17 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) = 5.049 | 5.049 | 5.049 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1654.1075 0 -1654.1075 -254.71841 Loop time of 6.525e-06 on 1 procs for 0 steps with 402 atoms 183.9% 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 | | 6.525e-06 | | |100.00 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8047.00 ave 8047 max 8047 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: 151288.0 ave 151288 max 151288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 151288 Ave neighs/atom = 376.33831 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 17 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) = 5.049 | 5.049 | 5.049 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 -1654.1075 -1654.1075 20.779947 82.672899 2.7701456 -254.71841 -254.71841 -195.94173 -174.45631 -393.75717 2.3558893 228.47843 Loop time of 8.65e-06 on 1 procs for 0 steps with 402 atoms 219.7% 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 | | 8.65e-06 | | |100.00 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8047.00 ave 8047 max 8047 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 75644.0 ave 75644 max 75644 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 151288.0 ave 151288 max 151288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 151288 Ave neighs/atom = 376.33831 Neighbor list builds = 0 Dangerous builds = 0 402 -1654.10745222788 eV 2.35588933731954 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05