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 = 4.0499858 4.0499858 4.0499858 Created orthogonal box = (0.0000000 -76.414980 0.0000000) to (38.207490 76.414980 4.0499858) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5808693 5.5808693 4.0499858 Created 712 atoms using lattice units in orthogonal box = (0.0000000 -76.414980 0.0000000) to (38.207490 76.414980 4.0499858) create_atoms CPU = 0.003 seconds 712 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5808693 5.5808693 4.0499858 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -76.414980 0.0000000) to (38.207490 76.414980 4.0499858) create_atoms CPU = 0.002 seconds 714 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 ghost atom cutoff = 6 binsize = 3, bins = 13 51 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1426 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_022920256108_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 ghost atom cutoff = 6 binsize = 3, bins = 13 51 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.666 | 4.666 | 4.666 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4653.8521 0 -4653.8521 13862.162 29 0 -4771.0004 0 -4771.0004 3341.8441 Loop time of 3.03448 on 1 procs for 29 steps with 1426 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 = -4653.85210595974 -4770.99645115495 -4771.00040326486 Force two-norm initial, final = 182.31159 0.47152931 Force max component initial, final = 57.984166 0.087548198 Final line search alpha, max atom move = 0.14084558 0.012330777 Iterations, force evaluations = 29 58 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0174 | 3.0174 | 3.0174 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0077491 | 0.0077491 | 0.0077491 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009301 | | | 0.31 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5640.00 ave 5640 max 5640 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: 77108.0 ave 77108 max 77108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77108 Ave neighs/atom = 54.072931 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 ghost atom cutoff = 6 binsize = 3, bins = 13 51 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.666 | 4.666 | 4.666 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -4771.0004 0 -4771.0004 3341.8441 23648.876 38 0 -4771.3419 0 -4771.3419 74.382208 23764.248 Loop time of 0.585135 on 1 procs for 9 steps with 1426 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 = -4771.00040326486 -4771.34133151787 -4771.34188942725 Force two-norm initial, final = 103.75876 2.0687626 Force max component initial, final = 97.335704 1.5657647 Final line search alpha, max atom move = 0.00046082010 0.00072153585 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.56469 | 0.56469 | 0.56469 | 0.0 | 96.51 Neigh | 0.012265 | 0.012265 | 0.012265 | 0.0 | 2.10 Comm | 0.0017805 | 0.0017805 | 0.0017805 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006395 | | | 1.09 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5632.00 ave 5632 max 5632 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: 76700.0 ave 76700 max 76700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76700 Ave neighs/atom = 53.786816 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 ghost atom cutoff = 6 binsize = 3, bins = 13 52 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.805 | 4.805 | 4.805 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4771.3419 0 -4771.3419 74.382208 Loop time of 7.628e-06 on 1 procs for 0 steps with 1426 atoms 183.5% 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 | | 7.628e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5632.00 ave 5632 max 5632 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: 76696.0 ave 76696 max 76696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76696 Ave neighs/atom = 53.784011 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 ghost atom cutoff = 6 binsize = 3, bins = 13 52 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.805 | 4.805 | 4.805 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 -4771.3419 -4771.3419 38.230791 154.01575 4.035949 74.382208 74.382208 64.494607 106.38231 52.269708 2.5110056 490.01655 Loop time of 6.295e-06 on 1 procs for 0 steps with 1426 atoms 301.8% 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 | | 6.295e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5632.00 ave 5632 max 5632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38348.0 ave 38348 max 38348 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 76696.0 ave 76696 max 76696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76696 Ave neighs/atom = 53.784011 Neighbor list builds = 0 Dangerous builds = 0 1426 -4771.34188942725 eV 2.51100564655135 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04