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 = 2.8553246 2.8553246 2.8553246 Created orthogonal box = (0.0000000 -44.965697 0.0000000) to (27.535754 44.965697 6.9940884) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4412506 4.3515191 4.6627256 Created 740 atoms using lattice units in orthogonal box = (0.0000000 -44.965697 0.0000000) to (27.535754 44.965697 6.9940884) create_atoms CPU = 0.004 seconds 740 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4412506 4.3515191 4.6627256 Created 746 atoms using lattice units in orthogonal box = (0.0000000 -44.965697 0.0000000) to (27.535754 44.965697 6.9940884) create_atoms CPU = 0.004 seconds 746 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 25 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1478 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_737567242631_000#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.518 | 5.518 | 5.518 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5374.4359 0 -5374.4359 110231.04 88 0 -6065.8231 0 -6065.8231 -6348.2853 Loop time of 3.42259 on 1 procs for 88 steps with 1478 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 = -5374.43586958767 -6065.81787032817 -6065.82310958576 Force two-norm initial, final = 1257.3612 0.23645227 Force max component initial, final = 241.89030 0.022078114 Final line search alpha, max atom move = 1.0000000 0.022078114 Iterations, force evaluations = 88 150 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2794 | 3.2794 | 3.2794 | 0.0 | 95.82 Neigh | 0.090001 | 0.090001 | 0.090001 | 0.0 | 2.63 Comm | 0.026363 | 0.026363 | 0.026363 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02683 | | | 0.78 Nlocal: 1478.00 ave 1478 max 1478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6594.00 ave 6594 max 6594 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: 201172.0 ave 201172 max 201172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201172 Ave neighs/atom = 136.11096 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 88 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.515 | 5.515 | 5.515 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -6065.8231 0 -6065.8231 -6348.2853 17319.662 91 0 -6065.957 0 -6065.957 -1.3965651 17256.167 Loop time of 0.131882 on 1 procs for 3 steps with 1478 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 = -6065.82310958577 -6065.95506452249 -6065.95698996022 Force two-norm initial, final = 120.09610 0.66031055 Force max component initial, final = 78.427841 0.47301133 Final line search alpha, max atom move = 0.00012800279 6.0546769e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12789 | 0.12789 | 0.12789 | 0.0 | 96.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00084104 | 0.00084104 | 0.00084104 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003151 | | | 2.39 Nlocal: 1478.00 ave 1478 max 1478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6483.00 ave 6483 max 6483 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: 201324.0 ave 201324 max 201324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201324 Ave neighs/atom = 136.21380 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.654 | 5.654 | 5.654 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6065.957 0 -6065.957 -1.3965651 Loop time of 6.746e-06 on 1 procs for 0 steps with 1478 atoms 177.9% 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 | | 6.746e-06 | | |100.00 Nlocal: 1478.00 ave 1478 max 1478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6518.00 ave 6518 max 6518 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: 201464.0 ave 201464 max 201464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201464 Ave neighs/atom = 136.30853 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.654 | 5.654 | 5.654 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 -6065.957 -6065.957 27.495644 89.88733 6.9820341 -1.3965651 -1.3965651 -43.853523 6.0427849 33.621043 2.2351137 935.67217 Loop time of 6.785e-06 on 1 procs for 0 steps with 1478 atoms 280.0% 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 | | 6.785e-06 | | |100.00 Nlocal: 1478.00 ave 1478 max 1478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6518.00 ave 6518 max 6518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100732.0 ave 100732 max 100732 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 201464.0 ave 201464 max 201464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201464 Ave neighs/atom = 136.30853 Neighbor list builds = 0 Dangerous builds = 0 1478 -6065.95698996022 eV 2.23511365677191 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04