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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -51.865308 0.0000000) to (36.674311 51.865308 5.7275651) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2614678 6.9575413 5.7275651 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -51.865308 0.0000000) to (36.674311 51.865308 5.7275651) create_atoms CPU = 0.005 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2614678 6.9575413 5.7275651 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -51.865308 0.0000000) to (36.674311 51.865308 5.7275651) create_atoms CPU = 0.005 seconds 660 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 9 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 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1312 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_826591359508_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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 5.074 | 5.074 | 5.074 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4351.6565 0 -4351.6565 4461.3639 82 0 -4398.9905 0 -4398.9905 2378.5705 Loop time of 3.77011 on 1 procs for 82 steps with 1312 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 = -4351.65650561209 -4398.98780694953 -4398.99052917069 Force two-norm initial, final = 30.245794 0.11174037 Force max component initial, final = 6.1228578 0.0080400257 Final line search alpha, max atom move = 1.0000000 0.0080400257 Iterations, force evaluations = 82 149 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6621 | 3.6621 | 3.6621 | 0.0 | 97.14 Neigh | 0.054735 | 0.054735 | 0.054735 | 0.0 | 1.45 Comm | 0.028703 | 0.028703 | 0.028703 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02455 | | | 0.65 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7049.00 ave 7049 max 7049 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: 186488.0 ave 186488 max 186488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186488 Ave neighs/atom = 142.14024 Neighbor list builds = 2 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.074 | 5.074 | 5.074 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -4398.9905 0 -4398.9905 2378.5705 21789.083 89 0 -4399.2209 0 -4399.2209 55.335877 21852.857 Loop time of 0.227279 on 1 procs for 7 steps with 1312 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 = -4398.99052917076 -4399.2204908948 -4399.22091107832 Force two-norm initial, final = 79.413446 1.3438297 Force max component initial, final = 77.739477 0.89935295 Final line search alpha, max atom move = 0.00049884049 0.00044863366 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22012 | 0.22012 | 0.22012 | 0.0 | 96.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001563 | 0.001563 | 0.001563 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005599 | | | 2.46 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7049.00 ave 7049 max 7049 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: 185904.0 ave 185904 max 185904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185904 Ave neighs/atom = 141.69512 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 5.212 | 5.212 | 5.212 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4399.2209 0 -4399.2209 55.335877 Loop time of 6.946e-06 on 1 procs for 0 steps with 1312 atoms 172.8% 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 | | 6.946e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7070.00 ave 7070 max 7070 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: 185488.0 ave 185488 max 185488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185488 Ave neighs/atom = 141.37805 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 5.212 | 5.212 | 5.212 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 -4399.2209 -4399.2209 36.582751 104.37329 5.7232474 55.335877 55.335877 40.762658 66.34599 58.898983 2.6607756 766.54665 Loop time of 7.216e-06 on 1 procs for 0 steps with 1312 atoms 235.6% 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 | | 7.216e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7070.00 ave 7070 max 7070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 92744.0 ave 92744 max 92744 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 185488.0 ave 185488 max 185488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185488 Ave neighs/atom = 141.37805 Neighbor list builds = 0 Dangerous builds = 0 1312 -4399.22091107832 eV 2.66077559276119 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05