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 = 3.5200244 3.5200244 3.5200244 Created orthogonal box = (0.0000000 -41.649490 0.0000000) to (51.009999 41.649490 8.6222635) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8297142 5.3549344 5.7481757 Created 1662 atoms using lattice units in orthogonal box = (0.0000000 -41.649490 0.0000000) to (51.009999 41.649490 8.6222635) create_atoms CPU = 0.003 seconds 1662 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8297142 5.3549344 5.7481757 Created 1686 atoms using lattice units in orthogonal box = (0.0000000 -41.649490 0.0000000) to (51.009999 41.649490 8.6222635) create_atoms CPU = 0.002 seconds 1686 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 13 20 3 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 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3348 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_532072268679_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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 7.833 | 7.833 | 7.833 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13953.792 0 -13953.792 69173.636 58 0 -14825.721 0 -14825.721 1623.4809 Loop time of 3.07187 on 1 procs for 58 steps with 3348 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13953.791867551 -14825.7072211996 -14825.7207113013 Force two-norm initial, final = 2183.6470 0.38928251 Force max component initial, final = 454.55178 0.051556351 Final line search alpha, max atom move = 0.97331738 0.050180692 Iterations, force evaluations = 58 81 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8661 | 2.8661 | 2.8661 | 0.0 | 93.30 Neigh | 0.17383 | 0.17383 | 0.17383 | 0.0 | 5.66 Comm | 0.013156 | 0.013156 | 0.013156 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01877 | | | 0.61 Nlocal: 3348.00 ave 3348 max 3348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12300.0 ave 12300 max 12300 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: 746890.0 ave 746890 max 746890 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 746890 Ave neighs/atom = 223.08542 Neighbor list builds = 4 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.832 | 7.832 | 7.832 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -14825.721 0 -14825.721 1623.4809 36636.695 60 0 -14825.75 0 -14825.75 -2.0094845 36670.627 Loop time of 0.175618 on 1 procs for 2 steps with 3348 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 = -14825.7207113013 -14825.7456979276 -14825.7503994615 Force two-norm initial, final = 72.369624 1.7804309 Force max component initial, final = 57.839295 1.4515421 Final line search alpha, max atom move = 5.1618677e-05 7.4926681e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17227 | 0.17227 | 0.17227 | 0.0 | 98.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050332 | 0.00050332 | 0.00050332 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002845 | | | 1.62 Nlocal: 3348.00 ave 3348 max 3348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12149.0 ave 12149 max 12149 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: 746996.0 ave 746996 max 746996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 746996 Ave neighs/atom = 223.11708 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 13 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 7.970 | 7.970 | 7.970 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14825.75 0 -14825.75 -2.0094845 Loop time of 2.64e-06 on 1 procs for 0 steps with 3348 atoms 189.4% 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 | | 2.64e-06 | | |100.00 Nlocal: 3348.00 ave 3348 max 3348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12149.0 ave 12149 max 12149 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: 746834.0 ave 746834 max 746834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 746834 Ave neighs/atom = 223.06870 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 13 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 7.970 | 7.970 | 7.970 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 -14825.75 -14825.75 51.030273 83.365118 8.6199764 -2.0094845 -2.0094845 -63.444536 35.058807 22.357276 2.1595403 1774.7277 Loop time of 2.734e-06 on 1 procs for 0 steps with 3348 atoms 256.0% 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 | | 2.734e-06 | | |100.00 Nlocal: 3348.00 ave 3348 max 3348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12149.0 ave 12149 max 12149 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 373417.0 ave 373417 max 373417 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 746834.0 ave 746834 max 746834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 746834 Ave neighs/atom = 223.06870 Neighbor list builds = 0 Dangerous builds = 0 3348 -14734.4792262351 eV 2.15954028582159 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04