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 = 3.1582519 3.1582519 3.1582519 Created orthogonal box = (0.0000000 -36.831230 0.0000000) to (18.415615 36.831230 3.1582519) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3330859 4.3330859 3.1582519 Created 136 atoms using lattice units in orthogonal box = (0.0000000 -36.831230 0.0000000) to (18.415615 36.831230 3.1582519) create_atoms CPU = 0.002 seconds 136 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3330859 4.3330859 3.1582519 Created 138 atoms using lattice units in orthogonal box = (0.0000000 -36.831230 0.0000000) to (18.415615 36.831230 3.1582519) create_atoms CPU = 0.001 seconds 138 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 5 18 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 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 272 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_228581001644_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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 5 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.435 | 4.435 | 4.435 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1342.448 0 -1342.448 217498.02 65 0 -1723.7679 0 -1723.7679 17303.842 Loop time of 0.607564 on 1 procs for 65 steps with 272 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 = -1342.44798342419 -1723.76624173123 -1723.76792985538 Force two-norm initial, final = 860.38088 0.23022962 Force max component initial, final = 248.56519 0.029091719 Final line search alpha, max atom move = 1.0000000 0.029091719 Iterations, force evaluations = 65 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.58462 | 0.58462 | 0.58462 | 0.0 | 96.22 Neigh | 0.005443 | 0.005443 | 0.005443 | 0.0 | 0.90 Comm | 0.010511 | 0.010511 | 0.010511 | 0.0 | 1.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006988 | | | 1.15 Nlocal: 272.000 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3562.00 ave 3562 max 3562 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: 44928.0 ave 44928 max 44928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44928 Ave neighs/atom = 165.17647 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 5 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.433 | 4.433 | 4.433 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -1723.7679 0 -1723.7679 17303.842 4284.2936 753 0 -1746.2552 0 -1746.2552 -967.25862 4270.1718 Loop time of 4.71765 on 1 procs for 688 steps with 272 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 = -1723.76792985538 -1746.25362735405 -1746.25522807403 Force two-norm initial, final = 174.86337 6.0048166 Force max component initial, final = 145.63594 2.9296183 Final line search alpha, max atom move = 0.00024528706 0.00071859746 Iterations, force evaluations = 688 891 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.383 | 4.383 | 4.383 | 0.0 | 92.91 Neigh | 0.029157 | 0.029157 | 0.029157 | 0.0 | 0.62 Comm | 0.075029 | 0.075029 | 0.075029 | 0.0 | 1.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2304 | | | 4.88 Nlocal: 272.000 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4159.00 ave 4159 max 4159 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: 42912.0 ave 42912 max 42912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42912 Ave neighs/atom = 157.76471 Neighbor list builds = 5 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 5 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.576 | 4.576 | 4.576 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1746.2552 0 -1746.2552 -967.25862 Loop time of 6.485e-06 on 1 procs for 0 steps with 272 atoms 185.0% 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 | | 6.485e-06 | | |100.00 Nlocal: 272.000 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4159.00 ave 4159 max 4159 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: 42584.0 ave 42584 max 42584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42584 Ave neighs/atom = 156.55882 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 5 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.576 | 4.576 | 4.576 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 -1746.2552 -1746.2552 18.965944 78.76596 2.8584613 -967.25862 -967.25862 -928.16618 -978.75054 -994.85915 2.6525806 516.64903 Loop time of 7.016e-06 on 1 procs for 0 steps with 272 atoms 242.3% 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 | | 7.016e-06 | | |100.00 Nlocal: 272.000 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4159.00 ave 4159 max 4159 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21292.0 ave 21292 max 21292 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 42584.0 ave 42584 max 42584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42584 Ave neighs/atom = 156.55882 Neighbor list builds = 0 Dangerous builds = 0 272 -1746.25522807403 eV 2.65258060862701 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05