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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -40.476452 0.0000000) to (19.827557 40.476452 8.8671532) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2873486 4.8567398 5.9114354 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -40.476452 0.0000000) to (19.827557 40.476452 8.8671532) create_atoms CPU = 0.001 seconds 612 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2873486 4.8567398 5.9114354 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -40.476452 0.0000000) to (19.827557 40.476452 8.8671532) create_atoms CPU = 0.001 seconds 612 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 21 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 48 atoms, new total = 1176 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.437 | 5.437 | 5.437 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4124.9046 0 -4124.9046 -4020.9621 46 0 -4144.1453 0 -4144.1453 -17796.713 Loop time of 0.823804 on 1 procs for 46 steps with 1176 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 = -4124.9046222473 -4144.14138665249 -4144.14534652846 Force two-norm initial, final = 18.316289 0.22497772 Force max component initial, final = 2.5705554 0.031210768 Final line search alpha, max atom move = 1.0000000 0.031210768 Iterations, force evaluations = 46 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.81605 | 0.81605 | 0.81605 | 0.0 | 99.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0037068 | 0.0037068 | 0.0037068 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004046 | | | 0.49 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5647.00 ave 5647 max 5647 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: 202248.0 ave 202248 max 202248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202248 Ave neighs/atom = 171.97959 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.437 | 5.437 | 5.437 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -4144.1453 0 -4144.1453 -17796.713 14232.653 54 0 -4144.9433 0 -4144.9433 -3897.3673 14080.808 Loop time of 0.095156 on 1 procs for 8 steps with 1176 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 = -4144.14534652851 -4144.9393796846 -4144.94333937279 Force two-norm initial, final = 198.86662 4.0014303 Force max component initial, final = 154.98441 3.4002308 Final line search alpha, max atom move = 0.00012376663 0.00042083511 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.092647 | 0.092647 | 0.092647 | 0.0 | 97.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040961 | 0.00040961 | 0.00040961 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002099 | | | 2.21 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5647.00 ave 5647 max 5647 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: 203304.0 ave 203304 max 203304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203304 Ave neighs/atom = 172.87755 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.575 | 5.575 | 5.575 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4144.9433 0 -4144.9433 -3897.3673 Loop time of 1.69e-06 on 1 procs for 0 steps with 1176 atoms 118.3% 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 | | 1.69e-06 | | |100.00 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5671.00 ave 5671 max 5671 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: 203424.0 ave 203424 max 203424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203424 Ave neighs/atom = 172.97959 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.575 | 5.575 | 5.575 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 -4144.9433 -4144.9433 19.680131 80.952904 8.8382682 -3897.3673 -3897.3673 -384.01655 -11071.399 -236.68585 2.3630854 701.38163 Loop time of 2.13e-06 on 1 procs for 0 steps with 1176 atoms 187.8% 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 | | 2.13e-06 | | |100.00 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5671.00 ave 5671 max 5671 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101712.0 ave 101712 max 101712 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 203424.0 ave 203424 max 203424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203424 Ave neighs/atom = 172.97959 Neighbor list builds = 0 Dangerous builds = 0 1176 -4144.94333937279 eV 2.36308535112697 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01