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 -81.202249 0.0000000) to (46.882140 81.202249 7.0148059) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2976009 6.4638606 7.0148059 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -81.202249 0.0000000) to (46.882140 81.202249 7.0148059) create_atoms CPU = 0.004 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2976009 6.4638606 7.0148059 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -81.202249 0.0000000) to (46.882140 81.202249 7.0148059) create_atoms CPU = 0.004 seconds 1610 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 13 43 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 3216 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_418978237058_005#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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 13 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.642 | 6.642 | 6.642 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10527.313 0 -10527.313 10082.288 39 0 -10794.719 0 -10794.719 4369.0948 Loop time of 1.14007 on 1 procs for 39 steps with 3216 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10527.3129020273 -10794.7096709453 -10794.719296803 Force two-norm initial, final = 143.75024 0.21554496 Force max component initial, final = 20.923930 0.035467522 Final line search alpha, max atom move = 1.0000000 0.035467522 Iterations, force evaluations = 39 59 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0651 | 1.0651 | 1.0651 | 0.0 | 93.42 Neigh | 0.051486 | 0.051486 | 0.051486 | 0.0 | 4.52 Comm | 0.010974 | 0.010974 | 0.010974 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01254 | | | 1.10 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12335.0 ave 12335 max 12335 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: 423864.0 ave 423864 max 423864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 423864 Ave neighs/atom = 131.79851 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 13 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.642 | 6.642 | 6.642 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -10794.719 0 -10794.719 4369.0948 53409.823 47 0 -10795.515 0 -10795.515 2.8932646 53704.225 Loop time of 0.193675 on 1 procs for 8 steps with 3216 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 = -10794.7192968029 -10795.5145554514 -10795.5149425842 Force two-norm initial, final = 282.43900 0.71821530 Force max component initial, final = 247.90372 0.41364073 Final line search alpha, max atom move = 0.00017234495 7.1288889e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16284 | 0.16284 | 0.16284 | 0.0 | 84.08 Neigh | 0.023808 | 0.023808 | 0.023808 | 0.0 | 12.29 Comm | 0.0012884 | 0.0012884 | 0.0012884 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005738 | | | 2.96 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12317.0 ave 12317 max 12317 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: 422512.0 ave 422512 max 422512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 422512 Ave neighs/atom = 131.37811 Neighbor list builds = 1 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 13 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.780 | 6.780 | 6.780 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10795.515 0 -10795.515 2.8932646 Loop time of 2.473e-06 on 1 procs for 0 steps with 3216 atoms 161.7% 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 | | 2.473e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12317.0 ave 12317 max 12317 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: 422540.0 ave 422540 max 422540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 422540 Ave neighs/atom = 131.38682 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 13 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.780 | 6.780 | 6.780 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 -10795.515 -10795.515 46.876934 163.53846 7.0053423 2.8932646 2.8932646 -12.338915 10.657647 10.361062 2.578159 1458.8123 Loop time of 2.617e-06 on 1 procs for 0 steps with 3216 atoms 229.3% 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 | | 2.617e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12317.0 ave 12317 max 12317 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 211270.0 ave 211270 max 211270 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 422540.0 ave 422540 max 422540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 422540 Ave neighs/atom = 131.38682 Neighbor list builds = 0 Dangerous builds = 0 3216 -10795.5149425842 eV 2.57815896039164 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01