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 = 3.6150017 3.6150017 3.6150017 Created orthogonal box = (0.0000000 -43.978394 0.0000000) to (21.989197 43.978394 3.6150017) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1601183 4.1601183 3.6150017 Created 296 atoms using lattice units in orthogonal box = (0.0000000 -43.978394 0.0000000) to (21.989197 43.978394 3.6150017) create_atoms CPU = 0.002 seconds 296 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1601183 4.1601183 3.6150017 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -43.978394 0.0000000) to (21.989197 43.978394 3.6150017) create_atoms CPU = 0.001 seconds 298 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 6 21 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 588 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_592013496703_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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 4.929 | 4.929 | 4.929 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1994.3244 0 -1994.3244 19638.106 47 0 -2073.2916 0 -2073.2916 -2432.2553 Loop time of 1.31824 on 1 procs for 47 steps with 588 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 = -1994.32442194668 -2073.29004231586 -2073.29164914449 Force two-norm initial, final = 147.06132 0.11247567 Force max component initial, final = 49.774511 0.016292935 Final line search alpha, max atom move = 1.0000000 0.016292935 Iterations, force evaluations = 47 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2806 | 1.2806 | 1.2806 | 0.0 | 97.15 Neigh | 0.016049 | 0.016049 | 0.016049 | 0.0 | 1.22 Comm | 0.013079 | 0.013079 | 0.013079 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008472 | | | 0.64 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6216.00 ave 6216 max 6216 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: 122164.0 ave 122164 max 122164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122164 Ave neighs/atom = 207.76190 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.929 | 4.929 | 4.929 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -2073.2916 0 -2073.2916 -2432.2553 6991.7715 50 0 -2073.3038 0 -2073.3038 -59.56358 6979.7171 Loop time of 0.0905294 on 1 procs for 3 steps with 588 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 = -2073.29164914453 -2073.30380827784 -2073.30384941739 Force two-norm initial, final = 18.700225 0.46684924 Force max component initial, final = 12.676024 0.28064875 Final line search alpha, max atom move = 0.0026732936 0.00075025650 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.087476 | 0.087476 | 0.087476 | 0.0 | 96.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076274 | 0.00076274 | 0.00076274 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00229 | | | 2.53 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6209.00 ave 6209 max 6209 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: 118940.0 ave 118940 max 118940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118940 Ave neighs/atom = 202.27891 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 6 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.067 | 5.067 | 5.067 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2073.3038 0 -2073.3038 -59.56358 Loop time of 6.345e-06 on 1 procs for 0 steps with 588 atoms 173.4% 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 | | 6.345e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6221.00 ave 6221 max 6221 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: 119060.0 ave 119060 max 119060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119060 Ave neighs/atom = 202.48299 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 6 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.067 | 5.067 | 5.067 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 -2073.3038 -2073.3038 21.956389 87.874096 3.6175625 -59.56358 -59.56358 -64.326095 -61.939222 -52.425424 2.3444681 206.58713 Loop time of 6.685e-06 on 1 procs for 0 steps with 588 atoms 239.3% 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 | | 6.685e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6221.00 ave 6221 max 6221 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59530.0 ave 59530 max 59530 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119060.0 ave 119060 max 119060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119060 Ave neighs/atom = 202.48299 Neighbor list builds = 0 Dangerous builds = 0 588 -2073.30384941739 eV 2.34446805374135 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02