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 = 4.0320000 4.0320000 4.0320000 Created orthogonal box = (0.0000000 -77.136701 0.0000000) to (44.534895 77.136701 6.9836288) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5707223 5.9011684 6.9836288 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -77.136701 0.0000000) to (44.534895 77.136701 6.9836288) create_atoms CPU = 0.009 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5707223 5.9011684 6.9836288 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -77.136701 0.0000000) to (44.534895 77.136701 6.9836288) create_atoms CPU = 0.007 seconds 1466 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 11 35 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 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2926 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_519613893196_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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 11 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 10.89 | 10.89 | 10.89 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9625.614 0 -9625.614 10496.665 125 0 -9812.5594 0 -9812.5594 2025.62 Loop time of 14.186 on 1 procs for 125 steps with 2926 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 = -9625.61395304027 -9812.5503744214 -9812.55938200939 Force two-norm initial, final = 199.96813 0.22722315 Force max component initial, final = 62.491177 0.024061655 Final line search alpha, max atom move = 1.0000000 0.024061655 Iterations, force evaluations = 125 233 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.653 | 13.653 | 13.653 | 0.0 | 96.24 Neigh | 0.36692 | 0.36692 | 0.36692 | 0.0 | 2.59 Comm | 0.085747 | 0.085747 | 0.085747 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08041 | | | 0.57 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13743.0 ave 13743 max 13743 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: 513900.0 ave 513900 max 513900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 513900 Ave neighs/atom = 175.63226 Neighbor list builds = 5 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 11 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 125 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.89 | 10.89 | 10.89 Mbytes Step Temp E_pair E_mol TotEng Press Volume 125 0 -9812.5594 0 -9812.5594 2025.62 47981.37 128 0 -9812.6599 0 -9812.6599 1.9010717 48100.914 Loop time of 0.354458 on 1 procs for 3 steps with 2926 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 = -9812.55938200941 -9812.65659914622 -9812.65988225773 Force two-norm initial, final = 110.69605 1.8862847 Force max component initial, final = 86.160776 1.4502725 Final line search alpha, max atom move = 6.2054544e-05 8.9996000e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34546 | 0.34546 | 0.34546 | 0.0 | 97.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021091 | 0.0021091 | 0.0021091 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006891 | | | 1.94 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13751.0 ave 13751 max 13751 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: 513964.0 ave 513964 max 513964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 513964 Ave neighs/atom = 175.65414 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 11 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 10.40 | 10.40 | 10.40 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9812.6599 0 -9812.6599 1.9010717 Loop time of 7.036e-06 on 1 procs for 0 steps with 2926 atoms 213.2% 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 | | 7.036e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13751.0 ave 13751 max 13751 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: 513720.0 ave 513720 max 513720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 513720 Ave neighs/atom = 175.57075 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 11 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 10.40 | 10.40 | 10.40 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 -9812.6599 -9812.6599 44.565562 154.56956 6.9828058 1.9010717 1.9010717 -48.339883 20.129005 33.914093 2.5976933 1384.4422 Loop time of 6.926e-06 on 1 procs for 0 steps with 2926 atoms 274.3% 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 | | 6.926e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13751.0 ave 13751 max 13751 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 256860.0 ave 256860 max 256860 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 513720.0 ave 513720 max 513720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 513720 Ave neighs/atom = 175.57075 Neighbor list builds = 0 Dangerous builds = 0 2926 -9812.65988225773 eV 2.59769333620013 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15