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 = 3.3116877 3.3116877 3.3116877 Created orthogonal box = (0.0000000 -47.300361 0.0000000) to (33.446406 47.300361 4.6834336) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2464950 4.1735613 4.6834336 Created 815 atoms using lattice units in orthogonal box = (0.0000000 -47.300361 0.0000000) to (33.446406 47.300361 4.6834336) create_atoms CPU = 0.001 seconds 815 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2464950 4.1735613 4.6834336 Created 823 atoms using lattice units in orthogonal box = (0.0000000 -47.300361 0.0000000) to (33.446406 47.300361 4.6834336) create_atoms CPU = 0.001 seconds 823 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 9 26 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 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 1631 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_255315407910_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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.951 | 5.951 | 5.951 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5891.7676 0 -5891.7676 116119.43 369 0 -6351.2969 0 -6351.2969 194878.05 Loop time of 13.2106 on 1 procs for 369 steps with 1631 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5891.76763514613 -6351.29071011624 -6351.29692525699 Force two-norm initial, final = 467.35111 0.52115218 Force max component initial, final = 66.686736 0.054812350 Final line search alpha, max atom move = 0.52780486 0.028930225 Iterations, force evaluations = 369 735 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.03 | 13.03 | 13.03 | 0.0 | 98.63 Neigh | 0.020412 | 0.020412 | 0.020412 | 0.0 | 0.15 Comm | 0.091997 | 0.091997 | 0.091997 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06828 | | | 0.52 Nlocal: 1631.00 ave 1631 max 1631 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9957.00 ave 9957 max 9957 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: 318742.0 ave 318742 max 318742 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 318742 Ave neighs/atom = 195.42735 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 369 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.950 | 5.950 | 5.950 Mbytes Step Temp E_pair E_mol TotEng Press Volume 369 0 -6351.2969 0 -6351.2969 194878.05 14818.637 585 0 -6442.339 0 -6442.339 -555.41586 17474.192 Loop time of 3.91207 on 1 procs for 216 steps with 1631 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6351.29692525702 -6442.33362745243 -6442.33895174673 Force two-norm initial, final = 3185.3629 17.931559 Force max component initial, final = 2104.6359 14.698269 Final line search alpha, max atom move = 0.00017671223 0.0025973640 Iterations, force evaluations = 216 222 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5399 | 3.5399 | 3.5399 | 0.0 | 90.49 Neigh | 0.25862 | 0.25862 | 0.25862 | 0.0 | 6.61 Comm | 0.021257 | 0.021257 | 0.021257 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.09229 | | | 2.36 Nlocal: 1631.00 ave 1631 max 1631 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9650.00 ave 9650 max 9650 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: 273896.0 ave 273896 max 273896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 273896 Ave neighs/atom = 167.93133 Neighbor list builds = 15 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.706 | 5.706 | 5.706 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6442.339 0 -6442.339 -555.41586 Loop time of 2.149e-06 on 1 procs for 0 steps with 1631 atoms 139.6% 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 | | 2.149e-06 | | |100.00 Nlocal: 1631.00 ave 1631 max 1631 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9634.00 ave 9634 max 9634 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: 272698.0 ave 272698 max 272698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272698 Ave neighs/atom = 167.19681 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 5.706 | 5.706 | 5.706 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 -6442.339 -6442.339 33.44919 110.91466 4.7100179 -555.41586 -555.41586 -1347.7694 -395.9038 77.42561 2.2756359 3632.6576 Loop time of 2.456e-06 on 1 procs for 0 steps with 1631 atoms 244.3% 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 | | 2.456e-06 | | |100.00 Nlocal: 1631.00 ave 1631 max 1631 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9634.00 ave 9634 max 9634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 136349.0 ave 136349 max 136349 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 272698.0 ave 272698 max 272698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272698 Ave neighs/atom = 167.19681 Neighbor list builds = 0 Dangerous builds = 0 1631 -6442.33895174673 eV 2.27563592502956 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18