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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -51.576804 0.0000000) to (36.470308 51.576804 5.1068646) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7208326 4.5508945 5.1068646 Created 816 atoms using lattice units in orthogonal box = (0.0000000 -51.576804 0.0000000) to (36.470308 51.576804 5.1068646) create_atoms CPU = 0.002 seconds 816 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7208326 4.5508945 5.1068646 Created 824 atoms using lattice units in orthogonal box = (0.0000000 -51.576804 0.0000000) to (36.470308 51.576804 5.1068646) create_atoms CPU = 0.001 seconds 824 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1640 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_179158257180_001#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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.110 | 5.110 | 5.110 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6375.6779 0 -6375.6779 79181.88 410 0 -6960.2676 0 -6960.2676 13087.887 Loop time of 45.4508 on 1 procs for 410 steps with 1640 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6375.67792361258 -6960.26091101836 -6960.26760771507 Force two-norm initial, final = 521.37933 0.26738517 Force max component initial, final = 133.52769 0.062392741 Final line search alpha, max atom move = 1.0000000 0.062392741 Iterations, force evaluations = 410 773 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 45.214 | 45.214 | 45.214 | 0.0 | 99.48 Neigh | 0.094107 | 0.094107 | 0.094107 | 0.0 | 0.21 Comm | 0.062273 | 0.062273 | 0.062273 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08069 | | | 0.18 Nlocal: 1640.00 ave 1640 max 1640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6625.00 ave 6625 max 6625 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: 117240.0 ave 117240 max 117240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117240 Ave neighs/atom = 71.487805 Neighbor list builds = 10 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 410 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.113 | 5.113 | 5.113 Mbytes Step Temp E_pair E_mol TotEng Press Volume 410 0 -6960.2676 0 -6960.2676 13087.887 19212.248 442 0 -6966.0759 0 -6966.0759 -9.1302556 19346.788 Loop time of 1.9263 on 1 procs for 32 steps with 1640 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 = -6960.26760771507 -6966.07317135839 -6966.07590442369 Force two-norm initial, final = 439.35236 1.6547824 Force max component initial, final = 438.20775 0.27258218 Final line search alpha, max atom move = 5.6745430e-05 1.5467793e-05 Iterations, force evaluations = 32 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8946 | 1.8946 | 1.8946 | 0.0 | 98.35 Neigh | 0.017994 | 0.017994 | 0.017994 | 0.0 | 0.93 Comm | 0.0023634 | 0.0023634 | 0.0023634 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01137 | | | 0.59 Nlocal: 1640.00 ave 1640 max 1640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6689.00 ave 6689 max 6689 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: 115612.0 ave 115612 max 115612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 115612 Ave neighs/atom = 70.495122 Neighbor list builds = 2 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.252 | 5.252 | 5.252 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6966.0759 0 -6966.0759 -9.1302556 Loop time of 2.07e-06 on 1 procs for 0 steps with 1640 atoms 193.2% 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 | | 2.07e-06 | | |100.00 Nlocal: 1640.00 ave 1640 max 1640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6689.00 ave 6689 max 6689 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: 115772.0 ave 115772 max 115772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 115772 Ave neighs/atom = 70.592683 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.252 | 5.252 | 5.252 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 -6966.0759 -6966.0759 36.088374 105.89929 5.0623074 -9.1302556 -9.1302556 -11.123048 6.1088308 -22.37655 2.344943 4278.9581 Loop time of 2.166e-06 on 1 procs for 0 steps with 1640 atoms 230.8% 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 | | 2.166e-06 | | |100.00 Nlocal: 1640.00 ave 1640 max 1640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6689.00 ave 6689 max 6689 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57886.0 ave 57886 max 57886 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 115772.0 ave 115772 max 115772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 115772 Ave neighs/atom = 70.592683 Neighbor list builds = 0 Dangerous builds = 0 1640 -6966.07590442369 eV 2.34494297415075 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:47