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 = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -39.102204 0.0000000) to (13.034068 39.102204 3.6150001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0131031 5.0131031 3.6150001 Created 156 atoms using lattice units in orthogonal box = (0.0000000 -39.102204 0.0000000) to (13.034068 39.102204 3.6150001) create_atoms CPU = 0.002 seconds 156 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0131031 5.0131031 3.6150001 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -39.102204 0.0000000) to (13.034068 39.102204 3.6150001) create_atoms CPU = 0.001 seconds 158 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 5 25 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 6.4274528135 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 312 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_179025990738_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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 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) = 4.432 | 4.432 | 4.432 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1077.2744 0 -1077.2744 12628.859 19 0 -1092.7009 0 -1092.7009 12813.435 Loop time of 0.164391 on 1 procs for 19 steps with 312 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1077.27437204979 -1092.700300461 -1092.70094622641 Force two-norm initial, final = 25.790691 0.066543414 Force max component initial, final = 8.5009423 0.012179135 Final line search alpha, max atom move = 1.0000000 0.012179135 Iterations, force evaluations = 19 34 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15811 | 0.15811 | 0.15811 | 0.0 | 96.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0036807 | 0.0036807 | 0.0036807 | 0.0 | 2.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0026 | | | 1.58 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3238.00 ave 3238 max 3238 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: 26976.0 ave 26976 max 26976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26976 Ave neighs/atom = 86.461538 Neighbor list builds = 0 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.432 | 4.432 | 4.432 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -1092.7009 0 -1092.7009 12813.435 3684.8477 30 0 -1092.925 0 -1092.925 -222.06671 3714.5808 Loop time of 0.0690382 on 1 procs for 11 steps with 312 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 = -1092.70094622641 -1092.92481887781 -1092.92503610294 Force two-norm initial, final = 58.777309 0.96772197 Force max component initial, final = 52.540814 0.69308742 Final line search alpha, max atom move = 0.0017683981 0.0012256545 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.061905 | 0.061905 | 0.061905 | 0.0 | 89.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016587 | 0.0016587 | 0.0016587 | 0.0 | 2.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005475 | | | 7.93 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3238.00 ave 3238 max 3238 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: 26736.0 ave 26736 max 26736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26736 Ave neighs/atom = 85.692308 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 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) = 4.569 | 4.569 | 4.569 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1092.925 0 -1092.925 -222.06671 Loop time of 7.136e-06 on 1 procs for 0 steps with 312 atoms 154.1% 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 | | 7.136e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3238.00 ave 3238 max 3238 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: 26704.0 ave 26704 max 26704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26704 Ave neighs/atom = 85.589744 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 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) = 4.569 | 4.569 | 4.569 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 -1092.925 -1092.925 13.034576 78.966356 3.6088664 -222.06671 -222.06671 -106.32182 -261.44243 -298.4359 2.2951856 125.63163 Loop time of 6.425e-06 on 1 procs for 0 steps with 312 atoms 264.6% 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 | | 6.425e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3238.00 ave 3238 max 3238 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13352.0 ave 13352 max 13352 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26704.0 ave 26704 max 26704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26704 Ave neighs/atom = 85.589744 Neighbor list builds = 0 Dangerous builds = 0 312 -1092.92503610294 eV 2.29518564377154 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00