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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -58.567254 0.0000000) to (20.705377 58.567254 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6469210 6.2112962 5.0973115 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.567254 0.0000000) to (20.705377 58.567254 5.0973115) create_atoms CPU = 0.002 seconds 530 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6469210 6.2112962 5.0973115 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.567254 0.0000000) to (20.705377 58.567254 5.0973115) create_atoms CPU = 0.001 seconds 530 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 7 39 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 1046 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 7 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.621 | 4.621 | 4.621 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4412.0472 0 -4412.0472 -2141.1774 80 0 -4435.7155 0 -4435.7155 -13705.558 Loop time of 5.06867 on 1 procs for 80 steps with 1046 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 = -4412.04724106004 -4435.71200996731 -4435.7155116219 Force two-norm initial, final = 18.288764 0.16160630 Force max component initial, final = 6.8806580 0.022184696 Final line search alpha, max atom move = 1.0000000 0.022184696 Iterations, force evaluations = 80 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0422 | 5.0422 | 5.0422 | 0.0 | 99.48 Neigh | 0.011651 | 0.011651 | 0.011651 | 0.0 | 0.23 Comm | 0.0071251 | 0.0071251 | 0.0071251 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007731 | | | 0.15 Nlocal: 1046.00 ave 1046 max 1046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4902.00 ave 4902 max 4902 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: 81176.0 ave 81176 max 81176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81176 Ave neighs/atom = 77.606119 Neighbor list builds = 2 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 7 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.621 | 4.621 | 4.621 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -4435.7155 0 -4435.7155 -13705.558 12362.582 96 0 -4437.5121 0 -4437.5121 6160.2545 12208.118 Loop time of 0.634089 on 1 procs for 16 steps with 1046 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 = -4435.7155116219 -4437.51111100301 -4437.5120548358 Force two-norm initial, final = 265.74145 0.53870725 Force max component initial, final = 248.75824 0.31875859 Final line search alpha, max atom move = 0.00033263717 0.00010603095 Iterations, force evaluations = 16 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62965 | 0.62965 | 0.62965 | 0.0 | 99.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00068097 | 0.00068097 | 0.00068097 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003759 | | | 0.59 Nlocal: 1046.00 ave 1046 max 1046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4902.00 ave 4902 max 4902 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: 81140.0 ave 81140 max 81140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81140 Ave neighs/atom = 77.571702 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 7 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.760 | 4.760 | 4.760 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4437.5121 0 -4437.5121 6160.2545 Loop time of 1.79e-06 on 1 procs for 0 steps with 1046 atoms 223.5% 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 | | 1.79e-06 | | |100.00 Nlocal: 1046.00 ave 1046 max 1046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4932.00 ave 4932 max 4932 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: 81308.0 ave 81308 max 81308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81308 Ave neighs/atom = 77.732314 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 7 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.760 | 4.760 | 4.760 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 -4437.5121 -4437.5121 20.387887 117.13451 5.1120093 6160.2545 6160.2545 41.191975 18399.613 39.958836 2.3461401 1173.826 Loop time of 2.275e-06 on 1 procs for 0 steps with 1046 atoms 175.8% 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 | | 2.275e-06 | | |100.00 Nlocal: 1046.00 ave 1046 max 1046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4932.00 ave 4932 max 4932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40654.0 ave 40654 max 40654 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 81308.0 ave 81308 max 81308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81308 Ave neighs/atom = 77.732314 Neighbor list builds = 0 Dangerous builds = 0 1046 -4437.5120548358 eV 2.34614013492827 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06