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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -55.403918 0.0000000) to (27.700000 55.403918 3.9173716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4320000 4.4320000 3.9173716 Created 402 atoms using lattice units in orthogonal box = (0.0000000 -55.403918 0.0000000) to (27.700000 55.403918 3.9173716) create_atoms CPU = 0.002 seconds 402 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4320000 4.4320000 3.9173716 Created 402 atoms using lattice units in orthogonal box = (0.0000000 -55.403918 0.0000000) to (27.700000 55.403918 3.9173716) create_atoms CPU = 0.001 seconds 402 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 799 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_070797404269_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.539 | 4.539 | 4.539 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4522.8608 0 -4522.8608 25315.261 42 0 -4593.3161 0 -4593.3161 5787.0262 Loop time of 2.73912 on 1 procs for 42 steps with 799 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 = -4522.86079117907 -4593.31320464057 -4593.31610667062 Force two-norm initial, final = 92.365266 0.17152300 Force max component initial, final = 23.998970 0.057594081 Final line search alpha, max atom move = 1.0000000 0.057594081 Iterations, force evaluations = 42 74 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7218 | 2.7218 | 2.7218 | 0.0 | 99.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0085652 | 0.0085652 | 0.0085652 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008768 | | | 0.32 Nlocal: 799.000 ave 799 max 799 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4449.00 ave 4449 max 4449 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: 62244.0 ave 62244 max 62244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62244 Ave neighs/atom = 77.902378 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.539 | 4.539 | 4.539 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -4593.3161 0 -4593.3161 5787.0262 12023.891 45 0 -4593.3731 0 -4593.3731 996.17292 12055.635 Loop time of 0.201106 on 1 procs for 3 steps with 799 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 = -4593.31610667062 -4593.37039203287 -4593.3730821651 Force two-norm initial, final = 55.408189 0.18105046 Force max component initial, final = 44.685969 0.047662264 Final line search alpha, max atom move = 0.00021984208 1.0478171e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19853 | 0.19853 | 0.19853 | 0.0 | 98.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00058729 | 0.00058729 | 0.00058729 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001985 | | | 0.99 Nlocal: 799.000 ave 799 max 799 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4453.00 ave 4453 max 4453 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: 61856.0 ave 61856 max 61856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61856 Ave neighs/atom = 77.416771 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.677 | 4.677 | 4.677 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4593.3731 0 -4593.3731 996.17292 Loop time of 6.194e-06 on 1 procs for 0 steps with 799 atoms 177.6% 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 | | 6.194e-06 | | |100.00 Nlocal: 799.000 ave 799 max 799 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4449.00 ave 4449 max 4449 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: 61812.0 ave 61812 max 61812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61812 Ave neighs/atom = 77.361702 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.677 | 4.677 | 4.677 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 -4593.3731 -4593.3731 27.764514 110.80784 3.9185874 996.17292 996.17292 -1.9559244 2991.1575 -0.68280914 2.5117947 278.00087 Loop time of 6.585e-06 on 1 procs for 0 steps with 799 atoms 318.9% 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 | | 6.585e-06 | | |100.00 Nlocal: 799.000 ave 799 max 799 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4449.00 ave 4449 max 4449 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30906.0 ave 30906 max 30906 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61812.0 ave 61812 max 61812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61812 Ave neighs/atom = 77.361702 Neighbor list builds = 0 Dangerous builds = 0 799 -4593.3730821651 eV 2.51179469779197 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03