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 = 4.0409265 4.0409265 4.0409265 Created orthogonal box = (0.0000000 -51.749108 0.0000000) to (36.592146 51.749108 5.7147330) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2474395 6.9419536 5.7147330 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -51.749108 0.0000000) to (36.592146 51.749108 5.7147330) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2474395 6.9419536 5.7147330 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -51.749108 0.0000000) to (36.592146 51.749108 5.7147330) create_atoms CPU = 0.001 seconds 660 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 8 21 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1304 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_338600200739_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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 5.894 | 5.894 | 5.894 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5020.2157 0 -5020.2157 7871.8333 72 0 -5082.6284 0 -5082.6284 -867.07044 Loop time of 2.47354 on 1 procs for 72 steps with 1304 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 = -5020.21573274834 -5082.62364902108 -5082.6284258225 Force two-norm initial, final = 88.247848 0.15263410 Force max component initial, final = 21.438169 0.013230155 Final line search alpha, max atom move = 1.0000000 0.013230155 Iterations, force evaluations = 72 130 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4185 | 2.4185 | 2.4185 | 0.0 | 97.78 Neigh | 0.035128 | 0.035128 | 0.035128 | 0.0 | 1.42 Comm | 0.011046 | 0.011046 | 0.011046 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008832 | | | 0.36 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9496.00 ave 9496 max 9496 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: 321760.0 ave 321760 max 321760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 321760 Ave neighs/atom = 246.74847 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.895 | 5.895 | 5.895 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -5082.6284 0 -5082.6284 -867.07044 21642.962 74 0 -5082.6364 0 -5082.6364 -1.5855365 21620.001 Loop time of 0.094431 on 1 procs for 2 steps with 1304 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 = -5082.6284258225 -5082.63565447562 -5082.6363861383 Force two-norm initial, final = 21.201380 0.16342566 Force max component initial, final = 15.507536 0.043145169 Final line search alpha, max atom move = 0.00029170363 1.2585602e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.092709 | 0.092709 | 0.092709 | 0.0 | 98.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003458 | 0.0003458 | 0.0003458 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001376 | | | 1.46 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9514.00 ave 9514 max 9514 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: 321880.0 ave 321880 max 321880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 321880 Ave neighs/atom = 246.84049 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 6.033 | 6.033 | 6.033 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5082.6364 0 -5082.6364 -1.5855365 Loop time of 1.987e-06 on 1 procs for 0 steps with 1304 atoms 151.0% 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 | | 1.987e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9514.00 ave 9514 max 9514 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: 321952.0 ave 321952 max 321952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 321952 Ave neighs/atom = 246.89571 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 6.033 | 6.033 | 6.033 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 -5082.6364 -5082.6364 36.576135 103.50627 5.7107253 -1.5855365 -1.5855365 1.2352627 -3.1975739 -2.7942984 2.656355 784.42363 Loop time of 4.032e-06 on 1 procs for 0 steps with 1304 atoms 272.8% 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 | | 4.032e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9514.00 ave 9514 max 9514 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 160976.0 ave 160976 max 160976 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 321952.0 ave 321952 max 321952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 321952 Ave neighs/atom = 246.89571 Neighbor list builds = 0 Dangerous builds = 0 1304 -5082.6363861383 eV 2.65635495697529 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03