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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -63.945568 0.0000000) to (36.916901 63.945568 6.2700239) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6795232 5.7383800 6.2700239 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -63.945568 0.0000000) to (36.916901 63.945568 6.2700239) create_atoms CPU = 0.008 seconds 1249 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6795232 5.7383800 6.2700239 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -63.945568 0.0000000) to (36.916901 63.945568 6.2700239) create_atoms CPU = 0.008 seconds 1249 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 43 3 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 26 atoms, new total = 2472 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_227887284491_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 43 3 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) = 5.243 | 5.243 | 5.243 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8688.8413 0 -8688.8413 860.75019 51 0 -8723.9394 0 -8723.9394 -9322.3644 Loop time of 20.8445 on 1 procs for 51 steps with 2472 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 = -8688.84131960819 -8723.93205649764 -8723.93943210704 Force two-norm initial, final = 50.314474 0.23960000 Force max component initial, final = 9.9739422 0.032776824 Final line search alpha, max atom move = 1.0000000 0.032776824 Iterations, force evaluations = 51 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.743 | 20.743 | 20.743 | 0.0 | 99.51 Neigh | 0.058342 | 0.058342 | 0.058342 | 0.0 | 0.28 Comm | 0.017566 | 0.017566 | 0.017566 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02591 | | | 0.12 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7033.00 ave 7033 max 7033 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: 191172.0 ave 191172 max 191172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191172 Ave neighs/atom = 77.334951 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 ghost atom cutoff = 6 binsize = 3, bins = 13 43 3 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 : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.243 | 5.243 | 5.243 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -8723.9394 0 -8723.9394 -9322.3644 29602.942 54 0 -8724.2122 0 -8724.2122 -3395.0332 29478.522 Loop time of 1.09896 on 1 procs for 3 steps with 2472 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 = -8723.93943210708 -8724.20512352248 -8724.21224697002 Force two-norm initial, final = 181.18649 3.6253629 Force max component initial, final = 141.95417 3.1275373 Final line search alpha, max atom move = 3.9357807e-05 0.00012309301 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0937 | 1.0937 | 1.0937 | 0.0 | 99.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00082997 | 0.00082997 | 0.00082997 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004436 | | | 0.40 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7031.00 ave 7031 max 7031 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: 191144.0 ave 191144 max 191144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191144 Ave neighs/atom = 77.323625 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 43 3 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) = 5.381 | 5.381 | 5.381 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8724.2122 0 -8724.2122 -3395.0332 Loop time of 6.435e-06 on 1 procs for 0 steps with 2472 atoms 170.9% 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 | | 6.435e-06 | | |100.00 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7034.00 ave 7034 max 7034 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: 191174.0 ave 191174 max 191174 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191174 Ave neighs/atom = 77.335761 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 43 3 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) = 5.381 | 5.381 | 5.381 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 -8724.2122 -8724.2122 36.851163 127.89114 6.2548091 -3395.0332 -3395.0332 169.68096 -10256.43 -98.350693 2.3325624 1016.0016 Loop time of 6.836e-06 on 1 procs for 0 steps with 2472 atoms 307.2% 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 | | 6.836e-06 | | |100.00 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7034.00 ave 7034 max 7034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 95587.0 ave 95587 max 95587 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 191174.0 ave 191174 max 191174 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191174 Ave neighs/atom = 77.335761 Neighbor list builds = 0 Dangerous builds = 0 2472 -8724.21224697002 eV 2.33256240321711 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:23