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 = 4.0320382 4.0320382 4.0320382 Created orthogonal box = (0.0000000 -46.324592 0.0000000) to (32.756433 46.324592 5.7021631) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9630960 6.3169898 5.7021631 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -46.324592 0.0000000) to (32.756433 46.324592 5.7021631) create_atoms CPU = 0.004 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9630960 6.3169898 5.7021631 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -46.324592 0.0000000) to (32.756433 46.324592 5.7021631) create_atoms CPU = 0.003 seconds 532 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 8 22 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 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1048 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_019873715786_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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.026 | 5.026 | 5.026 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3455.3961 0 -3455.3961 3734.8693 86 0 -3511.2449 0 -3511.2449 -903.2673 Loop time of 3.15388 on 1 procs for 86 steps with 1048 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 = -3455.39612884554 -3511.24194651982 -3511.24486921779 Force two-norm initial, final = 33.957134 0.14256060 Force max component initial, final = 6.4150932 0.021933300 Final line search alpha, max atom move = 1.0000000 0.021933300 Iterations, force evaluations = 86 152 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0601 | 3.0601 | 3.0601 | 0.0 | 97.03 Neigh | 0.048572 | 0.048572 | 0.048572 | 0.0 | 1.54 Comm | 0.024289 | 0.024289 | 0.024289 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02092 | | | 0.66 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6605.00 ave 6605 max 6605 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: 181104.0 ave 181104 max 181104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181104 Ave neighs/atom = 172.80916 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 86 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.027 | 5.027 | 5.027 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -3511.2449 0 -3511.2449 -903.2673 17305.249 90 0 -3511.3315 0 -3511.3315 84.257338 17285.034 Loop time of 0.124826 on 1 procs for 4 steps with 1048 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 = -3511.24486921778 -3511.32850944505 -3511.33149548422 Force two-norm initial, final = 39.183915 1.7316633 Force max component initial, final = 29.940084 1.3140074 Final line search alpha, max atom move = 0.00019222225 0.00025258146 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.121 | 0.121 | 0.121 | 0.0 | 96.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0008472 | 0.0008472 | 0.0008472 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002974 | | | 2.38 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6991.00 ave 6991 max 6991 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: 181304.0 ave 181304 max 181304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181304 Ave neighs/atom = 173.00000 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.165 | 5.165 | 5.165 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3511.3315 0 -3511.3315 84.257338 Loop time of 6.375e-06 on 1 procs for 0 steps with 1048 atoms 156.9% 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 | | 6.375e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7012.00 ave 7012 max 7012 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: 181272.0 ave 181272 max 181272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181272 Ave neighs/atom = 172.96947 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.165 | 5.165 | 5.165 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 -3511.3315 -3511.3315 32.705012 92.95388 5.6857583 84.257338 84.257338 34.192159 97.132879 121.44698 2.6251682 683.37602 Loop time of 6.526e-06 on 1 procs for 0 steps with 1048 atoms 275.8% 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 | | 6.526e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7012.00 ave 7012 max 7012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90636.0 ave 90636 max 90636 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 181272.0 ave 181272 max 181272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181272 Ave neighs/atom = 172.96947 Neighbor list builds = 0 Dangerous builds = 0 1048 -3511.33149548422 eV 2.62516815197453 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03