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 = 3.6147282 3.6147282 3.6147282 Created orthogonal box = (0.0000000 -71.567966 0.0000000) to (43.826250 71.567966 8.8542395) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0683418 5.1119976 5.9028264 Created 2351 atoms using lattice units in orthogonal box = (0.0000000 -71.567966 0.0000000) to (43.826250 71.567966 8.8542395) create_atoms CPU = 0.003 seconds 2351 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0683418 5.1119976 5.9028264 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -71.567966 0.0000000) to (43.826250 71.567966 8.8542395) create_atoms CPU = 0.003 seconds 2357 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 11 33 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 8.682500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 29 atoms, new total = 4679 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_942551040047_005#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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 11 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 13.21 | 13.21 | 13.21 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16003.522 0 -16003.522 19374.107 103 0 -16446.101 0 -16446.101 -1880.1169 Loop time of 9.0225 on 1 procs for 103 steps with 4679 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -16003.5215062088 -16446.0853885581 -16446.1012054976 Force two-norm initial, final = 509.52909 0.42384747 Force max component initial, final = 92.531725 0.10158332 Final line search alpha, max atom move = 0.71897630 0.073036002 Iterations, force evaluations = 103 180 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.6888 | 8.6888 | 8.6888 | 0.0 | 96.30 Neigh | 0.24237 | 0.24237 | 0.24237 | 0.0 | 2.69 Comm | 0.040271 | 0.040271 | 0.040271 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05107 | | | 0.57 Nlocal: 4679.00 ave 4679 max 4679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16899.0 ave 16899 max 16899 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: 1.04507e+06 ave 1.04507e+06 max 1.04507e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1045074 Ave neighs/atom = 223.35414 Neighbor list builds = 4 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 11 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 103 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 13.21 | 13.21 | 13.21 Mbytes Step Temp E_pair E_mol TotEng Press Volume 103 0 -16446.101 0 -16446.101 -1880.1169 55543.628 105 0 -16446.171 0 -16446.171 -3.9494259 55468.748 Loop time of 0.240831 on 1 procs for 2 steps with 4679 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 = -16446.1012054977 -16446.1594554143 -16446.1705351874 Force two-norm initial, final = 119.32548 5.8941779 Force max component initial, final = 90.785183 4.8621240 Final line search alpha, max atom move = 4.0428416e-05 0.00019656797 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23626 | 0.23626 | 0.23626 | 0.0 | 98.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00068898 | 0.00068898 | 0.00068898 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003883 | | | 1.61 Nlocal: 4679.00 ave 4679 max 4679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17227.0 ave 17227 max 17227 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: 1.04489e+06 ave 1.04489e+06 max 1.04489e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1044886 Ave neighs/atom = 223.31396 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 11 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 12.73 | 12.73 | 12.73 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16446.171 0 -16446.171 -3.9494259 Loop time of 2.327e-06 on 1 procs for 0 steps with 4679 atoms 171.9% 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 | | 2.327e-06 | | |100.00 Nlocal: 4679.00 ave 4679 max 4679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17227.0 ave 17227 max 17227 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: 1.04494e+06 ave 1.04494e+06 max 1.04494e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1044942 Ave neighs/atom = 223.32592 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 11 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 12.73 | 12.73 | 12.73 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 -16446.171 -16446.171 43.800877 143.18748 8.8442396 -3.9494259 -3.9494259 -140.35779 43.90848 84.601032 2.2718119 1757.3381 Loop time of 2.279e-06 on 1 procs for 0 steps with 4679 atoms 351.0% 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 | | 2.279e-06 | | |100.00 Nlocal: 4679.00 ave 4679 max 4679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17227.0 ave 17227 max 17227 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 522471.0 ave 522471 max 522471 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.04494e+06 ave 1.04494e+06 max 1.04494e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1044942 Ave neighs/atom = 223.32592 Neighbor list builds = 0 Dangerous builds = 0 4679 -16446.1705351874 eV 2.2718119194563 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10