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 = 4.2107003 4.2107003 4.2107003 Created orthogonal box = (0.0000000 -53.593465 0.0000000) to (12.632101 53.593465 5.9548295) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 7.0178338 5.9548295 5.9548295 Created 216 atoms using lattice units in orthogonal box = (0.0000000 -53.593465 0.0000000) to (12.632101 53.593465 5.9548295) create_atoms CPU = 0.001 seconds 216 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 7.0178338 5.9548295 5.9548295 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -53.593465 0.0000000) to (12.632101 53.593465 5.9548295) create_atoms CPU = 0.000 seconds 218 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 3 24 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 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 434 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_878712978062_003#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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 3 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 4.513 | 4.513 | 4.513 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -900.73263 0 -900.73263 369985.43 49 0 -1616.3853 0 -1616.3853 3623.1738 Loop time of 0.509192 on 1 procs for 49 steps with 434 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 = -900.73262620787 -1616.38381846221 -1616.38526304497 Force two-norm initial, final = 3187.7743 0.064024182 Force max component initial, final = 764.79495 0.0099454088 Final line search alpha, max atom move = 1.0000000 0.0099454088 Iterations, force evaluations = 49 82 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4988 | 0.4988 | 0.4988 | 0.0 | 97.96 Neigh | 0.0050109 | 0.0050109 | 0.0050109 | 0.0 | 0.98 Comm | 0.0031932 | 0.0031932 | 0.0031932 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002186 | | | 0.43 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4418.00 ave 4418 max 4418 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: 74888.0 ave 74888 max 74888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74888 Ave neighs/atom = 172.55300 Neighbor list builds = 1 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 3 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.513 | 4.513 | 4.513 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -1616.3853 0 -1616.3853 3623.1738 8062.816 58 0 -1616.4947 0 -1616.4947 67.236459 8132.0321 Loop time of 0.0709962 on 1 procs for 9 steps with 434 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 = -1616.38526304498 -1616.49457098211 -1616.49474308282 Force two-norm initial, final = 32.869085 0.78067866 Force max component initial, final = 25.644806 0.72408418 Final line search alpha, max atom move = 0.0011380280 0.00082402811 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.068698 | 0.068698 | 0.068698 | 0.0 | 96.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042249 | 0.00042249 | 0.00042249 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001876 | | | 2.64 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4512.00 ave 4512 max 4512 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: 74780.0 ave 74780 max 74780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74780 Ave neighs/atom = 172.30415 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 3 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 4.651 | 4.651 | 4.651 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1616.4947 0 -1616.4947 67.236459 Loop time of 1.985e-06 on 1 procs for 0 steps with 434 atoms 151.1% 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 | | 1.985e-06 | | |100.00 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4464.00 ave 4464 max 4464 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: 74216.0 ave 74216 max 74216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74216 Ave neighs/atom = 171.00461 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 3 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 4.651 | 4.651 | 4.651 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 -1616.4947 -1616.4947 12.643069 108.05163 5.9527175 67.236459 67.236459 54.068781 143.81024 3.8303533 2.80853 452.99052 Loop time of 4.381e-06 on 1 procs for 0 steps with 434 atoms 205.4% 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 | | 4.381e-06 | | |100.00 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4464.00 ave 4464 max 4464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37108.0 ave 37108 max 37108 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74216.0 ave 74216 max 74216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74216 Ave neighs/atom = 171.00461 Neighbor list builds = 0 Dangerous builds = 0 434 -1616.49474308282 eV 2.80852999441862 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01