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 = 3.6284291 3.6284291 3.6284291 Created orthogonal box = (0.0000000 -46.466564 0.0000000) to (23.233282 46.466564 3.6284291) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0999887 5.0999887 3.6284291 Created 327 atoms using lattice units in orthogonal box = (0.0000000 -46.466564 0.0000000) to (23.233282 46.466564 3.6284291) create_atoms CPU = 0.002 seconds 327 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0999887 5.0999887 3.6284291 Created 329 atoms using lattice units in orthogonal box = (0.0000000 -46.466564 0.0000000) to (23.233282 46.466564 3.6284291) create_atoms CPU = 0.001 seconds 329 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 7 25 1 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 7.549891471862793 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 656 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_650279905230_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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 4.548 | 4.548 | 4.548 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2549.8338 0 -2549.8338 82585.717 155 0 -2747.7711 0 -2747.7711 -4095.6466 Loop time of 3.1867 on 1 procs for 155 steps with 656 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2549.83380909886 -2747.76848535187 -2747.77112862027 Force two-norm initial, final = 464.23312 0.17574177 Force max component initial, final = 132.47066 0.052220066 Final line search alpha, max atom move = 1.0000000 0.052220066 Iterations, force evaluations = 155 287 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0812 | 3.0812 | 3.0812 | 0.0 | 96.69 Neigh | 0.038217 | 0.038217 | 0.038217 | 0.0 | 1.20 Comm | 0.038964 | 0.038964 | 0.038964 | 0.0 | 1.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02828 | | | 0.89 Nlocal: 656.000 ave 656 max 656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5763.00 ave 5763 max 5763 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: 94566.0 ave 94566 max 94566 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94566 Ave neighs/atom = 144.15549 Neighbor list builds = 3 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 155 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.549 | 4.549 | 4.549 Mbytes Step Temp E_pair E_mol TotEng Press Volume 155 0 -2747.7711 0 -2747.7711 -4095.6466 7834.292 260 0 -2762.6649 0 -2762.6649 579.48164 7758.625 Loop time of 1.43073 on 1 procs for 105 steps with 656 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 = -2747.77112862027 -2762.6634216205 -2762.66490103188 Force two-norm initial, final = 272.84036 5.6374139 Force max component initial, final = 200.81838 2.9441194 Final line search alpha, max atom move = 0.00051272300 0.0015095177 Iterations, force evaluations = 105 117 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3264 | 1.3264 | 1.3264 | 0.0 | 92.71 Neigh | 0.040471 | 0.040471 | 0.040471 | 0.0 | 2.83 Comm | 0.014654 | 0.014654 | 0.014654 | 0.0 | 1.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0492 | | | 3.44 Nlocal: 656.000 ave 656 max 656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5674.00 ave 5674 max 5674 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: 99808.0 ave 99808 max 99808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99808 Ave neighs/atom = 152.14634 Neighbor list builds = 3 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 5.055 | 5.055 | 5.055 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2762.6649 0 -2762.6649 579.48164 Loop time of 6.395e-06 on 1 procs for 0 steps with 656 atoms 187.6% 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 | | 6.395e-06 | | |100.00 Nlocal: 656.000 ave 656 max 656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5659.00 ave 5659 max 5659 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: 100986.0 ave 100986 max 100986 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100986 Ave neighs/atom = 153.94207 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 5.055 | 5.055 | 5.055 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 -2762.6649 -2762.6649 22.374369 89.423907 3.8777546 579.48164 579.48164 509.17643 585.01108 644.25742 2.2836102 234.0261 Loop time of 6.756e-06 on 1 procs for 0 steps with 656 atoms 222.0% 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 | | 6.756e-06 | | |100.00 Nlocal: 656.000 ave 656 max 656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5659.00 ave 5659 max 5659 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50493.0 ave 50493 max 50493 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 100986.0 ave 100986 max 100986 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100986 Ave neighs/atom = 153.94207 Neighbor list builds = 0 Dangerous builds = 0 656 -2762.66474462929 eV 2.28361018355549 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05