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 = 3.6583648 3.6583648 3.6583648 Created orthogonal box = (0.0000000 -38.018843 0.0000000) to (8.9611271 38.018843 5.1737092) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9740848 6.3364738 5.1737092 Created 143 atoms using lattice units in orthogonal box = (0.0000000 -38.018843 0.0000000) to (8.9611271 38.018843 5.1737092) create_atoms CPU = 0.001 seconds 143 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9740848 6.3364738 5.1737092 Created 151 atoms using lattice units in orthogonal box = (0.0000000 -38.018843 0.0000000) to (8.9611271 38.018843 5.1737092) create_atoms CPU = 0.000 seconds 151 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 3 21 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 287 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_737567242631_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 3 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.458 | 4.458 | 4.458 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1145.6397 0 -1145.6397 -3439.3991 244 0 -1153.5037 0 -1153.5037 -37571.131 Loop time of 0.986202 on 1 procs for 244 steps with 287 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 = -1145.63969615584 -1153.5025538427 -1153.5036793147 Force two-norm initial, final = 3.4518106 0.11442870 Force max component initial, final = 0.70402481 0.015451466 Final line search alpha, max atom move = 1.0000000 0.015451466 Iterations, force evaluations = 244 480 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.95572 | 0.95572 | 0.95572 | 0.0 | 96.91 Neigh | 0.012223 | 0.012223 | 0.012223 | 0.0 | 1.24 Comm | 0.011405 | 0.011405 | 0.011405 | 0.0 | 1.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006851 | | | 0.69 Nlocal: 287.000 ave 287 max 287 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3072.00 ave 3072 max 3072 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: 39210.0 ave 39210 max 39210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39210 Ave neighs/atom = 136.62021 Neighbor list builds = 5 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 3 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 244 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.458 | 4.458 | 4.458 Mbytes Step Temp E_pair E_mol TotEng Press Volume 244 0 -1153.5037 0 -1153.5037 -37571.131 3525.2794 374 0 -1160.8888 0 -1160.8888 -515.55095 3440.7795 Loop time of 0.317977 on 1 procs for 130 steps with 287 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 = -1153.50367931471 -1160.88787435331 -1160.88882717938 Force two-norm initial, final = 192.77795 2.6919550 Force max component initial, final = 171.56278 1.7397682 Final line search alpha, max atom move = 0.00054330851 0.00094523089 Iterations, force evaluations = 130 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29557 | 0.29557 | 0.29557 | 0.0 | 92.95 Neigh | 0.0048358 | 0.0048358 | 0.0048358 | 0.0 | 1.52 Comm | 0.003498 | 0.003498 | 0.003498 | 0.0 | 1.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01407 | | | 4.43 Nlocal: 287.000 ave 287 max 287 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3181.00 ave 3181 max 3181 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: 40618.0 ave 40618 max 40618 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40618 Ave neighs/atom = 141.52613 Neighbor list builds = 2 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 3 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.597 | 4.597 | 4.597 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1160.8888 0 -1160.8888 -515.55095 Loop time of 1.521e-06 on 1 procs for 0 steps with 287 atoms 0.0% 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 | | 1.521e-06 | | |100.00 Nlocal: 287.000 ave 287 max 287 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3230.00 ave 3230 max 3230 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: 41000.0 ave 41000 max 41000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41000 Ave neighs/atom = 142.85714 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 3 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.597 | 4.597 | 4.597 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 -1160.8888 -1160.8888 8.4415634 73.581476 5.5394349 -515.55095 -515.55095 -245.54304 -433.73188 -867.37792 2.3766864 639.91066 Loop time of 1.416e-06 on 1 procs for 0 steps with 287 atoms 141.2% 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 | | 1.416e-06 | | |100.00 Nlocal: 287.000 ave 287 max 287 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3230.00 ave 3230 max 3230 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20500.0 ave 20500 max 20500 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 41000.0 ave 41000 max 41000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41000 Ave neighs/atom = 142.85714 Neighbor list builds = 0 Dangerous builds = 0 287 -1160.88882717938 eV 2.37668635750384 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01