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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -44.734621 0.0000000) to (22.365879 44.734621 2.8636573) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0331912 4.0331912 2.8636573 Created 245 atoms using lattice units in orthogonal box = (0.0000000 -44.734621 0.0000000) to (22.365879 44.734621 2.8636573) create_atoms CPU = 0.002 seconds 245 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0331912 4.0331912 2.8636573 Created 245 atoms using lattice units in orthogonal box = (0.0000000 -44.734621 0.0000000) to (22.365879 44.734621 2.8636573) create_atoms CPU = 0.001 seconds 245 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 30 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 486 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_179158257180_001#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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.472 | 4.472 | 4.472 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2053.0581 0 -2053.0581 15790.706 44 0 -2078.3096 0 -2078.3096 -2848.6422 Loop time of 2.83625 on 1 procs for 44 steps with 486 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 = -2053.05813474029 -2078.30792612485 -2078.30959943764 Force two-norm initial, final = 49.892054 0.13799100 Force max component initial, final = 20.475772 0.040421732 Final line search alpha, max atom move = 1.0000000 0.040421732 Iterations, force evaluations = 44 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8157 | 2.8157 | 2.8157 | 0.0 | 99.28 Neigh | 0.0061385 | 0.0061385 | 0.0061385 | 0.0 | 0.22 Comm | 0.0078882 | 0.0078882 | 0.0078882 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006497 | | | 0.23 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3833.00 ave 3833 max 3833 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: 31256.0 ave 31256 max 31256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31256 Ave neighs/atom = 64.312757 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.473 | 4.473 | 4.473 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -2078.3096 0 -2078.3096 -2848.6422 5730.3449 49 0 -2078.3577 0 -2078.3577 856.04106 5717.7815 Loop time of 0.288482 on 1 procs for 5 steps with 486 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 = -2078.30959943763 -2078.35764683391 -2078.35766512228 Force two-norm initial, final = 24.762316 0.15186149 Force max component initial, final = 24.761133 0.041611993 Final line search alpha, max atom move = 0.0018750806 7.8025841e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28552 | 0.28552 | 0.28552 | 0.0 | 98.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0006599 | 0.0006599 | 0.0006599 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0023 | | | 0.80 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3863.00 ave 3863 max 3863 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: 31288.0 ave 31288 max 31288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31288 Ave neighs/atom = 64.378601 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 30 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.611 | 4.611 | 4.611 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2078.3577 0 -2078.3577 856.04106 Loop time of 6.605e-06 on 1 procs for 0 steps with 486 atoms 181.7% 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 | | 6.605e-06 | | |100.00 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3897.00 ave 3897 max 3897 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: 31298.0 ave 31298 max 31298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31298 Ave neighs/atom = 64.399177 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 30 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.611 | 4.611 | 4.611 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 -2078.3577 -2078.3577 22.403712 89.469242 2.8525536 856.04106 856.04106 5.4848435 2556.8127 5.8256735 2.3200687 134.18004 Loop time of 6.745e-06 on 1 procs for 0 steps with 486 atoms 266.9% 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 | | 6.745e-06 | | |100.00 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3897.00 ave 3897 max 3897 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15649.0 ave 15649 max 15649 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 31298.0 ave 31298 max 31298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31298 Ave neighs/atom = 64.399177 Neighbor list builds = 0 Dangerous builds = 0 486 -2078.35766512228 eV 2.32006868010118 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03