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 = 4.0397985 4.0397985 4.0397985 Created orthogonal box = (0.0000000 -53.593983 0.0000000) to (18.948334 53.593983 5.7131378) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8903034 6.0902253 5.7131378 Created 349 atoms using lattice units in orthogonal box = (0.0000000 -53.593983 0.0000000) to (18.948334 53.593983 5.7131378) create_atoms CPU = 0.001 seconds 349 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8903034 6.0902253 5.7131378 Created 357 atoms using lattice units in orthogonal box = (0.0000000 -53.593983 0.0000000) to (18.948334 53.593983 5.7131378) create_atoms CPU = 0.001 seconds 357 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 4 19 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 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 704 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_279544746097_004#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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 4 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 5.814 | 5.814 | 5.814 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2009.1788 0 -2009.1788 5412.2711 25 0 -2028.9981 0 -2028.9981 1030.7356 Loop time of 0.621192 on 1 procs for 25 steps with 704 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2009.178815492 -2028.99640456517 -2028.9980705696 Force two-norm initial, final = 29.360495 0.11740444 Force max component initial, final = 9.0384972 0.0096629912 Final line search alpha, max atom move = 1.0000000 0.0096629912 Iterations, force evaluations = 25 44 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.6157 | 0.6157 | 0.6157 | 0.0 | 99.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.003341 | 0.003341 | 0.003341 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002152 | | | 0.35 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8836.00 ave 8836 max 8836 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: 300512.0 ave 300512 max 300512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 300512 Ave neighs/atom = 426.86364 Neighbor list builds = 0 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 4 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.815 | 5.815 | 5.815 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -2028.9981 0 -2028.9981 1030.7356 11603.574 30 0 -2029.0921 0 -2029.0921 -17.364369 11619.095 Loop time of 0.102213 on 1 procs for 5 steps with 704 atoms 97.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2028.9980705696 -2029.09019749133 -2029.09209172783 Force two-norm initial, final = 34.768559 0.26797624 Force max component initial, final = 30.656625 0.15200445 Final line search alpha, max atom move = 0.00026265656 3.9924965e-05 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.099616 | 0.099616 | 0.099616 | 0.0 | 97.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048945 | 0.00048945 | 0.00048945 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002107 | | | 2.06 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8911.00 ave 8911 max 8911 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: 295164.0 ave 295164 max 295164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 295164 Ave neighs/atom = 419.26705 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 4 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 5.572 | 5.572 | 5.572 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2029.0921 0 -2029.0921 -17.364369 Loop time of 2.136e-06 on 1 procs for 0 steps with 704 atoms 140.4% 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 | | 2.136e-06 | | |100.00 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9010.00 ave 9010 max 9010 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: 289272.0 ave 289272 max 289272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289272 Ave neighs/atom = 410.89773 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 4 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 5.572 | 5.572 | 5.572 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 -2029.0921 -2029.0921 18.943768 107.68866 5.6955541 -17.364369 -17.364369 -13.923165 -17.274305 -20.895638 2.7303684 184.33443 Loop time of 4.294e-06 on 1 procs for 0 steps with 704 atoms 232.9% 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 | | 4.294e-06 | | |100.00 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9010.00 ave 9010 max 9010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 144636.0 ave 144636 max 144636 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 289272.0 ave 289272 max 289272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289272 Ave neighs/atom = 410.89773 Neighbor list builds = 0 Dangerous builds = 0 704 -2029.09209172783 eV 2.73036840812275 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01