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 -77.641477 0.0000000) to (38.820739 77.641477 4.2107003) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9372894 5.9372894 4.2107003 Created 680 atoms using lattice units in orthogonal box = (0.0000000 -77.641477 0.0000000) to (38.820739 77.641477 4.2107003) create_atoms CPU = 0.003 seconds 680 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9372894 5.9372894 4.2107003 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -77.641477 0.0000000) to (38.820739 77.641477 4.2107003) create_atoms CPU = 0.002 seconds 682 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 = 9 35 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 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1362 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 = 9 35 1 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) = 5.510 | 5.510 | 5.510 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4882.9381 0 -4882.9381 33234.483 27 0 -5072.6912 0 -5072.6912 1385.7374 Loop time of 1.70901 on 1 procs for 27 steps with 1362 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 = -4882.93807183938 -5072.68636408712 -5072.69115912969 Force two-norm initial, final = 612.01787 0.13783842 Force max component initial, final = 285.40728 0.034746460 Final line search alpha, max atom move = 1.0000000 0.034746460 Iterations, force evaluations = 27 42 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6906 | 1.6906 | 1.6906 | 0.0 | 98.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010385 | 0.010385 | 0.010385 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007973 | | | 0.47 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10882.0 ave 10882 max 10882 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: 239012.0 ave 239012 max 239012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 239012 Ave neighs/atom = 175.48605 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 9 35 1 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 : 27 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.510 | 5.510 | 5.510 Mbytes Step Temp E_pair E_mol TotEng Press Volume 27 0 -5072.6912 0 -5072.6912 1385.7374 25382.939 31 0 -5072.7475 0 -5072.7475 -69.173829 25476.165 Loop time of 0.256468 on 1 procs for 4 steps with 1362 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 = -5072.69115912969 -5072.74691756451 -5072.74752938519 Force two-norm initial, final = 39.886060 2.6043392 Force max component initial, final = 31.288247 1.9106737 Final line search alpha, max atom move = 0.00028082914 0.00053657285 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2509 | 0.2509 | 0.2509 | 0.0 | 97.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014653 | 0.0014653 | 0.0014653 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004106 | | | 1.60 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10853.0 ave 10853 max 10853 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: 235884.0 ave 235884 max 235884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235884 Ave neighs/atom = 173.18943 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 = 9 35 1 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) = 5.648 | 5.648 | 5.648 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5072.7475 0 -5072.7475 -69.173829 Loop time of 8.219e-06 on 1 procs for 0 steps with 1362 atoms 182.5% 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 | | 8.219e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10853.0 ave 10853 max 10853 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: 235256.0 ave 235256 max 235256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235256 Ave neighs/atom = 172.72834 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 = 9 35 1 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) = 5.648 | 5.648 | 5.648 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 -5072.7475 -5072.7475 38.847121 155.80126 4.2092455 -69.173829 -69.173829 -120.24247 21.542234 -108.82125 2.7238569 223.06907 Loop time of 7.287e-06 on 1 procs for 0 steps with 1362 atoms 205.8% 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 | | 7.287e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10853.0 ave 10853 max 10853 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117628.0 ave 117628 max 117628 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 235256.0 ave 235256 max 235256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235256 Ave neighs/atom = 172.72834 Neighbor list builds = 0 Dangerous builds = 0 1362 -5072.74752938519 eV 2.72385688784257 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03