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 = 4.0499990 4.0499990 4.0499990 Created orthogonal box = (0.0000000 -51.548072 0.0000000) to (12.149997 51.548072 5.7275635) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7499983 5.7275635 5.7275635 Created 216 atoms using lattice units in orthogonal box = (0.0000000 -51.548072 0.0000000) to (12.149997 51.548072 5.7275635) create_atoms CPU = 0.001 seconds 216 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7499983 5.7275635 5.7275635 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -51.548072 0.0000000) to (12.149997 51.548072 5.7275635) create_atoms CPU = 0.001 seconds 218 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 26 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 432 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_093637366498_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.505 | 4.505 | 4.505 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1367.0394 0 -1367.0394 31610.886 93 0 -1447.3075 0 -1447.3075 3387.7618 Loop time of 5.90073 on 1 procs for 93 steps with 432 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 = -1367.03935480032 -1447.30610661265 -1447.30751110923 Force two-norm initial, final = 183.62153 0.10054267 Force max component initial, final = 62.401680 0.0097045989 Final line search alpha, max atom move = 1.0000000 0.0097045989 Iterations, force evaluations = 93 175 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.8832 | 5.8832 | 5.8832 | 0.0 | 99.70 Neigh | 0.0036563 | 0.0036563 | 0.0036563 | 0.0 | 0.06 Comm | 0.008197 | 0.008197 | 0.008197 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005729 | | | 0.10 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3864.00 ave 3864 max 3864 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: 57628.0 ave 57628 max 57628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57628 Ave neighs/atom = 133.39815 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.502 | 4.502 | 4.502 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -1447.3075 0 -1447.3075 3387.7618 7174.4482 103 0 -1447.486 0 -1447.486 2.8372851 7203.9783 Loop time of 0.405914 on 1 procs for 10 steps with 432 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 = -1447.30751110923 -1447.48482029529 -1447.48600362757 Force two-norm initial, final = 38.898131 0.19525855 Force max component initial, final = 38.074014 0.066634029 Final line search alpha, max atom move = 0.00049322518 3.2865581e-05 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4001 | 0.4001 | 0.4001 | 0.0 | 98.57 Neigh | 0.003495 | 0.003495 | 0.003495 | 0.0 | 0.86 Comm | 0.00048139 | 0.00048139 | 0.00048139 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001834 | | | 0.45 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3872.00 ave 3872 max 3872 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: 57544.0 ave 57544 max 57544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57544 Ave neighs/atom = 133.20370 Neighbor list builds = 1 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.641 | 4.641 | 4.641 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1447.486 0 -1447.486 2.8372851 Loop time of 2.374e-06 on 1 procs for 0 steps with 432 atoms 168.5% 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 | | 2.374e-06 | | |100.00 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3872.00 ave 3872 max 3872 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: 57544.0 ave 57544 max 57544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57544 Ave neighs/atom = 133.20370 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.641 | 4.641 | 4.641 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 -1447.486 -1447.486 12.099945 104.10352 5.7190462 2.8372851 2.8372851 14.758467 1.7137574 -7.9603694 2.6506003 291.61528 Loop time of 1.99e-06 on 1 procs for 0 steps with 432 atoms 402.0% 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 | | 1.99e-06 | | |100.00 Nlocal: 432.000 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3872.00 ave 3872 max 3872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28772.0 ave 28772 max 28772 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 57544.0 ave 57544 max 57544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57544 Ave neighs/atom = 133.20370 Neighbor list builds = 0 Dangerous builds = 0 432 -1447.48600362757 eV 2.65060034631674 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06