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 = 3.4986965 3.4986965 3.4986965 Created orthogonal box = (0.0000000 -45.754892 0.0000000) to (21.567414 45.754892 4.9479041) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5405082 5.6185922 4.9479041 Created 460 atoms using lattice units in orthogonal box = (0.0000000 -45.754892 0.0000000) to (21.567414 45.754892 4.9479041) create_atoms CPU = 0.001 seconds 460 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5405082 5.6185922 4.9479041 Created 460 atoms using lattice units in orthogonal box = (0.0000000 -45.754892 0.0000000) to (21.567414 45.754892 4.9479041) create_atoms CPU = 0.001 seconds 460 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 6 25 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 908 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 6 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.005 | 5.005 | 5.005 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3674.9822 0 -3674.9822 30751.571 38 0 -3723.22 0 -3723.22 -1135.1702 Loop time of 0.590607 on 1 procs for 38 steps with 908 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 = -3674.98224462667 -3723.21678056824 -3723.22004648874 Force two-norm initial, final = 108.74579 0.24683152 Force max component initial, final = 19.322752 0.064438822 Final line search alpha, max atom move = 1.0000000 0.064438822 Iterations, force evaluations = 38 75 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.58431 | 0.58431 | 0.58431 | 0.0 | 98.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0035317 | 0.0035317 | 0.0035317 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002769 | | | 0.47 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6292.00 ave 6292 max 6292 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: 158544.0 ave 158544 max 158544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158544 Ave neighs/atom = 174.60793 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 6 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.005 | 5.005 | 5.005 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -3723.22 0 -3723.22 -1135.1702 9765.329 43 0 -3723.304 0 -3723.304 2254.6549 9738.4522 Loop time of 0.0561578 on 1 procs for 5 steps with 908 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 = -3723.22004648874 -3723.30217844445 -3723.30404583985 Force two-norm initial, final = 36.748512 0.87194923 Force max component initial, final = 36.746593 0.60384118 Final line search alpha, max atom move = 0.00025711380 0.00015525590 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.054443 | 0.054443 | 0.054443 | 0.0 | 96.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032748 | 0.00032748 | 0.00032748 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001388 | | | 2.47 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6292.00 ave 6292 max 6292 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: 158436.0 ave 158436 max 158436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158436 Ave neighs/atom = 174.48899 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 6 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.143 | 5.143 | 5.143 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3723.304 0 -3723.304 2254.6549 Loop time of 1.596e-06 on 1 procs for 0 steps with 908 atoms 188.0% 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 | | 1.596e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6308.00 ave 6308 max 6308 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: 158472.0 ave 158472 max 158472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158472 Ave neighs/atom = 174.52863 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 6 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.143 | 5.143 | 5.143 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 -3723.304 -3723.304 21.466372 91.509785 4.9575118 2254.6549 2254.6549 73.868919 6590.5586 99.537248 2.2530084 547.17375 Loop time of 1.553e-06 on 1 procs for 0 steps with 908 atoms 193.2% 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 | | 1.553e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6308.00 ave 6308 max 6308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79236.0 ave 79236 max 79236 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 158472.0 ave 158472 max 158472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158472 Ave neighs/atom = 174.52863 Neighbor list builds = 0 Dangerous builds = 0 908 -3723.30404583985 eV 2.2530083906332 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00