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 -34.601703 0.0000000) to (42.378259 34.601703 7.0144993) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0636686 4.2659634 4.6763329 Created 875 atoms using lattice units in orthogonal box = (0.0000000 -34.601703 0.0000000) to (42.378259 34.601703 7.0144993) create_atoms CPU = 0.001 seconds 875 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0636686 4.2659634 4.6763329 Created 881 atoms using lattice units in orthogonal box = (0.0000000 -34.601703 0.0000000) to (42.378259 34.601703 7.0144993) create_atoms CPU = 0.001 seconds 881 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 16 25 3 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1752 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_856956178669_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 16 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.015 | 5.015 | 5.015 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5806.0907 0 -5806.0907 140185.14 127 0 -7472.9621 0 -7472.9621 8522.0822 Loop time of 8.36257 on 1 procs for 127 steps with 1752 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 = -5806.09067628052 -7472.95534685011 -7472.9620597262 Force two-norm initial, final = 1674.3915 0.38318956 Force max component initial, final = 249.44419 0.10089925 Final line search alpha, max atom move = 1.0000000 0.10089925 Iterations, force evaluations = 127 231 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.3178 | 8.3178 | 8.3178 | 0.0 | 99.46 Neigh | 0.018283 | 0.018283 | 0.018283 | 0.0 | 0.22 Comm | 0.010305 | 0.010305 | 0.010305 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01621 | | | 0.19 Nlocal: 1752.00 ave 1752 max 1752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4849.00 ave 4849 max 4849 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: 102296.0 ave 102296 max 102296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102296 Ave neighs/atom = 58.388128 Neighbor list builds = 2 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 16 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 127 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.019 | 5.019 | 5.019 Mbytes Step Temp E_pair E_mol TotEng Press Volume 127 0 -7472.9621 0 -7472.9621 8522.0822 20571.561 134 0 -7473.568 0 -7473.568 -107.2569 20671.578 Loop time of 0.325166 on 1 procs for 7 steps with 1752 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 = -7472.9620597262 -7473.56761162067 -7473.56797636279 Force two-norm initial, final = 226.45145 3.2155610 Force max component initial, final = 208.36005 2.8376610 Final line search alpha, max atom move = 0.00021465293 0.00060911223 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32264 | 0.32264 | 0.32264 | 0.0 | 99.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035987 | 0.00035987 | 0.00035987 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002162 | | | 0.66 Nlocal: 1752.00 ave 1752 max 1752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5111.00 ave 5111 max 5111 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: 102304.0 ave 102304 max 102304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102304 Ave neighs/atom = 58.392694 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 16 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.157 | 5.157 | 5.157 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7473.568 0 -7473.568 -107.2569 Loop time of 1.663e-06 on 1 procs for 0 steps with 1752 atoms 180.4% 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 | | 1.663e-06 | | |100.00 Nlocal: 1752.00 ave 1752 max 1752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5111.00 ave 5111 max 5111 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: 102190.0 ave 102190 max 102190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102190 Ave neighs/atom = 58.327626 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 16 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.157 | 5.157 | 5.157 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 -7473.568 -7473.568 42.37077 69.626573 7.0070021 -107.2569 -107.2569 -219.8976 -3.0055248 -98.867582 2.2865183 1764.609 Loop time of 1.725e-06 on 1 procs for 0 steps with 1752 atoms 173.9% 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 | | 1.725e-06 | | |100.00 Nlocal: 1752.00 ave 1752 max 1752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5111.00 ave 5111 max 5111 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51095.0 ave 51095 max 51095 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 102190.0 ave 102190 max 102190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102190 Ave neighs/atom = 58.327626 Neighbor list builds = 0 Dangerous builds = 0 1752 -7473.56797636279 eV 2.28651830752865 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09