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 -44.534635 0.0000000) to (31.488269 44.534635 4.9479041) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8311609 6.0474383 4.9479041 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -44.534635 0.0000000) to (31.488269 44.534635 4.9479041) create_atoms CPU = 0.002 seconds 650 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8311609 6.0474383 4.9479041 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -44.534635 0.0000000) to (31.488269 44.534635 4.9479041) create_atoms CPU = 0.001 seconds 650 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 = 9 24 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 = 1288 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 = 9 24 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) = 5.472 | 5.472 | 5.472 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5212.1191 0 -5212.1191 34691.27 53 0 -5291.495 0 -5291.495 -6526.4808 Loop time of 1.07841 on 1 procs for 53 steps with 1288 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 = -5212.1190755591 -5291.4901043384 -5291.49504330323 Force two-norm initial, final = 148.50547 0.31053614 Force max component initial, final = 46.019418 0.062897171 Final line search alpha, max atom move = 0.87284230 0.054899311 Iterations, force evaluations = 53 97 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0534 | 1.0534 | 1.0534 | 0.0 | 97.68 Neigh | 0.012934 | 0.012934 | 0.012934 | 0.0 | 1.20 Comm | 0.0064219 | 0.0064219 | 0.0064219 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005676 | | | 0.53 Nlocal: 1288.00 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8214.00 ave 8214 max 8214 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: 224952.0 ave 224952 max 224952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224952 Ave neighs/atom = 174.65217 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 24 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 : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.472 | 5.472 | 5.472 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -5291.495 0 -5291.495 -6526.4808 13877.075 56 0 -5291.5515 0 -5291.5515 -4418.9693 13852.789 Loop time of 0.0555045 on 1 procs for 3 steps with 1288 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 = -5291.49504330323 -5291.54879744916 -5291.55149035102 Force two-norm initial, final = 47.755514 0.57033191 Force max component initial, final = 47.719684 0.32674533 Final line search alpha, max atom move = 0.00014159175 4.6264443e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.053988 | 0.053988 | 0.053988 | 0.0 | 97.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029355 | 0.00029355 | 0.00029355 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001223 | | | 2.20 Nlocal: 1288.00 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8205.00 ave 8205 max 8205 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: 224976.0 ave 224976 max 224976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224976 Ave neighs/atom = 174.67081 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 = 9 24 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) = 5.610 | 5.610 | 5.610 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5291.5515 0 -5291.5515 -4418.9693 Loop time of 1.653e-06 on 1 procs for 0 steps with 1288 atoms 121.0% 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 | | 1.653e-06 | | |100.00 Nlocal: 1288.00 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8213.00 ave 8213 max 8213 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: 225112.0 ave 225112 max 225112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225112 Ave neighs/atom = 174.77640 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 = 9 24 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) = 5.610 | 5.610 | 5.610 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 -5291.5515 -5291.5515 31.413608 89.069271 4.9509837 -4418.9693 -4418.9693 -37.700887 -13183.191 -36.016075 2.3080918 445.3112 Loop time of 1.538e-06 on 1 procs for 0 steps with 1288 atoms 195.1% 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 | | 1.538e-06 | | |100.00 Nlocal: 1288.00 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8213.00 ave 8213 max 8213 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112556.0 ave 112556 max 112556 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 225112.0 ave 225112 max 225112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225112 Ave neighs/atom = 174.77640 Neighbor list builds = 0 Dangerous builds = 0 1288 -5291.55149035102 eV 2.30809181336228 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01