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 -42.378258 0.0000000) to (34.601703 42.378258 7.0144992) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2659634 4.0636686 4.6763328 Created 876 atoms using lattice units in orthogonal box = (0.0000000 -42.378258 0.0000000) to (34.601703 42.378258 7.0144992) create_atoms CPU = 0.001 seconds 876 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2659634 4.0636686 4.6763328 Created 878 atoms using lattice units in orthogonal box = (0.0000000 -42.378258 0.0000000) to (34.601703 42.378258 7.0144992) create_atoms CPU = 0.001 seconds 878 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 12 29 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1754 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_321233176498_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 12 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.062 | 5.062 | 5.062 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6798.3501 0 -6798.3501 72745.403 69 0 -7486.845 0 -7486.845 10383.433 Loop time of 5.77645 on 1 procs for 69 steps with 1754 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 = -6798.3500813958 -7486.83784167939 -7486.84501171459 Force two-norm initial, final = 883.61032 0.28114514 Force max component initial, final = 206.76336 0.049628575 Final line search alpha, max atom move = 1.0000000 0.049628575 Iterations, force evaluations = 69 116 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.722 | 5.722 | 5.722 | 0.0 | 99.06 Neigh | 0.033224 | 0.033224 | 0.033224 | 0.0 | 0.58 Comm | 0.0084075 | 0.0084075 | 0.0084075 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01281 | | | 0.22 Nlocal: 1754.00 ave 1754 max 1754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5450.00 ave 5450 max 5450 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: 113228.0 ave 113228 max 113228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113228 Ave neighs/atom = 64.554162 Neighbor list builds = 3 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 12 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.062 | 5.062 | 5.062 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -7486.845 0 -7486.845 10383.433 20571.561 78 0 -7487.937 0 -7487.937 -97.821851 20694.806 Loop time of 0.534433 on 1 procs for 9 steps with 1754 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7486.8450117146 -7487.93350844411 -7487.93695146462 Force two-norm initial, final = 287.54256 2.3085229 Force max component initial, final = 270.31495 1.4805452 Final line search alpha, max atom move = 0.00011462480 0.00016970720 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53011 | 0.53011 | 0.53011 | 0.0 | 99.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00054567 | 0.00054567 | 0.00054567 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003779 | | | 0.71 Nlocal: 1754.00 ave 1754 max 1754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5439.00 ave 5439 max 5439 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: 113184.0 ave 113184 max 113184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113184 Ave neighs/atom = 64.529076 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.200 | 5.200 | 5.200 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7487.937 0 -7487.937 -97.821851 Loop time of 2.477e-06 on 1 procs for 0 steps with 1754 atoms 161.5% 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 | | 2.477e-06 | | |100.00 Nlocal: 1754.00 ave 1754 max 1754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5437.00 ave 5437 max 5437 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: 113064.0 ave 113064 max 113064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113064 Ave neighs/atom = 64.460661 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.200 | 5.200 | 5.200 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 -7487.937 -7487.937 34.499865 85.471417 7.0181568 -97.821851 -97.821851 -114.28535 -98.731476 -80.448722 2.2779226 1633.6568 Loop time of 2.55e-06 on 1 procs for 0 steps with 1754 atoms 235.3% 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 | | 2.55e-06 | | |100.00 Nlocal: 1754.00 ave 1754 max 1754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5437.00 ave 5437 max 5437 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56532.0 ave 56532 max 56532 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 113064.0 ave 113064 max 113064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113064 Ave neighs/atom = 64.460661 Neighbor list builds = 0 Dangerous builds = 0 1754 -7487.93695146462 eV 2.27792261671863 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06