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 = 3.5200244 3.5200244 3.5200244 Created orthogonal box = (0.0000000 -41.653010 0.0000000) to (51.009999 41.653010 8.6222635) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8297142 5.3549344 5.7481757 Created 1686 atoms using lattice units in orthogonal box = (0.0000000 -41.653010 0.0000000) to (51.009999 41.653010 8.6222635) create_atoms CPU = 0.007 seconds 1686 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8297142 5.3549344 5.7481757 Created 1686 atoms using lattice units in orthogonal box = (0.0000000 -41.653010 0.0000000) to (51.009999 41.653010 8.6222635) create_atoms CPU = 0.006 seconds 1686 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 13 20 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 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 60 atoms, new total = 3312 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_532072268679_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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 7.874 | 7.874 | 7.874 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14566.285 0 -14566.285 6813.2376 49 0 -14669.232 0 -14669.232 -17611.634 Loop time of 6.3928 on 1 procs for 49 steps with 3312 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 = -14566.2851151114 -14669.2205877696 -14669.2315639764 Force two-norm initial, final = 80.532008 0.32599080 Force max component initial, final = 6.8423401 0.023273872 Final line search alpha, max atom move = 1.0000000 0.023273872 Iterations, force evaluations = 49 87 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.2464 | 6.2464 | 6.2464 | 0.0 | 97.71 Neigh | 0.093547 | 0.093547 | 0.093547 | 0.0 | 1.46 Comm | 0.024156 | 0.024156 | 0.024156 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02871 | | | 0.45 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12211.0 ave 12211 max 12211 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: 734866.0 ave 734866 max 734866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 734866 Ave neighs/atom = 221.87983 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.887 | 7.887 | 7.887 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -14669.232 0 -14669.232 -17611.634 36639.791 54 0 -14670.34 0 -14670.34 -5739.7589 36389.457 Loop time of 0.565618 on 1 procs for 5 steps with 3312 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 = -14669.2315639765 -14670.3398266101 -14670.3398721343 Force two-norm initial, final = 455.80551 0.42082035 Force max component initial, final = 323.30194 0.077614373 Final line search alpha, max atom move = 0.00067271036 5.2211993e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.55492 | 0.55492 | 0.55492 | 0.0 | 98.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020819 | 0.0020819 | 0.0020819 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008621 | | | 1.52 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12582.0 ave 12582 max 12582 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: 736200.0 ave 736200 max 736200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 736200 Ave neighs/atom = 222.28261 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 13 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 8.025 | 8.025 | 8.025 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14670.34 0 -14670.34 -5739.7589 Loop time of 6.465e-06 on 1 procs for 0 steps with 3312 atoms 185.6% 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 | | 6.465e-06 | | |100.00 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12582.0 ave 12582 max 12582 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: 736750.0 ave 736750 max 736750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 736750 Ave neighs/atom = 222.44867 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 13 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 8.025 | 8.025 | 8.025 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 -14670.34 -14670.34 50.839524 83.30602 8.5920681 -5739.7589 -5739.7589 -3.4058311 -17217.464 1.5935238 2.3253342 1595.1135 Loop time of 6.946e-06 on 1 procs for 0 steps with 3312 atoms 331.1% 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 | | 6.946e-06 | | |100.00 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12582.0 ave 12582 max 12582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 368375.0 ave 368375 max 368375 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 736750.0 ave 736750 max 736750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 736750 Ave neighs/atom = 222.44867 Neighbor list builds = 0 Dangerous builds = 0 3312 -14580.0501093727 eV 2.32533423938342 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08