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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -51.865308 0.0000000) to (25.932654 51.865308 4.0500001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6925338 5.6925338 4.0500001 Created 327 atoms using lattice units in orthogonal box = (0.0000000 -51.865308 0.0000000) to (25.932654 51.865308 4.0500001) create_atoms CPU = 0.002 seconds 327 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6925338 5.6925338 4.0500001 Created 329 atoms using lattice units in orthogonal box = (0.0000000 -51.865308 0.0000000) to (25.932654 51.865308 4.0500001) create_atoms CPU = 0.001 seconds 329 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 7 25 1 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 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 656 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_826591359508_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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 4.549 | 4.549 | 4.549 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2169.6985 0 -2169.6985 4554.1502 63 0 -2199.4697 0 -2199.4697 2171.8275 Loop time of 1.59524 on 1 procs for 63 steps with 656 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 = -2169.69853925071 -2199.46803260905 -2199.46974899705 Force two-norm initial, final = 17.874437 0.11489414 Force max component initial, final = 3.2954689 0.038802121 Final line search alpha, max atom move = 1.0000000 0.038802121 Iterations, force evaluations = 63 111 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.54 | 1.54 | 1.54 | 0.0 | 96.54 Neigh | 0.026388 | 0.026388 | 0.026388 | 0.0 | 1.65 Comm | 0.016993 | 0.016993 | 0.016993 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01189 | | | 0.75 Nlocal: 656.000 ave 656 max 656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5995.00 ave 5995 max 5995 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: 93826.0 ave 93826 max 93826 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93826 Ave neighs/atom = 143.02744 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.554 | 4.554 | 4.554 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -2199.4697 0 -2199.4697 2171.8275 10894.542 69 0 -2199.5611 0 -2199.5611 -60.385677 10924.808 Loop time of 0.113071 on 1 procs for 6 steps with 656 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 = -2199.46974899705 -2199.56009984852 -2199.5611120767 Force two-norm initial, final = 35.861693 0.77792575 Force max component initial, final = 35.081625 0.61818812 Final line search alpha, max atom move = 0.00039417956 0.00024367713 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10858 | 0.10858 | 0.10858 | 0.0 | 96.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010945 | 0.0010945 | 0.0010945 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003393 | | | 3.00 Nlocal: 656.000 ave 656 max 656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6290.00 ave 6290 max 6290 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: 93380.0 ave 93380 max 93380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93380 Ave neighs/atom = 142.34756 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 7 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 4.692 | 4.692 | 4.692 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2199.5611 0 -2199.5611 -60.385677 Loop time of 6.304e-06 on 1 procs for 0 steps with 656 atoms 206.2% 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 | | 6.304e-06 | | |100.00 Nlocal: 656.000 ave 656 max 656 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: 93174.0 ave 93174 max 93174 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93174 Ave neighs/atom = 142.03354 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 7 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 4.692 | 4.692 | 4.692 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 -2199.5611 -2199.5611 25.88796 104.31077 4.0456363 -60.385677 -60.385677 -33.851108 -56.743298 -90.562625 2.583852 200.84778 Loop time of 1.0143e-05 on 1 procs for 0 steps with 656 atoms 167.6% 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 | | 1.014e-05 | | |100.00 Nlocal: 656.000 ave 656 max 656 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: 46587.0 ave 46587 max 46587 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 93174.0 ave 93174 max 93174 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93174 Ave neighs/atom = 142.03354 Neighbor list builds = 0 Dangerous builds = 0 656 -2199.5611120767 eV 2.58385203303009 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02