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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -42.677732 0.0000000) to (34.846222 42.677732 8.6222039) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9780317 4.9355200 5.7481359 Created 1175 atoms using lattice units in orthogonal box = (0.0000000 -42.677732 0.0000000) to (34.846222 42.677732 8.6222039) create_atoms CPU = 0.002 seconds 1175 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9780317 4.9355200 5.7481359 Created 1183 atoms using lattice units in orthogonal box = (0.0000000 -42.677732 0.0000000) to (34.846222 42.677732 8.6222039) create_atoms CPU = 0.001 seconds 1183 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 11 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 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 2336 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_800536961967_003#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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 5.956 | 5.956 | 5.956 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10207.879 0 -10207.879 5855.9611 66 0 -10350.289 0 -10350.289 3321.7568 Loop time of 1.6248 on 1 procs for 66 steps with 2336 atoms 98.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10207.8785243569 -10350.2807817194 -10350.2891551127 Force two-norm initial, final = 66.785485 0.30291317 Force max component initial, final = 9.4188499 0.064694061 Final line search alpha, max atom move = 1.0000000 0.064694061 Iterations, force evaluations = 66 118 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5576 | 1.5576 | 1.5576 | 0.0 | 95.87 Neigh | 0.043034 | 0.043034 | 0.043034 | 0.0 | 2.65 Comm | 0.0093379 | 0.0093379 | 0.0093379 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01478 | | | 0.91 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7386.00 ave 7386 max 7386 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: 308156.0 ave 308156 max 308156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 308156 Ave neighs/atom = 131.91610 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.957 | 5.957 | 5.957 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -10350.289 0 -10350.289 3321.7568 25645.154 70 0 -10350.481 0 -10350.481 -138.83636 25695.908 Loop time of 0.0791 on 1 procs for 4 steps with 2336 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 = -10350.2891551127 -10350.4793200964 -10350.4808685818 Force two-norm initial, final = 127.75250 6.0866227 Force max component initial, final = 122.25008 5.9743556 Final line search alpha, max atom move = 8.4217400e-05 0.00050314470 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.076316 | 0.076316 | 0.076316 | 0.0 | 96.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038456 | 0.00038456 | 0.00038456 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002399 | | | 3.03 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7580.00 ave 7580 max 7580 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: 307872.0 ave 307872 max 307872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 307872 Ave neighs/atom = 131.79452 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 11 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 6.096 | 6.096 | 6.096 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10350.481 0 -10350.481 -138.83636 Loop time of 2.175e-06 on 1 procs for 0 steps with 2336 atoms 137.9% 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 | | 2.175e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7644.00 ave 7644 max 7644 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: 307744.0 ave 307744 max 307744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 307744 Ave neighs/atom = 131.73973 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 11 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 6.096 | 6.096 | 6.096 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 -10350.481 -10350.481 34.838513 85.627953 8.6136811 -138.83636 -138.83636 -372.42719 20.768128 -64.850024 2.2349454 1415.167 Loop time of 2.869e-06 on 1 procs for 0 steps with 2336 atoms 278.8% 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 | | 2.869e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7644.00 ave 7644 max 7644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 153872.0 ave 153872 max 153872 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 307744.0 ave 307744 max 307744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 307744 Ave neighs/atom = 131.73973 Neighbor list builds = 0 Dangerous builds = 0 2336 -10350.4808685818 eV 2.23494537272189 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02