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 = 3.1435003 3.1435003 3.1435003 Created orthogonal box = (0.0000000 -40.744420 0.0000000) to (23.523802 40.744420 5.4447022) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0408147 4.8505262 5.4447022 Created 336 atoms using lattice units in orthogonal box = (0.0000000 -40.744420 0.0000000) to (23.523802 40.744420 5.4447022) create_atoms CPU = 0.003 seconds 336 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0408147 4.8505262 5.4447022 Created 339 atoms using lattice units in orthogonal box = (0.0000000 -40.744420 0.0000000) to (23.523802 40.744420 5.4447022) create_atoms CPU = 0.002 seconds 339 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 17 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 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 675 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_534363225491_004#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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.969 | 4.969 | 4.969 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3068.9373 0 -3068.9373 244157.45 313 0 -4527.918 0 -4527.918 20062.561 Loop time of 13.9206 on 1 procs for 313 steps with 675 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 = -3068.93725269151 -4527.91386555946 -4527.91798692465 Force two-norm initial, final = 3305.9121 0.38322757 Force max component initial, final = 1017.3494 0.081730062 Final line search alpha, max atom move = 0.65565897 0.053587049 Iterations, force evaluations = 313 605 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.47 | 13.47 | 13.47 | 0.0 | 96.76 Neigh | 0.29342 | 0.29342 | 0.29342 | 0.0 | 2.11 Comm | 0.093623 | 0.093623 | 0.093623 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06378 | | | 0.46 Nlocal: 675.000 ave 675 max 675 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6697.00 ave 6697 max 6697 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: 186926.0 ave 186926 max 186926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186926 Ave neighs/atom = 276.92741 Neighbor list builds = 12 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 313 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.969 | 4.969 | 4.969 Mbytes Step Temp E_pair E_mol TotEng Press Volume 313 0 -4527.918 0 -4527.918 20062.561 10437.099 343 0 -4535.9025 0 -4535.9025 -385.58415 10499.564 Loop time of 0.813118 on 1 procs for 30 steps with 675 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 = -4527.9179869246 -4535.89946876298 -4535.90253762391 Force two-norm initial, final = 701.67885 6.9850512 Force max component initial, final = 667.58542 5.1779685 Final line search alpha, max atom move = 7.1762772e-05 0.00037158538 Iterations, force evaluations = 30 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.79156 | 0.79156 | 0.79156 | 0.0 | 97.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0048829 | 0.0048829 | 0.0048829 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01668 | | | 2.05 Nlocal: 675.000 ave 675 max 675 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6581.00 ave 6581 max 6581 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: 187032.0 ave 187032 max 187032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187032 Ave neighs/atom = 277.08444 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.106 | 5.106 | 5.106 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4535.9025 0 -4535.9025 -385.58415 Loop time of 6.515e-06 on 1 procs for 0 steps with 675 atoms 199.5% 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 | | 6.515e-06 | | |100.00 Nlocal: 675.000 ave 675 max 675 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6471.00 ave 6471 max 6471 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: 184906.0 ave 184906 max 184906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184906 Ave neighs/atom = 273.93481 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 5 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.106 | 5.106 | 5.106 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 -4535.9025 -4535.9025 23.429459 80.61811 5.5587405 -385.58415 -385.58415 -400.09492 -781.68712 25.029603 2.5405796 4057.6943 Loop time of 6.977e-06 on 1 procs for 0 steps with 675 atoms 229.3% 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 | | 6.977e-06 | | |100.00 Nlocal: 675.000 ave 675 max 675 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6471.00 ave 6471 max 6471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 92453.0 ave 92453 max 92453 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 184906.0 ave 184906 max 184906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184906 Ave neighs/atom = 273.93481 Neighbor list builds = 0 Dangerous builds = 0 675 -4535.90253762391 eV 2.54057961508643 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15