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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -46.362241 0.0000000) to (23.179311 46.362241 3.6200001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0881413 5.0881413 3.6200001 Created 330 atoms using lattice units in orthogonal box = (0.0000000 -46.362241 0.0000000) to (23.179311 46.362241 3.6200001) create_atoms CPU = 0.001 seconds 330 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0881413 5.0881413 3.6200001 Created 330 atoms using lattice units in orthogonal box = (0.0000000 -46.362241 0.0000000) to (23.179311 46.362241 3.6200001) create_atoms CPU = 0.001 seconds 330 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 24 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 654 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.933 | 4.933 | 4.933 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2274.9089 0 -2274.9089 11751.528 66 0 -2309.2411 0 -2309.2411 -240.36399 Loop time of 0.792484 on 1 procs for 66 steps with 654 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 = -2274.90893299874 -2309.23878613625 -2309.24108439604 Force two-norm initial, final = 25.574590 0.16834991 Force max component initial, final = 7.1411583 0.055249917 Final line search alpha, max atom move = 0.72950365 0.040305016 Iterations, force evaluations = 66 118 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.76722 | 0.76722 | 0.76722 | 0.0 | 96.81 Neigh | 0.014282 | 0.014282 | 0.014282 | 0.0 | 1.80 Comm | 0.0062355 | 0.0062355 | 0.0062355 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004748 | | | 0.60 Nlocal: 654.000 ave 654 max 654 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5721.00 ave 5721 max 5721 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: 113464.0 ave 113464 max 113464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113464 Ave neighs/atom = 173.49235 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.933 | 4.933 | 4.933 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -2309.2411 0 -2309.2411 -240.36399 7780.4285 67 0 -2309.2424 0 -2309.2424 570.97921 7775.7351 Loop time of 0.0205548 on 1 procs for 1 steps with 654 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 = -2309.24108439604 -2309.24108439604 -2309.24242635467 Force two-norm initial, final = 5.6203324 2.5764889 Force max component initial, final = 5.3392043 2.4478548 Final line search alpha, max atom move = 0.00018729383 0.00045846809 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.019884 | 0.019884 | 0.019884 | 0.0 | 96.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000133 | 0.000133 | 0.000133 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005382 | | | 2.62 Nlocal: 654.000 ave 654 max 654 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5731.00 ave 5731 max 5731 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: 113468.0 ave 113468 max 113468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113468 Ave neighs/atom = 173.49847 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.071 | 5.071 | 5.071 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2309.2424 0 -2309.2424 570.97921 Loop time of 1.993e-06 on 1 procs for 0 steps with 654 atoms 150.5% 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 | | 1.993e-06 | | |100.00 Nlocal: 654.000 ave 654 max 654 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5731.00 ave 5731 max 5731 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: 113492.0 ave 113492 max 113492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113492 Ave neighs/atom = 173.53517 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.071 | 5.071 | 5.071 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 -2309.2424 -2309.2424 23.175863 92.724482 3.6183546 570.97921 570.97921 504.30114 1370.4524 -161.81594 2.3151416 152.18401 Loop time of 2.129e-06 on 1 procs for 0 steps with 654 atoms 234.9% 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 | | 2.129e-06 | | |100.00 Nlocal: 654.000 ave 654 max 654 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5731.00 ave 5731 max 5731 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56746.0 ave 56746 max 56746 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 113492.0 ave 113492 max 113492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113492 Ave neighs/atom = 173.53517 Neighbor list builds = 0 Dangerous builds = 0 654 -2309.24242635467 eV 2.31514161540567 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01