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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -43.251492 0.0000000) to (35.314696 43.251492 8.7381210) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0449565 5.0018733 5.8254140 Created 1174 atoms using lattice units in orthogonal box = (0.0000000 -43.251492 0.0000000) to (35.314696 43.251492 8.7381210) create_atoms CPU = 0.002 seconds 1174 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0449565 5.0018733 5.8254140 Created 1182 atoms using lattice units in orthogonal box = (0.0000000 -43.251492 0.0000000) to (35.314696 43.251492 8.7381210) create_atoms CPU = 0.001 seconds 1182 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 31 4 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2352 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 31 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.090 | 5.090 | 5.090 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8574.4955 0 -8574.4955 98263.594 77 0 -9905.3249 0 -9905.3249 46141.253 Loop time of 8.26417 on 1 procs for 77 steps with 2352 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8574.49552964855 -9905.31563542646 -9905.32490527878 Force two-norm initial, final = 1288.7931 0.44057545 Force max component initial, final = 172.44388 0.12520238 Final line search alpha, max atom move = 0.73490618 0.092012001 Iterations, force evaluations = 77 137 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.2147 | 8.2147 | 8.2147 | 0.0 | 99.40 Neigh | 0.024975 | 0.024975 | 0.024975 | 0.0 | 0.30 Comm | 0.0085335 | 0.0085335 | 0.0085335 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01597 | | | 0.19 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5507.00 ave 5507 max 5507 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: 137094.0 ave 137094 max 137094 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137094 Ave neighs/atom = 58.288265 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 31 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.089 | 5.089 | 5.089 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -9905.3249 0 -9905.3249 46141.253 26693.444 85 0 -9910.6746 0 -9910.6746 450.83048 27042.035 Loop time of 0.646327 on 1 procs for 8 steps with 2352 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 = -9905.32490527876 -9910.66721124263 -9910.67462187675 Force two-norm initial, final = 1349.4526 21.905012 Force max component initial, final = 875.11315 16.430746 Final line search alpha, max atom move = 2.7179952e-05 0.00044658687 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.64242 | 0.64242 | 0.64242 | 0.0 | 99.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047458 | 0.00047458 | 0.00047458 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003437 | | | 0.53 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5493.00 ave 5493 max 5493 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: 136526.0 ave 136526 max 136526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136526 Ave neighs/atom = 58.046769 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 32 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.228 | 5.228 | 5.228 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9910.6746 0 -9910.6746 450.83048 Loop time of 2.128e-06 on 1 procs for 0 steps with 2352 atoms 141.0% 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 | | 2.128e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5493.00 ave 5493 max 5493 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: 133120.0 ave 133120 max 133120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133120 Ave neighs/atom = 56.598639 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 32 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.228 | 5.228 | 5.228 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 -9910.6746 -9910.6746 35.351337 87.012271 8.7912986 450.83048 450.83048 -384.49231 757.57669 979.40705 2.1935524 2059.1951 Loop time of 2.169e-06 on 1 procs for 0 steps with 2352 atoms 138.3% 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 | | 2.169e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5493.00 ave 5493 max 5493 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 66560.0 ave 66560 max 66560 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 133120.0 ave 133120 max 133120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133120 Ave neighs/atom = 56.598639 Neighbor list builds = 0 Dangerous builds = 0 2352 -9910.67462187676 eV 2.19355244978274 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09