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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -35.955885 0.0000000) to (12.711235 35.955885 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2340380 5.2871768 4.3599177 Created 137 atoms using lattice units in orthogonal box = (0.0000000 -35.955885 0.0000000) to (12.711235 35.955885 4.3599177) create_atoms CPU = 0.000 seconds 137 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2340380 5.2871768 4.3599177 Created 137 atoms using lattice units in orthogonal box = (0.0000000 -35.955885 0.0000000) to (12.711235 35.955885 4.3599177) create_atoms CPU = 0.000 seconds 137 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 22 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 274 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.799 | 4.799 | 4.799 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1567.66 0 -1567.66 207020.61 178 0 -1775.1193 0 -1775.1193 21223.864 Loop time of 10.0039 on 1 procs for 178 steps with 274 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 = -1567.65996080004 -1775.11755172079 -1775.11925413961 Force two-norm initial, final = 409.90009 0.19703094 Force max component initial, final = 97.628704 0.057884981 Final line search alpha, max atom move = 1.0000000 0.057884981 Iterations, force evaluations = 178 346 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.9782 | 9.9782 | 9.9782 | 0.0 | 99.74 Neigh | 0.016063 | 0.016063 | 0.016063 | 0.0 | 0.16 Comm | 0.0070959 | 0.0070959 | 0.0070959 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002468 | | | 0.02 Nlocal: 274.000 ave 274 max 274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2498.00 ave 2498 max 2498 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: 21560.0 ave 21560 max 21560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21560 Ave neighs/atom = 78.686131 Neighbor list builds = 3 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 178 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.801 | 4.801 | 4.801 Mbytes Step Temp E_pair E_mol TotEng Press Volume 178 0 -1775.1193 0 -1775.1193 21223.864 3985.346 187 0 -1775.4305 0 -1775.4305 5802.4581 4013.0781 Loop time of 0.356323 on 1 procs for 9 steps with 274 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 = -1775.11925413961 -1775.43034938928 -1775.43046634996 Force two-norm initial, final = 84.210503 1.3007863 Force max component initial, final = 82.133153 0.77730914 Final line search alpha, max atom move = 0.0015164642 0.0011787615 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35569 | 0.35569 | 0.35569 | 0.0 | 99.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000151 | 0.000151 | 0.000151 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004766 | | | 0.13 Nlocal: 274.000 ave 274 max 274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2722.00 ave 2722 max 2722 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: 21402.0 ave 21402 max 21402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21402 Ave neighs/atom = 78.109489 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.939 | 4.939 | 4.939 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1775.4305 0 -1775.4305 5802.4581 Loop time of 1.9e-06 on 1 procs for 0 steps with 274 atoms 157.9% 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 | | 1.9e-06 | | |100.00 Nlocal: 274.000 ave 274 max 274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2704.00 ave 2704 max 2704 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: 20998.0 ave 20998 max 20998 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20998 Ave neighs/atom = 76.635036 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.939 | 4.939 | 4.939 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 -1775.4305 -1775.4305 12.81074 71.911771 4.3561558 5802.4581 5802.4581 229.53001 16867.78 310.06421 2.4878722 929.37989 Loop time of 2.1e-06 on 1 procs for 0 steps with 274 atoms 142.9% 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 | | 2.1e-06 | | |100.00 Nlocal: 274.000 ave 274 max 274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2704.00 ave 2704 max 2704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 10499.0 ave 10499 max 10499 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 20998.0 ave 20998 max 20998 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20998 Ave neighs/atom = 76.635036 Neighbor list builds = 0 Dangerous builds = 0 274 -1775.43046634996 eV 2.48787217933132 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10