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 = 4.0310361 4.0310361 4.0310361 Created orthogonal box = (0.0000000 -47.695862 0.0000000) to (58.415263 47.695862 9.8739816) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6760300 6.1323252 6.5826544 Created 1666 atoms using lattice units in orthogonal box = (0.0000000 -47.695862 0.0000000) to (58.415263 47.695862 9.8739816) create_atoms CPU = 0.003 seconds 1666 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6760300 6.1323252 6.5826544 Created 1690 atoms using lattice units in orthogonal box = (0.0000000 -47.695862 0.0000000) to (58.415263 47.695862 9.8739816) create_atoms CPU = 0.002 seconds 1690 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 16 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 3352 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_699137396381_005#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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 16 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.501 | 6.501 | 6.501 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10980.016 0 -10980.016 6080.4857 111 0 -11227.578 0 -11227.578 2153.0509 Loop time of 3.90046 on 1 procs for 111 steps with 3352 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 = -10980.0161046286 -11227.5671116043 -11227.5782240916 Force two-norm initial, final = 65.980908 0.32574791 Force max component initial, final = 6.8061195 0.086993150 Final line search alpha, max atom move = 0.98515477 0.085701717 Iterations, force evaluations = 111 171 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6105 | 3.6105 | 3.6105 | 0.0 | 92.57 Neigh | 0.23333 | 0.23333 | 0.23333 | 0.0 | 5.98 Comm | 0.021752 | 0.021752 | 0.021752 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03491 | | | 0.90 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9261.00 ave 9261 max 9261 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: 439938.0 ave 439938 max 439938 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 439938 Ave neighs/atom = 131.24642 Neighbor list builds = 7 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 16 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 111 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.500 | 6.500 | 6.500 Mbytes Step Temp E_pair E_mol TotEng Press Volume 111 0 -11227.578 0 -11227.578 2153.0509 55021.11 115 0 -11227.814 0 -11227.814 43.737431 55177.752 Loop time of 0.103258 on 1 procs for 4 steps with 3352 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 = -11227.5782240916 -11227.8043644221 -11227.814372523 Force two-norm initial, final = 147.18762 2.6495515 Force max component initial, final = 130.81823 1.5780508 Final line search alpha, max atom move = 6.4247502e-05 0.00010138582 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10018 | 0.10018 | 0.10018 | 0.0 | 97.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042601 | 0.00042601 | 0.00042601 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002649 | | | 2.57 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9261.00 ave 9261 max 9261 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: 440138.0 ave 440138 max 440138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 440138 Ave neighs/atom = 131.30609 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 16 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.638 | 6.638 | 6.638 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11227.814 0 -11227.814 43.737431 Loop time of 2.592e-06 on 1 procs for 0 steps with 3352 atoms 192.9% 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 | | 2.592e-06 | | |100.00 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9269.00 ave 9269 max 9269 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: 439908.0 ave 439908 max 439908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 439908 Ave neighs/atom = 131.23747 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 16 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.638 | 6.638 | 6.638 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 -11227.814 -11227.814 58.427554 95.750512 9.8629126 43.737431 43.737431 41.311672 45.993637 43.906985 2.5276467 2539.4162 Loop time of 2.588e-06 on 1 procs for 0 steps with 3352 atoms 231.8% 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 | | 2.588e-06 | | |100.00 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9269.00 ave 9269 max 9269 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 219954.0 ave 219954 max 219954 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 439908.0 ave 439908 max 439908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 439908 Ave neighs/atom = 131.23747 Neighbor list builds = 0 Dangerous builds = 0 3352 -11227.814372523 eV 2.52764672975809 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04