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 = 3.1582519 3.1582519 3.1582519 Created orthogonal box = (0.0000000 -49.333472 0.0000000) to (24.666736 49.333472 3.1582519) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4481000 4.4481000 3.1582519 Created 244 atoms using lattice units in orthogonal box = (0.0000000 -49.333472 0.0000000) to (24.666736 49.333472 3.1582519) create_atoms CPU = 0.002 seconds 244 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4481000 4.4481000 3.1582519 Created 245 atoms using lattice units in orthogonal box = (0.0000000 -49.333472 0.0000000) to (24.666736 49.333472 3.1582519) create_atoms CPU = 0.001 seconds 245 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, 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 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 486 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_228581001644_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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 6 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.497 | 4.497 | 4.497 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1702.4552 0 -1702.4552 282827.47 115 0 -3090.5257 0 -3090.5257 -1315.6637 Loop time of 1.83704 on 1 procs for 115 steps with 486 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 = -1702.45523591256 -3090.52283923652 -3090.52568683268 Force two-norm initial, final = 3343.4360 0.31741978 Force max component initial, final = 1603.5165 0.062881092 Final line search alpha, max atom move = 0.89124834 0.056042669 Iterations, force evaluations = 115 209 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7667 | 1.7667 | 1.7667 | 0.0 | 96.17 Neigh | 0.023441 | 0.023441 | 0.023441 | 0.0 | 1.28 Comm | 0.028541 | 0.028541 | 0.028541 | 0.0 | 1.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01834 | | | 1.00 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5817.00 ave 5817 max 5817 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: 79504.0 ave 79504 max 79504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79504 Ave neighs/atom = 163.58848 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 6 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 115 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.498 | 4.498 | 4.498 Mbytes Step Temp E_pair E_mol TotEng Press Volume 115 0 -3090.5257 0 -3090.5257 -1315.6637 7686.5267 164 0 -3097.3658 0 -3097.3658 -478.38253 7678.1217 Loop time of 0.464689 on 1 procs for 49 steps with 486 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 = -3090.52568683268 -3097.36461805882 -3097.36575282426 Force two-norm initial, final = 191.22284 5.4435332 Force max component initial, final = 157.66194 3.0950813 Final line search alpha, max atom move = 0.00021606283 0.00066873202 Iterations, force evaluations = 49 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41619 | 0.41619 | 0.41619 | 0.0 | 89.56 Neigh | 0.021739 | 0.021739 | 0.021739 | 0.0 | 4.68 Comm | 0.0066515 | 0.0066515 | 0.0066515 | 0.0 | 1.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02011 | | | 4.33 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5745.00 ave 5745 max 5745 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: 78512.0 ave 78512 max 78512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78512 Ave neighs/atom = 161.54733 Neighbor list builds = 2 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 6 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.635 | 4.635 | 4.635 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3097.3658 0 -3097.3658 -478.38253 Loop time of 6.545e-06 on 1 procs for 0 steps with 486 atoms 183.3% 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 | | 6.545e-06 | | |100.00 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5745.00 ave 5745 max 5745 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: 78392.0 ave 78392 max 78392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78392 Ave neighs/atom = 161.30041 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 6 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.635 | 4.635 | 4.635 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 -3097.3658 -3097.3658 25.294117 100.96146 3.0066289 -478.38253 -478.38253 -410.22405 -410.08584 -614.8377 2.6496206 153.60229 Loop time of 6.685e-06 on 1 procs for 0 steps with 486 atoms 224.4% 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 | | 6.685e-06 | | |100.00 Nlocal: 486.000 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5745.00 ave 5745 max 5745 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39196.0 ave 39196 max 39196 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 78392.0 ave 78392 max 78392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78392 Ave neighs/atom = 161.30041 Neighbor list builds = 0 Dangerous builds = 0 486 -3097.36575282426 eV 2.64962056431762 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02