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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -40.901208 0.0000000) to (28.921521 40.901208 4.0498230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5367092 3.6089301 4.0498230 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -40.901208 0.0000000) to (28.921521 40.901208 4.0498230) create_atoms CPU = 0.003 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5367092 3.6089301 4.0498230 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -40.901208 0.0000000) to (28.921521 40.901208 4.0498230) create_atoms CPU = 0.002 seconds 410 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 ghost atom cutoff = 6 binsize = 3, bins = 10 28 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, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 816 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_321233176498_001#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 ghost atom cutoff = 6 binsize = 3, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.539 | 4.539 | 4.539 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3035.11 0 -3035.11 87088.284 57 0 -3482.2853 0 -3482.2853 8835.6637 Loop time of 5.10135 on 1 procs for 57 steps with 816 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 = -3035.10997495674 -3482.28209228438 -3482.28534074146 Force two-norm initial, final = 812.79402 0.17516187 Force max component initial, final = 258.55537 0.018923561 Final line search alpha, max atom move = 1.0000000 0.018923561 Iterations, force evaluations = 57 91 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0597 | 5.0597 | 5.0597 | 0.0 | 99.18 Neigh | 0.020196 | 0.020196 | 0.020196 | 0.0 | 0.40 Comm | 0.010691 | 0.010691 | 0.010691 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01075 | | | 0.21 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4464.00 ave 4464 max 4464 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: 52484.0 ave 52484 max 52484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52484 Ave neighs/atom = 64.318627 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.538 | 4.538 | 4.538 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -3482.2853 0 -3482.2853 8835.6637 9581.275 65 0 -3482.5771 0 -3482.5771 214.60611 9628.8402 Loop time of 0.538783 on 1 procs for 8 steps with 816 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 = -3482.28534074146 -3482.57669088814 -3482.57706639721 Force two-norm initial, final = 102.70469 2.4954122 Force max component initial, final = 90.885582 2.1635610 Final line search alpha, max atom move = 0.00053944499 0.0011671222 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53392 | 0.53392 | 0.53392 | 0.0 | 99.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010493 | 0.0010493 | 0.0010493 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003812 | | | 0.71 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4456.00 ave 4456 max 4456 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: 52420.0 ave 52420 max 52420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52420 Ave neighs/atom = 64.240196 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 ghost atom cutoff = 6 binsize = 3, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.676 | 4.676 | 4.676 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3482.5771 0 -3482.5771 214.60611 Loop time of 6.465e-06 on 1 procs for 0 steps with 816 atoms 201.1% 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 | | 6.465e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4456.00 ave 4456 max 4456 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: 52416.0 ave 52416 max 52416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52416 Ave neighs/atom = 64.235294 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 ghost atom cutoff = 6 binsize = 3, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.676 | 4.676 | 4.676 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 -3482.5771 -3482.5771 28.893581 82.384863 4.045062 214.60611 214.60611 142.32806 362.56579 138.92449 2.3132802 475.27951 Loop time of 7.327e-06 on 1 procs for 0 steps with 816 atoms 259.3% 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 | | 7.327e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4456.00 ave 4456 max 4456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26208.0 ave 26208 max 26208 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 52416.0 ave 52416 max 52416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52416 Ave neighs/atom = 64.235294 Neighbor list builds = 0 Dangerous builds = 0 816 -3482.57706639721 eV 2.31328022352647 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06