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 = 4.1288715 4.1288715 4.1288715 Created orthogonal box = (0.0000000 -42.106392 0.0000000) to (21.053196 42.106392 4.1288715) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8584299 4.8584299 4.1288715 Created 208 atoms using lattice units in orthogonal box = (0.0000000 -42.106392 0.0000000) to (21.053196 42.106392 4.1288715) create_atoms CPU = 0.001 seconds 208 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8584299 4.8584299 4.1288715 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -42.106392 0.0000000) to (21.053196 42.106392 4.1288715) create_atoms CPU = 0.000 seconds 210 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 5 19 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 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 416 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_122703700223_003#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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 4.482 | 4.482 | 4.482 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1445.0811 0 -1445.0811 26297.038 45 0 -1540.1483 0 -1540.1483 3262.2209 Loop time of 0.573687 on 1 procs for 45 steps with 416 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1445.0811443018 -1540.14742654418 -1540.14831736753 Force two-norm initial, final = 188.79364 0.066895221 Force max component initial, final = 60.277614 0.011400476 Final line search alpha, max atom move = 1.0000000 0.011400476 Iterations, force evaluations = 45 84 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.56284 | 0.56284 | 0.56284 | 0.0 | 98.11 Neigh | 0.0044942 | 0.0044942 | 0.0044942 | 0.0 | 0.78 Comm | 0.0035029 | 0.0035029 | 0.0035029 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002847 | | | 0.50 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4324.00 ave 4324 max 4324 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: 76188.0 ave 76188 max 76188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76188 Ave neighs/atom = 183.14423 Neighbor list builds = 1 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 45 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.482 | 4.482 | 4.482 Mbytes Step Temp E_pair E_mol TotEng Press Volume 45 0 -1540.1483 0 -1540.1483 3262.2209 7320.2755 50 0 -1540.1925 0 -1540.1925 212.25923 7341.9772 Loop time of 0.0476565 on 1 procs for 5 steps with 416 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 = -1540.14831736752 -1540.19124326531 -1540.19247842039 Force two-norm initial, final = 27.324138 1.9329143 Force max component initial, final = 21.942217 1.7400455 Final line search alpha, max atom move = 0.00025751016 0.00044807940 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.046233 | 0.046233 | 0.046233 | 0.0 | 97.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025664 | 0.00025664 | 0.00025664 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001167 | | | 2.45 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4349.00 ave 4349 max 4349 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: 74996.0 ave 74996 max 74996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74996 Ave neighs/atom = 180.27885 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 5 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 4.620 | 4.620 | 4.620 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1540.1925 0 -1540.1925 212.25923 Loop time of 2.121e-06 on 1 procs for 0 steps with 416 atoms 141.4% 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 | | 2.121e-06 | | |100.00 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4349.00 ave 4349 max 4349 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: 74308.0 ave 74308 max 74308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74308 Ave neighs/atom = 178.62500 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 5 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 4.620 | 4.620 | 4.620 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 -1540.1925 -1540.1925 21.023907 84.574562 4.1291422 212.25923 212.25923 109.89217 381.3464 145.53911 2.6601396 255.02374 Loop time of 1.924e-06 on 1 procs for 0 steps with 416 atoms 207.9% 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 | | 1.924e-06 | | |100.00 Nlocal: 416.000 ave 416 max 416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4349.00 ave 4349 max 4349 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37154.0 ave 37154 max 37154 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74308.0 ave 74308 max 74308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74308 Ave neighs/atom = 178.62500 Neighbor list builds = 0 Dangerous builds = 0 416 -1540.19247842039 eV 2.66013963459497 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01