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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -60.995816 0.0000000) to (24.900000 60.995816 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9760000 5.2859988 5.7504086 Created 1203 atoms using lattice units in orthogonal box = (0.0000000 -60.995816 0.0000000) to (24.900000 60.995816 8.6256130) create_atoms CPU = 0.002 seconds 1203 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9760000 5.2859988 5.7504086 Created 1203 atoms using lattice units in orthogonal box = (0.0000000 -60.995816 0.0000000) to (24.900000 60.995816 8.6256130) create_atoms CPU = 0.002 seconds 1203 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 8 40 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 2384 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 8 40 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.568 | 5.568 | 5.568 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10542.105 0 -10542.105 3184.1802 26 0 -10576.48 0 -10576.48 -6936.7354 Loop time of 4.30728 on 1 procs for 26 steps with 2384 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10542.1048449538 -10576.4692906844 -10576.4797037186 Force two-norm initial, final = 40.539444 0.34145753 Force max component initial, final = 5.8126907 0.052419904 Final line search alpha, max atom move = 1.0000000 0.052419904 Iterations, force evaluations = 26 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2788 | 4.2788 | 4.2788 | 0.0 | 99.34 Neigh | 0.017479 | 0.017479 | 0.017479 | 0.0 | 0.41 Comm | 0.0046233 | 0.0046233 | 0.0046233 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006416 | | | 0.15 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7174.00 ave 7174 max 7174 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: 204498.0 ave 204498 max 204498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204498 Ave neighs/atom = 85.779362 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 8 40 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.568 | 5.568 | 5.568 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -10576.48 0 -10576.48 -6936.7354 26201.09 29 0 -10576.628 0 -10576.628 -1935.1215 26130.164 Loop time of 0.493476 on 1 procs for 3 steps with 2384 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10576.4797037186 -10576.6265569587 -10576.6284181283 Force two-norm initial, final = 141.07771 0.35584893 Force max component initial, final = 121.96035 0.053916540 Final line search alpha, max atom move = 9.0116120e-05 4.8587494e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49082 | 0.49082 | 0.49082 | 0.0 | 99.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040187 | 0.00040187 | 0.00040187 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002258 | | | 0.46 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7172.00 ave 7172 max 7172 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: 204516.0 ave 204516 max 204516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204516 Ave neighs/atom = 85.786913 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 8 40 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.705 | 5.705 | 5.705 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10576.628 0 -10576.628 -1935.1215 Loop time of 1.954e-06 on 1 procs for 0 steps with 2384 atoms 153.5% 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 | | 1.954e-06 | | |100.00 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7172.00 ave 7172 max 7172 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: 204522.0 ave 204522 max 204522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204522 Ave neighs/atom = 85.789430 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 8 40 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.705 | 5.705 | 5.705 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 -10576.628 -10576.628 24.88364 121.99163 8.607919 -1935.1215 -1935.1215 -1.0067958 -5804.666 0.30834553 2.2945412 582.16439 Loop time of 2.193e-06 on 1 procs for 0 steps with 2384 atoms 228.0% 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 | | 2.193e-06 | | |100.00 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7172.00 ave 7172 max 7172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 102261.0 ave 102261 max 102261 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 204522.0 ave 204522 max 204522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204522 Ave neighs/atom = 85.789430 Neighbor list builds = 0 Dangerous builds = 0 2384 -10576.6284181283 eV 2.29454124870325 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05