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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -43.251493 0.0000000) to (35.314696 43.251493 8.7381211) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0449566 5.0018733 5.8254141 Created 1175 atoms using lattice units in orthogonal box = (0.0000000 -43.251493 0.0000000) to (35.314696 43.251493 8.7381211) create_atoms CPU = 0.005 seconds 1175 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0449566 5.0018733 5.8254141 Created 1183 atoms using lattice units in orthogonal box = (0.0000000 -43.251493 0.0000000) to (35.314696 43.251493 8.7381211) create_atoms CPU = 0.002 seconds 1183 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 31 4 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 2351 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_058735400462_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 31 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.088 | 5.088 | 5.088 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9031.7282 0 -9031.7282 77673.036 64 0 -9898.5835 0 -9898.5835 44032.106 Loop time of 6.69902 on 1 procs for 64 steps with 2351 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 = -9031.72817958391 -9898.57814543317 -9898.58354414894 Force two-norm initial, final = 820.17828 0.39131366 Force max component initial, final = 117.79700 0.094684602 Final line search alpha, max atom move = 0.96111766 0.091003043 Iterations, force evaluations = 64 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.6674 | 6.6674 | 6.6674 | 0.0 | 99.53 Neigh | 0.012431 | 0.012431 | 0.012431 | 0.0 | 0.19 Comm | 0.0068024 | 0.0068024 | 0.0068024 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01238 | | | 0.18 Nlocal: 2351.00 ave 2351 max 2351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5512.00 ave 5512 max 5512 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: 132652.0 ave 132652 max 132652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132652 Ave neighs/atom = 56.423650 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 31 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.087 | 5.087 | 5.087 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -9898.5835 0 -9898.5835 44032.106 26693.445 72 0 -9903.4681 0 -9903.4681 705.09189 27019.644 Loop time of 0.590335 on 1 procs for 8 steps with 2351 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 = -9898.583544149 -9903.46054392307 -9903.46806575563 Force two-norm initial, final = 1289.8626 21.976519 Force max component initial, final = 859.26203 14.944793 Final line search alpha, max atom move = 3.9406481e-05 0.00058892169 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.58656 | 0.58656 | 0.58656 | 0.0 | 99.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00043058 | 0.00043058 | 0.00043058 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003346 | | | 0.57 Nlocal: 2351.00 ave 2351 max 2351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5501.00 ave 5501 max 5501 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: 135898.0 ave 135898 max 135898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135898 Ave neighs/atom = 57.804339 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 32 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.226 | 5.226 | 5.226 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9903.4681 0 -9903.4681 705.09189 Loop time of 2.028e-06 on 1 procs for 0 steps with 2351 atoms 197.2% 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 | | 2.028e-06 | | |100.00 Nlocal: 2351.00 ave 2351 max 2351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5497.00 ave 5497 max 5497 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: 132678.0 ave 132678 max 132678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132678 Ave neighs/atom = 56.434709 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 32 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.226 | 5.226 | 5.226 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 -9903.4681 -9903.4681 35.331367 87.056302 8.784539 705.09189 705.09189 336.89566 891.84574 886.53426 2.184918 1995.1267 Loop time of 2.37e-06 on 1 procs for 0 steps with 2351 atoms 211.0% 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 | | 2.37e-06 | | |100.00 Nlocal: 2351.00 ave 2351 max 2351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5497.00 ave 5497 max 5497 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 66339.0 ave 66339 max 66339 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 132678.0 ave 132678 max 132678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132678 Ave neighs/atom = 56.434709 Neighbor list builds = 0 Dangerous builds = 0 2351 -9903.46806575564 eV 2.18491797413949 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07