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 = 3.6073527 3.6073527 3.6073527 Created orthogonal box = (0.0000000 -43.736827 0.0000000) to (35.710970 43.736827 8.8361734) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1015671 5.0580004 5.8907823 Created 1175 atoms using lattice units in orthogonal box = (0.0000000 -43.736827 0.0000000) to (35.710970 43.736827 8.8361734) create_atoms CPU = 0.002 seconds 1175 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1015671 5.0580004 5.8907823 Created 1183 atoms using lattice units in orthogonal box = (0.0000000 -43.736827 0.0000000) to (35.710970 43.736827 8.8361734) create_atoms CPU = 0.001 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 6 15 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 2336 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_151002396060_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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 6 15 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 14.40 | 14.40 | 14.40 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7906.654 0 -7906.654 20692.189 67 0 -8191.5137 0 -8191.5137 -1700.8167 Loop time of 7.26317 on 1 procs for 67 steps with 2336 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7906.65403983655 -8191.50645937186 -8191.51365552568 Force two-norm initial, final = 272.94349 0.34232081 Force max component initial, final = 40.965379 0.084868106 Final line search alpha, max atom move = 1.0000000 0.084868106 Iterations, force evaluations = 67 124 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.065 | 7.065 | 7.065 | 0.0 | 97.27 Neigh | 0.14702 | 0.14702 | 0.14702 | 0.0 | 2.02 Comm | 0.031978 | 0.031978 | 0.031978 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01914 | | | 0.26 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16393.0 ave 16393 max 16393 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: 1.46184e+06 ave 1.46184e+06 max 1.46184e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1461844 Ave neighs/atom = 625.78938 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 6 15 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 14.40 | 14.40 | 14.40 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -8191.5137 0 -8191.5137 -1700.8167 27602.165 70 0 -8191.5893 0 -8191.5893 -14.208926 27568.245 Loop time of 0.341278 on 1 procs for 3 steps with 2336 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 = -8191.51365552562 -8191.5889784313 -8191.58928028499 Force two-norm initial, final = 79.843059 1.3894574 Force max component initial, final = 79.193912 1.2306964 Final line search alpha, max atom move = 0.00018307733 0.00022531261 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3374 | 0.3374 | 0.3374 | 0.0 | 98.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00075646 | 0.00075646 | 0.00075646 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003123 | | | 0.91 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16416.0 ave 16416 max 16416 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: 1.46019e+06 ave 1.46019e+06 max 1.46019e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1460190 Ave neighs/atom = 625.08134 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 6 15 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 13.91 | 13.91 | 13.91 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8191.5893 0 -8191.5893 -14.208926 Loop time of 2.099e-06 on 1 procs for 0 steps with 2336 atoms 190.6% 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 | | 2.099e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16410.0 ave 16410 max 16410 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: 1.46045e+06 ave 1.46045e+06 max 1.46045e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1460448 Ave neighs/atom = 625.19178 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 6 15 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 13.91 | 13.91 | 13.91 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 -8191.5893 -8191.5893 35.715536 87.522187 8.8192933 -14.208926 -14.208926 -71.533208 30.950429 -2.0439991 2.2655347 1315.9891 Loop time of 5.027e-06 on 1 procs for 0 steps with 2336 atoms 198.9% 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 | | 5.027e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16410.0 ave 16410 max 16410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 730224.0 ave 730224 max 730224 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.46045e+06 ave 1.46045e+06 max 1.46045e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1460448 Ave neighs/atom = 625.19178 Neighbor list builds = 0 Dangerous builds = 0 2336 -8191.58928028499 eV 2.26553470848708 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08