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 = 3.6131481 3.6131481 3.6131481 Created orthogonal box = (0.0000000 -54.557340 0.0000000) to (38.577865 54.557340 5.1097631) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0912419 5.2643048 5.1097631 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -54.557340 0.0000000) to (38.577865 54.557340 5.1097631) create_atoms CPU = 0.002 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0912419 5.2643048 5.1097631 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -54.557340 0.0000000) to (38.577865 54.557340 5.1097631) create_atoms CPU = 0.002 seconds 916 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 8 21 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 10.45965 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1820 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_173787283511_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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 8 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 11.49 | 11.49 | 11.49 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5821.8824 0 -5821.8824 37356.974 204 0 -6337.6357 0 -6337.6357 -569.65407 Loop time of 15.8168 on 1 procs for 204 steps with 1820 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5821.88238288833 -6337.6293812385 -6337.63568442762 Force two-norm initial, final = 625.79325 0.31732513 Force max component initial, final = 151.90100 0.042209779 Final line search alpha, max atom move = 0.68074548 0.028734116 Iterations, force evaluations = 204 365 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.338 | 15.338 | 15.338 | 0.0 | 96.97 Neigh | 0.31431 | 0.31431 | 0.31431 | 0.0 | 1.99 Comm | 0.10201 | 0.10201 | 0.10201 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06236 | | | 0.39 Nlocal: 1820.00 ave 1820 max 1820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15578.0 ave 15578 max 15578 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: 703080.0 ave 703080 max 703080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 703080 Ave neighs/atom = 386.30769 Neighbor list builds = 6 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 8 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 204 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.49 | 11.49 | 11.49 Mbytes Step Temp E_pair E_mol TotEng Press Volume 204 0 -6337.6357 0 -6337.6357 -569.65407 21509.095 209 0 -6337.9325 0 -6337.9325 -10.354457 21498 Loop time of 0.221077 on 1 procs for 5 steps with 1820 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 = -6337.63568442763 -6337.92766294767 -6337.93250314067 Force two-norm initial, final = 102.21475 0.52801057 Force max component initial, final = 74.700148 0.16402963 Final line search alpha, max atom move = 9.5473399e-05 1.5660466e-05 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21594 | 0.21594 | 0.21594 | 0.0 | 97.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00089366 | 0.00089366 | 0.00089366 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004248 | | | 1.92 Nlocal: 1820.00 ave 1820 max 1820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15447.0 ave 15447 max 15447 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: 705368.0 ave 705368 max 705368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 705368 Ave neighs/atom = 387.56484 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 8 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 11.01 | 11.01 | 11.01 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6337.9325 0 -6337.9325 -10.354457 Loop time of 2.565e-06 on 1 procs for 0 steps with 1820 atoms 194.9% 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 | | 2.565e-06 | | |100.00 Nlocal: 1820.00 ave 1820 max 1820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15496.0 ave 15496 max 15496 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: 704904.0 ave 704904 max 704904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 704904 Ave neighs/atom = 387.30989 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 8 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 11.01 | 11.01 | 11.01 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 -6337.9325 -6337.9325 38.479852 109.61769 5.0966406 -10.354457 -10.354457 -12.19354 -10.860101 -8.0097304 2.4038402 868.82364 Loop time of 2.847e-06 on 1 procs for 0 steps with 1820 atoms 281.0% 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 | | 2.847e-06 | | |100.00 Nlocal: 1820.00 ave 1820 max 1820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15496.0 ave 15496 max 15496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 352452.0 ave 352452 max 352452 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 704904.0 ave 704904 max 704904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 704904 Ave neighs/atom = 387.30989 Neighbor list builds = 0 Dangerous builds = 0 1820 -6337.93250314067 eV 2.40384024109653 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16