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 # Using KIM Simulator Model : Sim_LAMMPS_ADP_StarikovSmirnovaPradhan_2021_Fe__SM_906654900816_000 # For Simulator : LAMMPS 30 Jul 2021 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 3.5225141 3.5225141 3.5225141 Created orthogonal box = (0.0000000 -67.393186 0.0000000) to (38.907440 67.393186 6.1011734) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7404420 5.1554934 6.1011734 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -67.393186 0.0000000) to (38.907440 67.393186 6.1011734) create_atoms CPU = 0.003 seconds 1466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7404420 5.1554934 6.1011734 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -67.393186 0.0000000) to (38.907440 67.393186 6.1011734) create_atoms CPU = 0.003 seconds 1466 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 = 8.1965966 ghost atom cutoff = 8.1965966 binsize = 4.0982983, bins = 10 33 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 adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Deleted 28 atoms, new total = 2904 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/SM_906654900816_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 = 8.1965966 ghost atom cutoff = 8.1965966 binsize = 4.0982983, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 15.19 | 15.19 | 15.19 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12355.234 0 -12355.234 1461.1895 227 0 -12480.96 0 -12480.96 -6833.0133 Loop time of 14.3362 on 1 procs for 227 steps with 2904 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 = -12355.2336319776 -12480.9477457828 -12480.9595094658 Force two-norm initial, final = 37.457330 0.37505668 Force max component initial, final = 7.1022357 0.10525246 Final line search alpha, max atom move = 0.58568359 0.061644636 Iterations, force evaluations = 227 407 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.183 | 14.183 | 14.183 | 0.0 | 98.93 Neigh | 0.041761 | 0.041761 | 0.041761 | 0.0 | 0.29 Comm | 0.05959 | 0.05959 | 0.05959 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05188 | | | 0.36 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14010.0 ave 14010 max 14010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 303302.0 ave 303302 max 303302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 303302 Ave neighs/atom = 104.44284 Neighbor list builds = 3 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Setting up cg style minimization ... Unit style : metal Current step : 227 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 15.57 | 15.57 | 15.57 Mbytes Step Temp E_pair E_mol TotEng Press Volume 227 0 -12480.96 0 -12480.96 -6833.0133 31995.729 245 0 -12486.679 0 -12486.679 -10345.573 32147.036 Loop time of 0.714209 on 1 procs for 18 steps with 2904 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 = -12480.9595094659 -12486.6712406498 -12486.6786073094 Force two-norm initial, final = 540.79052 2.5870636 Force max component initial, final = 420.57385 1.2260050 Final line search alpha, max atom move = 6.2090699e-05 7.6123509e-05 Iterations, force evaluations = 18 19 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.70106 | 0.70106 | 0.70106 | 0.0 | 98.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020972 | 0.0020972 | 0.0020972 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01105 | | | 1.55 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14018.0 ave 14018 max 14018 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 303276.0 ave 303276 max 303276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 303276 Ave neighs/atom = 104.43388 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 = 8.1965966 ghost atom cutoff = 8.1965966 binsize = 4.0982983, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/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, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 14.45 | 14.45 | 14.45 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12486.679 0 -12486.679 -10345.573 Loop time of 2.005e-06 on 1 procs for 0 steps with 2904 atoms 149.6% 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 | | 2.005e-06 | | |100.00 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14081.0 ave 14081 max 14081 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 303056.0 ave 303056 max 303056 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 303056 Ave neighs/atom = 104.35813 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 14.45 | 14.45 | 14.45 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 -12486.679 -12486.679 38.417633 134.78637 6.2081808 -10345.573 -10345.573 60.333652 -31136.678 39.626276 2.2252271 12684.979 Loop time of 2.018e-06 on 1 procs for 0 steps with 2904 atoms 247.8% 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 | | 2.018e-06 | | |100.00 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14081.0 ave 14081 max 14081 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 303056.0 ave 303056 max 303056 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 606112.0 ave 606112 max 606112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 606112 Ave neighs/atom = 208.71625 Neighbor list builds = 0 Dangerous builds = 0 2904 -12486.6786073094 eV 2.22522712193395 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15