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_TersoffZBL_ByggmastarGranberg_2020_Fe__SM_958863895234_000 # For Simulator : LAMMPS 19 Sep 2019 # Running on : LAMMPS 30 Jul 2021 # Lattice spacing in x,y,z = 3.6122691 3.6122691 3.6122691 Created orthogonal box = (0.0000000 -66.997610 0.0000000) to (23.687232 66.997610 5.1085199) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0595245 6.2323358 5.1085199 Created 688 atoms using lattice units in orthogonal box = (0.0000000 -66.997610 0.0000000) to (23.687232 66.997610 5.1085199) create_atoms CPU = 0.002 seconds 688 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0595245 6.2323358 5.1085199 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -66.997610 0.0000000) to (23.687232 66.997610 5.1085199) create_atoms CPU = 0.002 seconds 690 atoms in group lower Displacing atoms ... Reading tersoff/zbl potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXQ7q4vU/Fe_Byggmastar.tersoff.zbl with DATE: 2018-09-11 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 = 5.46 ghost atom cutoff = 5.46 binsize = 2.73, bins = 9 50 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional, copy from (2) attributes: full, newton on pair build: copy stencil: none bin: none (2) pair tersoff/zbl, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1374 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_958863895234_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 = 5.46 ghost atom cutoff = 5.46 binsize = 2.73, bins = 9 50 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair tersoff/zbl, perpetual attributes: full, newton on 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) = 4.554 | 4.554 | 4.554 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5339.1379 0 -5339.1379 80058.96 168 0 -5852.286 0 -5852.286 -1888.6335 Loop time of 17.9324 on 1 procs for 168 steps with 1374 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 = -5339.13793020141 -5852.28199155557 -5852.28599641336 Force two-norm initial, final = 1440.1737 0.20329010 Force max component initial, final = 490.64417 0.035921943 Final line search alpha, max atom move = 1.0000000 0.035921943 Iterations, force evaluations = 168 316 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.885 | 17.885 | 17.885 | 0.0 | 99.74 Neigh | 0.0066234 | 0.0066234 | 0.0066234 | 0.0 | 0.04 Comm | 0.017966 | 0.017966 | 0.017966 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02271 | | | 0.13 Nlocal: 1374.00 ave 1374 max 1374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5297.00 ave 5297 max 5297 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: 74996.0 ave 74996 max 74996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74996 Ave neighs/atom = 54.582242 Neighbor list builds = 1 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 : 168 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.558 | 4.558 | 4.558 Mbytes Step Temp E_pair E_mol TotEng Press Volume 168 0 -5852.286 0 -5852.286 -1888.6335 16214.319 172 0 -5852.3979 0 -5852.3979 31.060478 16196.556 Loop time of 0.399591 on 1 procs for 4 steps with 1374 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 = -5852.28599641337 -5852.39786136119 -5852.39793123385 Force two-norm initial, final = 67.666654 0.93594091 Force max component initial, final = 54.176505 0.78484051 Final line search alpha, max atom move = 0.00044216165 0.00034702638 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39755 | 0.39755 | 0.39755 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032521 | 0.00032521 | 0.00032521 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001719 | | | 0.43 Nlocal: 1374.00 ave 1374 max 1374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5636.00 ave 5636 max 5636 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: 75764.0 ave 75764 max 75764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75764 Ave neighs/atom = 55.141194 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 = 5.46 ghost atom cutoff = 5.46 binsize = 2.73, bins = 9 49 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair tersoff/zbl, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional, copy from (1) attributes: full, newton on pair build: copy stencil: none bin: none (3) compute pair/local, occasional, half/full from (1) attributes: half, newton on pair build: halffull/newton 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) = 4.189 | 4.189 | 4.189 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5852.3979 0 -5852.3979 31.060478 Loop time of 1.71e-06 on 1 procs for 0 steps with 1374 atoms 175.4% 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 | | 1.71e-06 | | |100.00 Nlocal: 1374.00 ave 1374 max 1374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5635.00 ave 5635 max 5635 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: 75788.0 ave 75788 max 75788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75788 Ave neighs/atom = 55.158661 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) = 4.189 | 4.189 | 4.189 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 -5852.3979 -5852.3979 23.658828 133.68874 5.1207624 31.060478 31.060478 -20.245223 77.459485 35.967173 2.3771929 827.6245 Loop time of 1.545e-06 on 1 procs for 0 steps with 1374 atoms 194.2% 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 | | 1.545e-06 | | |100.00 Nlocal: 1374.00 ave 1374 max 1374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5635.00 ave 5635 max 5635 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37894.0 ave 37894 max 37894 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75788.0 ave 75788 max 75788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75788 Ave neighs/atom = 55.158661 Neighbor list builds = 0 Dangerous builds = 0 1374 -5852.39793123385 eV 2.3771929166443 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18