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 = 2.8598780 2.8598780 2.8598780 Created orthogonal box = (0.0000000 -40.444782 0.0000000) to (20.222391 40.444782 2.8598780) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.2355826 3.2355826 2.8598780 Created 200 atoms using lattice units in orthogonal box = (0.0000000 -40.444782 0.0000000) to (20.222391 40.444782 2.8598780) create_atoms CPU = 0.001 seconds 200 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.2355826 3.2355826 2.8598780 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -40.444782 0.0000000) to (20.222391 40.444782 2.8598780) create_atoms CPU = 0.001 seconds 202 atoms in group lower Displacing atoms ... Reading tersoff/zbl potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXD1sTcr/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 = 8 30 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 0 atoms, new total = 402 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 = 8 30 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) = 4.309 | 4.309 | 4.309 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1641.6014 0 -1641.6014 83212.654 35 0 -1740.3905 0 -1740.3905 15193.019 Loop time of 3.52278 on 1 procs for 35 steps with 402 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 = -1641.60144762214 -1740.38906990107 -1740.39047345675 Force two-norm initial, final = 381.68661 0.12648544 Force max component initial, final = 186.70108 0.026843673 Final line search alpha, max atom move = 1.0000000 0.026843673 Iterations, force evaluations = 35 63 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5141 | 3.5141 | 3.5141 | 0.0 | 99.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.004499 | 0.004499 | 0.004499 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004162 | | | 0.12 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3108.00 ave 3108 max 3108 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: 23420.0 ave 23420 max 23420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23420 Ave neighs/atom = 58.258706 Neighbor list builds = 0 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 : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.309 | 4.309 | 4.309 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -1740.3905 0 -1740.3905 15193.019 4678.1323 47 0 -1740.7471 0 -1740.7471 -73.162259 4717.7088 Loop time of 0.766675 on 1 procs for 12 steps with 402 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 = -1740.39047345675 -1740.74603480196 -1740.7470937349 Force two-norm initial, final = 82.960970 0.69317186 Force max component initial, final = 69.337958 0.36583685 Final line search alpha, max atom move = 0.00063162800 0.00023107280 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.76242 | 0.76242 | 0.76242 | 0.0 | 99.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00091869 | 0.00091869 | 0.00091869 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003334 | | | 0.43 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3118.00 ave 3118 max 3118 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: 23256.0 ave 23256 max 23256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23256 Ave neighs/atom = 57.850746 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 = 8 30 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) = 3.940 | 3.940 | 3.940 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1740.7471 0 -1740.7471 -73.162259 Loop time of 6.014e-06 on 1 procs for 0 steps with 402 atoms 182.9% 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 | | 6.014e-06 | | |100.00 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3118.00 ave 3118 max 3118 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: 23252.0 ave 23252 max 23252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23252 Ave neighs/atom = 57.840796 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) = 3.940 | 3.940 | 3.940 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 -1740.7471 -1740.7471 20.236538 81.833697 2.8488051 -73.162259 -73.162259 -28.716991 -125.69163 -65.078158 2.3677606 107.90736 Loop time of 6.145e-06 on 1 procs for 0 steps with 402 atoms 244.1% 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 | | 6.145e-06 | | |100.00 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3118.00 ave 3118 max 3118 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11626.0 ave 11626 max 11626 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23252.0 ave 23252 max 23252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23252 Ave neighs/atom = 57.840796 Neighbor list builds = 0 Dangerous builds = 0 402 -1740.7470937349 eV 2.36776061341872 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04