LAMMPS (24 Jan 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_AryanpourVanDuinKubicki_2010_FeHO__SM_222964216001_001 # For Simulator : LAMMPS 28 Feb 2019 # Running on : LAMMPS 24 Jan 2020 # Lattice spacing in x,y,z = 3.62799 3.62799 3.62799 Created orthogonal box = (0 -37.002 0) to (18.4992 37.002 3.62799) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.26904 4.26904 3.62799 Created 210 atoms create_atoms CPU = 0.000249863 secs 210 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.26904 4.26904 3.62799 Created 210 atoms create_atoms CPU = 0.000102997 secs 210 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXmTjHrL/ffield.reax.Fe_O_C_H with DATE: 2011-02-18 System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 4 13 1 3 neighbor lists, perpetual/occasional/extra = 2 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: half/ghost/bin/3d/newtoff bin: standard (3) fix qeq/reax, perpetual, copy from (2) attributes: half, newton off, ghost pair build: copy stencil: none bin: none Deleted 7 atoms, new total = 413 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 4 13 1 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: half/ghost/bin/3d/newtoff bin: standard (2) fix qeq/reax, perpetual, copy from (1) attributes: half, newton off, ghost pair build: copy stencil: none bin: none Setting up cg style minimization ... Unit style : real Current step : 0 Per MPI rank memory allocation (min/avg/max) = 405.3 | 405.3 | 405.3 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -40677.323 0 -40677.323 2863.7923 143 0 -41244.152 0 -41244.152 -46664.098 Loop time of 45.3764 on 1 procs for 143 steps with 413 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 = -40677.3234257 -41244.1113905 -41244.1522016 Force two-norm initial, final = 378.204 3.08968 Force max component initial, final = 85.1739 0.63918 Final line search alpha, max atom move = 0.112229 0.0717342 Iterations, force evaluations = 143 272 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 40.91 | 40.91 | 40.91 | 0.0 | 90.16 Neigh | 0.17303 | 0.17303 | 0.17303 | 0.0 | 0.38 Comm | 0.022739 | 0.022739 | 0.022739 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 4.2642 | 4.2642 | 4.2642 | 0.0 | 9.40 Other | | 0.00615 | | | 0.01 Nlocal: 413 ave 413 max 413 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9611 ave 9611 max 9611 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 228032 ave 228032 max 228032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 228032 Ave neighs/atom = 552.136 Neighbor list builds = 3 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : real Current step : 143 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 405.3 | 405.3 | 405.3 Mbytes Step Temp E_pair E_mol TotEng Press Volume 143 0 -41244.152 0 -41244.152 -46664.098 4966.7655 507 0 -41958.255 0 -41958.255 -7835.1754 4732.0957 Loop time of 52.9167 on 1 procs for 364 steps with 413 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 = -41244.1522016 -41958.2165894 -41958.2550686 Force two-norm initial, final = 5225.41 75.6896 Force max component initial, final = 5192.24 42.9635 Final line search alpha, max atom move = 1.11205e-05 0.000477777 Iterations, force evaluations = 364 380 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 48.707 | 48.707 | 48.707 | 0.0 | 92.04 Neigh | 0.10551 | 0.10551 | 0.10551 | 0.0 | 0.20 Comm | 0.020081 | 0.020081 | 0.020081 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 4.0256 | 4.0256 | 4.0256 | 0.0 | 7.61 Other | | 0.05879 | | | 0.11 Nlocal: 413 ave 413 max 413 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8988 ave 8988 max 8988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 233472 ave 233472 max 233472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 233472 Ave neighs/atom = 565.308 Neighbor list builds = 2 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 3 13 1 4 neighbor lists, perpetual/occasional/extra = 2 2 0 (1) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: half/ghost/bin/3d/newtoff 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/newton bin: standard (4) fix qeq/reax, perpetual, copy from (1) attributes: half, newton off, ghost pair build: copy stencil: none bin: none Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 404.9 | 404.9 | 404.9 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -41958.255 0 -41958.255 -7835.1754 Loop time of 9.53674e-07 on 1 procs for 0 steps with 413 atoms 314.6% 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 | | 9.537e-07 | | |100.00 Nlocal: 413 ave 413 max 413 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9142 ave 9142 max 9142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 237590 ave 237590 max 237590 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237590 Ave neighs/atom = 575.278 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 404.9 | 404.9 | 404.9 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 -1819.4821 -41958.255 16.026518 74.003994 3.989874 -7835.1754 -7938.9914 -546.47886 -22987.372 -283.1236 2.1342681 856.95242 Loop time of 2.14577e-06 on 1 procs for 0 steps with 413 atoms 605.8% 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 | | 2.146e-06 | | |100.00 Nlocal: 413 ave 413 max 413 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9142 ave 9142 max 9142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 237590 ave 237590 max 237590 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 257724 ave 257724 max 257724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 257724 Ave neighs/atom = 624.029 Neighbor list builds = 0 Dangerous builds = 0 413 -1819.48213228249 eV 2.13426805830799 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:01:39