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 = 2.83671 2.83671 2.83671 Created orthogonal box = (0 -37.206 0) to (26.3066 37.206 4.01172) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.89425 4.75854 4.01172 Created 346 atoms create_atoms CPU = 0.000741005 secs 346 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.89425 4.75854 4.01172 Created 346 atoms create_atoms CPU = 0.000515938 secs 346 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXUAVAzn/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 = 5 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 4 atoms, new total = 688 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 = 5 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) = 397.4 | 397.4 | 397.4 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -69922.375 0 -69922.375 3704.5593 35 0 -70808.041 0 -70808.041 -1771.8215 Loop time of 10.9316 on 1 procs for 35 steps with 688 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 = -69922.375136 -70807.9740763 -70808.0406879 Force two-norm initial, final = 755.984 3.92419 Force max component initial, final = 158.116 0.376412 Final line search alpha, max atom move = 0.0803586 0.0302479 Iterations, force evaluations = 35 63 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.3919 | 9.3919 | 9.3919 | 0.0 | 85.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0052223 | 0.0052223 | 0.0052223 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 1.5328 | 1.5328 | 1.5328 | 0.0 | 14.02 Other | | 0.00176 | | | 0.02 Nlocal: 688 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10656 ave 10656 max 10656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 381302 ave 381302 max 381302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 381302 Ave neighs/atom = 554.218 Neighbor list builds = 0 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 : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 397.5 | 397.5 | 397.5 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -70808.041 0 -70808.041 -1771.8215 7853.0403 37 0 -70808.133 0 -70808.133 -1694.7021 7852.7727 Loop time of 0.824867 on 1 procs for 2 steps with 688 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 = -70808.0406879 -70808.1331163 -70808.1332028 Force two-norm initial, final = 215.796 4.60204 Force max component initial, final = 160.029 1.85234 Final line search alpha, max atom move = 0.00019539 0.000361928 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.73288 | 0.73288 | 0.73288 | 0.0 | 88.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037408 | 0.00037408 | 0.00037408 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.090776 | 0.090776 | 0.090776 | 0.0 | 11.00 Other | | 0.0008397 | | | 0.10 Nlocal: 688 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10596 ave 10596 max 10596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 384494 ave 384494 max 384494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 384494 Ave neighs/atom = 558.858 Neighbor list builds = 0 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 = 5 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) = 397.6 | 397.6 | 397.6 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -70808.133 0 -70808.133 -1694.7021 Loop time of 9.53674e-07 on 1 procs for 0 steps with 688 atoms 524.3% 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: 688 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10596 ave 10596 max 10596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 384533 ave 384533 max 384533 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 = 384533 Ave neighs/atom = 558.914 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) = 397.6 | 397.6 | 397.6 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 -3070.5312 -70808.133 26.322103 74.411962 4.0092181 -1694.7021 -1717.1569 -16.398096 -5122.0884 -12.984228 2.1363561 432.20454 Loop time of 2.14577e-06 on 1 procs for 0 steps with 688 atoms 139.8% 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: 688 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10596 ave 10596 max 10596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 384533 ave 384533 max 384533 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 424216 ave 424216 max 424216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 424216 Ave neighs/atom = 616.593 Neighbor list builds = 0 Dangerous builds = 0 688 -3070.53124521374 eV 2.13635610101354 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:13