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 -56.6746 0) to (28.3355 56.6746 3.62799) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.10968 5.10968 3.62799 Created 490 atoms create_atoms CPU = 0.000522137 secs 490 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.10968 5.10968 3.62799 Created 490 atoms create_atoms CPU = 0.000427008 secs 490 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXJK7cwV/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 19 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 1 atoms, new total = 979 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 19 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) = 726.8 | 726.8 | 726.8 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -96914.658 0 -96914.658 4325.1235 232 0 -98474.45 0 -98474.45 -43314.946 Loop time of 229.277 on 1 procs for 232 steps with 979 atoms 67.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -96914.6578122 -98474.3554628 -98474.450311 Force two-norm initial, final = 545.289 4.8273 Force max component initial, final = 109.187 0.525977 Final line search alpha, max atom move = 0.120681 0.0634752 Iterations, force evaluations = 232 433 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 203.14 | 203.14 | 203.14 | 0.0 | 88.60 Neigh | 1.2623 | 1.2623 | 1.2623 | 0.0 | 0.55 Comm | 0.18705 | 0.18705 | 0.18705 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 24.595 | 24.595 | 24.595 | 0.0 | 10.73 Other | | 0.09253 | | | 0.04 Nlocal: 979 ave 979 max 979 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16581 ave 16581 max 16581 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 538367 ave 538367 max 538367 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 538367 Ave neighs/atom = 549.915 Neighbor list builds = 6 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 : 232 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 726.8 | 726.8 | 726.8 Mbytes Step Temp E_pair E_mol TotEng Press Volume 232 0 -98474.45 0 -98474.45 -43314.946 11652.399 299 0 -98987.402 0 -98987.402 -39988.937 11693.131 Loop time of 34.7784 on 1 procs for 67 steps with 979 atoms 63.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -98474.450311 -98987.3270711 -98987.4021602 Force two-norm initial, final = 13470.8 71.5055 Force max component initial, final = 12936 25.1809 Final line search alpha, max atom move = 7.97738e-06 0.000200878 Iterations, force evaluations = 67 68 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 31.861 | 31.861 | 31.861 | 0.0 | 91.61 Neigh | 0.17029 | 0.17029 | 0.17029 | 0.0 | 0.49 Comm | 0.0092044 | 0.0092044 | 0.0092044 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 2.66 | 2.66 | 2.66 | 0.0 | 7.65 Other | | 0.07768 | | | 0.22 Nlocal: 979 ave 979 max 979 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14589 ave 14589 max 14589 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 542661 ave 542661 max 542661 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 542661 Ave neighs/atom = 554.301 Neighbor list builds = 1 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 19 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) = 722.4 | 722.4 | 722.4 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -98987.402 0 -98987.402 -39988.937 Loop time of 1.90735e-06 on 1 procs for 0 steps with 979 atoms 157.3% 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 | | 1.907e-06 | | |100.00 Nlocal: 979 ave 979 max 979 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14708 ave 14708 max 14708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 537722 ave 537722 max 537722 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 = 537722 Ave neighs/atom = 549.256 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) = 722.4 | 722.4 | 722.4 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 -4292.5 -98987.402 26.881098 113.34924 3.8376485 -39988.937 -40518.79 76.552367 -121474.66 -158.26363 2.196144 280.46638 Loop time of 2.14577e-06 on 1 procs for 0 steps with 979 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: 979 ave 979 max 979 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14708 ave 14708 max 14708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 537722 ave 537722 max 537722 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 591292 ave 591292 max 591292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 591292 Ave neighs/atom = 603.975 Neighbor list builds = 0 Dangerous builds = 0 979 -4292.49999212481 eV 2.19614398483425 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:04:29