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 -38.5697 0) to (38.566 38.5697 3.62799) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.11939 5.11939 3.62799 Created 453 atoms create_atoms CPU = 0.00048995 secs 453 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.11939 5.11939 3.62799 Created 453 atoms create_atoms CPU = 0.000320911 secs 453 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXUYS1OT/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 = 7 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 14 atoms, new total = 892 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 = 7 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) = 618.1 | 618.1 | 618.1 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -88249.542 0 -88249.542 -3675.0987 301 0 -89525.115 0 -89525.115 -62832.442 Loop time of 240.499 on 1 procs for 301 steps with 892 atoms 74.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -88249.5424752 -89525.0265471 -89525.1146135 Force two-norm initial, final = 378.569 4.78966 Force max component initial, final = 83.643 0.424752 Final line search alpha, max atom move = 0.0951191 0.040402 Iterations, force evaluations = 301 581 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 211.87 | 211.87 | 211.87 | 0.0 | 88.09 Neigh | 1.4019 | 1.4019 | 1.4019 | 0.0 | 0.58 Comm | 0.19263 | 0.19263 | 0.19263 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 26.867 | 26.867 | 26.867 | 0.0 | 11.17 Other | | 0.1713 | | | 0.07 Nlocal: 892 ave 892 max 892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14348 ave 14348 max 14348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 480082 ave 480082 max 480082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 480082 Ave neighs/atom = 538.209 Neighbor list builds = 8 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 : 301 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 618 | 618 | 618 Mbytes Step Temp E_pair E_mol TotEng Press Volume 301 0 -89525.115 0 -89525.115 -62832.442 10793.12 394 0 -90232.466 0 -90232.466 -41088.677 10644.663 Loop time of 39.8701 on 1 procs for 93 steps with 892 atoms 69.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -89525.1146135 -90232.4302383 -90232.4655428 Force two-norm initial, final = 16947.8 92.6673 Force max component initial, final = 16944.5 54.5976 Final line search alpha, max atom move = 8.49113e-06 0.000463595 Iterations, force evaluations = 93 96 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 36.398 | 36.398 | 36.398 | 0.0 | 91.29 Neigh | 0.32703 | 0.32703 | 0.32703 | 0.0 | 0.82 Comm | 0.021487 | 0.021487 | 0.021487 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 3.0567 | 3.0567 | 3.0567 | 0.0 | 7.67 Other | | 0.06672 | | | 0.17 Nlocal: 892 ave 892 max 892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12660 ave 12660 max 12660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 491111 ave 491111 max 491111 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 491111 Ave neighs/atom = 550.573 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 = 6 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) = 615.2 | 615.2 | 615.2 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -90232.466 0 -90232.466 -41088.677 Loop time of 2.14577e-06 on 1 procs for 0 steps with 892 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: 892 ave 892 max 892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12891 ave 12891 max 12891 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 487383 ave 487383 max 487383 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 = 487383 Ave neighs/atom = 546.393 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) = 615.2 | 615.2 | 615.2 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 -3912.85 -90232.466 35.904999 77.139351 3.8432712 -41088.677 -41633.102 -331.7662 -124547.66 -19.884624 2.2233966 246.95941 Loop time of 9.53674e-07 on 1 procs for 0 steps with 892 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: 892 ave 892 max 892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12891 ave 12891 max 12891 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 487383 ave 487383 max 487383 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 538080 ave 538080 max 538080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 538080 Ave neighs/atom = 603.229 Neighbor list builds = 0 Dangerous builds = 0 892 -3912.85001100275 eV 2.22339655414225 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:04:44