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 -51.0637 0) to (36.1055 51.0637 4.01172) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.90321 4.72786 4.01172 Created 649 atoms create_atoms CPU = 0.00138617 secs 649 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.90321 4.72786 4.01172 Created 649 atoms create_atoms CPU = 0.00107384 secs 649 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXePsCYT/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 18 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 3 atoms, new total = 1295 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 18 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) = 657.7 | 657.7 | 657.7 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -132376.31 0 -132376.31 2349.6749 21 0 -133510.64 0 -133510.64 -2261.8887 Loop time of 9.99412 on 1 procs for 21 steps with 1295 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 = -132376.309538 -133510.511346 -133510.643187 Force two-norm initial, final = 950.325 5.77056 Force max component initial, final = 237.61 1.20284 Final line search alpha, max atom move = 0.0333098 0.0400663 Iterations, force evaluations = 21 33 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.4489 | 8.4489 | 8.4489 | 0.0 | 84.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0046198 | 0.0046198 | 0.0046198 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 1.5389 | 1.5389 | 1.5389 | 0.0 | 15.40 Other | | 0.001658 | | | 0.02 Nlocal: 1295 ave 1295 max 1295 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17374 ave 17374 max 17374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 708700 ave 708700 max 708700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 708700 Ave neighs/atom = 547.259 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 : 21 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 657.8 | 657.8 | 657.8 Mbytes Step Temp E_pair E_mol TotEng Press Volume 21 0 -133510.64 0 -133510.64 -2261.8887 14792.63 22 0 -133510.72 0 -133510.72 -1372.2652 14784.859 Loop time of 0.859953 on 1 procs for 1 steps with 1295 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 = -133510.643187 -133510.643187 -133510.718025 Force two-norm initial, final = 337.089 85.2109 Force max component initial, final = 329.859 83.1964 Final line search alpha, max atom move = 3.0316e-06 0.000252218 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.76319 | 0.76319 | 0.76319 | 0.0 | 88.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003109 | 0.0003109 | 0.0003109 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.095804 | 0.095804 | 0.095804 | 0.0 | 11.14 Other | | 0.0006499 | | | 0.08 Nlocal: 1295 ave 1295 max 1295 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17325 ave 17325 max 17325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 714030 ave 714030 max 714030 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 714030 Ave neighs/atom = 551.375 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 = 7 18 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) = 657.4 | 657.4 | 657.4 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -133510.72 0 -133510.72 -1372.2652 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1295 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: 1295 ave 1295 max 1295 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17325 ave 17325 max 17325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 714370 ave 714370 max 714370 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 = 714370 Ave neighs/atom = 551.637 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) = 657.4 | 657.4 | 657.4 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 -5789.5726 -133510.72 36.102175 102.12735 4.0099761 -1372.2652 -1390.4477 390.92041 -4480.1182 -82.145335 2.1367269 512.01328 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1295 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: 1295 ave 1295 max 1295 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17325 ave 17325 max 17325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 714370 ave 714370 max 714370 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 796458 ave 796458 max 796458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 796458 Ave neighs/atom = 615.025 Neighbor list builds = 0 Dangerous builds = 0 1295 -5789.57264826909 eV 2.13672693059088 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:12