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 -45.8945 0) to (11.4727 45.8945 3.62799) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.58908 4.58908 3.62799 Created 162 atoms create_atoms CPU = 0.000386 secs 162 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.58908 4.58908 3.62799 Created 162 atoms create_atoms CPU = 0.000159979 secs 162 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXGXDRME/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 = 2 16 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 2 atoms, new total = 322 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 = 2 16 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) = 404.4 | 404.4 | 404.4 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -31630.481 0 -31630.481 10174.514 85 0 -32203.186 0 -32203.186 -35666.285 Loop time of 30.1603 on 1 procs for 85 steps with 322 atoms 80.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -31630.4806994 -32203.1555023 -32203.1861282 Force two-norm initial, final = 479.105 2.60392 Force max component initial, final = 89.029 0.337889 Final line search alpha, max atom move = 0.111343 0.0376217 Iterations, force evaluations = 85 143 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 27.535 | 27.535 | 27.535 | 0.0 | 91.29 Neigh | 0.1909 | 0.1909 | 0.1909 | 0.0 | 0.63 Comm | 0.013149 | 0.013149 | 0.013149 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 2.4183 | 2.4183 | 2.4183 | 0.0 | 8.02 Other | | 0.003295 | | | 0.01 Nlocal: 322 ave 322 max 322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9694 ave 9694 max 9694 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 183271 ave 183271 max 183271 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 183271 Ave neighs/atom = 569.165 Neighbor list builds = 2 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 : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 404.3 | 404.3 | 404.3 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -32203.186 0 -32203.186 -35666.285 3820.5163 351 0 -32598.555 0 -32598.555 -23980.89 3739.7086 Loop time of 52.6296 on 1 procs for 266 steps with 322 atoms 76.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -32203.1861282 -32598.5322949 -32598.5554636 Force two-norm initial, final = 3702.38 52.2493 Force max component initial, final = 3478.52 39.2657 Final line search alpha, max atom move = 5.27176e-05 0.00207 Iterations, force evaluations = 266 277 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 49.247 | 49.247 | 49.247 | 0.0 | 93.57 Neigh | 0.061608 | 0.061608 | 0.061608 | 0.0 | 0.12 Comm | 0.016356 | 0.016356 | 0.016356 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 3.2539 | 3.2539 | 3.2539 | 0.0 | 6.18 Other | | 0.05104 | | | 0.10 Nlocal: 322 ave 322 max 322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9002 ave 9002 max 9002 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 187659 ave 187659 max 187659 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187659 Ave neighs/atom = 582.792 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 = 2 16 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) = 403.8 | 403.8 | 403.8 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -32598.555 0 -32598.555 -23980.89 Loop time of 1.19209e-06 on 1 procs for 0 steps with 322 atoms 251.7% 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 | | 1.192e-06 | | |100.00 Nlocal: 322 ave 322 max 322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9163 ave 9163 max 9163 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 186284 ave 186284 max 186284 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 = 186284 Ave neighs/atom = 578.522 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) = 403.8 | 403.8 | 403.8 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 -1413.6071 -32598.555 10.283084 91.788914 3.9620883 -23980.89 -24298.637 -653.84416 -72551.267 309.20027 2.1745858 763.12354 Loop time of 2.14577e-06 on 1 procs for 0 steps with 322 atoms 186.4% 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: 322 ave 322 max 322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9163 ave 9163 max 9163 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 186284 ave 186284 max 186284 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 197810 ave 197810 max 197810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 197810 Ave neighs/atom = 614.317 Neighbor list builds = 0 Dangerous builds = 0 322 -1413.60714613267 eV 2.17458578369657 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:01:24