LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_AryanpourVanDuinKubicki_2010_FeHO__SM_222964216001_000 # For Simulator : LAMMPS 28 Feb 2019 # Running on : LAMMPS 7 Aug 2019 # Lattice spacing in x,y,z = 2.83671 2.83671 2.83671 Created orthogonal box = (0 -30.2906 0) to (21.4167 30.2906 4.01172) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.13305 4.78229 4.01172 Created 230 atoms create_atoms CPU = 0.00020504 secs 230 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.13305 4.78229 4.01172 Created 230 atoms create_atoms CPU = 8.89301e-05 secs 230 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXX7CxXSF/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 = 4 11 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 0 atoms, new total = 460 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) 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 = 4 11 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) = 338.7 | 338.7 | 338.7 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -45914.336 0 -45914.336 14672.415 37 0 -46921.51 0 -46921.51 11443.332 Loop time of 8.04642 on 1 procs for 37 steps with 460 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -45914.3356608 -46921.4964226 -46921.510116 Force two-norm initial, final = 991.429 9.12685 Force max component initial, final = 197.342 0.858229 Final line search alpha, max atom move = 0.0589296 0.050575 Iterations, force evaluations = 37 69 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.1023 | 7.1023 | 7.1023 | 0.0 | 88.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0033534 | 0.0033534 | 0.0033534 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.9397 | 0.9397 | 0.9397 | 0.0 | 11.68 Other | | 0.001045 | | | 0.01 Nlocal: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9123 ave 9123 max 9123 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 259513 ave 259513 max 259513 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 259513 Ave neighs/atom = 564.159 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : real Current step : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 338.7 | 338.7 | 338.7 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -46921.509 0 -46921.509 11443.335 5205.0127 40 0 -46921.831 0 -46921.831 9374.4289 5211.4958 Loop time of 3.16087 on 1 procs for 3 steps with 460 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 = -46921.5093924 -46921.8247 -46921.830507 Force two-norm initial, final = 900.255 621.554 Force max component initial, final = 824.466 586.278 Final line search alpha, max atom move = 5.2553e-08 3.08106e-05 Iterations, force evaluations = 3 29 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9067 | 2.9067 | 2.9067 | 0.0 | 91.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012672 | 0.0012672 | 0.0012672 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.25007 | 0.25007 | 0.25007 | 0.0 | 7.91 Other | | 0.002879 | | | 0.09 Nlocal: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8431 ave 8431 max 8431 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 261896 ave 261896 max 261896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261896 Ave neighs/atom = 569.339 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 = 4 11 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) = 337.3 | 337.3 | 337.3 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -46921.834 0 -46921.834 9374.4327 Loop time of 1.90735e-06 on 1 procs for 0 steps with 460 atoms 0.0% 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: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8419 ave 8419 max 8419 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 261565 ave 261565 max 261565 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 = 261565 Ave neighs/atom = 568.62 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) = 337.3 | 337.3 | 337.3 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 -2034.7234 -46921.836 21.424574 60.58129 4.0152415 9374.4289 9498.6401 2750.1054 17923.049 7822.7659 2.0357822 313.80237 Loop time of 9.53674e-07 on 1 procs for 0 steps with 460 atoms 0.0% 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: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8419 ave 8419 max 8419 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 261565 ave 261565 max 261565 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 286592 ave 286592 max 286592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 286592 Ave neighs/atom = 623.026 Neighbor list builds = 0 Dangerous builds = 0 460 -2034.72337252456 eV 2.03578221998171 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