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 -52.3092 0) to (26.1532 52.3092 2.83671) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9999 3.9999 2.83671 Created 341 atoms create_atoms CPU = 0.000307798 secs 341 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9999 3.9999 2.83671 Created 341 atoms create_atoms CPU = 0.000201941 secs 341 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXaXwwR8/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 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 2 atoms, new total = 680 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 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) = 525.9 | 525.9 | 525.9 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -69514.027 0 -69514.027 2100.7517 42 0 -70129.749 0 -70129.749 -1185.535 Loop time of 19.1825 on 1 procs for 42 steps with 680 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -69514.0272277 -70129.6945056 -70129.7492658 Force two-norm initial, final = 656.042 3.70426 Force max component initial, final = 198.657 0.523012 Final line search alpha, max atom move = 0.127795 0.0668381 Iterations, force evaluations = 42 71 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.305 | 17.305 | 17.305 | 0.0 | 90.21 Neigh | 0.086362 | 0.086362 | 0.086362 | 0.0 | 0.45 Comm | 0.0084991 | 0.0084991 | 0.0084991 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 1.78 | 1.78 | 1.78 | 0.0 | 9.28 Other | | 0.002323 | | | 0.01 Nlocal: 680 ave 680 max 680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14487 ave 14487 max 14487 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 390390 ave 390390 max 390390 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 390390 Ave neighs/atom = 574.103 Neighbor list builds = 1 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 : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 525.9 | 525.9 | 525.9 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -70129.749 0 -70129.749 -1185.535 7761.555 45 0 -70130.376 0 -70130.376 616.87074 7753.2783 Loop time of 1.27581 on 1 procs for 3 steps with 680 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -70129.7492658 -70130.3680201 -70130.3760552 Force two-norm initial, final = 551.008 29.2165 Force max component initial, final = 545.439 28.0533 Final line search alpha, max atom move = 1.51363e-05 0.000424624 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1941 | 1.1941 | 1.1941 | 0.0 | 93.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053883 | 0.00053883 | 0.00053883 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.080064 | 0.080064 | 0.080064 | 0.0 | 6.28 Other | | 0.001081 | | | 0.08 Nlocal: 680 ave 680 max 680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14540 ave 14540 max 14540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 389814 ave 389814 max 389814 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 389814 Ave neighs/atom = 573.256 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 = 5 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) = 526.1 | 526.1 | 526.1 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -70130.376 0 -70130.376 616.87074 Loop time of 9.53674e-07 on 1 procs for 0 steps with 680 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: 680 ave 680 max 680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14513 ave 14513 max 14513 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 390419 ave 390419 max 390419 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 = 390419 Ave neighs/atom = 574.146 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) = 526.1 | 526.1 | 526.1 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 -3041.1409 -70130.376 26.179167 104.61849 2.8308777 616.87074 625.04428 -65.114246 2191.115 -250.86793 2.180271 102.52939 Loop time of 9.53674e-07 on 1 procs for 0 steps with 680 atoms 419.4% 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 | | 9.537e-07 | | |100.00 Nlocal: 680 ave 680 max 680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14513 ave 14513 max 14513 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 390419 ave 390419 max 390419 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 418602 ave 418602 max 418602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 418602 Ave neighs/atom = 615.591 Neighbor list builds = 0 Dangerous builds = 0 680 -3041.1409138466 eV 2.18027097152015 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:22