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 -50.1092 0) to (28.9289 50.1092 4.91333) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4506 4.49672 4.91333 Created 626 atoms create_atoms CPU = 0.000344038 secs 626 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4506 4.49672 4.91333 Created 627 atoms create_atoms CPU = 0.000247002 secs 627 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXgualTi/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 17 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 5 atoms, new total = 1248 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 = 5 17 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) = 594.2 | 594.2 | 594.2 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -126527.18 0 -126527.18 7468.3966 42 0 -127880.13 0 -127880.13 214.11598 Loop time of 24.0133 on 1 procs for 42 steps with 1248 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -126527.175317 -127880.049719 -127880.134579 Force two-norm initial, final = 1048.91 6.09076 Force max component initial, final = 189.264 0.905032 Final line search alpha, max atom move = 0.0740562 0.0670233 Iterations, force evaluations = 42 76 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.039 | 21.039 | 21.039 | 0.0 | 87.61 Neigh | 0.089301 | 0.089301 | 0.089301 | 0.0 | 0.37 Comm | 0.008657 | 0.008657 | 0.008657 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 2.8733 | 2.8733 | 2.8733 | 0.0 | 11.97 Other | | 0.002788 | | | 0.01 Nlocal: 1248 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15700 ave 15700 max 15700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 679289 ave 679289 max 679289 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 679289 Ave neighs/atom = 544.302 Neighbor list builds = 1 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 : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 594.3 | 594.3 | 594.3 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -127880.14 0 -127880.14 214.09936 14244.77 43 0 -127880.14 0 -127880.14 213.69249 14244.774 Loop time of 3.90059 on 1 procs for 1 steps with 1248 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -127880.137733 -127880.137733 -127880.138054 Force two-norm initial, final = 935.221 935.054 Force max component initial, final = 934.174 934.009 Final line search alpha, max atom move = 2.61344e-10 2.44098e-07 Iterations, force evaluations = 1 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.569 | 3.569 | 3.569 | 0.0 | 91.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012445 | 0.0012445 | 0.0012445 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.32768 | 0.32768 | 0.32768 | 0.0 | 8.40 Other | | 0.002687 | | | 0.07 Nlocal: 1248 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15708 ave 15708 max 15708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 677534 ave 677534 max 677534 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 677534 Ave neighs/atom = 542.896 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 17 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) = 593.8 | 593.8 | 593.8 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -127880.14 0 -127880.14 213.68081 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1248 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 | | 1.192e-06 | | |100.00 Nlocal: 1248 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15708 ave 15708 max 15708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 677534 ave 677534 max 677534 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 = 677534 Ave neighs/atom = 542.896 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) = 593.8 | 593.8 | 593.8 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 -5545.4075 -127880.14 28.928912 100.21836 4.9133325 213.67594 216.50715 213.5123 -4119.4969 4555.506 2.1766792 483.22355 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1248 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 | | 2.146e-06 | | |100.00 Nlocal: 1248 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15708 ave 15708 max 15708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 677534 ave 677534 max 677534 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 765882 ave 765882 max 765882 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 765882 Ave neighs/atom = 613.688 Neighbor list builds = 0 Dangerous builds = 0 1248 -5545.40748764502 eV 2.17667918935761 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:29