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 -28.9317 0) to (14.4645 28.9317 2.83671) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.33795 3.33795 2.83671 Created 106 atoms create_atoms CPU = 0.000277042 secs 106 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.33795 3.33795 2.83671 Created 106 atoms create_atoms CPU = 9.60827e-05 secs 106 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXU3n3Mi/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 = 3 10 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 8 atoms, new total = 204 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 = 3 10 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) = 235.1 | 235.1 | 235.1 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20738.493 0 -20738.493 -7112.2249 28 0 -20904.318 0 -20904.318 -20035.941 Loop time of 5.02883 on 1 procs for 28 steps with 204 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 = -20738.4932016 -20904.3014152 -20904.3181049 Force two-norm initial, final = 187.831 2.00605 Force max component initial, final = 60.7702 0.2488 Final line search alpha, max atom move = 0.160494 0.0399309 Iterations, force evaluations = 28 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6498 | 4.6498 | 4.6498 | 0.0 | 92.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026703 | 0.0026703 | 0.0026703 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.37562 | 0.37562 | 0.37562 | 0.0 | 7.47 Other | | 0.0007026 | | | 0.01 Nlocal: 204 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6690 ave 6690 max 6690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 116225 ave 116225 max 116225 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116225 Ave neighs/atom = 569.73 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 : 28 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 235.1 | 235.1 | 235.1 Mbytes Step Temp E_pair E_mol TotEng Press Volume 28 0 -20904.318 0 -20904.318 -20035.941 2374.2268 35 0 -20907.866 0 -20907.866 -3375.411 2349.9752 Loop time of 0.906622 on 1 procs for 7 steps with 204 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 = -20904.3181049 -20907.8582657 -20907.8661268 Force two-norm initial, final = 957.349 4.84901 Force max component initial, final = 743.737 2.31599 Final line search alpha, max atom move = 4.4405e-05 0.000102842 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.85743 | 0.85743 | 0.85743 | 0.0 | 94.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049448 | 0.00049448 | 0.00049448 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.047674 | 0.047674 | 0.047674 | 0.0 | 5.26 Other | | 0.001021 | | | 0.11 Nlocal: 204 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6735 ave 6735 max 6735 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 116907 ave 116907 max 116907 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116907 Ave neighs/atom = 573.074 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 = 3 10 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) = 237.6 | 237.6 | 237.6 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20907.866 0 -20907.866 -3375.411 Loop time of 9.53674e-07 on 1 procs for 0 steps with 204 atoms 209.7% 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 | | 9.537e-07 | | |100.00 Nlocal: 204 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7506 ave 7506 max 7506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 119973 ave 119973 max 119973 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 = 119973 Ave neighs/atom = 588.103 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) = 237.6 | 237.6 | 237.6 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 -906.65088 -20907.866 14.408882 57.863497 2.8185667 -3375.411 -3420.1352 59.62112 -10388.061 68.034245 2.3156566 141.97483 Loop time of 1.90735e-06 on 1 procs for 0 steps with 204 atoms 104.9% 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: 204 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7506 ave 7506 max 7506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 119973 ave 119973 max 119973 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 126444 ave 126444 max 126444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126444 Ave neighs/atom = 619.824 Neighbor list builds = 0 Dangerous builds = 0 204 -906.650879061203 eV 2.31565656440697 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:06