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 -46.4646 0) to (23.2305 46.4646 3.62799) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.09937 5.09937 3.62799 Created 329 atoms create_atoms CPU = 0.000447035 secs 329 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.09937 5.09937 3.62799 Created 329 atoms create_atoms CPU = 0.000266075 secs 329 atoms in group lower Displacing atoms ... Reading potential file /tmp/kim-simulator-model-parameter-file-directory-XXXXXXzIpBkh/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 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 3 atoms, new total = 655 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 = 4 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) = 549.4 | 549.4 | 549.4 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -64762.542 0 -64762.542 1800.1007 329 0 -65814.897 0 -65814.897 -50407.99 Loop time of 245.973 on 1 procs for 329 steps with 655 atoms 66.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -64762.5420656 -65814.8424498 -65814.8972205 Force two-norm initial, final = 423.777 3.70943 Force max component initial, final = 104.737 0.332134 Final line search alpha, max atom move = 0.0819004 0.0272019 Iterations, force evaluations = 329 640 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 219.64 | 219.64 | 219.64 | 0.0 | 89.30 Neigh | 1.0385 | 1.0385 | 1.0385 | 0.0 | 0.42 Comm | 0.15186 | 0.15186 | 0.15186 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 25.042 | 25.042 | 25.042 | 0.0 | 10.18 Other | | 0.09783 | | | 0.04 Nlocal: 655 ave 655 max 655 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12665 ave 12665 max 12665 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 360032 ave 360032 max 360032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 360032 Ave neighs/atom = 549.667 Neighbor list builds = 6 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 : 329 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 549.4 | 549.4 | 549.4 Mbytes Step Temp E_pair E_mol TotEng Press Volume 329 0 -65814.897 0 -65814.897 -50407.99 7832.0507 399 0 -66185.282 0 -66185.282 -41598.29 7828.0767 Loop time of 28.0035 on 1 procs for 70 steps with 655 atoms 60.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -65814.8972205 -66185.2203818 -66185.2815055 Force two-norm initial, final = 9918.74 69.3911 Force max component initial, final = 9734.09 32.9013 Final line search alpha, max atom move = 1.26055e-05 0.000414736 Iterations, force evaluations = 70 71 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 26.048 | 26.048 | 26.048 | 0.0 | 93.02 Neigh | 0.097728 | 0.097728 | 0.097728 | 0.0 | 0.35 Comm | 0.0067279 | 0.0067279 | 0.0067279 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 1.8323 | 1.8323 | 1.8323 | 0.0 | 6.54 Other | | 0.01894 | | | 0.07 Nlocal: 655 ave 655 max 655 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11280 ave 11280 max 11280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 363738 ave 363738 max 363738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 363738 Ave neighs/atom = 555.325 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 = 4 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) = 547.3 | 547.3 | 547.3 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -66185.282 0 -66185.282 -41598.29 Loop time of 9.53674e-07 on 1 procs for 0 steps with 655 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: 655 ave 655 max 655 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11364 ave 11364 max 11364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 361012 ave 361012 max 361012 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 = 361012 Ave neighs/atom = 551.163 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) = 547.3 | 547.3 | 547.3 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 -2870.0654 -66185.282 21.961844 92.929102 3.8356107 -41598.29 -42149.467 140.87925 -126280.56 -308.7214 2.186797 233.1939 Loop time of 2.14577e-06 on 1 procs for 0 steps with 655 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: 655 ave 655 max 655 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11364 ave 11364 max 11364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 361012 ave 361012 max 361012 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 394674 ave 394674 max 394674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 394674 Ave neighs/atom = 602.556 Neighbor list builds = 0 Dangerous builds = 0 655 -2870.065423893 eV 2.18679699853898 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:04:37