LAMMPS (2 Aug 2023 - Update 1) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_BrugnoliMiyataniAkaji_SiCeNaClHO_2023__SM_282799919035_000 # For Simulator : LAMMPS Stable release 29 September 2021 # Running on : LAMMPS 2 Aug 2023 # Lattice spacing in x,y,z = 5.3559572 5.3559572 5.3559572 Created orthogonal box = (0 0 0) to (53.559572 53.559572 53.559572) 1 by 1 by 1 MPI processor grid Created 8000 atoms using lattice units in orthogonal box = (0 0 0) to (53.559572 53.559572 53.559572) create_atoms CPU = 0.001 seconds WARNING: Van der Waals parameters for element SI indicate inner wall+shielding, but earlier atoms indicate a different van der Waals method. This may cause division-by-zero errors. Keeping van der Waals setting for earlier atoms. (src/REAXFF/reaxff_ffield.cpp:251) WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:296) Initial system volume: 153642.474252245 Angstroms^3 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM Project: doi:10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/SM_282799919035_000#item-citation - pair reaxff command: doi:10.1016/j.parco.2011.08.005 - fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005 The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE 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 = 9 9 9 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair reaxff, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: full/ghost/bin/3d bin: standard (2) fix qeq/reaxff, perpetual, copy from (1) attributes: half, newton off 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) = 609.5 | 609.5 | 609.5 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -830701.27 -36022.616 -838644.73 -36367.077 333.15 333.15 153642.47 153642.47 2363.3917 2394.7067 1000 -822995.79 -35688.475 -830649.15 -36020.356 320.98305 320.98305 153439.47 153439.47 33.28749 33.728549 Loop time of 347.114 on 1 procs for 1000 steps with 8000 atoms Performance: 0.249 ns/day, 96.421 hours/ns, 2.881 timesteps/s, 23.047 katom-step/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 264.45 | 264.45 | 264.45 | 0.0 | 76.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.064928 | 0.064928 | 0.064928 | 0.0 | 0.02 Output | 0.00013855 | 0.00013855 | 0.00013855 | 0.0 | 0.00 Modify | 82.57 | 82.57 | 82.57 | 0.0 | 23.79 Other | | 0.0339 | | | 0.01 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15171 ave 15171 max 15171 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1.8731e+06 ave 1.8731e+06 max 1.8731e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1873098 Ave neighs/atom = 234.13725 Neighbor list builds = 0 Dangerous builds = 0 flag: Temp = 332.884415056355, Press = -6.66716977920453 Setting up Verlet run ... Unit style : real Current step : 1000 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 608.6 | 608.6 | 608.6 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -822995.79 -35688.475 -830649.15 -36020.356 320.98305 320.98305 153439.47 153439.47 33.287491 33.72855 2000 -822845.35 -35681.951 -830761.32 -36025.22 331.99702 331.99702 153601 153601 -811.20552 -821.95399 Loop time of 349.398 on 1 procs for 1000 steps with 8000 atoms Performance: 0.247 ns/day, 97.055 hours/ns, 2.862 timesteps/s, 22.897 katom-step/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 266.26 | 266.26 | 266.26 | 0.0 | 76.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.063428 | 0.063428 | 0.063428 | 0.0 | 0.02 Output | 9.3906e-05 | 9.3906e-05 | 9.3906e-05 | 0.0 | 0.00 Modify | 83.045 | 83.045 | 83.045 | 0.0 | 23.77 Other | | 0.03194 | | | 0.01 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15828 ave 15828 max 15828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1.83366e+06 ave 1.83366e+06 max 1.83366e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1833656 Ave neighs/atom = 229.207 Neighbor list builds = 0 Dangerous builds = 0 153439.051561795 LAMMPS calculation completed