LAMMPS (23 Jun 2022) 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 23 Jun 2022 # Created orthogonal box = (-25 -25 -25) to (25 25 25) 1 by 1 by 1 MPI processor grid Scanning dump file ... Reading snapshot from dump file ... orthogonal box = (-25 -25 -25) to (25 25 25) 0 atoms before read 3 atoms in snapshot 0 atoms purged 0 atoms replaced 0 atoms trimmed 3 atoms added 3 atoms after read 3 atoms in group all Changing box ... orthogonal box = (-25 -25 -25) to (25 25 25) orthogonal box = (-25 -25 -25) to (25 25 25) orthogonal box = (-25 -25 -25) to (25 25 25) 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) CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/SM_282799919035_000#item-citation - pair reaxff command: - fix qeq/reaxff command: The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) 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 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair reaxff, perpetual attributes: half, newton off, ghost pair build: half/nsq/newtoff/ghost stencil: none bin: none (2) fix qeq/reaxff, perpetual, copy from (1) attributes: half, newton off 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) = 11.53 | 11.53 | 11.53 Mbytes v_pe_metal -4.2058331 -5.2920859 Loop time of 0.000362991 on 1 procs for 12 steps with 3 atoms 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -96.9888150611172 -122.038400647414 -122.038400650675 Force two-norm initial, final = 146.68019 9.5713649e-05 Force max component initial, final = 108.5171 5.8034562e-05 Final line search alpha, max atom move = 1 5.8034562e-05 Iterations, force evaluations = 12 20 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.3005e-05 | 9.3005e-05 | 9.3005e-05 | 0.0 | 25.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 2.152e-06 | 2.152e-06 | 2.152e-06 | 0.0 | 0.59 Output | 0.00020217 | 0.00020217 | 0.00020217 | 0.0 | 55.70 Modify | 2.7762e-05 | 2.7762e-05 | 2.7762e-05 | 0.0 | 7.65 Other | | 3.79e-05 | | | 10.44 Nlocal: 3 ave 3 max 3 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3 ave 3 max 3 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3 Ave neighs/atom = 1 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:00