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 dimension 3 boundary p p f units metal atom_style atomic neighbor 0.5 bin neigh_modify delay 0 check yes comm_modify cutoff 10.7 timestep 0.001 lattice diamond 5.43 Lattice spacing in x,y,z = 5.43 5.43 5.43 region box block -5 15 -5 20 -9 9 units lattice create_box 2 box Created orthogonal box = (-27.15 -27.15 -48.87) to (81.45 108.6 48.87) 1 by 1 by 1 MPI processor grid read_data 9-540Ncell_Sicore_9.5.data add append offset 0 0 0 0 0 Reading data file ... orthogonal box = (-27.15 -27.15 -48.87) to (81.45 108.6 48.87) 1 by 1 by 1 MPI processor grid reading atoms ... 6363 atoms reading velocities ... 6363 velocities read_data CPU = 0.030 seconds mass 1 28.0855 mass 2 12.0107 group Ncell type 1 2 6363 atoms in group Ncell write_data System.data System init for write_data ... pair_style hybrid sw lj/cut 10 airebo 3.0 1 1 pair_coeff * * airebo CH.airebo NULL C Reading airebo potential file CH.airebo with DATE: 2011-10-25 pair_coeff * * sw Si.sw Si NULL Reading sw potential file Si.sw with DATE: 2007-06-11 pair_coeff 1 2 lj/cut 0.008909 3.629 compute cluster Ncell cluster/atom 2.5 compute Nchunk Ncell chunk/atom c_cluster compress yes nchunk once ids once variable chunkID atom c_Nchunk fix st Ncell ave/chunk 1 1 1 Nchunk c_Nchunk v_chunkID norm none ave one file preNchunk.txt run 1 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.7 ghost atom cutoff = 10.7 binsize = 5.35, bins = 21 26 19 7 neighbor lists, perpetual/occasional/extra = 6 1 0 (1) pair sw, perpetual, skip from (5) attributes: full, newton on pair build: skip stencil: none bin: none (2) pair lj/cut, perpetual, skip from (6) attributes: half, newton on pair build: skip stencil: none bin: none (3) pair airebo, perpetual, skip from (7) attributes: full, newton on, ghost pair build: skip/ghost stencil: none bin: none (4) compute cluster/atom, occasional, copy from (5) attributes: full, newton on pair build: copy stencil: none bin: none (5) neighbor class addition, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (6) neighbor class addition, perpetual, half/full from (5) attributes: half, newton on pair build: halffull/newton stencil: none bin: none (7) neighbor class addition, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 28.78 | 28.78 | 28.78 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 6925579.2 0 6925579.2 31005183 1 0 6925579.2 0 6925579.2 31005183 Loop time of 0.0655124 on 1 procs for 1 steps with 6363 atoms Performance: 1.319 ns/day, 18.198 hours/ns, 15.264 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.065194 | 0.065194 | 0.065194 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 1.2507e-05 | 1.2507e-05 | 1.2507e-05 | 0.0 | 0.02 Output | 5.8555e-05 | 5.8555e-05 | 5.8555e-05 | 0.0 | 0.09 Modify | 0.00019201 | 0.00019201 | 0.00019201 | 0.0 | 0.29 Other | | 5.54e-05 | | | 0.08 Nlocal: 6363 ave 6363 max 6363 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 504 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.27953e+06 ave 1.27953e+06 max 1.27953e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1279530 Ave neighs/atom = 201.08911 Neighbor list builds = 0 Dangerous builds = 0 unfix st fix R Ncell rigid/nve custom v_chunkID 1 rigid bodies with 6363 atoms run 2 Per MPI rank memory allocation (min/avg/max) = 29.9 | 29.9 | 29.9 Mbytes Step Temp E_pair E_mol TotEng Press 1 0 6925579.2 0 6925579.2 1.0562547e-07 3 3.6699182e-17 6925579.2 0 6925579.2 1.2157285e-06 Loop time of 0.12419 on 1 procs for 2 steps with 6363 atoms Performance: 1.391 ns/day, 17.249 hours/ns, 16.104 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12319 | 0.12319 | 0.12319 | 0.0 | 99.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 1.7643e-05 | 1.7643e-05 | 1.7643e-05 | 0.0 | 0.01 Output | 5.2505e-05 | 5.2505e-05 | 5.2505e-05 | 0.0 | 0.04 Modify | 0.00082762 | 0.00082762 | 0.00082762 | 0.0 | 0.67 Other | | 0.0001007 | | | 0.08 Nlocal: 6363 ave 6363 max 6363 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 504 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.27953e+06 ave 1.27953e+06 max 1.27953e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1279530 Ave neighs/atom = 201.08911 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:00