LAMMPS (11 Aug 2017) ######################################################################## ### Pure diffusion with a reaction source term analog of a periodic ### ### Poiseuille flow problem using transport DPD (tDPD) simulation ### ### ### ### Created : Zhen Li (zhen_li@brown.edu) ### ### Division of Applied Mathematics, Brown University. ### ### ### ### tDPD system setup follows Fig.1 in the publication: ### ### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ### ### "Transport dissipative particle dynamics model for mesoscopic ### ### advection-diffusion-reaction problems. J. Chem. Phys., ### ### 2015, 143: 014101. DOI: 10.1063/1.4923254 ### ######################################################################## units lj dimension 3 boundary p p p neighbor 0.2 bin neigh_modify every 1 delay 0 check yes atom_style tdpd 2 region tdpd block -10 10 -10 10 -5 5 units box create_box 1 tdpd Created orthogonal box = (-10 -10 -5) to (10 10 5) 1 by 1 by 1 MPI processor grid create_atoms 1 random 16000 276438 NULL Created 16000 atoms mass 1 1.0 set atom * cc 1 1.0 16000 settings made for cc index 1 set atom * cc 2 1.0 16000 settings made for cc index 2 pair_style tdpd 1.0 1.58 9872598 pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0 compute mythermo all temp thermo 50 thermo_modify temp mythermo thermo_modify flush yes velocity all create 1.0 432982 loop local dist gaussian fix mvv all mvv/tdpd 0.5 fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01 fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01 fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01 fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01 timestep 0.01 run 500 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.78 ghost atom cutoff = 1.78 binsize = 0.89, bins = 23 23 12 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair tdpd, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 11.3 | 11.3 | 11.3 Mbytes Step Temp E_pair E_mol TotEng Press 0 1 48.948932 0 50.448838 202.19166 50 0.99837766 43.949877 0 45.447349 195.80936 100 0.99846831 43.756995 0 45.254604 198.22348 150 1.0026903 43.72408 0 45.228021 196.61676 200 1.0063144 43.722388 0 45.231765 194.17954 250 1.0032304 43.721864 0 45.226615 197.85829 300 0.9932656 43.703526 0 45.193331 196.57406 350 1.0002916 43.720498 0 45.220841 193.55346 400 0.99475486 43.722965 0 45.215004 196.81546 450 1.0011803 43.712447 0 45.214124 200.46118 500 1.0009006 43.708984 0 45.210241 197.38953 Loop time of 96.0326 on 1 procs for 500 steps with 16000 atoms Performance: 4498.474 tau/day, 5.207 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 90.083 | 90.083 | 90.083 | 0.0 | 93.80 Neigh | 5.049 | 5.049 | 5.049 | 0.0 | 5.26 Comm | 0.34141 | 0.34141 | 0.34141 | 0.0 | 0.36 Output | 0.00092816 | 0.00092816 | 0.00092816 | 0.0 | 0.00 Modify | 0.45991 | 0.45991 | 0.45991 | 0.0 | 0.48 Other | | 0.09865 | | | 0.10 Nlocal: 16000 ave 16000 max 16000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14091 ave 14091 max 14091 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 749379 ave 749379 max 749379 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 749379 Ave neighs/atom = 46.8362 Neighbor list builds = 183 Dangerous builds = 0 reset_timestep 0 compute cc1 all tdpd/cc/atom 1 compute cc2 all tdpd/cc/atom 2 compute bin all chunk/atom bin/1d y 0.0 1.0 fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile run 100 Per MPI rank memory allocation (min/avg/max) = 11.8 | 11.8 | 11.8 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.0009006 43.708984 0 45.210241 199.3205 50 1.0007276 43.704844 0 45.205842 197.77053 100 1.0039032 43.714201 0 45.219961 197.31118 Loop time of 19.0326 on 1 procs for 100 steps with 16000 atoms Performance: 4539.577 tau/day, 5.254 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.842 | 17.842 | 17.842 | 0.0 | 93.74 Neigh | 0.98674 | 0.98674 | 0.98674 | 0.0 | 5.18 Comm | 0.066013 | 0.066013 | 0.066013 | 0.0 | 0.35 Output | 0.00016284 | 0.00016284 | 0.00016284 | 0.0 | 0.00 Modify | 0.11795 | 0.11795 | 0.11795 | 0.0 | 0.62 Other | | 0.02012 | | | 0.11 Nlocal: 16000 ave 16000 max 16000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14126 ave 14126 max 14126 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 748927 ave 748927 max 748927 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 748927 Ave neighs/atom = 46.8079 Neighbor list builds = 37 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:01:55