######################################################################## ### 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 create_atoms 1 random 16000 276438 NULL mass 1 1.0 set atom * cc 1 1.0 set atom * cc 2 1.0 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 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