sdpd-polymer-run.lmp

echo               both
#atom_modify	sort 3.0e-6 3.0e-6
dimension          2
units              si
atom_style       hybrid bond meso
boundary          p p p

# create simulation box
#2D box
variable          Lx equal 2.00e-3

region             box block 0.0000e-3 ${Lx}  0.0000e-3 ${Lx} -1.0e-6 1.0e-6 units box
read_data           poly.txt

# create fluid particles
lattice         sq 0.025e-3
bond_style      fene
special_bonds   lj 1 1 1
#H*ro^2/(kT)=100
variable    H_fene equal 5   
#variable        H_fene equal 0.5e-1
variable        r0_fene equal 5e-5
bond_coeff  1 ${H_fene} ${r0_fene} 0.0 0.0


variable           sdpd_mass equal 2.778E-6
mass               1 ${sdpd_mass}
set                group all meso_rho 1000.0

# use Tait's EOS in combination with Morris' laminar viscosity.
# We set rho_0 = 1000 kg/m^3, c = 0.1 m/s, h = 6.5e-5 m.
# The dynamic viscosity is set to 1.0e-3 Pa s, corresponding to a kinematic viscosity of 1.0e-6 m^2/s
#The temperature is set to 1e14.
variable           sdpd_temp index 1e14
pair_style         hybrid sdpd
pair_coeff         * *    sdpd 1000 0.1 1.0e-3 6.5e-5 ${sdpd_temp}

compute            rho_peratom all meso_rho/atom
compute            e_peratom all meso_e/atom
compute            ke_peratom all ke/atom
compute            esph all reduce sum c_e_peratom
compute            ke all ke
compute            sdpd_kin all temp
variable           etot equal c_ke+c_esph


# do full time integration for shear driver and fluid, but keep walls stationary
fix                integrate_fix_full all meso
variable            A_kol equal 5
variable            var_kol atom ${A_kol}*${sdpd_mass}*cos(2*PI*y/${Lx})
fix                 kol_force all addforce v_var_kol 0.0 0.0


#dump               dump_id all custom 10000 dump*.dat id type x y vx vy c_rho_peratom c_e_peratom
dump               dump_id all custom 100000 dump*.dat x y vx vy id type c_rho_peratom
dump_modify        dump_id first yes
dump_modify        dump_id sort id
dump_modify        dump_id pad 8
thermo             10
thermo_style       custom step  c_sdpd_kin
thermo_modify      norm no

dump imgDump all image 100000 image.*.jpg type type bond atom 1e-5 adiam 1e-5 view 0 0 zoom 1.75
dump_modify        imgDump pad 9

neighbor           1.0e-6 bin
#timestep <0.5*delta/Cs
#include detime
timestep            1.0e-8

run                100000000