gen

#!/usr/bin/env python3

import aphros
import numpy
import numpy as np
from scipy.interpolate import make_interp_spline


def V(x, y, z):
    return np.array([x, y, z])


class Default(aphros.Parameters):
    np = 256
    ny = 128
    bs = 16
    tl = 1440
    dumpdt = 0.1
    dumplist = "omm ebvf vm"
    tmax = 2000
    Re = 1000
    Ca = 0.04
    rho = 0.01

    dim = 3

    resist = 1000  # Resistivity of bubbles.

    Win = 0.2  # Width of inlet.
    Lin = 0.71
    Wout = 1  # Width of device.
    Lout = 0  # Buffer after last bone.
    Wbone = 0.2  # Width of bone.
    Lbone = 0.15  # Length of bone, distance between posts.
    Lshift = 0.4  # Shift between bones.
    Lstart = 0.  # Buffer before first bone.
    H = 0.2  # Height (depth) of the device.

    Sc_top = 160  # Schmidt number for gas from top electrode.
    Sc_btm = 400  # Schmidt number for gas from bottom electrode.
    flux_top = 0.0002 * 3  # Target flux of dissolved gas through top electrode.

    inletvel = 1.  # Inlet velocity.

    tracer_interface_diffusion_factor = 0.1

    electro = True
    stepwise = True
    particles = True
    nucleation = True
    nucldens = 10000.  # Areal number density of nucleation sites.
    resistivity_estimate = 0.6  # Estimate of average resistivity depending
    # on distance between bones.
    nucl_cmax = 0.05


def AppendVolcano(g, par, domain):
    """
    Appends a Volcano electrolyzer to geometry.
    g: instance of aphros.Geometry
    Returns:
    box_top, box_btm: insances of aphros.Geometry describing
                         boxes containing the two electrodes
    """
    lx = domain.lx
    ly = domain.ly
    lz = domain.lz
    inf = lx * 10
    eps = 1e-4
    epsh = 0.5 * domain.h if par.stepwise else eps
    lxh = lx * 0.5
    lyh = ly * 0.5
    lzh = lz * 0.5
    H = par.H if par.dim == 3 else inf
    Hh = H * 0.5

    Wgap = par.Win + par.Wbone  # Distance between centers of bones.

    # Add inlet.
    g.Box(V(lxh, lyh, lzh), V(inf, par.Win / 2, Hh))
    # Add device after inlet.
    g.Box(V(lx, lyh, lzh), V(lx - par.Lin, par.Wout / 2, Hh))
    # Subtract box containin all top and bottom bones.
    g.Box(V(lx, lyh + Wgap / 2, lzh),
          V(lx - par.Lin, par.Wbone / 2, Hh),
          intersect=True,
          invert=True)
    g.Box(V(lx, lyh - Wgap / 2, lzh),
          V(lx - par.Lin, par.Wbone / 2, Hh),
          intersect=True,
          invert=True)
    # Bone is a gap between two posts, liquid flows in bones.
    nbones = int((lx - par.Lin + par.Lbone) / par.Lshift)
    dLout = lx - (par.Lin + (nbones - 1) * par.Lshift + par.Lbone + par.Lout)
    # Subtract box near outlet.
    g.Box(V(lx, lyh, lzh), V(dLout, Wgap / 2, Hh), intersect=True, invert=True)
    for i in range(nbones):
        bonestart = i * par.Lshift
        g.Box(
            V(par.Lin + par.Lbone / 2 + par.Lstart + bonestart, lyh + Wgap / 2,
              lzh), V(par.Lbone / 2, par.Wbone / 2, Hh))
        g.Box(
            V(par.Lin + par.Lbone / 2 + par.Lstart + bonestart, lyh - Wgap / 2,
              lzh), V(par.Lbone / 2, par.Wbone / 2, Hh))

    hh = domain.h * 0.5
    box_top = aphros.Geometry().Box(  #
        [(par.Lin + lx - dLout) / 2, lyh + (Wgap + par.Wbone) / 2, lzh],
        [(lx - par.Lin - dLout) / 2, epsh * 2, Hh - epsh])
    box_btm = aphros.Geometry().Box(  #
        [(par.Lin + lx - dLout) / 2, lyh - (Wgap + par.Wbone) / 2, lzh],
        [(lx - par.Lin - dLout) / 2, epsh * 2, Hh - epsh])

    area_top = (nbones + 1) * par.Lbone * par.H

    return box_top, box_btm, area_top


par = Default("par.py")

lx = 4
ly = 1
lz = 0.25

domain = aphros.AdjustedDomain(lx=lx,
                               ly=ly,
                               lz=lz,
                               ny=par.ny,
                               nproc_factor=0.7,
                               size_factor=1,
                               nproc=par.np,
                               bs=par.bs)

lx = domain.lx
ly = domain.ly
lz = domain.lz
lxh = lx * 0.5
lyh = ly * 0.5
lzh = lz * 0.5

inf = ly * 100
eps = 1e-4

geom = aphros.Geometry()
box_top, box_btm, area_top = AppendVolcano(geom, par, domain)

conf = aphros.Config()
conf.extent = domain.extent
conf.mu1 = par.Win / par.Re
conf.mu2 = conf.mu1 * par.rho
conf.rho1 = 1.
conf.rho2 = conf.rho1 * par.rho
conf.dump_field_dt = par.dumpdt
conf.dump_traj_dt = par.dumpdt
conf.tmax = float(par.tmax)
conf.dumplist = par.dumplist
conf.sigma = conf.mu1 / par.Ca

potential = par.flux_top * par.resistivity_estimate

conf.sim_Re = par.Re
conf.sim_Ca = par.Ca
conf.sim_Sc_top = par.Sc_top
conf.sim_Sc_btm = par.Sc_btm
conf.sim_Win = par.Win
conf.sim_H = par.H
conf.sim_nucldens = par.nucldens
conf.sim_nucl_cmax = par.nucl_cmax
conf.sim_potential = potential
conf.sim_area_top = area_top
conf.sim_flux_top = par.flux_top
conf.sim_resistivity_estimate = par.resistivity_estimate
conf.sim_inletvel = par.inletvel

if par.stepwise:
    conf.body_init = "list"
    conf.enable_embed = 0
    conf.enable_stepwise_body = 1
    conf.dump_stepwise_body = 1
    conf.stepwise_threshold = 0.001
    conf.body_list_path = 'inline{}\n'.format(''.join(
        ['\n  ' + l for l in geom.Generate().split('\n')]))
else:
    conf.eb_list_path = 'inline{}\n'.format(''.join(
        ['\n  ' + l for l in geom.Generate().split('\n')]))

conf.enable_tracer = 1
conf.tracer_override_mixture = 0
conf.tracer_layers = 2
conf.tracer_density = [1.] * 2
conf.tracer_viscosity = [0.] * 2
nu1 = conf.mu1 / conf.rho1
diffusion_top = nu1 / par.Sc_top
diffusion_btm = nu1 / par.Sc_btm
conf.tracer_diffusion = [diffusion_top, diffusion_btm]
conf.tracer0_init = "list"
conf.tracer0_list_path = "b.dat"
conf.tracer1_init = "list"
conf.tracer1_list_path = "b.dat"
conf.dumplist += " tu0 tu1"
conf.tracer_interface_diffusion_factor = par.tracer_interface_diffusion_factor

if par.electro:
    conf.enable_electro = 1
    conf.dumplist += " elpot"
    conf.resist1 = 1.
    conf.resist2 = float(par.resist)
    conf.tracer0_init = "zero"
    conf.tracer1_init = "zero"
    conf.flux_from_current = 1.
    conf.hypre_electro_tol = potential * 0.1

if par.particles:
    conf.enable_particles = 1
    conf.particles_mode = "tracer"
    conf.particles_density = par.rho
    conf.particles_to_vof = 1
    conf.particles_coal = 1
    conf.particles_to_vof_radius = 2.
    conf.particles_growth_diffusion_factor = 1.

if par.nucleation:
    conf.enable_nucleation_points = 1
    conf.nucleation_number_density = par.nucldens
    conf.nucleation_cmax0 = par.nucl_cmax
    conf.nucleation_cpost0 = 0.
    conf.nucleation_cmax1 = par.nucl_cmax
    conf.nucleation_cpost1 = 0.
    conf.dump_nucl = 1

bc = aphros.BoundaryConditions()
bcel = ", electro_neumann 0, tracer0_neumann 0, tracer1_neumann 0"
bc.Wall(aphros.Geometry().Box([0, 0, 0], [inf, inf, inf]), extra=bcel)

bc.Inlet(aphros.Geometry().Box([0, 0, 0], [eps, inf, inf]),
         velocity=[par.inletvel, 0, 0],
         extra=bcel)
bc.Outlet(aphros.Geometry().Box([lx, 0, 0], [eps, inf, inf]), extra=bcel)

bc_nucleation = ", nucleation 1" if par.nucleation else ""
bc_top = ", electro_dirichlet 0, tracer0_neumann 1, tracer1_neumann 0"
bc_btm = ", electro_dirichlet {:}, tracer0_neumann 0, tracer1_neumann 0.5".format(
    potential)
bc.Wall(box_top, extra=bc_top + bc_nucleation)
bc.Wall(box_btm, extra=bc_btm + bc_nucleation)

bc.GenerateFile("bc.dat")
conf.bc_path = 'inline{}\n'.format(''.join(
    ['\n  ' + l for l in bc.Generate().split('\n')]))

conf.GenerateFile("par.conf")

domain = aphros.PartitionDomain(domain)
domain.GenerateMeshConfig()
aphros.GenerateJobConfig(domain.nproc, par.tl)