Commit 1efb2d33 authored by Johannes Blaschke's avatar Johannes Blaschke
Browse files

rename modules to make more sense moving forward

parent abdfc5f2

1d_diffusion.ipynb

+19 −19
Original line number Diff line number Diff line 
%% Cell type:code id: tags:



``` julia

include("src/fp.jl")

include("src/flux_array.jl")

```



%% Output



    Main.FP

    Main.ModFluxArray



%% Cell type:code id: tags:



``` julia

using .FP

using .ModFluxArray

```



%% Cell type:code id: tags:



``` julia

N = 10

D = 1.;

h = 1e-3;

k = 1.;

```



%% Cell type:code id: tags:



``` julia

n = DistributionArray{Float64}(0., 1., N);

f = FluxArray{Float64}(N);

```



%% Cell type:code id: tags:



``` julia

n.p[Integer(size(n)/2)] = 1;

n.p

```



%% Output



    10-element Array{Float64,1}:

     0.0

     0.0

     0.0

     0.0

     1.0

     0.0

     0.0

     0.0

     0.0

     0.0



%% Cell type:code id: tags:



``` julia

fill_fr!(f);

fill_lr!(f, n.p);

```



%% Cell type:code id: tags:



``` julia

f.left

```



%% Output



    10-element Array{Float64,1}:

     0.0

     0.0

     0.0

     0.0

     0.0022742765607139948

     0.1936697622933632

     0.0

     0.0

     0.0

     0.0

     0.0



%% Cell type:code id: tags:



``` julia

f.right

```



%% Output



    10-element Array{Float64,1}:

     0.0

     0.0

     0.0

     0.0

     0.997725723439286

     0.8063302377066368

     0.0

     0.0

     0.0

     0.0

     0.0



%% Cell type:code id: tags:



``` julia

f.left .+ f.right

```



%% Output



    10-element Array{Float64,1}:

     0.0

     0.0

     0.0

     0.0

     1.0

     0.0

     0.0

     0.0

     0.0

     0.0



%% Cell type:code id: tags:



``` julia

fill_df!(f, D, h);

```



%% Cell type:code id: tags:



``` julia

f.diffusive

```



%% Output



    11-element Array{Float64,1}:

        0.0

        0.0

        0.0

        0.0

        2.2742765607139948

     -997.725723439286

      193.6697622933632

     -806.3302377066368

        0.0

        0.0

        0.0

        0.0

        0.0



%% Cell type:code id: tags:



``` julia

fill_sf!(f, D, h, k);

```



%% Cell type:code id: tags:



``` julia

f.stochastic

```



%% Output



    11-element Array{Float64,1}:

     -0.8640646960498399

      0.0

      1.662956306086986

      0.0

     -0.0

      0.3672085709169771

     -2.924360797089483

      0.0

      0.0

     -0.0

      4.240011808025856

      2.710972258785979

     -0.0

      0.0

      0.3838915655069409

     -0.0

     -0.0

     -0.3416384648516665



%% Cell type:code id: tags:



``` julia

apply_bc!(f);

```



%% Cell type:code id: tags:



``` julia

f.stochastic

```



%% Output



    11-element Array{Float64,1}:

      0.0

      0.0

      0.0

     -0.0

      0.3672085709169771

     -2.924360797089483

      0.0

      0.0

     -0.0

      4.240011808025856

      2.710972258785979

     -0.0

      0.0

     -0.0

     -0.0

      0.0



%% Cell type:code id: tags:



``` julia

```

src/fp.jl→src/flux_array.jl

+2 −52
Original line number Diff line number Diff line 
module FP

module StochFluxArray



export DistributionArray

export size
@@ -172,7 +172,7 @@ function fill_ft!(flx::FluxArray{T}, h::T, k::T) where T 
    

    for i=2:size_cc(flx)

        # Total particle number

        P::T  = flx.right[i-1] + flx.left[i]

        P::T  = flx.right[i-1] + flx.left[i];

        # Number in right box (i.e. number of particles going left)

        x0::T = flx.left[i];

        # Valid range of fluxes
@@ -182,55 +182,6 @@ function fill_ft!(flx::FluxArray{T}, h::T, k::T) where T 
end





#function getFlux(n, h, N, k, D, FP, time)

#    #get the diffusive flux for FV solver

#    

#    #create flux vectors

#    Ftot = zeros(1,N+1); #total flux

#    Fd = zeros(1,N+1);   #diffusive flux

#    Fs = zeros(1,N+1);   #stochastic flux

#    

#    #get the fraction of particles going in each direction

#    fr = rand(1,N);  #fraction going right, 1-fr is fraction going left

#    left = n.*(1-fr);right = n.*fr; #define left and right particle numbers

#    

#    #compute the diffusive flux

#    for i = 2:N

#        Fd(i) = D/h * (left(i) - right(i-1)); #random fractions

#        #Fd(i) = D/h * (n(i) - n(i-1)); #usual fv

#    end

#    

#    #compute the stochastic flux - assume gaussian

#    R = randn(1,N+1);  #standard normals

#    for i = 2:N

#        avg = left(i) + right(i-1);  #average over cell, ignore factor of 2

#        Fs(i) = R(i)*sqrt(D*avg/(k*sqrt(h)));  #set correct variance, 2 cancels

#    end

#    

#    #check if each box has a physical flux

#    nu = k/h;         #ratio of time to space step to propogate soln

#    Ftot = Fd + Fs;   #set total flux

#    Q = -Ftot*nu;     #take time step to get real fluxes 

#    for i=1:N-1

#        P = right(i)+left(i+1); #total particle number

#        x0 = left(i+1);         #number in right box

#        lower = -x0; upper = P-x0; #valid range of fluxes

#        if (Q(i+1)>upper || Q(i+1) < lower)

#            #if particle num is low enough, sample uniform - approx FP

#            if (P < 1e-3)

#                Ftot(i+1) = -1/nu*(P*rand()-x0);

#            else

#                #do a fokker planck solve - sample flux

#                #divide by nu to remain consistent.

#                flux = FPsample(P,x0,D,h,k);

#                Ftot(i+1) = -1/nu*flux;

#                FP{i}(time) = 1;

#            end

#        end

#    end

#    

#    return Ftot, FP

#end





end
 
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