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Questions tagged [diffusion]

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26
votes
2answers
5k views

Is Crank-Nicolson a stable discretization scheme for Reaction-Diffusion-Advection (convection) equation?

I am not very familiar with the common discretization schemes for PDEs. I know that Crank-Nicolson is popular scheme for discretizing the diffusion equation. Is also a good choice for the advection ...
24
votes
1answer
5k views

Conservation of a physical quantity when using Neumann boundary conditions applied to the advection-diffusion equation

I don't understand the different behaviour of the advection-diffusion equation when I apply different boundary conditions. My motivation is the simulation of a real physical quantity (particle density)...
8
votes
1answer
261 views

Computing geodesic distances with diffusion

I am trying to solve an APSP (All-Pair Shortest Path) problem on a weighted graph. This graph is actually a 1, 2 or 3 dimensional grid, and the weights on each edge represent the distance between its ...
7
votes
1answer
202 views

Optimal way to find stationary solutions of the PDE

I am researching heat diffusion in an optical element irradiated by laser. This problem is described by the PDE which I wrote down in this question. I am using an implicit numerical scheme to model ...
6
votes
3answers
2k views

Open boundary conditions with the advection-diffusion equation

Following on from my previous equation I'm would like to apply open boundary condition to the advection-diffusion equation (with reaction term), $$ \frac{\partial \phi}{\partial t} = \frac{\partial}{\...
6
votes
1answer
161 views

Can heat distribution in an optical element irradiated by laser be oscillating?

I am modelling a heat distribution in optical element irradiated by laser. System is radially symmetric, and element is thin, i.e. heat value depends only on distance from center. Heat is received via ...
6
votes
2answers
1k views

9-point stencil finite difference Laplacian with variable diffusion coefficients

So I'm trying to implement a 9-point stencil discretization to the 2D difussion equation. The stencil is here. However, most of the literature deals with a Laplacian that has a constant diffusion ...
5
votes
2answers
173 views

Is this system of diffusion equations well-posed?

I’m using a standard Crank-Nicholson algorithm to solve this system of two coupled diffusion equations: $\dot{u} - \dot{v} = \frac{\partial}{\partial x} \left( \alpha(x) \frac{\partial u}{\partial x} ...
5
votes
2answers
678 views

Are the drift-diffusion equations from semiconductor physics analogous to solving an advection-diffusion problem?

I am trying to understand an extra terms that appears when I derive the drift-diffusion equations for semiconductors. The extra term (see below) comes from applying the chain rule to the advection ...
4
votes
2answers
206 views

Mean-squared displacement in Monte Carlo studies

Is measuring mean-squared-displacement in Monte Carlo simulations uncommon? I'm very interested to find out if this has actually ever been tried. For instance, in the context of spheres, or ...
4
votes
2answers
571 views

Diffusion coefficient when simulating in 2D

Suppose I want to simulate the well-known diffusion partial differential equation in 2D, for example with finite elements or finite differences. Can I directly take physical diffusion coefficients ...
4
votes
1answer
2k views

Numerical solution of non-linear diffusion equation via finite-difference with the Crank-Nicolson method

I want to numerically solve the non-linear diffusion equation: $$ \frac{\partial}{\partial t} T(x,t)= \frac{\partial}{\partial x}\left(T^{5/2} \frac{\partial T}{\partial x} \right) $$ I want to use ...
4
votes
1answer
210 views

The most efficient way to solve diffusion equation with concentrated initial condition

I want to solve the diffusion equation, i.e. $$ \dot{f} - f'' = 0 $$ with a boundary condition $f(0) = f(1) = 0$ and with an initial condition that $f$ is a boxcar function concentrated over some ...
4
votes
1answer
475 views

Two approaches to solving diffusion equation in Fourier space

I want to numerically solve the diffusion equation $\partial_t u = D \partial_x^2 u$ in Fourier space, and can think of multiple ways to do it. Setup Option 1 Differentiating $u$ twice in Fourier ...
3
votes
1answer
222 views

High frequency noise at solving diffusion equation

I'm trying to simulate a simple diffusion based on Fick's 2nd law. ...
3
votes
2answers
781 views

Molecular Dynamics: Diffusion with PBC

How can I implement the computation of the diffusion coefficient $D$ using periodic boundary conditions (PBC)? I use molecular dynamics of a set of $nboby$ particles with positions $pos(3,nbody)$ in ...
3
votes
1answer
116 views

Diffusion properties of hard spheres in Monte Carlo simulation

In standard Monte Carlo simulations, say for hard sphere systems, how should one compute the mean-squared displacement of the spheres in order to extract dynamical properties such as the diffusion ...
3
votes
0answers
99 views

How to account for the interface between two different phases in a discretized diffusion model?

I have tried to set up a model for the diffusion of a gas into a liquid. The two media are next to each other and the geometry is spherical because the system should simulate the diffusion out of a ...
3
votes
0answers
181 views

Spurious oscillations in diffusion-reaction problems with finite volume

I have successfully solved the multi-species diffusion-reaction equation \begin{equation} \frac{\partial c_i}{\partial t} = \nabla \cdot (d_i(x)\nabla c_i) + s_i(x,t), \quad \quad (1) \end{equation} ...
2
votes
2answers
684 views

Determining if samples fit a 3D Gaussian distribution

I have a collection of sample particles, with (x,y,z) coordinates generated by a simplified Monte Carlo-like code. I expect that these particles will follow an anisotropic diffusion process, which ...
2
votes
1answer
128 views

Problem with Richardson extrapolation method for weak convergence in SDE

I have implemented the Richardson extrapolation of the Euler-Maruyama method to 4th order, to estimate the moments of SDE. The Euler-Maruyama works, and I would expect the Richardson extrapolation to ...
2
votes
1answer
174 views

Not getting correct numerical solution for Advection-Diffusion-Reaction eqn

Objective: I am trying to numerically solve $C(x,y,t)$ from the following advection-diffusion-reaction equation in 2D space (x,y) and time. I will be testing my numerical solution with an approximate ...
2
votes
1answer
127 views

Modified diffusion equation and unstabilities

I am trying to simulate the phase separation of a binary mixture. If the free energy F is known as a function of the concentration $c$, the dynamical equation is: $ \frac{\partial c(x,t)}{\partial t}=...
2
votes
2answers
232 views

Model of heat sink problem with fan

I am trying to solve this problem using advection-diffusion model and finite element method for the solution, due to the complex geometry. Basically the problem i'm trying to solve using OpenFOAM is ...
2
votes
2answers
348 views

Neumann boundary conditions diffusion equations methods of lines

I want to solve the diffusion equation using the method of lines with Neumann boundary conditions $$ \frac{\partial p}{\partial t}=\frac{\partial^2p}{\partial x^2}\\ \frac{\partial p}{\partial x}(x=0)=...
2
votes
2answers
332 views

Computing element stiffness matrices with variable coefficients

I am trying to implement a simple FEM approach, using p1 triangular elements, for solving the diffusion equation with variable nodal diffusivities and I was wondering how to incorporate the variable ...
2
votes
0answers
72 views

Numerical solution to N-dimensional diffusion on simplex?

Assume I have a system of at least (but generally only) $N+1$ points in an $N$-dimensional space ($N > 3$ is possible). At each of these points $x_i, i=1,...,N+1$ I know an initial potential/...
2
votes
0answers
66 views

Harmonic average of Diffusion Tensors in Finite Volume Method

I want to implement a Bilinear Finite Volume discretisation of the anisotropic diffusion problem: $$\frac{du}{dt} = \nabla \cdot (\textbf{D} \nabla u)$$ Both my degrees of freedom as well as the ...
2
votes
0answers
220 views

1 D Diffusion equation FDM with different layers

I'm trying to solve this particular equation $\frac{\partial u}{\partial t} = \frac{\partial}{\partial x} \big[D_{i}(x)\frac{\partial u}{\partial x} \big] + S(x,t)$ where the $i$ index denotes ...
1
vote
1answer
69 views

Transforming a 1D cartesian variable-coefficient diffusion code into a 1D adially symmetric one

So I have a code that I use which solves a 1D variable coefficient diffusion problem in cartesian coordinates: $\frac{\partial u}{\partial t}=\frac{\partial}{\partial x}\left(D(x)\frac{\partial u}{\...
1
vote
1answer
56 views

What is the right way to set up two random tensor fields which have an identical average diffusivity

I want to compare some properties of traveling waves through two randomly diffusive media. The traveling waves follow the fisher equation: $$\frac{du}{dt} = \nabla(\mathbf{D}_{\gamma} \nabla u) + u(1-...
1
vote
1answer
64 views

Numerical methods for non-linear diffusion

I have the following non-linear diffusion equation, for $\ z(x,t)$: $\ z_t = -C(\sin(\omega t))^m x^{hm}(hm x^{-1}(z_x)^n + n z_{xx} (z_x)^{n-1}) $ Any advice for numerical (or analytical) solutions?...
1
vote
1answer
3k views

How to simulate 3D diffusion in python?

I want to simulate a simple 3D diffusion (e.g., an ink released from one side of a vessel) using SciPy. There are some tutorials for one-dimensional diffusion. ...
1
vote
3answers
383 views

2D simulation of a particle with different diffusion coefficient in different directions of the particle

How can one simulate diffusion of a particle which has a natural axis and diffusion coefficient of the particle in the direction of the axis is D_1 and in perpendicular to the axis is D_2? Could ...
1
vote
1answer
74 views

Reaction-Diffusion problem A->B, solving for B

I need to solve a Reaction-Diffusion using Finite Elements, piecewise linear elements. In this problem, a reaction $A \rightarrow B$, with rate law $ r_A = - k_A \cdot u_A $, takes part, where $u_i$ ...
1
vote
2answers
1k views

How to handle floating point operations in HLSL?

I'm trying to write a perona malik anisotropic diffusion filter for the GPU. I'm basing my shader off a matlab implementation of the filter. I'm running into trouble because of what I suspect is ...
1
vote
1answer
52 views

Minimizing the used memory in diffusion simulation using Python

I am recently dealing with a diffusion simulation project and I have come up with the following code: ...
1
vote
1answer
99 views

Analytical testcase for 2D/3D anisotropic Diffusion (Heat Kernel)

I want to verify and compare different Discretizations of the anisotropic diffusion equation in 2D / 3D. In order to both test the timestepping and the spatial discretisations I had a look at using ...
1
vote
2answers
192 views

Conservation violation in axisymmetric Diffusion Equation

1d diffusion equation Integrating the diffusion equation, $$ \frac{\partial u}{\partial t} = D \frac{\partial^2 u}{\partial x^2}, $$ with a constant diffusion coefficient D using forward Euler for ...
1
vote
2answers
140 views

Computational Physics: Finding the Diffusion Coefficient from the Discretized Diffusion Equation

I'm pretty new to translating simulation to reality so please forgive the perhaps naive approach I'm taking here. If we have a (quasi-2D) experimental video of a certain concentration changing with ...
1
vote
1answer
265 views

Unfolding folded trajectories for Diffusivity calculation - MD

I have just started using dl_poly classic to work in Molecular Dynamics simulations. It produces a HISTORY file which records the trajectory after applying boundary conditions. Now, here I don't ...
1
vote
0answers
23 views

Setting up diffusion with integral B.C. in Fenics

I'm trying to model diffusion through a cylindrical domain $D = \{ (x,y,z) : x^2 + y^2 \leq 1, \;\; 0 \leq z \leq 1\}$. The is an initial concentration of the diffusant at the upper flat surface, ...
1
vote
0answers
39 views

Limit to volume change in a discretized mathematical model?

I have set up a mathematical model describing the diffusion of ozone out of a gas bubble. The bubble is surrounded by a thin gas film. So actually, the model describes the diffusion of ozone through ...
1
vote
0answers
150 views

Neumann boundary condition FD implementation for instationnary diffusion equation

I am trying to solve this diffusion equation : $\dfrac{\partial D\dfrac{\partial f}{\partial x}}{\partial x}+S = \dfrac{\partial f}{\partial t}$ ($D$ is not constant and varies according to $x$) with ...
1
vote
0answers
104 views

Hello word in FEniCS? [closed]

I am trying to start using FEniCS, but have a problem with the simple hello world examples given in the books. Could you please give me the simplest hello world ...
1
vote
0answers
46 views

How is the Gastner-Newman equation implemented to create value-by-area cartograms?

There is a paper called "Density-equalizing map projections: Diffusion-based algorithm and applications" by Michael T. Gastner and M. E. J. Newman, which explains their algorithm (which is based in ...
1
vote
0answers
57 views

elliptic equation with exponential coefficient

I'm trying to solve the following equation $$\dfrac{\partial}{\partial x}\left(e^{au}\dfrac{\partial u}{\partial x}\right) = 0$$ Of course, this equation can be solved analytically. I am trying to ...
1
vote
0answers
202 views

Reaction-diffusion equations

I'm simulating a biological phenomena with reaction diffusion equations. There are multiple diffusing materials and there are some complex relations about consumption and production of such materials. ...
1
vote
0answers
130 views

Discontinuity at Interface

The equation at the left of the interface is \begin{equation} \displaystyle\frac{\partial C_i}{\partial t} = D_i \nabla^2 C_i - z_i \frac{D_i}{RT}F \nabla \cdot (C_i \nabla \phi_2) \end{equation} ...
1
vote
0answers
107 views

Reducing oscillations a 3D Alternating direction explicit scheme for the diffusion equation?

Hi I have made a 3D alternating direction explicit scheme for solving the diffusion equation, which will eventually replace a FTCS scheme in model of bubble dynamics in tissue. I have been testing it ...