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% 
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% Copyright (c) 20032010 by University of Queensland 
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% Earth Systems Science Computational Center (ESSCC) 
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% http://www.uq.edu.au/esscc 
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% 
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% Primary Business: Queensland, Australia 
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% Licensed under the Open Software License version 3.0 
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\begin{figure}[h!] 
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\centerline{\includegraphics[width=4.in]{figures/onedheatdiff001}} 
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\caption{Example 1: Temperature differential along a single interface between 
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two granite blocks.} 
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\label{fig:onedgbmodel} 
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\end{figure} 
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\section{Example 1: One Dimensional Heat Diffusion in Granite} 
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\label{Sec:1DHDv00} 
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The first model consists of two blocks of isotropic material, for instance 
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granite, sitting next to each other. 
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Initial temperature in \textit{Block 1} is \verbT1 and in \textit{Block 2} is 
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\verbT2. 
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We assume that the system is insulated. 
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What would happen to the temperature distribution in each block over time? 
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Intuition tells us that heat will be transported from the hotter block to the 
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cooler one until both 
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blocks have the same temperature. 
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\subsection{1D Heat Diffusion Equation} 
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We can model the heat distribution of this problem over time using the one 
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dimensional heat diffusion equation\footnote{A detailed discussion on how the 
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heat diffusion equation is derived can be found at 
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\url{ 
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http://online.redwoods.edu/instruct/darnold/DEProj/sp02/AbeRichards/paper.pdf}}; 
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which is defined as: 
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\begin{equation} 
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\rho c_p \frac{\partial T}{\partial t}  \kappa \frac{\partial^{2} 
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T}{\partial x^{2}} = q_H 
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\label{eqn:hd} 
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\end{equation} 
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where $\rho$ is the material density, $c_p$ is the specific heat and 
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$\kappa$ is the thermal 
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conductivity\footnote{A list of some common thermal conductivities is available 
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from Wikipedia 
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\url{http://en.wikipedia.org/wiki/List_of_thermal_conductivities}}. Here we 
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assume that these material 
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parameters are \textbf{constant}. 
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The heat source is defined by the right hand side of \refEq{eqn:hd} as 
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$q_{H}$; this can take the form of a constant or a function of time and 
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space. For example $q_{H} = q_{0}e^{\gamma t}$ where we have 
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the output of our heat source decaying with time. There are also two partial 
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derivatives in \refEq{eqn:hd}; $\frac{\partial T}{\partial t}$ describes the 
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change in temperature with time while $\frac{\partial ^2 T}{\partial x^2}$ is 
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the spatial change of temperature. As there is only a single spatial dimension 
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to our problem, our temperature solution $T$ is only dependent on the time $t$ 
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and our signed distance from the blockblock interface $x$. 
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\subsection{PDEs and the General Form} 
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It is possible to solve PDE \refEq{eqn:hd} analytically and obtain an exact 
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solution to our problem. However, it is not always practical to solve the 
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problem this way. Alternatively, computers can be used to find the solution. To 
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do this, a numerical approach is required to discretise 
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the PDE \refEq{eqn:hd} across time and space, this reduces the problem to a 
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finite number of equations for a finite number of spatial points and time steps. 
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These parameters together define the model. While discretisation introduces 
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approximations and a degree of error, a sufficiently sampled model is generally 
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accurate enough to satisfy the accuracy requirements for the final solution. 
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Firstly, we discretise the PDE \refEq{eqn:hd} in time. This leaves us with a 
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steady linear PDE which involves spatial derivatives only and needs to be solved 
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in each time step to progress in time. \esc can help us here. 
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For time discretisation we use the Backward Euler approximation 
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scheme\footnote{see \url{http://en.wikipedia.org/wiki/Euler_method}}. It is 
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based on the approximation 
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\begin{equation} 
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\frac{\partial T(t)}{\partial t} \approx \frac{T(t)T(th)}{h} 
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\label{eqn:beuler} 
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\end{equation} 
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for $\frac{\partial T}{\partial t}$ at time $t$ 
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where $h$ is the time step size. This can also be written as; 
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\begin{equation} 
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\frac{\partial T}{\partial t}(t^{(n)}) \approx \frac{T^{(n)}  T^{(n1)}}{h} 
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\label{eqn:Tbeuler} 
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\end{equation} 
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where the upper index $n$ denotes the n\textsuperscript{th} time step. So one 
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has 
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\begin{equation} 
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\begin{array}{rcl} 
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t^{(n)} & = & t^{(n1)}+h \\ 
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T^{(n)} & = & T(t^{(n1)}) \\ 
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\end{array} 
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\label{eqn:Neuler} 
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\end{equation} 
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Substituting \refEq{eqn:Tbeuler} into \refEq{eqn:hd} we get; 
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\begin{equation} 
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\frac{\rho c_p}{h} (T^{(n)}  T^{(n1)})  \kappa \frac{\partial^{2} 
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T^{(n)}}{\partial x^{2}} = q_H 
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\label{eqn:hddisc} 
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\end{equation} 
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Notice that we evaluate the spatial derivative term at the current time 
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$t^{(n)}$  therefore the name \textbf{backward Euler} scheme. Alternatively, 
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one can evaluate the spatial derivative term at the previous time $t^{(n1)}$. 
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This approach is called the \textbf{forward Euler} scheme. This scheme can 
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provide some computational advantages, which 
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are not discussed here. However, the \textbf{forward Euler} scheme has a major 
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disadvantage. Namely, depending on the 
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material parameters as well as the domain discretization of the spatial 
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derivative term, the time step size $h$ needs to be chosen sufficiently small to 
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achieve a stable temperature when progressing in time. Stability is achieved if 
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the temperature does not grow beyond its initial bounds and becomes 
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nonphysical. 
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The backward Euler scheme, which we use here, is unconditionally stable meaning 
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that under the assumption of a 
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physically correct problem setup the temperature approximation remains physical 
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for all time steps. 
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The user needs to keep in mind that the discretisation error introduced by 
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\refEq{eqn:beuler} 
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is sufficiently small, thus a good approximation of the true temperature is 
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computed. It is therefore very important that any results are viewed with 
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caution. For example, one may compare the results for different time and 
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spatial step sizes. 
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To get the temperature $T^{(n)}$ at time $t^{(n)}$ we need to solve the linear 
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differential equation \refEq{eqn:hddisc} which only includes spatial 
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derivatives. To solve this problem we want to use \esc. 
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In \esc any given PDE can be described by the general form. For the purpose of 
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this introduction we illustrate a simpler version of the general form for full 
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linear PDEs which is available in the \esc user's guide. A simplified form that 
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suits our heat diffusion problem\footnote{The form in the \esc users guide which 
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uses the Einstein convention is written as 
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$(A_{jl} u_{,l})_{,j}+D u =Y$} 
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is described by; 
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\begin{equation}\label{eqn:commonform nabla} 
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\nabla\cdot(A\cdot\nabla u) + Du = f 
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\end{equation} 
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where $A$, $D$ and $f$ are known values and $u$ is the unknown solution. The 
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symbol $\nabla$ which is called the \textit{Nabla operator} or \textit{del 
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operator} represents 
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the spatial derivative of its subject  in this case $u$. Lets assume for a 
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moment that we deal with a onedimensional problem then ; 
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\begin{equation} 
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\nabla = \frac{\partial}{\partial x} 
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\end{equation} 
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and we can write \refEq{eqn:commonform nabla} as; 
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\begin{equation}\label{eqn:commonform} 
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A\frac{\partial^{2}u}{\partial x^{2}} + Du = f 
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\end{equation} 
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if $A$ is constant. To match this simplified general form to our problem 
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\refEq{eqn:hddisc} 
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we rearrange \refEq{eqn:hddisc}; 
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\begin{equation} 
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\frac{\rho c_p}{h} T^{(n)}  \kappa \frac{\partial^2 T^{(n)}}{\partial 
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x^2} = q_H + \frac{\rho c_p}{h} T^{(n1)} 
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\label{eqn:hdgenf} 
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\end{equation} 
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The PDE is now in a form that satisfies \refEq{eqn:commonform nabla} which is 
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required for \esc to solve our PDE. This can be done by generating a solution 
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for successive increments in the time nodes $t^{(n)}$ where 
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$t^{(0)}=0$ and $t^{(n)}=t^{(n1)}+h$ where $h>0$ is the step size and assumed 
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to be constant. 
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In the following the upper index ${(n)}$ refers to a value at time $t^{(n)}$. 
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Finally, by comparing \refEq{eqn:hdgenf} with \refEq{eqn:commonform} one can see 
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that; 
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\begin{equation}\label{ESCRIPT SET} 
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u=T^{(n)}; 
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A = \kappa; D = \frac{\rho c _{p}}{h}; f = q _{H} + \frac{\rho 
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c_p}{h} T^{(n1)} 
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\end{equation} 
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\subsection{Boundary Conditions} 
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\label{SEC BOUNDARY COND} 
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With the PDE sufficiently modified, consideration must now be given to the 
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boundary conditions of our model. Typically there are two main types of boundary 
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conditions known as \textbf{Neumann} and \textbf{Dirichlet} boundary 
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conditions\footnote{More information on Boundary Conditions is available at 
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Wikipedia \url{http://en.wikipedia.org/wiki/Boundary_conditions}}, 
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respectively. 
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A \textbf{Dirichlet boundary condition} is conceptually simpler and is used to 
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prescribe a known value to the unknown solution (in our example the temperature) 
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on parts of the boundary or on the entire boundary of the region of interest. 
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We discuss the Dirichlet boundary condition in our second example presented in 
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Section~\ref{Sec:1DHDv0}. 
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However, for this example we have made the model assumption that the system is 
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insulated, so we need to add an appropriate boundary condition to prevent 
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any loss or inflow of energy at the boundary of our domain. Mathematically this 
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is expressed by prescribing 
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the heat flux $\kappa \frac{\partial T}{\partial x}$ to zero. In our simplified 
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one dimensional model this is expressed 
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in the form; 
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\begin{equation} 
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\kappa \frac{\partial T}{\partial x} = 0 
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\end{equation} 
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or in a more general case as 
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\begin{equation}\label{NEUMAN 1} 
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\kappa \nabla T \cdot n = 0 
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\end{equation} 
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where $n$ is the outer normal field \index{outer normal field} at the surface 
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of the domain. 
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The $\cdot$ (dot) refers to the dot product of the vectors $\nabla T$ and $n$. 
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In fact, the term $\nabla T \cdot n$ is the normal derivative of 
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the temperature $T$. Other notations used here are\footnote{The \esc notation 
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for the normal 
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derivative is $T_{,i} n_i$.}; 
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\begin{equation} 
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\nabla T \cdot n = \frac{\partial T}{\partial n} \; . 
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\end{equation} 
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A condition of the type \refEq{NEUMAN 1} defines a \textbf{Neumann boundary 
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condition} for the PDE. 
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The PDE \refEq{eqn:hdgenf} 
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and the Neumann boundary condition~\ref{eqn:hdgenf} (potentially together with 
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the Dirichlet boundary conditions) define a \textbf{boundary value problem}. 
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It is the nature of a boundary value problem to allow making statements about 
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the solution in the 
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interior of the domain from information known on the boundary only. In most 
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cases we use the term partial differential equation but in fact it is a 
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boundary value problem. 
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It is important to keep in mind that boundary conditions need to be complete and 
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consistent in the sense that 
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at any point on the boundary either a Dirichlet or a Neumann boundary condition 
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must be set. 
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Conveniently, \esc makes a default assumption on the boundary conditions which 
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the user may modify where appropriate. 
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For a problem of the form in~\refEq{eqn:commonform nabla} the default 
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condition\footnote{In the \esc user guide which uses the Einstein convention 
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this is written as 
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$n_{j}A_{jl} u_{,l}=0$.} is; 
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\begin{equation}\label{NEUMAN 2} 
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n\cdot A \cdot\nabla u = 0 
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\end{equation} 
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which is used everywhere on the boundary. Again $n$ denotes the outer normal 
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field. 
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Notice that the coefficient $A$ is the same as in the \esc 
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PDE~\ref{eqn:commonform nabla}. 
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With the settings for the coefficients we have already identified in 
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\refEq{ESCRIPT SET} this 
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condition translates into 
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\begin{equation}\label{NEUMAN 2b} 
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\kappa \frac{\partial T}{\partial x} = 0 
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\end{equation} 
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for the boundary of the domain. This is identical to the Neumann boundary 
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condition we want to set. \esc will take care of this condition for us. We 
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discuss the Dirichlet boundary condition later. 
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\subsection{Outline of the Implementation} 
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\label{sec:outline} 
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To solve the heat diffusion equation (\refEq{eqn:hd}) we write a simple \pyt 
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script. At this point we assume that you have some basic understanding of the 
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\pyt programming language. If not, there are some pointers and links available 
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in Section \ref{sec:escpybas}. The script (discussed in \refSec{sec:key}) has 
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four major steps. Firstly, we need to define the domain where we want to 
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calculate the temperature. For our problem this is the joint blocks of granite 
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which has a rectangular shape. Secondly, we need to define the PDE to solve in 
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each time step to get the updated temperature. Thirdly, we need to define the 
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coefficients of the PDE and finally we need to solve the PDE. The last two steps 
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need to be repeated until the final time marker has been reached. The work flow 
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is described in \reffig{fig:wf}. 
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% \begin{enumerate} 
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% \item create domain 
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% \item create PDE 
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% \item while end time not reached: 
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% \begin{enumerate} 
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% \item set PDE coefficients 
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% \item solve PDE 
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% \item update time marker 
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% \end{enumerate} 
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% \item end of calculation 
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% \end{enumerate} 
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\begin{figure}[h!] 
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\centering 
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\includegraphics[width=1in]{figures/workflow.png} 
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\caption{Workflow for developing an \esc model and solution} 
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\label{fig:wf} 
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\end{figure} 
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In the terminology of \pyt, the domain and PDE are represented by 
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\textbf{objects}. The nice feature of an object is that it is defined by its 
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usage and features 
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rather than its actual representation. So we will create a domain object to 
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describe the geometry of the two 
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granite blocks. Then we define PDEs and spatially distributed values such as the 
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temperature 
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on this domain. Similarly, to define a PDE object we use the fact that one needs 
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only to define the coefficients of the PDE and solve the PDE. The PDE object has 
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advanced features, but these are not required in simple cases. 
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\begin{figure}[htp] 
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\centering 
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\includegraphics[width=6in]{figures/functionspace.pdf} 
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\caption{\esc domain construction overview} 
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\label{fig:fs} 
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\end{figure} 
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\subsection{The Domain Constructor in \esc} 
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\label{ss:domcon} 
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Whilst it is not strictly relevant or necessary, a better understanding of 
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how values are spatially distributed (\textit{e.g.} Temperature) and how PDE 
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coefficients are interpreted in \esc can be helpful. 
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There are various ways to construct domain objects. The simplest form is a 
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rectangular shaped region with a length and height. There is 
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a ready to use function for this named \verb rectangle(). Besides the spatial 
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dimensions this function requires to specify the number of 
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elements or cells to be used along the length and height, see \reffig{fig:fs}. 
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Any spatially distributed value 
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and the PDE is represented in discrete form using this element 
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representation\footnote{We use the finite element method (FEM), see 
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\url{http://en.wikipedia.org/wiki/Finite_element_method} for details.}. 
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Therefore we will have access to an approximation of the true PDE solution 
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only. 
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The quality of the approximation depends  besides other factors  mainly on the 
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number of elements being used. In fact, the 
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approximation becomes better when more elements are used. However, computational 
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cost grows with the number of 
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elements being used. It is therefore important that you find the right balance 
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between the demand in accuracy and acceptable resource usage. 
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In general, one can think about a domain object as a composition of nodes and 
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elements. 
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As shown in \reffig{fig:fs}, an element is defined by the nodes that are used to 
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describe its vertices. 
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To represent spatially distributed values the user can use 
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the values at the nodes, at the elements in the interior of the domain or at the 
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elements located on the surface of the domain. 
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The different approach used to represent values is called \textbf{function 
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space} and is attached to all objects 
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in \esc representing a spatially distributed value such as the solution of 
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a PDE. The three function spaces we use at the moment are; 
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\begin{enumerate} 
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\item the nodes, called by \verbContinuousFunction(domain) ; 
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\item the elements/cells, called by \verbFunction(domain) ; and 
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\item the boundary, called by \verbFunctionOnBoundary(domain). 
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\end{enumerate} 
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A function space object such as \verbContinuousFunction(domain) has the method 
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\verbgetX attached to it. This method returns the 
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location of the socalled \textbf{sample points} used to represent values of the 
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particular function space. So the 
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call \verbContinuousFunction(domain).getX() will return the coordinates of the 
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nodes used to describe the domain while 
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\verbFunction(domain).getX() returns the coordinates of numerical 
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integration points within elements, see \reffig{fig:fs}. 
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This distinction between different representations of spatially distributed 
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values 
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is important in order to be able to vary the degrees of smoothness in a PDE 
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problem. 
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The coefficients of a PDE do not need to be continuous, thus this qualifies as a 
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\verbFunction() type. 
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On the other hand a temperature distribution must be continuous and needs to be 
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represented with a \verbContinuousFunction() function space. 
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An influx may only be defined at the boundary and is therefore a 
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\verbFunctionOnBoundary() object. 
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\esc allows certain transformations of the function spaces. A 
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\verbContinuousFunction() can be transformed into a 
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\verbFunctionOnBoundary() or \verbFunction(). On the other hand there is 
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not enough information in a \verbFunctionOnBoundary() to transform it to a 
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\verbContinuousFunction(). 
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These transformations, which are called \textbf{interpolation} are invoked 
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automatically by \esc if needed. 
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Later in this introduction we discuss how 
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to define specific areas of geometry with different materials which are 
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represented by different material coefficients such as the 
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thermal conductivities $\kappa$. A very powerful technique to define these types 
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of PDE 
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coefficients is tagging. Blocks of materials and boundaries can be named and 
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values can be defined on subregions based on their names. 
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This is a method for simplifying PDE coefficient and flux definitions. It makes 
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scripting much easier and we will discuss this technique in 
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Section~\ref{STEADYSTATE HEAT REFRACTION}. 
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\subsection{A Clarification for the 1D Case} 
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\label{SEC: 1D CLARIFICATION} 
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It is necessary for clarification that we revisit our general PDE from 
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\refeq{eqn:commonform nabla} for a two dimensional domain. \esc is inherently 
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designed to solve problems that are multidimensional and so 
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\refEq{eqn:commonform nabla} needs to be read as a higher dimensional problem. 
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In the case of two spatial dimensions the \textit{Nabla operator} has in fact 
391 


two components $\nabla = (\frac{\partial}{\partial x}, \frac{\partial}{\partial 
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y})$. Assuming the coefficient $A$ is constant, the \refEq{eqn:commonform nabla} 
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takes the following form; 
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\begin{equation}\label{eqn:commonform2D} 
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A_{00}\frac{\partial^{2}u}{\partial x^{2}} 
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A_{01}\frac{\partial^{2}u}{\partial x\partial y} 
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A_{10}\frac{\partial^{2}u}{\partial y\partial x} 
398 


A_{11}\frac{\partial^{2}u}{\partial y^{2}} 
399 
gross 
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+ Du = f 
400 


\end{equation} 
401 
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Notice that for the higher dimensional case $A$ becomes a matrix. It is also 
402 
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important to notice that the usage of the Nabla operator creates 
403 


a compact formulation which is also independent from the spatial dimension. 
404 
artak 
2963 
To make the general PDE \refEq{eqn:commonform2D} one dimensional as 
405 
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shown in \refEq{eqn:commonform} we need to set 
406 
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2606 
\begin{equation} 
407 
jfenwick 
3308 
A_{00}=A; A_{01}=A_{10}=A_{11}=0 
408 
gross 
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\end{equation} 
409 



410 
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2867 

411 
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\subsection{Developing a PDE Solution Script} 
412 
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\label{sec:key} 
413 
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2949 
\sslist{example01a.py} 
414 
ahallam 
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We write a simple \pyt script which uses the \modescript, \modfinley and \modmpl 
415 


modules. 
416 


By developing a script for \esc, the heat diffusion equation can be solved at 
417 


successive time steps for a predefined period using our general form 
418 


\refEq{eqn:hdgenf}. Firstly it is necessary to import all the 
419 


libraries\footnote{The libraries contain predefined scripts that are required to 
420 


solve certain problems, these can be simple like sine and cosine functions or 
421 


more complicated like those from our \esc library.} 
422 
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that we will require. 
423 
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\begin{python} 
424 
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from esys.escript import * 
425 
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# This defines the LinearPDE module as LinearPDE 
426 


from esys.escript.linearPDEs import LinearPDE 
427 


# This imports the rectangle domain function from finley. 
428 


from esys.finley import Rectangle 
429 


# A useful unit handling package which will make sure all our units 
430 


# match up in the equations under SI. 
431 


from esys.escript.unitsSI import * 
432 
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\end{python} 
433 
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It is generally a good idea to import all of the \modescript library, although 
434 


if the functions and classes required are known they can be specified 
435 


individually. The function \verbLinearPDE has been imported explicitly for 
436 


ease of use later in the script. \verbRectangle is going to be our type of 
437 
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2982 
domain. The module \verbunitsSI provides support for SI unit definitions with 
438 
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2979 
our variables. 
439 
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440 
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Once our library dependencies have been established, defining the problem 
441 


specific variables is the next step. In general the number of variables needed 
442 


will vary between problems. These variables belong to two categories. They are 
443 


either directly related to the PDE and can be used as inputs into the \esc 
444 


solver, or they are script variables used to control internal functions and 
445 


iterations in our problem. For this PDE there are a number of constants which 
446 


need values. Firstly, the domain upon which we wish to solve our problem needs 
447 


to be defined. There are different types of domains in \modescript which we 
448 


demonstrate in later tutorials but for our granite blocks, we simply use a 
449 


rectangular domain. 
450 
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Using a rectangular domain simplifies our granite blocks (which would in reality 
452 


be a \textit{3D} object) into a single dimension. The granite blocks will have a 
453 


lengthways cross section that looks like a rectangle. As a result we do not 
454 


need to model the volume of the block due to symmetry. There are four arguments 
455 


we must consider when we decide to create a rectangular domain, the domain 
456 


\textit{length}, \textit{width} and \textit{step size} in each direction. When 
457 


defining the size of our problem it will help us determine appropriate values 
458 


for our model arguments. If we make our dimensions large but our step sizes very 
459 


small we increase the accuracy of our solution. Unfortunately we also increase 
460 


the number of calculations that must be solved per time step. This means more 
461 


computational time is required to produce a solution. In this \textit{1D} 
462 


problem, the bar is defined as being 1 metre long. An appropriate step size 
463 
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\verbndx would be 1 to 10\% of the length. Our \verbndy needs only be 1, 
464 


this is because our problem stipulates no partial derivatives in the $y$ 
465 


direction. 
466 
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Thus the temperature does not vary with $y$. Hence, the model parameters can be 
467 
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defined as follows; note we have used the \verbunitsSI convention to make sure 
468 
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all our input units are converted to SI. 
469 
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\begin{python} 
470 
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mx = 500.*m #meters  model length 
471 


my = 100.*m #meters  model width 
472 


ndx = 50 # mesh steps in x direction 
473 


ndy = 1 # mesh steps in y direction 
474 


boundloc = mx/2 # location of boundary between the two blocks 
475 
ahallam 
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\end{python} 
476 
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The material constants and the temperature variables must also be defined. For 
477 


the granite in the model they are defined as: 
478 
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\begin{python} 
479 
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#PDE related 
480 
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rho = 2750. *kg/m**3 #kg/m^{3} density of iron 
481 


cp = 790.*J/(kg*K) # J/Kg.K thermal capacity 
482 
gross 
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rhocp = rho*cp 
483 
gross 
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kappa = 2.2*W/m/K # watts/m.Kthermal conductivity 
484 
gross 
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qH=0 * J/(sec*m**3) # J/(sec.m^{3}) no heat source 
485 
gross 
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T1=20 * Celsius # initial temperature at Block 1 
486 


T2=2273. * Celsius # base temperature at Block 2 
487 
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\end{python} 
488 
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Finally, to control our script we will have to specify our timing controls and 
489 


where we would like to save the output from the solver. This is simple enough: 
490 
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\begin{python} 
491 
gross 
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t=0 * day #our start time, usually zero 
492 


tend=1. * day #  time to end simulation 
493 
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outputs = 200 # number of time steps required. 
494 


h=(tendt)/outputs #size of time step 
495 
ahallam 
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#user warning statement 
496 


print "Expected Number of time outputs is: ", (tendt)/h 
497 


i=0 #loop counter 
498 
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\end{python} 
499 
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Now that we know our inputs we will build a domain using the 
500 
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\verbRectangle() function from \FINLEY. The four arguments allow us to 
501 


define our domain \verbmodel as: 
502 
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\begin{python} 
503 
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#generate domain using rectangle 
504 
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blocks = Rectangle(l0=mx,l1=my,n0=ndx, n1=ndy) 
505 
ahallam 
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\end{python} 
506 
caltinay 
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\verbblocks now describes a domain in the manner of Section \ref{ss:domcon}. 
507 
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508 
caltinay 
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With a domain and all the required variables established, it is now possible to 
509 
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set up our PDE so that it can be solved by \esc. The first step is to define the 
510 


type of PDE that we are trying to solve in each time step. In this example it is 
511 
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a single linear PDE\footnote{in contrast to a system of PDEs which we discuss 
512 
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later.}. We also need to state the values of our general form variables. 
513 
ahallam 
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\begin{python} 
514 
gross 
2905 
mypde=LinearPDE(blocks) 
515 
gross 
2878 
A=zeros((2,2))) 
516 


A[0,0]=kappa 
517 
gross 
2905 
mypde.setValue(A=A, D=rhocp/h) 
518 
ahallam 
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\end{python} 
519 
caltinay 
2982 
In many cases it may be possible to decrease the computational time of the 
520 
ahallam 
2979 
solver if the PDE is symmetric. 
521 
gross 
2878 
Symmetry of a PDE is defined by; 
522 
ahallam 
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\begin{equation}\label{eqn:symm} 
523 
jfenwick 
3308 
A_{jl}=A_{lj} 
524 
ahallam 
2495 
\end{equation} 
525 
ahallam 
2979 
Symmetry is only dependent on the $A$ coefficient in the general form and the 
526 


other coefficients $D$ as well as the right hand side $Y$. From the above 
527 
caltinay 
2982 
definition we can see that our PDE is symmetric. The \verbLinearPDE class 
528 
ahallam 
2979 
provides the method \method{checkSymmetry} to check if the given PDE is 
529 


symmetric. As our PDE is symmetrical we enable symmetry via; 
530 
ahallam 
2775 
\begin{python} 
531 
caltinay 
2982 
myPDE.setSymmetryOn() 
532 
ahallam 
2775 
\end{python} 
533 
ahallam 
2979 
Next we need to establish the initial temperature distribution \verbT. We need 
534 


to 
535 


assign the value \verbT1 to all sample points left to the contact interface at 
536 
jfenwick 
3308 
$x_{0}=\frac{mx}{2}$ 
537 
gross 
2905 
and the value \verbT2 right to the contact interface. \esc 
538 
caltinay 
2982 
provides the \verbwhereNegative function to construct this. More 
539 


specifically, \verbwhereNegative returns the value $1$ at those sample points 
540 


where the argument has a negative value. Otherwise zero is returned. 
541 
jfenwick 
3308 
If \verbx are the $x_{0}$ 
542 
gross 
2905 
coordinates of the sample points used to represent the temperature distribution 
543 


then \verbx[0]boundloc gives us a negative value for 
544 


all sample points left to the interface and nonnegative value to 
545 


the right of the interface. So with; 
546 
gross 
2878 
\begin{python} 
547 


# ... set initial temperature .... 
548 
gross 
2905 
T= T1*whereNegative(x[0]boundloc)+T2*(1whereNegative(x[0]boundloc)) 
549 
gross 
2878 
\end{python} 
550 
ahallam 
2979 
we get the desired temperature distribution. To get the actual sample points 
551 
caltinay 
2982 
\verbx we use the \verbgetX() method of the function space 
552 


\verbSolution(blocks) which is used to represent the solution of a PDE; 
553 
gross 
2878 
\begin{python} 
554 
gross 
2905 
x=Solution(blocks).getX() 
555 


\end{python} 
556 
ahallam 
2979 
As \verbx are the sample points for the function space 
557 


\verbSolution(blocks) 
558 


the initial temperature \verbT is using these sample points for 
559 


representation. 
560 


Although \esc is trying to be forgiving with the choice of sample points and to 
561 
caltinay 
2982 
convert 
562 
ahallam 
2979 
where necessary the adjustment of the function space is not always possible. So 
563 
caltinay 
2982 
it is advisable to make a careful choice on the function space used. 
564 
gross 
2905 

565 
ahallam 
2979 
Finally we initialise an iteration loop to solve our PDE for all the time steps 
566 


we specified in the variable section. As the right hand side of the general form 
567 


is dependent on the previous values for temperature \verb T across the bar this 
568 


must be updated in the loop. Our output at each time step is \verb T the heat 
569 


distribution and \verb totT the total heat in the system. 
570 
gross 
2905 
\begin{python} 
571 
gross 
2878 
while t < tend: 
572 


i+=1 #increment the counter 
573 


t+=h #increment the current time 
574 


mypde.setValue(Y=qH+rhocp/h*T) # set variable PDE coefficients 
575 


T=mypde.getSolution() #get the PDE solution 
576 


totE = integrate(rhocp*T) #get the total heat (energy) in the system 
577 


\end{python} 
578 
ahallam 
2979 
The last statement in this script calculates the total energy in the system as 
579 
jfenwick 
3308 
the volume integral of $\rho c_{p} T$ over the block. 
580 
caltinay 
2982 
As the blocks are insulated no energy should be lost or added. 
581 
gross 
2905 
The total energy should stay constant for the example discussed here. 
582 
ahallam 
2401 

583 
gross 
2905 
\subsection{Running the Script} 
584 
ahallam 
2975 
The script presented so far is available under 
585 
gross 
2949 
\verbexample01a.py. You can edit this file with your favourite text editor. 
586 
caltinay 
2982 
On most operating systems\footnote{The \texttt{runescript} launcher is not 
587 


supported under {\it MS Windows} yet.} you can use the 
588 
ahallam 
2979 
\program{runescript} command 
589 
gross 
2905 
to launch {\it escript} scripts. For the example script use; 
590 


\begin{verbatim} 
591 
gross 
2949 
runescript example01a.py 
592 
gross 
2905 
\end{verbatim} 
593 


The program will print a progress report. Alternatively, you can use 
594 


the python interpreter directly; 
595 


\begin{verbatim} 
596 
gross 
2949 
python example01a.py 
597 
gross 
2905 
\end{verbatim} 
598 
caltinay 
2982 
if the system is configured correctly (please talk to your system 
599 
ahallam 
2979 
administrator). 
600 
gross 
2905 

601 
gross 
2878 
\subsection{Plotting the Total Energy} 
602 
gross 
2949 
\sslist{example01b.py} 
603 
gross 
2878 

604 
ahallam 
2979 
\esc does not include its own plotting capabilities. However, it is possible to 
605 


use a variety of free \pyt packages for visualisation. 
606 


Two types will be demonstrated in this cookbook; 
607 


\mpl\footnote{\url{http://matplotlib.sourceforge.net/}} and 
608 
caltinay 
2982 
\verbVTK\footnote{\url{http://www.vtk.org/}}. 
609 
ahallam 
2979 
The \mpl package is a component of SciPy\footnote{\url{http://www.scipy.org}} 
610 


and is good for basic graphs and plots. 
611 
caltinay 
2982 
For more complex visualisation tasks, in particular two and three dimensional 
612 
ahallam 
2979 
problems we recommend the use of more advanced tools. For instance, \mayavi 
613 


\footnote{\url{http://code.enthought.com/projects/mayavi/}} 
614 
ahallam 
2975 
which is based upon the \verbVTK toolkit. The usage of \verbVTK based 
615 
caltinay 
2982 
visualisation is discussed in Chapter~\ref{Sec:2DHD} which focuses on a two 
616 
ahallam 
2979 
dimensional PDE. 
617 
gross 
2878 

618 
ahallam 
2979 
For our simple granite block problem, we have two plotting tasks. Firstly, we 
619 


are interested in showing the 
620 


behaviour of the total energy over time and secondly, how the temperature 
621 
caltinay 
2982 
distribution within the block is developing over time. 
622 


Let us start with the first task. 
623 
gross 
2878 

624 
caltinay 
2982 
The idea is to create a record of the time marks and the corresponding total 
625 
ahallam 
2979 
energies observed. 
626 
gross 
2878 
\pyt provides the concept of lists for this. Before 
627 
ahallam 
2979 
the time loop is opened we create empty lists for the time marks \verbt_list 
628 


and the total energies \verbE_list. 
629 


After the new temperature has been calculated by solving the PDE we append the 
630 


new time marker and the total energy value for that time 
631 


to the corresponding list using the \verbappend method. With these 
632 


modifications our script looks as follows: 
633 
ahallam 
2775 
\begin{python} 
634 
gross 
2878 
t_list=[] 
635 


E_list=[] 
636 


# ... start iteration: 
637 


while t<tend: 
638 


t+=h 
639 


mypde.setValue(Y=qH+rhocp/h*T) # set variable PDE coefficients 
640 


T=mypde.getSolution() #get the PDE solution 
641 


totE=integrate(rhocp*T) 
642 


t_list.append(t) # add current time mark to record 
643 


E_list.append(totE) # add current total energy to record 
644 
ahallam 
2775 
\end{python} 
645 
ahallam 
2979 
To plot $t$ over $totE$ we use \mpl a module contained within \pylab which needs 
646 
caltinay 
2982 
to be loaded before use; 
647 
ahallam 
2775 
\begin{python} 
648 
gross 
2878 
import pylab as pl # plotting package. 
649 
ahallam 
2775 
\end{python} 
650 
caltinay 
2982 
Here we are not using \verbfrom pylab import * in order to avoid name 
651 


clashes for function names within \esc. 
652 
ahallam 
2401 

653 
ahallam 
2979 
The following statements are added to the script after the time loop has been 
654 


completed; 
655 
ahallam 
2775 
\begin{python} 
656 
gross 
2878 
pl.plot(t_list,E_list) 
657 


pl.title("Total Energy") 
658 
gross 
2905 
pl.axis([0,max(t_list),0,max(E_list)*1.1]) 
659 
gross 
2878 
pl.savefig("totE.png") 
660 
ahallam 
2775 
\end{python} 
661 
ahallam 
2979 
The first statement hands over the time marks and corresponding total energies 
662 
caltinay 
2982 
to the plotter. 
663 


The second statement sets the title for the plot. The third statement 
664 
ahallam 
2979 
sets the axis ranges. In most cases these are set appropriately by the plotter. 
665 



666 
caltinay 
2982 
The last statement generates the plot and writes the result into the file 
667 


\verbtotE.png which can be displayed by (almost) any image viewer. 
668 
ahallam 
2979 
As expected the total energy is constant over time, see 
669 


\reffig{fig:onedheatout1}. 
670 
ahallam 
2401 

671 
ahallam 
3029 
\begin{figure} 
672 


\begin{center} 
673 


\includegraphics[width=4in]{figures/ttblockspyplot150} 
674 


\caption{Example 1b: Total Energy in the Blocks over Time (in seconds)} 
675 


\label{fig:onedheatout1} 
676 


\end{center} 
677 


\end{figure} 
678 


\clearpage 
679 



680 
gross 
2878 
\subsection{Plotting the Temperature Distribution} 
681 
gross 
2931 
\label{sec: plot T} 
682 
gross 
2949 
\sslist{example01c.py} 
683 
ahallam 
2979 
For plotting the spatial distribution of the temperature we need to modify the 
684 
caltinay 
2982 
strategy we have used for the total energy. 
685 


Instead of producing a final plot at the end we will generate a 
686 
ahallam 
2979 
picture at each time step which can be browsed as a slide show or composed into 
687 


a movie. 
688 


The first problem we encounter is that if we produce an image at each time step 
689 
caltinay 
2982 
we need to make sure that the images previously generated are not overwritten. 
690 
gross 
2878 

691 
ahallam 
2979 
To develop an incrementing file name we can use the following convention. It is 
692 
caltinay 
2982 
convenient to put all image files showing the same variable  in our case the 
693 


temperature distribution  into a separate directory. 
694 


As part of the \verbos module\footnote{The \texttt{os} module provides 
695 
ahallam 
2979 
a powerful interface to interact with the operating system, see 
696 


\url{http://docs.python.org/library/os.html}.} \pyt 
697 
caltinay 
2982 
provides the \verbos.path.join command to build file and directory names in a 
698 


platform independent way. Assuming that 
699 


\verbsave_path is the name of the directory we want to put the results in the 
700 


command is; 
701 
ahallam 
2775 
\begin{python} 
702 
gross 
2878 
import os 
703 


os.path.join(save_path, "tempT%03d.png"%i ) 
704 
ahallam 
2775 
\end{python} 
705 
gross 
2878 
where \verbi is the time step counter. 
706 
caltinay 
2982 
There are two arguments to the \verbjoin command. The \verbsave_path 
707 


variable is a predefined string pointing to the directory we want to save our 
708 


data, for example a single subfolder called \verbdata would be defined by; 
709 
gross 
2878 
\begin{verbatim} 
710 


save_path = "data" 
711 


\end{verbatim} 
712 
caltinay 
2982 
while a subfolder of \verbdata called \verbexample01 would be defined by; 
713 
gross 
2878 
\begin{verbatim} 
714 
gross 
2949 
save_path = os.path.join("data","example01") 
715 
gross 
2878 
\end{verbatim} 
716 
caltinay 
2982 
The second argument of \verbjoin contains a string which is the file 
717 
ahallam 
2979 
name or subdirectory name. We can use the operator \verb% to use the value of 
718 
caltinay 
2982 
\verbi as part of our filename. The substring \verb%03d indicates that we 
719 


want to substitute a value into the name; 
720 
gross 
2878 
\begin{itemize} 
721 
jfenwick 
2961 
\item \verb 0 means that small numbers should have leading zeroes; 
722 
ahallam 
2979 
\item \verb 3 means that numbers should be written using at least 3 digits; 
723 


and 
724 
caltinay 
2982 
\item \verb d means that the value to substitute will be a decimal integer. 
725 
gross 
2878 
\end{itemize} 
726 
caltinay 
2982 
To actually substitute the value of \verbi into the name write \verb%i after 
727 
ahallam 
2979 
the string. 
728 
caltinay 
2982 
When done correctly, the output files from this command will be placed in the 
729 
ahallam 
2979 
directory defined by \verb save_path as; 
730 
gross 
2878 
\begin{verbatim} 
731 
jfenwick 
2961 
blockspyplot001.png 
732 


blockspyplot002.png 
733 


blockspyplot003.png 
734 
gross 
2878 
... 
735 


\end{verbatim} 
736 


and so on. 
737 



738 


A subfolder check/constructor is available in \esc. The command; 
739 


\begin{verbatim} 
740 


mkDir(save_path) 
741 


\end{verbatim} 
742 
caltinay 
2982 
will check for the existence of \verb save_path and if missing, create the 
743 
ahallam 
2979 
required directories. 
744 
gross 
2878 

745 
artak 
2964 
We start by modifying our solution script. 
746 
caltinay 
2982 
Prior to the \verbwhile loop we need to extract our finite solution 
747 
ahallam 
2979 
points to a data object that is compatible with \mpl. First we create the node 
748 


coordinates of the sample points used to represent 
749 


the temperature as a \pyt list of tuples or a \numpy array as requested by the 
750 


plotting function. 
751 


We need to convert the array \verbx previously set as 
752 


\verbSolution(blocks).getX() into a \pyt list 
753 
jfenwick 
3308 
and then to a \numpy array. The $x_{0}$ component is then extracted via 
754 
ahallam 
2979 
an array slice to the variable \verbplx; 
755 
ahallam 
2775 
\begin{python} 
756 
gross 
2878 
import numpy as np # array package. 
757 


#convert solution points for plotting 
758 
gross 
2905 
plx = x.toListOfTuples() 
759 
gross 
2878 
plx = np.array(plx) # convert to tuple to numpy array 
760 


plx = plx[:,0] # extract x locations 
761 
ahallam 
2775 
\end{python} 
762 
gross 
2878 

763 
ahallam 
2645 
\begin{figure} 
764 


\begin{center} 
765 
gross 
2905 
\includegraphics[width=4in]{figures/blockspyplot001} 
766 


\includegraphics[width=4in]{figures/blockspyplot050} 
767 


\includegraphics[width=4in]{figures/blockspyplot200} 
768 
ahallam 
2979 
\caption{Example 1c: Temperature ($T$) distribution in the blocks at time steps 
769 
caltinay 
2982 
$1$, $50$ and $200$} 
770 
ahallam 
2645 
\label{fig:onedheatout} 
771 


\end{center} 
772 


\end{figure} 
773 
ahallam 
3029 
\clearpage 
774 
ahallam 
2645 

775 
ahallam 
2979 
We use the same techniques provided by \mpl as we have used to plot the total 
776 


energy over time. 
777 


For each time step we generate a plot of the temperature distribution and save 
778 


each to a file. 
779 
caltinay 
2982 
The following is appended to the end of the \verbwhile loop and creates one 
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figure of the temperature distribution. We start by converting the solution to a 
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tuple and then plotting this against our \textit{x coordinates} \verbplx we 
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have generated before. We add a title to the diagram before it is rendered into 
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a file. 
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Finally, the figure is saved to a \verb*.png file and cleared for the 
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following iteration. 
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\begin{python} 
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# ... start iteration: 
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while t<tend: 
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.... 
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T=mypde.getSolution() #get the PDE solution 
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tempT = T.toListOfTuples() # convert to a tuple 
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pl.plot(plx,tempT) # plot solution 
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# set scale (Temperature should be between Tref and T0) 
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pl.axis([0,mx,Tref*.9,T0*1.1]) 
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# add title 
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pl.title("Temperature across the blocks at time %e minutes"%(t/day)) 
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#save figure to file 
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pl.savefig(os.path.join(save_path,"tempT","blockspyplot%03d.png") %i) 
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\end{python} 
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Some results are shown in \reffig{fig:onedheatout}. 
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\subsection{Making a Video} 
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Our saved plots from the previous section can be cast into a video using the 
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following command appended to the end of the script. The \verb mencoder command 
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is not available on every platform, so some users need to use an alternative 
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video encoder. 
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\begin{python} 
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# compile the *.png files to create a *.avi video that shows T change 
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# with time. This operation uses Linux mencoder. For other operating 
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# systems it is possible to use your favourite video compiler to 
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# convert image files to videos. 
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os.system("mencoder mf://"+save_path+"/tempT"+"/*.png mf type=png:\ 
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w=800:h=600:fps=25 ovc lavc lavcopts vcodec=mpeg4 oac copy o \ 
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example01tempT.avi") 
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\end{python} 
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