Hello World for Numerical Packages

# Hand Coded Heat

Why use numerical packages...

## At a Glance

Questions Objectives Key Points
What is a numerical algorithm? Implement a simple numerical algorithm.
Use it to solve a simple science problem.
Numerical Packages are used
to solve scientific problems involving PDEs.
What is discretization? Introduce basic concepts in solving continuous
PDEs using discrete computations.
Meshing (or discretization) is an
important first step.
How can numerical packages
help me with my software?
Understand the value numerical packages
offer in developing science applications
Numerical packages offer: rigorous/vetted numerics
greater generality, extreme scalability and more…

#### To begin this lesson

• Go to the directory for the hand-coded heat application
cd HandsOnLessons/hand_coded_heat


## A Simple Science Question

Will my pipes freeze during a long, cold storm?

You keep the inside temperature of the house always at 70 degrees F. But, there is an overnight storm coming. The outside temperature is expected to drop to -40 degrees F for 15.5 hours. Will your pipes freeze before the storm is over?

### Governing Equations

Heat conduction is governed by the partial differential (PDE)… $\frac{\partial u}{\partial t} - \nabla \cdot \alpha \nabla u = 0$

where u is the temperature through the wall at spatial positions, x, and times, t, $$\alpha$$, is the thermal diffusivity of the material(s) comprising the wall. This equation is known as the Diffusion Equation and also the Heat Equation.

We make some simplifying assumptions…

1. The wall can be treated as homogenous in material.
• In effect, we ignore the fact that part of the wall has a pipe filled with water running through it.
2. The thermal diffusivity of the wall material, $$\alpha$$ is constant for all space and time.
3. The only heat source is from initial and/or boundary conditions.
4. We will deal only with the one dimensional problem in Cartesian coordinates.
• That is heat along the dimension through the wall between inside and outside.
5. We will discretize with constant spacing in both space, $$\Delta x$$ and time, $$\Delta t$$.

The PDE simplifies to the one dimensional heat equation… $\frac{\partial u}{\partial t} = \alpha \frac{\partial^2 u}{\partial x^2}$

## Discretization

Using difference equations as approximations for derivatives, we can discretize, independently, the left- and right-hand sides of equation 2

For the left-hand side, we can approximate the first derivative of u with respect to time, t, by the forward difference equation… $\frac{\partial u}{\partial t} \Bigr\vert_{t_{k+1}} \approx \frac{u_i^{k+1}-u_i^k}{\Delta t}$

For the right-hand side, we can approximate the the second derivative of u with respect to space, x, by the centered difference equation… $\alpha \frac{\partial^2 u}{\partial x^2}\Bigr\vert_{x_i} \approx \alpha \frac{u_{i-1}^k-2u_i^k+u_{i+1}^k}{\Delta x^2}$

Setting equations 3 and 4 equal to each other and re-arranging terms, we arrive at the following update scheme for producing the temperatures at the next time, k+1, from temperatures at the current time, k, as $u_i^{k+1} = ru_{i+1}^k+(1-2r)u_i^k+ru_{i-1}^k$

where $$r=\alpha\frac{\Delta t}{\Delta x^2}$$

In the process of discretizing the PDE, we have defined a fixed spacing in x and a fixed spacing in t as shown in the figure here

This is essentially a uniform mesh. Later lessons here address more sophisticated discretizations in space and in time which depart from these often inflexible fixed spacings.

## Exercise #1: Implement FTCS

% ls
args.C    crankn.C  ftcs.C  heat.C  makefile  tools       utils.C
check.sh  exact.C   Half.H  heat.H  Number.H  upwind15.C


The function, solution_update_ftcs, is defined in ftcs.C without its body.

static bool             // false if unstable, true otherwise
solution_update_ftcs(
int n,              // # of temperature samples in space
Number *uk1,        // new temperatures @ t = k+1
Number const *uk0,  // old/last temperatures @ t = k
Number alpha,       // thermal diffusivity
Number dx,          // spacing in space, x
Number dt,          // spacing in time, t
Number bc_0,        // boundary condition @ x=0
Number bc_1         // boundary condition @ x=Lx
)
{


    Number const r = alpha * dt / (dx * dx);

// Sanity check for stability
if (r > 0.5) return false;

// Update the solution using FTCS algorithm
for (int i = 1; i < n-1; i++)
uk1[i] = r*uk0[i+1] + (1-2*r)*uk0[i] + r*uk0[i-1];

// Impose boundary conditions for solution indices 0 & n-1
uk1[0  ] = bc0;
uk1[n-1] = bc1;

return true;


}


Edit ftcs.C and implement the FTCS numerical algorithm by coding the body of this function.

## Exercise #2: Build and Test

To compile the code you have just written…

make heat


#### A note on getting help

% make


without any target specified will display a set of convenient make targets.

Targets:
heat: makes the default heat application (double precision)
heat-half: makes the heat application with half precision
heat-single: makes the heat application with single precision
heat-double: makes the heat application with double precision
heat-long-double: makes the heat application with long-double precision
PTOOL=[gnuplot,matplotlib,visit] RUNAME=<run-dir-name> plot: plots results
check: runs various tests confirming steady-state is linear


% ./heat --help


Usage: ./heat <arg>=<value> <arg>=<value>...
runame="heat_results"               name to give run and results dir (char*)
alpha=0.2         material thermal diffusivity (sq-meters/second) (fpnumber)
lenx=1                                   material length (meters) (fpnumber)
dx=0.1                x-incriment. Best if lenx/dx==int. (meters) (fpnumber)
dt=0.004                                    t-incriment (seconds) (fpnumber)
maxt=2       >0:max sim time (seconds) | <0:min l2 change in soln (fpnumber)
bc0=0                   boundary condition @ x=0: u(0,t) (Kelvin) (fpnumber)
bc1=1             boundary condition @ x=lenx: u(lenx,t) (Kelvin) (fpnumber)
ic="const(1)"               initial condition @ t=0: u(x,0) (Kelvin) (char*)
alg="ftcs"                            algorithm ftcs|upwind15|crankn (char*)
savi=0                                   save every i-th solution step (int)
save=0                              save error in every saved solution (int)
outi=100                      output progress every i-th solution step (int)
noout=0                                       disable all file outputs (int)
prec=2           precision 0=half/1=float/2=double/3=long double (int const)
Examples...
./heat dx=0.01 dt=0.0002 alg=ftcs
./heat dx=0.1 bc0=273 bc1=273 ic="spikes(273,5,373)"


The initial condition argument, ic, handles a few interesting cases

Constant, ic="const(V)"

Set initial condition to constant value, V

Ramp, ic="ramp(L,R)"

Set initial condition to a linear ramp having value L @ x=0 and R @ x=$$L_x$$.

Step, ic="step(L,Mx,R)"

Set initial condition to a step function having value L for all x<Mx and value R for all x>=Mx.

Random, ic="rand(S,B,A)"

Set initial condition to random values in the range [B-A,B+A] using seed value S.

Sin, ic="sin(Pi*x)"

Set initial condition to $$sin(\pi x)$$.

Spikes, ic="spikes(C,A0,X0,A1,X1,...)"

Set initial condition to a constant value, C with any number of spikes where each spike is the pair, Ai specifying the spike amplitude and Xi specifying its position in, x.

#### Default Run

Run the application with default arguments (e.g. don’t specify any) and see what happens…

% ./heat
runame="heat_results"
prec="double"
alpha=0.2
lenx=1
dx=0.1
dt=0.004
maxt=2
bc0=0
bc1=1
ic="const(1)"
alg="ftcs"
savi=0
save=0
outi=100
noout=0
Iteration 0000: last change l2=0.0909091
Iteration 0100: last change l2=2.42918e-06
Iteration 0200: last change l2=4.86446e-07
Iteration 0300: last change l2=1.00929e-07
Iteration 0400: last change l2=2.09483e-08
Iteration 0500: last change l2=4.41684e-09


Before running, the application dumps its command-line arguments so the user can see what parameters it was run with. In this case, you are seeing the default values. It then runs the problem as defined by the command-line arguments and saves result files, as needed, to the directory specified by the runame= argument.

#### Understanding the output and results

To list the most recently created entries in the current directory, run the following command…

% ls -1t | head -n 1
heat_results


The entry heat_results is a directory containing some files created by the application. To determine what kind of files they are, run the following command…

% file heat_results/*.*
heat_results/clargs.out:                    ASCII text
heat_results/heat_results_soln_00000.curve: ASCII text
heat_results/heat_results_soln_final.curve: ASCII text


For this simple application, the results are uncomplicated. They are ASCII text files containing two columns of data. To see an example, run the command

% cat heat_results/heat_results_soln_final.curve
# Temperature
0        0
0.1   0.1039
0.2   0.2073
0.3   0.3101
0.4   0.4119
0.5   0.5125
0.6   0.6119
0.7   0.7101
0.8   0.8073
0.9   0.9039
1        1


The first column is each spatial position, $$x_{i}$$ and the second column is the temperature, u, at that spatial position. The name of the file indicates the time of the solution data stored therein.

### Testing The heat Application

Before we use our new application to solve our simple science question, how can we assure ourselves that the code we have written is not somehow seriously broken?

• Compare it to known, validated numerical solutions.
• Compare it to known analytical solutions.
• Confirm its behavior at steady state.

In any case, think about how you would measure error.

We know, maybe even intuitively, that if we maintain constant temperatures at $$A @ x=0$$ and $$B @ x=L_x$$, then after a long time (e.g. when the solution reaches steady state), we expect it to be a simple linear variation between temperatures A and B. For example, observe what happens after a long time in the one dimensional example below.

Since the default length is 1 and the default boundary conditions are 0 and 1, we just need to run the problem for a long time. But, to be a little more thorough, it is even better to start with a random initial condition too.

% ./heat dx=0.25 maxt=100 ic="rand(125489,100,50)" runame=test


Examine the initial and final results file and confirm even a random input still yields a final result where $$u=x_{i}$$ for all rows of the results file

% cat test/test_soln_00000.curve
# Temperature
0    69.09
0.25    143.6
0.5     96.3
0.75    52.61
1    131.6
% cat test/test_soln_final.curve
# Temperature
0        0
0.25     0.25
0.5      0.5
0.75     0.75
1        1


## Exercise #3: Use Applicaton to Do Some Science

Back to our original problem…will our water pipes freeze?

 Material Thermal Diffusivity(sq-meters/second) Wood $$8.2 \times 10^{-8}$$ Adobe Brick $$2.7 \times 10^{-7}$$ Common (red) Brick $$5.2 \times 10^{-7}$$
• Outside temp has been same as inside temp for a long time, 70 degrees F
• Night/Storm will last 15.5 hours @ -40 degrees F
• Walls are 0.25 meters thick wood and pipe is 0.1 meters in diameter
• Pipe will freeze if center point drops below freezing.

Note: An all too common issue in simulation applications is being sure data is input in the correct units. Take care!

./heat runame=wall alpha=8.2e-8 lenx=0.25 dx=0.01 dt=100 outi=100 savi=1000 maxt=55800 bc0=233.15 bc1=294.261 ic="const(294.261)"

## Exercise #4: Analyze Results and Do Some Science

Its time to use the results from our simulation to answer the science question of interest. Below we plot results

make plot PTOOL=gnuplot RUNAME=wall


Depending on your situation, the above command may or may not produce a plot looking like below.

No

## Challenges with Custom Coding

We all like to write code and build useful tools. However, it is all too easy to see the unfamiliar as an impediment rather than enabler in reaching our sience goals. However, this is a slippery slope. We often start with relatively simple goals and over time wish to evolve our software solutions to ever more challenging science problems.

Examine the lines of code of the complete application here

% wc -l *.[CH]
125 args.C      # User interface
94 crankn.C    # Alternative (implicit) solver
43 exact.C     # Testing support (exact solns for some cases)
12 ftcs.C      # FTCS (explicit) solver
222 heat.C      # Main application
22 heat.H      # Modularization
115 Number.H    # Performance tracking
27 upwind15.C  # Alternative (explicit) solver
157 utils.C     # Utilities, I/O, Data formats
817 total

4575 Half.H      # Half precision floats (half.sourceforge.net)


Developing generally useful science applications involves many considerations and software engineering challenges.

• More complex physical phenomena
• More complex materials
• Laminated, anisotropic and/or non-linear materials
• More complex geometries
• More spatial dimensions
• Non-cartesian coordinate systems
• Larger objects involving billions of discretization points and requiring scalability in all phases of the solution.
• More generality in execution paradigm
• Performance portability and various parallel runtimes
• Interoperability of key components
• Discretizers, solvers, time-integrators, optimizers
• More sophsticated software design and implementation
• Documented, sustainable, maintaiable, portable, efficient, scalable, …

By employing numerical packages, we can leave some of the heavy lifting for others and focus more of our effort on the science and/or the parts of the problem we are most passionate about.

## Optional Exercises

For any of these optional exercises, we encourage you to submit a show your work upload of your work for review and feedback. It may take us a few days to respond but we would be happy to follow up.

Yes

0.3-0.4 meters

### Are the assumptions correct?

A common pitfal in numerical modeling is neglecting to ensure fundamental assumptions still hold. In this exercise, to make the problem tractable and a short lesson, we made a number of simplifying assumptions. If the picture below was a more accurate representation of the situation, the wall is composed more of water (in the pipe) than it is of wall

and our numerical model would fail.

Maybe. Certainly the pipe is wider than the original picture suggests.

### Determine Optimum Wall Thicknesses

What are the minimum thicknesses of walls of Wood, Adobe and Common brick to prevent the pipes from freezing?

When you are done, go to Intro->Submit A Show Your Work using the hands-on activity name Optimized Walls and upload evidence of your completed solution.

### Compare various precisions

The heat application can be made to run using half, single, double and long double precision. Try each of these and compare time and space performance as well as quality of the results. How do the various precisions compare in terms of # of operations, time to solution, memory used and quality of results?

### Compare FTCS, Crank-Nicholson and Upwind15 Algorithms

#### Crank-Nicolson Discretization

Using the Crank-Nicolson discretization, we arrive at the following discretization of equation 2… $-ru_{i+1}^{k+1}+(1+2r)u_i^{k+1}-ru_{i-1}^{k+1} = ru_{i+1}^k+(1-2r)u_i^k+ru_{i-1}^k$

where $r= \alpha \frac{\Delta t}{2 \Delta x^2}$

In equation 7, the solution at spatial position i and time k+1 now depends not only on values of u at time k but also on other values of u at time k+1. This means each time we advance the solution in time we must solve a linear system; in other words we must solve for all of the values at time k+1 in one step. This is an example of an implicit method. In this case, the system of equations is tri-diagonal – since each update for u at i only uses u at i-1 , i and i+1 – so it is easier to implement than a general matrix solve but is still more complicated than an explicit update.

The code to implement this method is more involved because it involves doing a tri-diagonal solve. It is in crankn.C. It involves code that sets up and LU factors the initial matrix. Then, the LU factored matrix is used on each solution timestep to solve for the new temperatures.

Run the same problems using each of these algorithms and observe total memory usage and operation counts (printed at the end) and provide your explanations for them and in comparison with the FTCS method.

When you are done, go to Intro->Submit A Show Your Work using the hands-on activity name Crank-Nicholson and upload evidence of your completed solution.

### Use The Application to Solve The Pipeline Problem

An pipeline carrying Ethenol-85 (E85) runs between a manure processing facility and a kerosene production factory. In the unlikely event that both facilities experience catastrophic explosion (burning methane at the manure facility and burning kerosene at the kerosene facility), that briefly increases the local air temperature on both sides of the pipe to the burning temperature of the respective materials, determine the minimum thermal diffusivity of the material used to coat/insulate the pipe to prevent the E-85 from exploding. Assume the pipe is 36 inches in diameter.

When you are done, go to Intro->Submit A Show Your Work using the hands-on activity name Pipeline and upload evidence of your completed solution.

### Modify the Application to Support Two Materials

Using other research, modify the application to work for a composite wall composed of two materials.

When you are done, go to Intro->Submit A Show Your Work using the hands-on activity name Composite Wall and upload evidence of your completed solution.