11/8/99

4810: p. 224 #1: Show your program is working by reproducing Fig. 8.8 and you will receive most of the credit for this problem.

The molecular dynamics simulation is temperamental and will tend to blow up due to the large force at small r. You can get this working by keeping your timestep small and not running the simulation too long. You can also set a minimum r for which you evaluate the force. That is, make the force some fixed value for r less than some minimum cut off value of r.

10/25/99 I was able to obtain a bunch of IDL hardware keys from the Physics Department. You may check them out from me, and borrow the CD-ROM to install IDL. You must return the CD-ROM when you are done with it and the hardware key by the end of the semester or you will receive an incomplete.

4810: For the forest fire problem: 1) Demonstrate that your simulation is working properly. 2) Try to reproduce Figure 7.35.

10/19/99 For Assignment 5, 4810 students should get the forest fire model working and produce results like in Figure 7.35.

There will be a tour of the NCAR high performance computer center Monday, November 8th at 3:10 pm. We will meet at NCAR, at the front door. Please car pool if necessary. I have room for 3 people. NCAR is at the very West End of Table Mesa Rd.

10/14/99 For Assignment 5, there is an example program to help you with the graphics for the forest fire problem. If you have a nice simulation, but are unsure what to hand in, you may want to show me the simulation in person so I know it works. Assignments are now posted below.

10/8/99 The extra credit problem is now referring to the correct problem. You should use bit-reversed numbers on the Monte-Carlo integration problem. There will be an example program on the web page shortly to help you with the forest-fire model, which is part of the next assignment.

10/1/99 For some reason a few people forgot to solve the Lorenz equations for the 3rd assignment. It will be re-assigned for the 4th assignment. If you did it, you have one less problem to do on Assignment 4.

The third assignment will be due Fri 10/1.

The second assignment will be due Fri 9/17.

 9/13/99

For the homework, to get the best resolution for the surface-of-section plots (especially the bifurcation diagram for 7820), you should use double precision floating point numbers.

Make sure to understand that in IDL 1/2 = 0. I always use floating point notation (e.g. a=1.0/2.0) if I am dealing with real numbers and always use the commands for type conversions to make things explicit. This is especially helpful if you are using different programming languages because different languages have different conventions. In addition, explicitly keeping the types of variables straight ensures you know what is going on.

I have combined the 4810 and 7820 assignments + hints and revisions, into one file. Look here for updates.

My office hours have changed to: Tues 2:30-4pm, Thurs 3:30-5pm. On Thurs 10/9 and 10/16 I will not be available 2pm-4:15pm. If you have any questions, please feel free to get in touch with me any time, I'll help then, or we can arrange a time when we both are free.

We will meet Mon 9/13 in the Computer Lab. Please take a look at the assignment and bring any questions you might have. Also, ask about any computing problems you are having.

Read Chapter 3, except you do not need to read Sections 3.5 and 3.6.

For example, p. 48 #2 means do problem number 2 on page 48.

1) p. 13 #3

2) p. 14 #6

3) p. 48 #1

4) This assignment is intended to help get started with IDL.

1) p. 48 # 2

2) p. 55 # 4

3) Reproduce Fig. 3.7 on p. 54.

4) p. 59 # 1

1) Reproduce Fig. 3.11 on p. 63.

2) p. 141 # 4 (Try a Gaussian shape and a guitar pluck shape as in Fig. 6.3.)

3) p. 142 # 6

4) p. 147 # 4

0) If you forgot to solve the Lorenz equations for Assignment 3 do so for Assignment 4.

1) p. 165 # 1. Plot the probability distribution function.

2) p. 169 # 3. Show convergence by plotting the error versus number of sample points.

3) Use the Box-Muller transformation to generate two Gaussian random number sequences. Plot the distribution function of the two sequences. Calculate the average and the average of the square numerically for both sequences and compare your result to what you obtain analytically using integrals of the probability distribution function.

Extra Credit (5 points) Re-do problem 2) using bit-reversed random numbers and compare the convergence using truly random numbers vs. bit-reversed numbers. Use "revers(num,n)" where num should be set to 2, 3, and 5 for the x, y and z dimensions respectively.

1) p. 173 # 2

2) p. 180 # 1

3) p. 202 # 6 (This problem will be simplified shortly. Only get the model working, check course examples to get you started.)

1) p. 224 #1 (This problem will be simplified further. Do not repeat the calculation for a triangular lattice.)

2) p. 242 #1 (Also show results like Figure 9.3.)

1) p. 271 # 5

2) p. 292 # 1

3) p. 292 # 3

4) p. 292 # 4

1) Build a protein folding simulation and reproduce results similar to Section 11.1.

2) p. 343 # 1

For example, p. 48 #2 means do problem number 2 on page 48.

1) p. 14 #6

2) p. 48 #1

3) p. 48 #2

This assignment is intended to help get started with IDL.

1) p. 55 # 4

2) p. 59 # 1

3) Generate the bifurcation diagram in the range of 1.476 to 1.480. Estimate the Feigenbaum parameter. (This is like problem p. 59 #2 except with a different range of the drive force.)

Hint: You may encounter a problem with your bifurcation results drifting and giving broader lines then you would like. This can be minimized by waiting for about 500-600 drive periods before gathering points to insure that the transient motion has died away.

1) Reproduce Fig. 3.11 on p. 63.

2) p. 146 # 1

3) p. 147 # 4

4) p. 150 # 1

5) p. 155 # 1

 Assignment 4 Due Wed 10/13

See 4810 assignment. Except the extra credit problem is not extra credit, it is required.

1) p. 173 # 2

2) p. 184 # 1

3) p. 202 # 6

1) p. 224 #1 (Do not repeat the calculation for a triangular lattice.)

2) p.242 #1

3) p. 251 #1

1) p. 271 # 7 (7820)

2) p. 292 # 1

3) p. 292 # 3

4) p. 292 # 4

1) Build a protein folding simulation and reproduce results similar to Section 11.1.

2) p. 343 # 1