12.010 Course

12.010 Computational Methods of Scientific Programming

Instructors: T. Herring (tah@mit.edu), Chris Hill (cnh@plume.mit.edu)

This course introduces programming languages and techniques used by physical scientists: FORTRAN, C, C++, Matlab, and Mathematica. Emphasis is placed on program design, algorithm development and verification, and comparative advantages and disadvantages of different languages. Students first learn the basic usage of each language, common types of problems encountered, and techniques for solving a variety of problems encountered in contemporary research: examination of data with visualization techniques, numerical analysis, and methods of dissemination and verification. No prior programming experience is required.

Prerequisite: 18.01, 18.02, 8.01

Aim of course:

The aim of this course is to give students an introduction to the uses of computer languages in the analysis of contemporary scientific problems. The course covers both conceptual areas of converting a problem to be solved into a computer-based solution, and specific aspects of individual languages and the types of problems they are best suited to solve. Emphasis is placed on the importance of structure, documentation, and levels of "user-hostility" of program interface. For each language, the basic syntax and structure of the language is covered with examples drawn from real applications. The major toolboxes and libraries, interfacing techniques and platform specific issues are also addressed.

Homework will be assigned for each of the languages and there will be a common project developed during the course that students will solve using the language of their choice. The final class will be used to compare the different solutions developed. Homework grading will be based not only on completing the assigned task but also on solution structure, robustness, human interface, documentation and transportability.

This class has no final exam.

Class grading: 80% homework, 20% final project

Office Hours for Prof. Herring; Tuesday 1:00-2:00 pm

There is an open courseware version of this course.

Course Outline:

Class	Date 2011	Instr.	Topic
1	09/08	TH	Introduction: Problem formulation, algorithm development, algorithm implementation, and algorithm verification. Structure and documentation
2	09/13	CH
3	09/15	CH	Fortran: "Formula Translation". Program creation, compilation and linking, variables and parameters, flow control, subroutines and functions. Structure and documentation. Use of libraries, internal and external communication, and interaction with other languages. Fortran: Implementation issues: Compilation errors, segmentation violations, Not-a-Number (NaN), Input/Output (IOSTAT) errors, Runtime errors. Transportable code, standard extensions. Fortran 90 differences and similarities to Fortran 77
4	09/20	TH
5	09/22	TH
6	09/27	TH
7	09/29	TH
8	10/04	TH	C for Scientific uses. Representation of data through arrays, pointers, and data structures. Function calls, argument passing and scoping rules, IO, profiling, system calls, and signals. C++ objects. Encapsulation and inheritance, polymorphic operators.
9	10/06	TH
10	10/11	TH
11	10/13	TH

12	10/18	TH	Mathematica. What it is and what it can do; structure of Mathematica; symbols, exact numbers, and machine numbers; lists, vectors, and matrices Working with Mathematica: numerical calculations, symbolic calculations, and graphics. Importing and exporting information
13	10/20	TH
14	10/25	TH	MatLab. "Matrix Laboratory". Matlab syntax, workspace, variables. Script M-files, IO, control flow, debugging, and profiling tools. Object-oriented programming Matlab applications, polynomials, interpolation, integration, differentiation, ODE. Graphics, 2-D, 3-D, Graphical User Interface (GUI)
15	10/27	TH
16	11/01	TH
17	11/04	TH
18	11/08	TH	Python scripting language program
19	11/15	TH	Python scripting language program
20	11/17	TH	Advanced graphics in Matlab, 3-D representation and exportable animations.
21	11/20	TH	Ordinary differential equation (ODE) solutions used Matlab and Mathematica
22	11/29	CH	Advanced Topics: Parallel computing with large memory and large numbers of CPUs. Advanced topics: Parallel MATLAB. Discussion of final projects. Order of the presentations will be decided in the last class.
23	12/01	CH
24	12/06	CH
	12/13	All	Final Project Presentations

Instructors: TH: T. Herring tah@mit.edu,; CH Chris Hill cnh@plume@mit.edu

Lecture Notes 2010 (shaded) and 2009 (non-shaded)

The lecture notes are converted from Microsoft Power Point documents portable document format (PDF). The most complete version of the documents is the power point files, which we make available for each lecture. Lecture notes are added as the class is taught. Check the date on the lecture notes to make sure you get this year’s version.

Lecture 01: Class introduction; overview of languages; Program development

Lec 01 PDF Lec01 Power Point Thursday, September 09, 2010.

Lecture 02: Discussion of aspects of computers and their operation. An example is given of program development for a simple case of computing the area of a figure. In this lecture there are notes that appear in the power point document. (These notes are often important for doing the homework and are not in the PDF file).

Lec 02 PDF Lec 02 Power Point Tuesday, September 14, 2010

In the lecture notes the poly_area.f Fortran program is referred to. This program implements the area determination algorithm discussed in the lecture. Links that are in the notes for this lecture:

http://www.webopedia.com/TERM/B/big_endian.html.

http://mathworld.wolfram.com/GreensTheorem.html

http://www.psc.edu/general/software/packages/ieee/ieee.html

Lecture 03: Started FORTRAN (Formula Translation). Went through the basic elements that make up this language. An on-line version of a Fortan77 manual can be found at the www.fortran.com. In reading these notes, you should think about operations you want to do and what command or commands do you use to do that. The list on Fortran intrinsic functions can be found at http://www.fortran.com/fortran/F77_std/rjcnf0001-sh-15.html - sh-15.10

Project Presentation: Thursday December 9, 2010

Project Presentation should be a total of 7-10 minutes long include (this is not very long): Groups with two people will have 10-minutes and single person groups will have 10 minutes. Some of the time should be left for questions.

1. Brief description of project

2. Role played by each member of team when more than one.

3. Demonstration of program.

All members of team should participate in the presentation.

Each project submission should include:

1. Written document that outlines the algorithms used in the project. The document should include:
Role of each person in the project
Methods that were used to verify that the code generated correct answers,

2. Program design and layout discussion

3. Program source code and instructions on installation

4. Examples of output of program and instructions for using the program.

Final electronic submissions are due Thursday December 9, 2010.

Project Groups 12.010 2010

Time	Group	Topics
2:05	Susan Flowers	Sudoku solver (Mathematica)
2:13	Shaena Berlin, Anna Merrifield	Predicting Run-up on the North Shore of O’ahu
2:24	Kirrah Jones, Ciara Sivels	Neuton Diffusion
2:35	Benjamin Nield	Checkers Game
2:43	Martina Coccia, Sedar Sahin	Expansion of Universe
2:54	Curran Oi	Tracking High-Energy Electrons
Break
3:15	Kimberly Huppert	Slope Stability analysis
3:23	Charles Hallam	Sudoku solver
3:31	Stephanie Sallum, Harriet Lau	Hangman
3:42	Lauren Jozwiak	Flexure models