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Practical Programming F17Q3. Spring 2017.

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[ NB | Lectures : 0 1 2 3 4 5 6 7 8 9 10 11 ]

NB

Christine, your assignment is [here].
[14/5] Klara, you only need to login to the examination server at the official reexamination date (12-13/06, I think) and upload, say, the archive of your exam folder.
[14/5] Christine, remember to supply the link to your repository at the Wiki above. Remember also to login to the examination server at the official reexamination date (12-13/6, I think) and upload, say, the archive of your homeworks so that the server registers you as participated in the exam. Then, on 27/6 you should come to this page and get the examination assignment.
The examination assignments for the 22/3 run will be available [here] on 22/3 at 10:00.
The examination assignments for the 16/3 run, (Magnus H. Geismar, Peter Granum Nielsen, Magnus Graf Skou, Laura Feuerhake) will be available [here] on 16/3 at 10:00.
[7/3] Makef sure that your server shows Makefiles (and other important files) directly in the browser. Dropbox users must rename their Makefile to Makefile.txt.
[5/3] The default target in the Makefile of your examination project must be, say, report.pdf file (built from report.tex, article style or your other favourite style)—one or two pages—with i) a short formulation of the problem at hand; ii) the way you solved it; iii) and an illustration indicating that you solved the problem correctly.
You must submit this pdf file to the examination server at the official examination date.
[5/3] Please, do not copy blindly my Makefiles -- make your own.
[4/3] I have reformatted our Wiki table -- for some of you I had to change the numbers (sorry, but we cannot have gaps in numbering) -- check that everything is ok with your name and link.
[] Requirements for the homework-projects (and for the examination-project):
1. The project files must be kept in a separate folder with an indicative name (like, e.g., exam) inside your folder for the Practical Programming.
2. The project must be built with the command make.
3. The project must be built when submitted.
4. The command make clean must clean the folder and leave only the files from which the project is built.
5. There must be output files—with indicative names (like out.txt, or efuns.png)—which must prove the exercise is done satisfactorily. If in doubt consult your fellow student.
[] Go to our Wiki page and put a link to your homework-folder-in-the-internet in the Homeworks-page at the Wiki.
[21/2] I have modified slightly the "eigen" problems by adding an extra simple warm-up exercise as number 1.
[9/2] Having listened to your questions I have expanded somewhat the exercise problems-gnuplot.
[1/2] I have clarified the formulation of the "komplex" exercise. You are now asked specifically to create files "komplex.h" with declarations, "komplex.c" with implementations, and "main.c" with testing.
[31/1] I have marked the more complicated parts of the exercises as "optional". The optional parts are not mandatory for the examination. You might want to make them though if you want a better grade ;)
[31/1] I have installed Clang on rpione and made the "komplex" example with Clang.
[26/1] Added section "Functions" to Note "C-program".
[26/1] Every exercise must be made in a separate folder with an indicative name, like ~/pprog/hello, using the make utility.
You have to divide yourselves into 3-person teams and work in teams at the classes.

Schedule

(included from here)

Plan

Introduction; UNIX/POSIX systems; C programming language; Free software.
- Prerequisite: an access to a POSIX system. You've got several options:
  1. Ubuntu. The latest version is 16.10. The latest long term support version is 16.04. You can either install it directly on your laptop (default) or as a virtual machine (VirtualBox is a popular hypervisor).
  2. Most of other Linux-based systems (like Debian or Fedora) would do just as well. Though some small details might differ.
  3. MacOS with homebrew is a proven possibility. Though, since it is FreeBSD-based, certain things are different from Ubuntu.
  4. If you have an account on a POSIX server you can well work on it. Bring a laptop from which you can ssh to your account.
  5. Microsoft Windows with Cygwin is also a possibility. Less explored though. Some things will certainly be different.
- Reading
  - Learn how to start a terminal.
  - Read about the man utility. Run man man and read the DESCRIPTION of the utility in your system. Hints: man usually uses less as the default pager; you quit from less by pressing the q-key.
  - Learn the following commands (file utilities) from the GNU Core Utilities: cp, ls, mkdir, mv, rm, and the bash built-in command cd. Hint: type, for example, man 1 mkdir in your terminal or into Google-search in your browser.
  - Read about the command line completion.
- Exercises
  - Install your favourite text editor. If you don't have one, install the Nano text editor with the command
    sudo apt-get install nano.
  - Learn to create, save, and edit text files with your favourite text editor.
  - Install the GNU C compiler — gcc — with the command
    sudo apt-get install build-essential.
  - Problems "hello". See also the exercise C Programming/A taste of C. Hint: examples/hello.
- Hints
  - You quit from man by pressing q.
  - Directory abbreviations:
    
    ~ home directory
    .. parent directory
    . current working directory
    $HOME home directory
  - cd - changes into the previous directory.
[lectures/math] Structure of a C program; Basics of compilation; Variables and basic data types: char, int, float, double, long double, complex; Operators +,-,*,/; Simple output with the printf function; C math functions, math library (remember -lm); type-generic math tgmath.h.
- Reading:
  - Note "C-program".
  - Note "printf".
  - Also:
    - C program: global structure.
    - Preprocessing, compiling, linking, and execution of a C-program.
    - C data types for numbers, also complex numbers.
    - Arithmetic and comparison C operators.
    - C mathematical functions; type generic functions; libm.
- Answer questions-1.
- Make problems-math. Hints: digits.
- Hints:
  - In bash prompt ↑ and ↓ keys scroll over the previously issued commands.
  - In bash prompt !text runs the latest command that begins with text. Useful for issuing the same command again.

[lectures/make] Make utility and makefiles; Conditional statements if, switch and loops while, for, do-while; Scope of variables: file, function, block.
- Reading:
  - Note "make".
  - Note "scope".
  - C Programming → Program Flow.
  - GNU make manual → Introduction To Makefiles.
  - Also:
    - Microsoft's makefile tutorial (just kidding).
    - Arithmetic, comparison, and compound assignment operators from the list of operators in C and C++.
    - Ternary conditional operator.
    - C syntax → Iteration statements (loops);
    - C syntax → Selection statements (switch is not so important).
    - Scope of variables.
- (Optional) Install additional man-pages with the command
  sudo apt-get install manpages-posix manpages-posix-dev
- Create a makefile for your "math" exercise and re-make the exercise using the make utility.
  Hint: examples/hello.
  From now on all your exercises (and also the examination project) must be managed using makefiles.
- Answer questions-2.
- Make problems-epsilon. Hint: examples/epsilon.
- Hints:
  - If you have GNU make version 3.82+ and you don't like your recipies to start with tabulator-sign, you can do .RECIPEPREFIX := ;.
  - For nano users: you can indicate the invisible tabulator-signs with a color by adding the following lines to your ~/.nanorc,
```
syntax "makefile" "[Mm]akefile"
color white,magenta "	"
```
    where the character in between the quotation marks in the second line should be the tabulator sign and where the colors are free for you to choose.
[lectures/pointers] Pointers; Arrays and structs.
- Note "pointers".
- Note "arrays".
- Note "structures".
- Also:
  - Pointers in computer programming;
  - C syntax → Pointers;
  - C syntax → Arrays;
  - C syntax → Structures ~~and Unions~~;
  - C dynamic memory allocation.
- Answer questions-3.
- Make problems-komplex. Hints: examples/komplex.
[lectures/io] Passing functions as arguments; Simple input and output; Streams and redirections.
- Note "passing functions as arguments".
- Note "input/output".
- Note "redirections and pipes".
- Also
  - C syntax → Command-line arguments.
  - man stdout
  - man atoi (ascii to integer) and man atof (ascii to double).
  - man scanf
  - Unix I/O redirection.
- Questions 4.
- Problems "nvector". Hints: examples/nvector.
[lectures/gnuplot] C-preprocessor; building a program from functions in different C-files; simple printf-debugging (tracing); gnuplot/pyxplot.
1. You have to make the folder with your homeworks (and later the examination project) visible in the internet via a browser. There are many possibilities, for example, (bitbucket is the coolest, you think?),
  - If you have a DropBox (or similar) account you can create a public folder there and syncronize it with the folder with your homeworks. If you provider does not show makefiles in browsers (DropBox doesn't) rename your Makefile to Makefile.txt and run your make as make -f Makefile.txt.
  - Go to bitbucket.org; get yourself an account there; create a mercurial project "pprog"; push your files there. Here is an example: https://bitbucket.org/dvfedorov/prog/src/default/examples.
  - Any other server visibile via http would do as well, for example, http://phys.au.dk/~fedorov/prog/examples or http://phys.au.dk/~fedorov/prog/examples.
2. Go to our Wiki page and put a link to your homework-folder-in-the-internet in the Homeworks-page at the Wiki.
3. Note "printf debugging".
4. Also:
  - C preprocessor → including files; macro definitions;
  - Debugging;
  - Pyxplot users' guide → "first steps with Pyxplot" (most of it applies also to Gnuplot).
  - Gnuplot documentation, the "Plotting" section.
5. Install Gnuplot and/or Pyxplot on your box. If you are one MacOS with homebrew you should probably use the command
```
brew install gnuplot
```
  On Debian based systems, like Ubuntu, the command is
```
sudo apt-get --yes install gnuplot
```
  and/or
```
sudo apt-get --yes install pyxplot gv
```
  Actually it seems there appeared a new gnuplot version 5, so if you want the latest, do
```
sudo apt-get --yes install gnuplot5
```
  The --yes option automatically answers 'yes' on all questions apt-get might ask.
  Some of you might have managed to install a special version of gnuplot, called gnuplot-nox where 'nox' means 'no X-window'. This version, predictably, has no x-window terminal. If you plan to use gnuplot interactively, you have to install 'gnuplot', not 'gnuplot-nox'.
  The two plotting utilities have very similar scripting languages but otherwise are somewhat different. Pyxplot uses LaTeX to render all text on the plot which is rather convenient. Gnuplot has more terminals. Look at their web-pages, gnuplot and pyxplot (specifically, the examples), and choose the one you like most (or both).
  Note: it seems the developement of pyxplot has stagnated at the moment, therefore gnuplot might indeed be a better option.
6. Questions 5.
7. Problems "io-gnuplot". Hints: examples/io-gnuplot.
[lectures/gsl-sf]
GNU Scientific Library (GSL): installation, including, linking; vectors and matrices.
1. Install GSL on your box. First search for the GSL developement library in you system,
```
apt-cache search libgsl | grep development
```
  It should return either libgsl0-dev or libgls-dev, depending on your system. Install this package,
```
sudo apt-get install libgsl0-dev
```
  or
```
sudo apt-get install libgsl-dev
```
  The HomeBrew users should (apparently) use the command
```
brew install gsl
```
  Alternatively, you can download the source code and build the library on your box. It will probably take more time though.
2. Read the GSL manual chapters 'Introduction', 'Using the library', 'Vectors and Matrices', and 'Eigensystems/Real Symmetric Matrices'.
3. Questions 6.
4. Problems "eigen". Hints: examples/eigen.
[lectures/odeiv]
GSL: vectors and matrices; vector and matrix operations; BLAS; Ordinary Differential Equations Initial Value (odeiv) problem.
- Read the corresponding chapters in the GSL manual; in particular, learn
  - The interface to the BLAS routines.
  - The data type gsl_odeiv2_system with the fields function, jacobian, dimension, params to hold an Ordinary Differential Equations Initial Value System.
  - The names of the available stepping algorithms: gsl_odeiv2_step_rk2, gsl_odeiv2_step_rk4, gsl_odeiv2_step_rk45, ... , gsl_odeiv2_step_bsimp. Note which of the algorithms require the Jacobian of the system.
  - The driver functions gsl_odeiv2_driver_alloc_y_new and gsl_odeiv2_driver_apply
- Questions 7.
- Problems "orbit". Hints: (examples/odeiv-orbit).
[lectures/latex]
L^AT_EX: basics; document structure; importing graphics.
1. Install LaTeX on your system:
  1. Debian based systems: install Tex Live distribution with the command
```
sudo apt-get install texlive texlive-latex-extra
```
  2. MacOS with HomeBrew: install MacTeX distribution. It seems that you first need to install homebrew cask and then
```
brew cask install mactex
```
    or
```
brew cask install basictex # allegedly a small but functional version of MacTeX
```
2. Read the chapter 'Basics', 'Document Structure', and 'Importing Graphics' in the LaTeX wikibook.
3. Another interesting reading is A brief and concise description of RevTeX 4 package.
4. Browse through the sections 'Mathematics', 'Advanced mathematics', 'Floats, Figures and Captions', 'Labels and Cross-referencing', and 'Bibliography Management/Embedded system' in the LaTeX wikibook.
5. Learn how to do the following things in LaTeX: math; displayed equation; floating figures and tables; cross-references; the bibliography.
6. Questions 8.
7. Problems "latex". Hints: lectures/latex.
[lectures/integ-gamma]
GSL: Numerical integration.
1. Read the Introduction to numerical integration in GSL manual;
2. Learn the interfaces to the following structures and functions:
  - gsl_function (providing the function to integrate)
  - gsl_integration_qag (adaptive Gauss-Kronrod integrator)
  - gsl_integration_qags (singular integrand)
  - gsl_integration_qagi (infinite interval)
  - gsl_integration_qagiu (infinite upper interval)
  - gsl_integration_qagil (infinite lower interval)
  - gsl_integration_cquad (new fashionable algorithm)
3. Look at the 'Numerical Integration Examples'.
4. Questions 9.
5. Problems "integ". Hints: lectures/integ-gamma.
[lectures/multimin]
GSL: Multidimensional minimization.
- Read the multidimensional minimization chapter in GSL manual, specifically the 'algorithms without derivatives' chapter.
- You can read more about the Nelder-Mead (downhill-simplex) algorithm in Wikipedia: Nelder-Mead method.
- Learn the interfaces to the following structures and functions:
  - gsl_multimin_function
  - gsl_multimin_fminimizer
  - gsl_multimin_fminimizer_nmsimplex2
  - gsl_multimin_fminimizer_alloc|free
  - gsl_multimin_fminimizer_set
  - gsl_multimin_fminimizer_iterate
  - gsl_multimin_fminimizer_size
  - gsl_multimin_fminimizer_test_size
- Understand the Nelder-Mead Simplex example in 'Multimin Examples'.
- Questions 10.
- Problems "optimization". Hint: examples/multimin-decay.
[lectures/multiroot]
GSL: nonlinear equations (multidimensional root-finding).
- Read the multidimensional root-finding chapter in GSL manual, specifically the 'algorithms without derivatives' chapter.
- Learn the following objects from the 'multidimensional root-finding' chapter:
  - gsl_multiroot_function
  - gsl_multiroot_fsolver_alloc|free
  - gsl_multiroot_fsolver_set
  - gsl_multiroot_fsolver_iterate
  - gsl_multiroot_test_residual
- Questions 11.
- Problems "multiroot" (Schrödinger equation for hydrogen atom: shooting method); Hint: examples/multiroot-H.
Tips on programming and debugging; FAQ.
- Good coding style:
  1. The code is segmented into small methods/functions spanning no more than a screenful.
  2. The names of functions, structures.members, and variables are meaningful and self-describing.
  3. The logic of the code is easy to follow and easy to modify (by somebody else); only a small number of comments are needed in a good code.
  4. Defensive programming: #include<assert.h> and use assertions plentifully: you can easily disable all assertions by simply recompiling the code with -DNDEBUG c-flag:
```
CFLAGS += -DNDEBUG
```

Lecturer:

Dmitri Fedorov

Literature:

Wikibooks, C programming (the link also provides a PDF version).
GNU Scientific Library manual.
Gnuplot documentation.
Pyxplot User's Manual.
Wikibooks, LaTeX.

Links:

Wikipedia

Sear wikipedia for c language.

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`..`	parent directory
`.`	current working directory
`$HOME`	home directory