PY3C01 Part II: Computational methods

Transcription

1 PY3C01 Part II: Computational methods lectures, Tuesday 9-10AM weeks 5-11 and hands on session, Friday 2-4PM weeks 7,8,14,15 Lecturer: Dr Thomas Archer Office: Lloyd 221 Phone: If there are computer problems please

2 Structure of PYC301 Lecture 1 Context Lecture 1-3: Linux and shell programming Lecture 4-11: C programming

3 Lecture 1 Why computational modelling Where computational physics is now Where computational physics is going Coding grammar Introduction to Linux

4 Why computational modelling?

5 Solution to physical models Newtons laws of motion or relativity Classical motion of objects Quantum mechanics describes atoms, molecules, all of chemistry, solids. We can write the equations to describe virtually anything (black holes are still a little tricky) but how do we solve them?

6 Experimental physics Expensive several million Euro per lab Time consuming low turnover of results Many practical difficulties Atomic scale Temperature Time scales If done carefully you get the final answer

7 Computational physics Inexpensive Numerical approximations often needed We don't always the correct answer

8 Theoretical physics Existing theories are almost exact for our everyday lives. Numerical approximations for computational physics

9 Physics now

10 Classical mechanics Examples Weather chaotic Astrophysics Galaxy formation Solar weather chaotic Usually classical mechanics but probably requires QM or relativity Finite element design Aerodynamics Optimization problems

11 Atomistic modelling Described almost exactly by quantum theory Solids Describes all chemistry Physical properties Optical properties Magnetic properties Biological processes Electronic transport Computationally expensive Small systems Numerical approximations Reduce complexity periodicity in solid sate physics ~10,000 atoms possible as of 2013

12 Atomistic modelling examples Bulk materials use periodicity - solid state physics Bulk Al Other systems without symmetry more computationally intensive Sale ~N3

13 Where things are going Time Magazine

14 What does more power allow us to do Reduce approximations Run more detailed calculations Study larger systems Study larger numbers of systems High-throughput computing/big data

15 Physics future

16 Transferable skills

17 Coding Grammar How many languages do you know?

18 Flow charts Commands executed sequentially

19 Multi-thread Multi core CPUs are now standard Thermal dissipation Small transistor size Multiple threads can run at the same times Threaded code is beyond the scope of this course

20 Universal Grammar Grammar if you can write a flow chart you can turn it into a code Universal grammar - Common to all languages Syntax can always be quickly looked up How many languages do you know? ALL OF THEM!

21 Linux

22 Linux GNU licence free to download change and redistribute Safe/secure no viruses Most new developments are built on top of Linux

23 Linux modular design

24 Linux distributions A good start would be You can boot from CD or flash drive to avoid any changes to your existing OS

25 All you need in in this course

26 Where are my files?

27 File permissions Permission User Group Size Date Modified File name

28 Commands Many Linux commands, some useful ones are given here:

29 Commands Many Linux commands, some useful ones are given here:

30 Commands Many Linux commands, some useful ones are given here:

31 Commands Many Linux commands, some useful ones are given here:

32 Commands Many Linux commands, some useful ones are given here:

33 Arguments Many commands require specification of one or more arguments: arg1 [arg2] Most commands can be fine-tuned using options: command [-o] [--long-option] Sometimes options can also have arguments

34 Editors nano [file] - simple terminal based text editor gedit [file] - simple GUI editor emacs [file] - complex text editor vi [file] - the classical unix text editor Many other programs available

35 Wildcards Wildcards allow to handle many files with similar names simultaneously * matches any string ls *.jpg (list all files ending with '.jpg')? matches any single character ls file?.dat (matches file1.dat, files.dat, but not file10.dat) [abcde] exactly one of the listed characters ls data[137] (matches data1, data7, but not data13 or data5) [2-7] exactly one character in the given range ls file[a-e] (matches filea, filee, but not filez or fileaa) {xy,linux,unix} exactly any of the given strings

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38 Combining commands ls wc -l - counts number of files/directories cat text.txt grep Linux wc -l - counts number of lines in text.txt that contain the word Linux cat word_list sort uniq > unique_word_list - alphabetically sorts all lines (words) in word_list, removes duplicate lines, and writes the resulting list into file unique_word_list echo 3*3 bc - calculates 3*3=9 (echo=writes the given string to stdout)

39 Exercise/homework Get familiar with the command line: Go to your home directory. How many files of different type are there? Go one level up and list the contents of that directory Go to the root directory (/). Inspect its contents Go to the /bin directory and list its contents. Do you recognize some of the filenames? Inspect the contents of the /usr/bin directorty without changing to that directory 1. Using absolute pathnames ii. Using relative pathnames Go back to your home directory Create a directory anynameyoulike and change into it Create a text file yourfavoritename.txt using an editor of your choice. Write something and save it. Inspect your newly created file with cat, more, and less Copy the file to anothername.txt Edit the new file and save it. Go back to your home directory Go into the directory anynameyoulike Print the contents of yourfavoritename.txt and then redirect its content to another file ofyourchoice.txt Inspect the content of ofyourchoice.txt Create a process in the foreground using sleep 1000 Suspend the foreground process Resume the suspended process in the foreground Terminate the process Kill the sleep process Check whether the sleep process was really killed

40 Lecture 1 Summary Why computational modelling Where computational physics is now Where computational physics is going Coding grammar Introduction to Linux Next time combining Linux commands to make a program shell scripting