1 Gnuplot. Installing and running. Plot

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1 1 Gnuplot gnuplot is a simple and popular scripting language and program for producing plots. You may use any software you want for producing the plots in your report. Here, we introduce gnuplot because it is free and available on any platform (Linux, Windows, Mac and others). Installing and running On Linux, gnuplot is available for download using your package manager. Once installed, you can run gnuplot by typing gnuplot in the command line terminal. Alternatively, for example if you do not have sudo access, you can download and run the binaries in a similar manner. Make sure that the installation folder is in your $PATH environment variable. On Windows, you can download the latest version from the gngnuplot homepage After installation, running gnuplot.exe will open a command line interface. On Windows 10, you may also use the Windows Subsystem for Linux, which allows you to run a fully functioning Linux (Ubuntu) command line terminal natively inside your Windows computer. On any platform, it is recommended to write and execute script les rather than using the gnuplot command line directly. On linux, type gnuplot script.gnu to execute script.gnu. On Windows, the GUI allows script execusion, and you can associate the.gnu le extension with gnuplot. Plot Plotting simple functions: plot x * plot sin(x) Dening and plotting a function: f(x,a) = x+a plot f(x,1) title ``a=1'', f(x,2) title ``a=2'' Setting ranges for the axes: set xrange [0:1] set yrange [0:*] (only lower bound set) 1

2 There is a replot command, which will let you add more plots in an existing window: replot cos(x) 3D Plots To generate 3D plots you use the command splot instead of plot otherwise everything works the same way as in the 2D case, with set zrange setting the range of the z-axis. For example: splot x*x + y*y Plotting data from a le Usually, you will want to plot data from a le, rather than an expression. Suppose you have a le called out.data that looks like this: This is the format of outputs used in the exercises. To plot the data from this le, you can type plot "out.data" using 1:3 with linespoints This will create a plot where x coordinates are taken from column 1 and y coordinates from column 3. If you don't specify the columns (i.e., you remove "using 1:3"), the rst columns will be used. linespoints means that the data points will be plotted as points connected with lines. Some other useful styles are lines, points, dots and yerrorbars. With yerrorbars you need to have a column with error values, and the using clause should specify three columns (e.g. using 1:3:5). To set the plotting style for all subsequent plot commands, use set data style, e.g.: set data style linespoints Of course you are also able to splot from a text le, simply type 2

3 splot "out.data" using 1:2:3 with linespoints You can transform the data in a column before plotting it. The following will plot the square of the data in the second column plot "out.data" using 1:($2**2) The operator ** means to the power of. Title and labels To give the diagram a title and set labels on the axes, you can type: set title "Title goes here" set xlabel "My x label" set ylabel "My y label" Log scale Once in a while you may need to plot something with a logarithmic scale on either axis. For instance, if you want a logarithmic y axis: set logscale y And to set the scale back to linear: unset logscale y Save your plot as postscript le By default, gnuplot displays its output in a new window on the screen. To include a plot into your report, you will need to save it to a le. Gnuplot can save to many dierent le formats, using the set terminal X command. It is recommended to use a vector graphics format like pdf or postscript for your reports. set terminal postscript set output "yourfilename.ps" or 3

4 set terminal pdfcairo set output "yourfilename.pdf" Any plots produced after one of these lines will be written to the appropriate le. Use set terminal X11 to return to the default behavior of printing plots to a window on the screen. Using gnuplot scripts It is often easier to save all plot commands in a script le. This allows you to organise your commands, and re-execute everything from a clean slate after a change. Writing a script that processes everything from loading the data to creating the output plot will allow you to create a streamlined pipeline. You can run scripts from the command line by typing gnuplot scriptfile on linux, or opening the script with gnuplot.exe on Windows. An example Create a le called mygnuplotfile.gnplt that looks like this: set terminal postscript set output "myoutput.ps" set title "My postscript plot" set xlabel "X" set ylabel "Y" set zlabel "Z" splot x*x + y*y with lines quit If you type gnuplot mygnuplotfile.gnplt in a terminal, a le called myoutput.ps that looks like this will automatically be created: 4

5 You can read postscript les with Adobe Acrobat Reader on Windows, or with gv or okular on Linux. Getting help In most cases, it is easiest to type in your problem in google, and someone will have asked your question on StackExchange. Alternatively, gnuplot has a help command which lists all of the available commands and their options, and provides some useful examples. To get a list of all help topics, type help. If you want a list of the available commands: help commands. If you want help with a specic command: help plot help set key help set term post There are also many tutorials to be found online. 2 Using the ODE simulator For this exercise, you are given a java program where all the reaction networks and numerical calculations are pre-dened. You do not need to program this yourselves. The software is provided on the course website. Running the ODE simulator The le is called ODE.jar. Save it to your computer. It will produce output les in the same folder it is in, so it is best to put it in an empty folder, or the folder with your plot scripts. 5

6 The ODE simulator is a.jar le. Jar les are zip archives containing text les which dene Java classes. This particular Jar le also has a main method, which means it can be executed. It uses Java's Swing system to produce a GUI. To run the jar le, type java -jar ODE.jar on Linux in the appropriate folder. On Windows,.jar les are probably already associated with Java and will execute when double-clicked. Otherwise, download and install Java (tip: use ninite.com). When the program is run, a new window should open with options for the simulation you want to run. Each time you run a simulation, the concentrations as a function of time will be displayed as a graph on your screen, and the output values will be printed to a space-separated values ASCII le. Make sure to change the name of the output le if you do not want to overwrite the output of the previous experiment. Single cell simulations The The most simple case is when you have set the number of cells to one, a typical data le will in this case look like this; Note: Some Windows text editors like Notepad may not recognize the line breaks between the rows, so that everything will appear on the same line. This is because Linux and Windows systems tend to use dierent characters to signify newlines (denoted \r and \n). The line breaks will be recognized when importing the data in your plotting software, or when using a better text editor. The rst column enumerates the outputs from 0 to the number of outputs you have chosen in the Simulation settings, the second column displays the time, the third shows which cell we are looking at (in this case we only have one cell and thus this column is 0 everywhere) and the following columns display the concentrations at that specic time point. In gnuplot we can write plot "out.data" u 2:4 with lines which will plot the rst molecule concentration as a function of time. 6

7 Simulations with multiple cells When you set the number of cells to something other then one, you will immediately see that the Initial Values panel changes. Instead of setting specic initial values you can now dene a range of values. Each cell will then use a random value within that range. In this way we can simulate systems with multiple cells with dierent initial conditions. The output from the program looks as above, with one row for each cell at each time point. An empty line separates outputs for dierent time points; gnuplot ignores these lines, but you may need to remove these empty lines before plotting in other languages, such as Mathematica If we want to create a 3D plot with time on one the x-axis, the spatial position on the y-axis and a concentration on the z-axis, simply type splot ``out.data'' using 2:3:4 with lines 7

Computational Approach to Materials Science and Engineering

Computational Approach to Materials Science and Engineering Prita Pant and M. P. Gururajan January, 2012 Copyright c 2012, Prita Pant and M P Gururajan. Permission is granted to copy, distribute and/or