Gnuplot

2013-01-22T22:08:17Z

Rthomas: /* Other Reading */

Gnuplot

2013-01-22T22:06:45Z

Rthomas: /* Other Reading */

Gnuplot

2013-01-22T22:06:23Z

Rthomas:

Gnuplot is a terminal based plotting application. This means that you interact with gnuplot by ''typing commands at a prompt''. This turns out to be very convenient, because it means that you can always save or create a gnuplot configuration into a plain text file.
==Installation==
If gnuplot is not already installed on your system, you need to install it. The method of install will depend on your OS and distribution. A few common examples are

;Gentoo
# must run as root
> emerge gnuplot

;Ubuntu
> sudo apt-get install gnuplot

;Fedora
# must run as root
> yum install gnuplot

;Debian
# must run as root
> apt-get install gnuplot

;Windows
: A windows install file can be downloaded from the gnuplot sourceforge page [http://sourceforge.net/projects/gnuplot/files/gnuplot/4.6.0/ here].

;Mac OS X
: First, download XQuartz from [http://xquartz.macosforge.org/landing/ here] and install. Then download the <code>gnuplot-4.6.0.tar.gz</code> from [http://sourceforge.net/projects/gnuplot/files/gnuplot/4.6.0/ here]. Now you will just unpack, configure, build and install gnuplot from source.
> tar xzf gnuplot-4.6.0.tar.gz
> cd gnuplot-4.6.0
> ./configure
> make
> make install # run as root.

;Other
: Of course, gnuplot can be built from source on any other Unix based machine such as Mac OS X and Linux.

==Getting Started==
Several good tutorial references exist for gnuplot.

Gnuplot Official Site (Tutorial/User Manual PDF): [http://www.gnuplot.info/ http://www.gnuplot.info/]

Gnuplot Not So Frequently Asked Questions: [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html http://t16web.lanl.gov/Kawano/gnuplot/index-e.html]

The book, Gnuplot in Action: [http://www.manning.com/janert/ http://www.manning.com/janert/]

===Plotting===
gnuplot is a program created to plot stuff. You can plot functions or data. There are two commands for plotting, <code>plot</code> and <code>splot</code>. <code>plot</code> is used to plot 2D functions while <code>splot</code> is used to plot 3D functions.

===Plotting Functions===
The <code>plot</code> command has the following form

gnuplot> plot [ function | 'filename' datafile-modifiers ]

gnuplot has great support for all common (and many uncommon) functions. For example, to plot sin(x),

gnuplot> plot sin(x)

[[File:gnuplot_tutorial_pic_001.png|400px]]

Note that <code>x</code> is a special variable that gnuplot reconizes as the dependent variable. Multiple functions can be plotted on the same graph, just separate each with a comma

gnuplot> plot sin(x), cos(x)

[[File:gnuplot_tutorial_pic_002.png|400px]]

We control the what and how our plot is displayed by setting ''options''. Options are set with the <code>set</code> command. For example, to set the graph title, we set the <code>title</code> option to a string containing the title.

gnuplot> set title "Sine and Cosine"

Notice that the graph does not change after you set the title option. gnuplot will not redraw the graph until we either issue another <code>plot</code> command, or tell it to ''replot'' what we previously plotted with the ...<code>replot</code> command.

gnuplot> replot # redraw the previous plot with new options

[[File:gnuplot_tutorial_pic_003.png|400px]]

Other important options include <code>xlabel</code> (the x-axis label), <code>ylabel</code> (the y-axis label) and <code>key</code> (sets the position of the legend). The legend is located in the top-right corner of the graph by default, which is in the way in the example above. To label the axis and move the key,

gnuplot> set xlabel "time (s)"
gnuplot> set ylabel "current (A)"
gnuplot> set key top left
gnuplot> replot

[[File:gnuplot_tutorial_pic_004.png|400px]]

By default, gnuplot will "autoscale" the y axis (when plotting data from a file, the x axis is autoscaled too). To set the x and y axis ranges, set the <code>xrange</code> and <code>yrange</code> options.

gnuplot> xrange[0:10]
gnuplot> yrange[-2:2]
gnuplot> replot

[[File:gnuplot_tutorial_pic_005.png|400px]]

You can also set the range directly in the plot command.

gnuplot> plot [x=0:10] sin(x)

Autoscaling can always be re-enabled by setting the <code>autoscale</code> option

gnuplot> set autoscale

or, to enable autoscaling for the x or y axis individually,

gnuplot> set autoscale x # autoscale the x axis
gnuplot> set autoscale y # autoscale the y axis

gnuplot allows aritrarly complex functions to be plotted. These can either be built directly in the <code>plot</code> command,

gnuplot> plot sin(x) + cos(2*x) + 3*sin(4*x)

or you can define a function and plot it

gnuplot> f(x) = sin(x) + cos(2*x) + 3*sin(4*x)
gnuplot> plot f(x)

[[File:gnuplot_tutorial_pic_006.png|400px]]

====user-defined functions====
gnuplot allows the user to define arbitrary functions. Function definitions have the following form

gnuplot> function_name(arg1, [arg2, ...] ) = expression

In the example above, we defined a function <code>f(x)</code> that was a function of only one variable. However, we can define function of multiple variables. This can be very handy if we would like to plot a function with a variable parameter. For example, we may want to plot a Gaussian, but allow the center and width to be changed. We could define a Gauss function,

gnuplot> gauss(sigma, x0, x) = exp( - (x - x0)**2 / (2*sigma*sigma))

To plot this function for different values of <code>x0</code> and <code>sigma</code>, we just provide values directly in the plot command

gnuplot> plot gauss(0.5,0,x), gauss(0.5,1,x), gausss(1.0,1,x)

[[file:gnuplot_tutorial_pic_007.png|400px]]

Note that, while we used the variable <code>x<\code> in the definition of <code>gauss</code>, it is not required. More importantly, we can plot a function agains ''any'' of its arguments.

gnuplot> plot gauss(0.5,x,1)

[[file:gnuplot_tutorial_pic_008.png|400px]]

gnuplot also also supports variables. You can set a variable, and then use it in plot commands or even function definitions. For example, we could set the width and position of a Gaussian function through two variables.

gnuplot> x0 = 1.5
gnuplot> sigma = 0.75
gnuplot> gauss2(x) = exp( - (x - x0)**2 / (2*sigma*sigma))

This function will use the values stored in <code>x0</code> and <code>sigma</code> when it is evaluated. Note that the <code>x0</code> and <code>sigma</code> in the function <code>gauss</code> will '''not''' use the variables. Function argument names will "hide" variable names. In other words, gnuplot variables have ''scope''.

gnuplot> plot gauss(0.5, 1, x), gauss2(x)

[[file:gnuplot_tutorial_pic_009.png|400px]]

===plotting data from a file===

We often need to plot data that is stored in a file. Typically this has either been generated from a computer model, or collected in an experiment. gnuplot has a very powerful set of utilities for plotting data from a file. The data files used in the examples that follow can be downloaded here.

[[Media:simple.txt|simple.txt]]

gnuplot reads plain text files in table format: one row per line with columns separated by white space. Each row in the table is used to create ''one'' data point on the graph. The simplest file that gnuplot can read contains just two columns of data points,
> cat simple.txt
0.0 1.1
0.1 1.3
0.2 1.4
0.3 1.9

gnuplot can plot this file directly,

gnuplot> plot 'simple.txt' # note the quote marks

[[file:gnuplot_tutorial_pic_010.png|400px]]

This turns out to be fairly convenient because it is not very difficult to write code to write files in this format

// C

for(i = 0; i < n; i++)
printf( fp, "%f %f\n", x[i], y[i] );

// C++

for(i = 0; i < n; i++)
std::cout<<x[i]<<" "<<y[i]<<std::endl;

When analyzing data, this is often all that is required to see trends. However, if we are going to show out graph to anybody else, we will certainly want to fix it up.

gnuplot> set xlabel 'x (arbitrary)' # arbitrary units on the x-axis
gnuplot> set ylabel 'y (arbitrary)' # arbitrary units on the y-axis
gnuplot> set title 'Simple Graph'
gnuplot> set xrange[-.1:.4] # widen xrange to see endpoints
gnuplot> set yrange[1:2] # same for yrange
gnuplot> set key left # move key to left, out of the way
gnuplot> replot # dont' forget to replot

[[file:gnuplot_tutorial_pic_011.png|400px]]

gnuplot can display data points as points (as above), lines, or points connected by lines. This is controlled by setting the <code>style</code> option for <code>data</code>

gnuplot> set style data lines
gnuplot> rep # rep is shorthand for replot

gnuplot> set style data linespoints
gnuplot> rep

=====choosing and manipulating data=====
The data we want to plot may be in a file with multiple columns. By default, gnuplot will read the file and use only the first two columns. The first column is used for the x coordinate, the second column is used for y.

> cat simple2.txt
0.0 1.1 2.4 5.4
0.1 1.3 2.7 6.3
0.2 1.4 2.9 7.5
0.3 1.9 3.1 9.1

Plotting this file will give the same graph as the previous file. However, to plot the 3rd column of data, we add the <code>using</code> modifier.

gnuplot> plot 'simple2.txt' using 1:3

The <code>using</code> modifier selects the columns to use in the plot. As expected, the above plot command selects the first and third columns.

;using
: select columns from

====lines vs. points====
By default, gnuplot will plot data as ''points''. To change this, we can set the data style to ''lines'' or ''linespoints'' (actually, other styles exist, but are much less common).

==Creating Pictures==
gnuplot separates the concept of ''creating'' a plot and ''outputting'' a plot. Basically, all of the work required to construct a plot (reading in data points from a file, evaluating functions, etc) is independent of how the plot will be displayed. For example, you may want to the plot to be displayed on the screen, or written to a jpg. gnuplot uses the idea of ''terminals'' to support outputting plots to multiple formats. To output a plot to a jpeg, you tell gnuplot to write to the jpeg terminal type. To output a plot a png, you tell gnuplot to write to the png terminal type. You get the idea.

To change the terminal type, set the <code>terminal</code> option. For example, to create a png, set the terminal type to png.

gnuplot> set terminal png

==Gnuplot Scripts==
The commands for creation of a gnuplot graph can be assembled as a text file and run as a gnuplot script by
executing a command:

>gnuplot "script_file_name"

Gnuplot will execute the commands within the file. Here, the common use is to set the output terminal to postscript or some other format and viewed by an external viewer, like Okular.

A second method is to load a file from within gnuplot with the load command.

gnuplot> load "script_file-name"

Using this method, additional changes may be made to the graph with the interactive command line.

==Graphical Interfaces==
A number of graphical user interfaces exist for gnuplot. A common interface within Linux is grace. The grace package can typically be found along with gnuplot and installed in a similar fashion as described above.

Graphical interfaces are categorically frowned upon by this Department and its collaborators.

==Other Reading==

* {{Official website|http://www.gnuplot.info/}}
* {{cite book|author=Lee Phillips|title=gnuplot Cookbook|isbn=978-1849517249|publisher=Packt Publishing|year=2012}}
* {{SourceForge|gnuplot}}
* [http://www-128.ibm.com/developerworks/library/l-gnuplot/ Visualize your data with gnuplot]: an IBM tutorial
* [http://www.gnuplotting.org/ gnuplotting]: a blog of gnuplot examples and tips
* [http://spplotters.blogspot.com/ spplotters]: a blog of gnuplot examples and tips
* [http://gnuplot-surprising.blogspot.com/ gnuplot surprising]: a blog of gnuplot examples and tips

LaTeX

2013-01-22T20:02:48Z

Rthomas: /* Using LaTeX */

Author: Jack Maseberg

Guide to getting LaTeX running on your computer (Windows, Mac, or Linux)!

1) Install TeX Live: 
Windows: download and run the install-tl.zip file from here (http://www.tug.org/texlive/acquire-netinstall.html) 
Macs: (http://www.tug.org/mactex/2011/) 
Linux (Ubuntu): use synaptic to install the texlive package 

Note that the net installers look deceptively small is size, but the texlive folder on my windows machine is about 2.5 GB in size, so make sure you have HD space before you start!

2) Install a LaTeX editor. I use the cross-platform Texmaker (http://www.xm1math.net/texmaker/)

3) Install REVTeX https://authors.aps.org/revtex4/

It may be useful to refer to this site: [http://www.math.uiuc.edu/~hildebr/tex/tips-customstyles.html http://www.math.uiuc.edu/~hildebr/tex/tips-customstyles.html] when installing the custom styles and bibliography formats.

4) Get this example template: [[File:Advanced lab.tar]] (Use 7-Zip, http://www.7-zip.org/, on Windows to extract this .tar file.)

5) Configure Texmaker: go to toolbar, choose options/quick build/User, add the following text

latex -interaction=nonstopmode %.tex|bibtex %.aux|latex -interaction=nonstopmode %.tex|latex -interaction=nonstopmode %.tex|dvips -t letter %.dvi -o %.ps|ps2pdf -dPDFSETTINGS=/prepress %.ps

== Using LaTeX ==

LaTeX Wikibook: http://en.wikibooks.org/wiki/LaTeX

LaTeX Cookbook: http://www.personal.ceu.hu/tex/cookbook.html

LaTeX

2013-01-22T20:02:33Z

Rthomas: /* Using LaTeX */

Author: Jack Maseberg

Guide to getting LaTeX running on your computer (Windows, Mac, or Linux)!

1) Install TeX Live: 
Windows: download and run the install-tl.zip file from here (http://www.tug.org/texlive/acquire-netinstall.html) 
Macs: (http://www.tug.org/mactex/2011/) 
Linux (Ubuntu): use synaptic to install the texlive package 

Note that the net installers look deceptively small is size, but the texlive folder on my windows machine is about 2.5 GB in size, so make sure you have HD space before you start!

2) Install a LaTeX editor. I use the cross-platform Texmaker (http://www.xm1math.net/texmaker/)

3) Install REVTeX https://authors.aps.org/revtex4/

It may be useful to refer to this site: [http://www.math.uiuc.edu/~hildebr/tex/tips-customstyles.html http://www.math.uiuc.edu/~hildebr/tex/tips-customstyles.html] when installing the custom styles and bibliography formats.

4) Get this example template: [[File:Advanced lab.tar]] (Use 7-Zip, http://www.7-zip.org/, on Windows to extract this .tar file.)

5) Configure Texmaker: go to toolbar, choose options/quick build/User, add the following text

latex -interaction=nonstopmode %.tex|bibtex %.aux|latex -interaction=nonstopmode %.tex|latex -interaction=nonstopmode %.tex|dvips -t letter %.dvi -o %.ps|ps2pdf -dPDFSETTINGS=/prepress %.ps

== Using LaTeX ==

LaTeX Wikibook: http://en.wikibooks.org/wiki/LaTeX
LaTeX Cookbook: http://www.personal.ceu.hu/tex/cookbook.html

Common C, C++, FORTRAN Libraries

2012-09-15T23:48:55Z

Rthomas:

There are a number of common libraries for computational physics and numerical analysis. Here are a few links for tutorials and information for installation of commonly-used tools.

== Special Functions ==

[http://www.gnu.org/software/gsl/ GNU Scientific Library(GSL)]

The GSL also has calls for C and C++ for a variety of linear algebra functions found in BLAS and other packages.

== Linear Algebra ==

=== BLAS under Linux ===

[http://www.seehuhn.de/pages/linear Linear Algebra in Linux (BLAS/LAPACK)]

[http://www.linuxquestions.org/questions/linux-software-2/blas-installation-using-yum-doesnt-install-header-files-887814/ Setting up BLAS in Linux (yum-based systems)]

[http://vibrationdata.wordpress.com/2011/11/04/matrix-multiplication-in-blas/ Matrix Multiplication with BLAS and CBLAS]

[http://www.gnu.org/software/gsl/manual/html_node/BLAS-Examples.html GSL BLAS Examples (such as matrix multiply)]

Common C, C++, FORTRAN Libraries

2012-09-15T23:47:14Z

Rthomas:

Common C, C++, FORTRAN Libraries

2012-09-15T23:33:15Z

Rthomas:

There are a number of common libraries for computational physics and numerical analysis. Here are a few links for tutorials and information for installation of commonly-used tools.

== Linear Algebra ==

=== BLAS under Linux ===

[http://www.seehuhn.de/pages/linear Linear Algebra in Linux (BLAS/LAPACK)]

[http://www.linuxquestions.org/questions/linux-software-2/blas-installation-using-yum-doesnt-install-header-files-887814/ Setting up BLAS in Linux (yum-based systems)]

[http://vibrationdata.wordpress.com/2011/11/04/matrix-multiplication-in-blas/ Matrix Multiplication with BLAS and CBLAS]

Common C, C++, FORTRAN Libraries

2012-09-15T22:37:49Z

Rthomas:

There are a number of common libraries for computational physics and numerical analysis. Here are a few links for tutorials and information for installation of commonly-used tools.

== Linear Algebra ==

=== BLAS under Linux ===

[http://www.seehuhn.de/pages/linear Linear Algebra in Linux (BLAS/LAPACK)]

[http://www.linuxquestions.org/questions/linux-software-2/blas-installation-using-yum-doesnt-install-header-files-887814/ Setting up BLAS in Linux (yum-based systems)]

Common C, C++, FORTRAN Libraries

2012-09-15T22:37:39Z

Rthomas: Created page with "There are a number of common libraries for computational physics and numerical analysis. Here are a few links for tutorials and information for installation of commonly-used too…"

There are a number of common libraries for computational physics and numerical analysis. Here are a few links for tutorials and information for installation of commonly-used tools.

== Linear Algebra ==

==- BLAS under Linux ===

[http://www.seehuhn.de/pages/linear Linear Algebra in Linux (BLAS/LAPACK)]

[http://www.linuxquestions.org/questions/linux-software-2/blas-installation-using-yum-doesnt-install-header-files-887814/ Setting up BLAS in Linux (yum-based systems)]

Linux

2012-09-15T22:33:13Z

Rthomas:

[[Scripting]]

[[Gnuplot]]

[[Common C, C++, FORTRAN Libraries]]