C2110 UNIX and programming Lesson 9 / Module 1 -1C2110
UNIX and programming
Petr Kulhanek
kulhanek@chemi.muni.cz
National Center for Biomolecular Research, Faculty of Science
Masaryk University, Kamenice 5, CZ-62500 Brno
PS / 2020 Distance form of teaching: Rev2
Lesson 9 / Module 1
C2110 UNIX and programming Lesson 9 / Module 1 -2-
Gnuplot
PM3
http://www.gnuplot.info/
(documentation, tutorials, source codes)
C2110 UNIX and programming Lesson 9 / Module 1 -3-
Content
➢ Presentation of scientific data
➢ Gnuplot
• language overview
• plot command, setting and description of axis
• terminals
• splot command
C2110 UNIX and programming Lesson 9 / Module 1 -4Presentation
of scientific data
Data presented using a graph:
▪ graph must not be flooded with data
▪ presentation of the data must be concise and unambiguous
▪ axes of the graph must be described, including units
▪ data series must be distinguished either by color or by line style (solid, dashed, dotted,
etc.) and provided with key indicated in the graph or in its key
C2110 UNIX and programming Lesson 9 / Module 1 -5-
Samples
Figure 1. Impact of total simulation time on the calculated
free energy DA (DD).
C2110 UNIX and programming Lesson 9 / Module 1 -6-
Samples
Figure 2. Impact of REWALD cut-off on the calculated free
energy DA (DD). The inset shows the region withthe largest
deviations.
C2110 UNIX and programming Lesson 9 / Module 1 -7Interactive
Run
Gnuplot is used to draw 2D and 3D graphs and enabled work in both interactive and
scripting mode.
[kulhanek@wolf ~]$ gnuplot
G N U P L O T
Version 4.4 patchlevel 3
last modified March 2011
System: Linux 3.2.0-31-generic
Copyright (C) 1986-1993, 1998, 2004, 2007-2010
Thomas Williams, Colin Kelley and many others
gnuplot home: http://www.gnuplot.info
faq, bugs, etc: type "help seeking-assistance"
immediate help: type "help"
plot window: hit 'h'
Terminal type set to 'wxt'
gnuplot>
Interactive mode
command line of gnuplot
command line of Bash shell
C2110 UNIX and programming Lesson 9 / Module 1 -8Non-interactive
startup
1) Indirect start
We run the language interpreter and give the name of the script as an argument.
$ gnuplot my_gnuplot_script
Scripts do not have to have the x flag set (executable).
2) Direct start
We run the script directly (shell automatically starts the interpreter).
$ chmod u+x my_gnuplot_script
$./my_gnuplot_script
Scripts must have the x flag (executable) and interpreter (part of script) set.
#!/usr/bin/gnuplot
plot sin(x)
pause -1
C2110 UNIX and programming Lesson 9 / Module 1 -9Command
- plot: functions
> plot function/file [display_settings] [, function/file...]
Displays an XY graph of a function or data series contained in a file.
Examples (functions):
> plot sin(x)
> plot cos(5.7*x+3.4)
> plot sin(x), cos(x)
> f(x) = sin(x)
> plot f(x)
C2110 UNIX and programming Lesson 9 / Module 1 -10Command
- plot: Data Series
> plot function/file [display_settings] [, function/file...]
Examples (functions):
> plot "input.txt"
> plot "input.txt", "teplota.log"
> plot "input.txt" using 2:3
> plot "input.txt" using 1:($2+10.7)
> plot "input.txt" using ($1/10):($2+$3)
name of file with data (name must be enclosed in quotation marks)
second column forms x-values
third column forms y-values
(…) an arithmetic expression at any position
$N is value in column N
Displays an XY graph of a function or data series contained in a file.
C2110 UNIX and programming Lesson 9 / Module 1 -11>
plot sin(x)
> plot cos(x) title "cos"
> plot f(x) with points linecolor rgb "red" linewidth 2
> plot "data.log" using 2:3 title "temperature" with lines \
linecolor rgb "red" linewidth 2 , \
"data.log" using 2:4 title "pressure" with lines \
linecolor rgb "blue" linewidth 2
Command – plot: Setting
Examples:
lines, points, linespoints, dots,…
line color
line width
> plot function/file [display_settings] [, function/file...]
Displays an XY graph of a function or data series contained in a file.
C2110 UNIX and programming Lesson 9 / Module 1 -12Exercise
I
1. Display the function y=x2
2. Display the function from the first exercise in blue
3. View the temperature profile over time contained in the file
/home/kulhanek/Documents/C2110/Lesson09/temp.txt
The time is given in the first column, the temperature is given in the second column.
4. Display the sin(x) function with a red line and the cos(x) function with an orange line
and dots in one graph.
Solve tasks in interactive mode.
C2110 UNIX and programming Lesson 9 / Module 1 -13Other
Commands
> set title "popis" # graph header (title)
> set xrange[min_value:max_value] # sets range of x-axis
> set xlabel “description" # sets description of x-axis
> set yrange[min_value:max_value] # sets range of y-axis
> set ylabel "popis" # sets description of y-axis
> set nokey # hides key to data series
> pause -1 # waits for press of a key
C2110 UNIX and programming Lesson 9 / Module 1 -14Exercise
II
1. Write a script that displays function y=x2 in range 0-10 for x-value. Run the script
indirectly using the interpreter gnuplot.
2. Write a script that displays the temperature over time contained in file
/home/kulhanek/Documents/C2110/Lesson09/temp.txt
In the graph, describe the axes, including the description of units. Time is given in
picoseconds, temperature in kelvins.
C2110 UNIX and programming Lesson 9 / Module 1 -15-
Terminals
Terminal determines where the graph will be drawn.
> set term x11 # output is plotted into a window
> set term qt # output is drawn into a window (better properties)
> set term png size 800,600
# output is plotted as an image in png format
> set output "output.png" # output will be saved to a file named output.png,
the name must be enclosed in quotation marks
> test # prints a page demonstrating the properties of the
terminal (not all terminals have the same output
options)
C2110 UNIX and programming Lesson 9 / Module 1 -16Output
from Various Terminals
wxt
postscript/eps
supports dashed lines
C2110 UNIX and programming Lesson 9 / Module 1 -17Exercise
III
1. What features do x11 and qt terminals provide? Work in interactive mode and use the
test command.
2. Write a script that displays the function y=5x3+6x2-7 in the range -10 to 5 for x-value.
Run the script directly with the interpreter in header of the script.
3. Modify the previous script so that the graph is rendered into an image in png format.
Size of the image will be 640x480. Use the display command to show the image.
4. View the result of the test command for the png and postscript terminals.
5. What terminals does gnuplot support (set terminal with no argument)?
C2110 UNIX and programming Lesson 9 / Module 1 -18-
Self-study
C2110 UNIX and programming Lesson 9 / Module 1 -19Command
- splot
> plot function/file [display_settings] [, function/file ...]
Displays XYZ graph of a function or data series contained in a file.
Command splot can be used to display the functions of two variables.
View direction is set by command set view a,b, where a and b are directional angles. The
top view can be set with set view map
To highlight an area with a function value, pm3d display can be used, e.g.:
> splot x*x+y*y with pm3d
When displaying functions, the sampling density for x- a y-directions can be entered with
the command set isosamples a, b, where a and b indicate the number of samples in the
given direction.
C2110 UNIX and programming Lesson 9 / Module 1 -20Exercise
IV
1. Display the function x2+ y2
2. Set top view (set view)
3. Disable top view (unset view)
4. Increase the dot density to display the function (set isosamples). Use values ​​of 10,20;
20,10 and 20,20
5. Use the pm3d visualization
6. Set top view (set view)
Solve tasks in interactive mode.