Introduction to Gnuplot

• Basic Use
• Numerical Data
• Experimental Data
• Functions
  • Functions
  • Values
  • Least-Squares
  • Postscript format
• Life with gnuplot
• Plotting Styles

Introducing to gnuplot — Functions

User-Defined Functions

If you can write an equation, gnuplot can calculate it. I mean,
functions to be plotted are expressed in a simple functional form,
for example, f(x)=a*x+b, and they do not contain a complicated
integration / differentiation which needs a numerical calculation.
Gnuplot has many basic functions such as sine, cosine, Bessel,
Gamma, etc, and it can plot them as well as combinations of those
functions.

Maybe gnuplot users are not so interested in plotting functions,
except for your Math homework (or some special purpose which I
don’t know), but this is extremely useful for a parameter-fitting to
experimental data, namely a least-squares fitting. Gnuplot can solve
not only linear least-squares problems but also non-linear ones.
In this section, we learn how we can use a user-defined function,
and how to fit this to experimental data.

The function we are thinking here is the Lorentzian plus background
term of 1/sqrt(x). This equation contains four parameters, a, b, c,
and d, those are determined by experimental data.

Definition of a function is similar to Fortran or C programming
language. In the example below,
f(x)=c/((x-a)*(x-a)+b)+d/sqrt(x) defines our
equation. Square of (x-a) term also can be written in a
Fortran manner, (x-a)**2 . The parameters, a,b,c, and d
are arbitrary.

gnuplot> a=0.25
gnuplot> b=0.02
gnuplot> c=0.05
gnuplot> d=0.1
gnuplot> f(x)=c/((x-a)*(x-a)+b)+d/sqrt(x)
gnuplot> set xrange [0:1]
gnuplot> set yrange [0:4]
gnuplot> plot f(x)

Values of the function

Since gnuplot calculates user-defined functions numerically
to draw a graph on your screen, you can look at the calculated
numbers with the print command. The value of function
depends on the parameters (a,b,c,d, and e). Gnuplot calculates
functions in a double-precision.

gnuplot> print f(0.25)
2.7
gnuplot> print f(0.4)
1.33458447124371
gnuplot> a=0.4
gnuplot> print f(0.4)
2.65811388300842

To obtain the calculated values in a tabulated format, which can be
processed with other applications such as a spread-sheet, use a
special terminal table . To write the result, specify a
file name with set output .

gnuplot> set term table
Terminal type set to 'table'
gnuplot> plot f(x)
#Curve 0, 100 points
#x y type
0 0 u
0.010101 1.63972 i
0.020202 1.39031 i
0.030303 1.30688 i
....

0.979798 0.191506 i
0.989899 0.188622 i
1 0.185837 i

gnuplot> set output "calc.plt"
gnuplot> replot

Search for the parameters with a Least-Squares Method

We now fit the function to experimental data, and obtain best values
of the parameters, a, b, c, and d. The experimental data are stored
in a file “exp.dat”.

2.5000E-03 3.0420E+00 6.47E-01
3.5000E-03 2.5700E+00 4.37E-01
4.5000E-03 2.3020E+00 2.53E-01
...

7.0000E-01 2.7420E-01 2.14E-03
7.5000E-01 2.5680E-01 1.81E-03
8.0000E-01 2.4630E-01 1.59E-03

The data file consists of 3 columns, each of which is (x,y,z) data
pair, the Z-data stand for an absolute uncertainty of the data
Y. It means Z has the same dimension as Y. For example (in the case
above), if your Y value is 3.04 cm, its uncertainty should be
0.647cm. The inverse of Z becomes a weight of this data point at
the data fitting. If no uncertainty is given, the weights for all
data points are the same.

First of all, we show the data and function in one plot. As shown in
Experimental Data or
Numerical Calculation section,
the axis names, ranges, tics, are adjusted properly.

gnuplot> set xlabel "Energy [MeV]"
gnuplot> set ylabel "Cross Section [b]"
gnuplot> set xtics 0.1
gnuplot> set ytics 0.5
gnuplot> plot f(x) title "Lorentzian",
> "exp.dat" using 1:2:3 title "experiment" with yerrors

As I said that the parameters, a,b,c, and d, are arbitrary, but they
were roughly determined for this experimental data. The parameter
‘a’ is a position of Lorentzian peak, and which is, say, about 0.25
from this plotting. For the parameter ‘b’, its square-root
corresponds to the width of this peak, and I estimated that b is
about 0.02.

It is quite easy to do a least-squares fitting with gnuplot.
Just use the fit command, and add parameters
to be searched for by the via option. When your
fitting function is strongly non-linear, you need to be careful
about the initial values of your parameters. Here we used
the values above as the initial parameters for this fitting.

gnuplot> fit f(x) "exp.dat" using 1:2:3 via a,b,c,d


Iteration 0
WSSR        : 96618.1           delta(WSSR)/WSSR   : 0
delta(WSSR) : 0                 limit for stopping : 1e-05
lambda    : 1150.73

initial set of free parameter values

...

After 17 iterations the fit converged.
final sum of squares of residuals : 3341.93
rel. change during last iteration : -5.29173e-06

degrees of freedom (ndf) : 47
rms of residuals      (stdfit) = sqrt(WSSR/ndf)      : 8.43237
variance of residuals (reduced chisquare) = WSSR/ndf : 71.1049

Final set of parameters            Asymptotic Standard Error
=======================            ==========================

a               = 0.26191          +/- 0.005759     (2.199%)
b               = 0.00251445       +/- 0.0008358    (33.24%)
c               = 0.00541346       +/- 0.0009206    (17.01%)
d               = 0.182469         +/- 0.007329     (4.016%)


correlation matrix of the fit parameters:

a      b      c      d
a               1.000
b               0.042  1.000
c              -0.229  0.783  1.000
d               0.210 -0.538 -0.768  1.000
gnuplot> replot

As shown above, the fitted function is not so good except for the
region where the data are off-resonance. This is because our
fitting function was not the best choice. Its peak shape looks fine
with the Lorentzian, so we modify d/sqrt(x) by
introducing a new parameter ‘e’ and express it as d*x**e
. The initial value of ‘e’ is -0.5.

gnuplot> e=-0.5
gnuplot> f(x)=c/((x-a)*(x-a)+b)+d*x**e
gnuplot> fit f(x) "exp.dat" using 1:2:3 via a,b,c,d,e

...
Final set of parameters            Asymptotic Standard Error
=======================            ==========================

a               = 0.25029          +/- 0.002106     (0.8412%)
b               = 0.00197707       +/- 0.0002747    (13.89%)
c               = 0.00550098       +/- 0.0003662    (6.657%)
d               = 0.21537          +/- 0.003743     (1.738%)
e               = -0.358371        +/- 0.0115       (3.208%)


correlation matrix of the fit parameters:

a      b      c      d      e
a               1.000
b               0.021  1.000
c              -0.078  0.788  1.000
d              -0.110 -0.384 -0.500  1.000
e              -0.304  0.198  0.335  0.381  1.000
gnuplot> replot

Still its not perfect. Fixing a=0.24 and search only for
via b,c,d,e gives you better looks, but its chi-square is
larger.

Output in the Postscript format

As shown in Experimental Data section.
we generate a Postscript figure. The data points are drawn with
solid line and seventh symbol (circle), and the function is shown
with the thick dashed line.

gnuplot> set linestyle 1 lt 1 pt 7
gnuplot> set linestyle 2 lt 2 lw 3
gnuplot> set size 0.6,0.6
gnuplot> set term postscript eps enhanced color
Terminal type set to 'postscript'
Options are 'eps enhanced color dashed defaultplex "Helvetica" 14'
gnuplot> set output "exp.ps"
gnuplot> plot"exp.dat" using 1:2:3 title "experiment" with yerrors ls 1,
>        f(x) title "Lorentzian" with line ls 2