Bubble Dynamics Code

Requirements:

• A working Fortran compiler. The makefile assumes you will be using gfortran. If this is not the case, you will need to edit it to suit your needs.
• LAPACK and BLAS libraries that can be linked to the compiler. You will probably be okay with the following

sudo apt install liblapack3 liblapack-dev liblapacke-dev
sudo apt install libopenblas-base libopenblas-dev

at least if you are on recent versions of Ubuntu. Earlier versions may need apt-get and other Linux flavours will require their own package-manager installs.

First run:

If this is the first time you are running the code, you will need to make the main file executable.

• Run chmod +x runcode.sh

Future runs:

Once the runcode.sh file is exectuable, the pressure_GAUSSIAN.f90 code can be made, compiled and run with the command:

./runcode.sh

The output of this run will create a folder called data, inside which a date-stamped folder will be created containing the data files.

Parameters:

Most of the code's parameters are set between lines 15-20 and lines 247-310. These may be cross-referenced with the parameters in the main paper paper.pdf in the directory. Some of the more numerical parameters are set between lines 136-143.

Plotting graphs from the data:

The current code setup populates the following data files:

bub_surf_before.dat
bub_surf_before2.dat
bub_surf_before2.dat
bub_surf_before3.dat
centroid_eqrad.dat
ENERGY.dat
ENERGYTERMS.dat
field_variables.dat
jet_vel.dat
pressurepulses.dat
rad_vs_time.dat
volume.dat

of which, most should be fairly self-explanatory in terms of their contents from the filenames, the code comments and the figures in the paper.

The files tend to follow a convention of

xdata ydata1 ... ydataN

with each of the ydata values explained in the code.

This allows for plotting of the data to be reasonably straightforward and consistent.

Plotting in gnuplot

In gnuplot, you can use the command

plot 'filename.dat' using 1:? w l

where the column number required replaces the ? in the command. For example, to plot column 2 against the xdata, use the command

plot 'filename.dat' using 1:2 w l

Further details about plotting from data files in gnuplot are avaiable here.

Plotting in MATLAB

To import the file into MATLAB, you can use something analagous to

A = dlmread('filename.dat');

which will store the data in MATLAB as an array. This can then be plotted in the usual way as

plot(A(:,1),A(:,?));

where the column number required replaces the ? in the command. For example, to plot column 2 against the xdata, use the command

plot(A(:,1),A(:,2));

Contact

Questions about running the code and analysing the output and can be directed to Scott Morgan - smorgan@bridgend.ac.uk - at any time.