2-D contour plot of a trajectory file obtained from lammps

I have done a simulation of a mixture of water and ethanol on a graphite surface. Now i have a trajectory file for visualisation. What I want to do is plot a 2-D contour of the mixture to show the density distribution of one of the molecule. can any body help me how to do it in Matlab. How can i basically call the trajectory file which i have in Matlab.

Answer 1

[Raag]

Hi Dani,

I am assuming that you are looking to visualize the density distribution of your simulation data using a 2-D contour plot in MATLAB.

Here are steps, to achieve the above-mentioned workflow:

• First, you need to import your trajectory data into MATLAB. If your file is in a text format, you can use the ‘readtable’ function or similar to load the data. For binary files, ‘fread’ might be necessary.
• Once you've loaded the data, you'll want to calculate the density distribution. This can be done by dividing the space into a grid and counting the number of molecules in each grid cell. MATLAB’s ‘histcounts2’ function is handy for this purpose.
• With the density data ready, you can use the ‘contourf’ function to create a 2-D contour plot. This will visually represent the density distribution of your molecules.

Here is an example code for the steps mentioned above:

% Load your trajectory data (replace 'trajectory.txt' with your file)
data = readtable('trajectory.txt'); % Adjust this line based on your file format

% Extract x, y coordinates (assuming your file contains these columns)
x = data.x;
y = data.y;

% Define the grid for the contour plot
xEdges = linspace(min(x), max(x), 100); % Adjust the number of bins as needed
yEdges = linspace(min(y), max(y), 100);

% Calculate 2D histogram for density
[N, xEdges, yEdges] = histcounts2(x, y, xEdges, yEdges);

% Plot the contour
contourf(xEdges(1:end-1), yEdges(1:end-1), N', 'LineColor', 'none');
colorbar;
xlabel('X');
ylabel('Y');
title('2-D Contour Plot of Density Distribution');

Additionally if your data file format is specific (e.g., LAMMPS dump), you may need a custom parser.

For more information on ‘countourf’ function, use this command to open the documentation:

>>web(fullfile(docroot, "techdoc/ref/contourf.html"))