I am writing in python and in the program I am using I need to define a box in cylindrical shape. To do so, i need to define a matrix(3*3) to make a cylindrical shape. Inside the package, they say you can have any shape for box as long as it is an upper triangular matrix.For example:
[[Lx, Ly * xy, Lz * xz], [0, Ly, Lz * yz], [0, 0, Lz]]
The Lx,Ly,Lz defined the length of a cube in each direction and xy,xz and yz show the tilt of each plane. https://hoomd-blue.readthedocs.io/en/latest/package-hoomd.html#hoomd.Box.from_box
How can I write a code that give me a matrix like this but for cylinder.
I tried using cylindrical coordinate but I don't know how to give a range of angles to the matrix. Specially in the program I can not use more than one matrix for the shape of the box.
