I experience a similar problem. I am trying to use mupad for physics.
My intention is to have a notebook with symbolic formulas for learning and understanding the theory.
In addition I want to use the capabilities of mupad for deduction of specialized formulas from theory for my project.
I found: The output of mupad is correct in a mathematical way. However, I cannot see the physics behind the formulas.
Example: Set up a vector equation:
assume([x, y, z, x0, y0, z0, kx, ky, kz], Type::Real)
r := matrix([x, y, z]); r0 := matrix([x0, y0, z0]); k := matrix(1, 3, [kx, ky, kz])
Now the vector equation:
linalg::scalarProduct(r  r0, k), [x, y, z] = 0
I found no way to get just a symbolic scalar product. The output of mupad is hardly usuable for further symbolic computation with more complex formulas.
There seems to be no control for some kind of symbolic physics. However, perhaps I just expect too much or I choosed the wrong program.
I am considering to use a formula editor, like that of OpenOffice, and do most symbolic computations by myself. There is still an advantage over pencil and paper: the possibility to reuse terms by copy and paste, and of course, good printout.
Mupad could still contribute to my project by performing complex computations, either for control of my own solutions or finding solutions, which I do not see.
Harry
