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Coordinate system and COMSOL solver

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Hi
This may sound silly but I need to understand the basics.
I am bit confused about how COMSOL handles coordinates. I have a circular geometry in 3D, preferably in theory it is usual to use a cylindrical coordinate system (r,theta,z). When I use comsol, the equation is generally expressed in cartesian coordinates. Does it matter to convert it to cylindrical coordinate? I guess comsol solver would eventually convert it back to x,y,z system.

For example, an equation is dependent on the stresses in x,y,z direction but the geometry is a circular. All the equations are in cartesian coordinate. Can some one please explain how comsol handles the equation in this case? I am using SM and heat trasnfer in solids together.

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