Which part of the parameter file tells Gerris where the half-cylinder is placed? How do I alter it?
The position of the solid object is defined (obviously) through the coordinates of its vertices. If you created it using a CAD or similar program, you can translate, rotate etc… the object using this same program. You can also specify simple transformations (scaling, translations, rotations) directly in the parameter file, have a look at the GfsSurface documentation. Alternatively, you can use the transform program which comes with GTS.