I think the best way is to discretize the heat pipe in several little portion of pipe. In this way, as for me, the initial condition does not affect so much the final solution, being each subportion linked to the previous one and, so, affected by the solution of the previous subportion only.
So you are suggesting me to separately model and simulate each part ?How will I then be able to visualize the characteristic contours on the entire heat pipe.How can I conduct parametric study on the entire heat pipe then because I would have to carryout study separately for each part which would be tedious right?