SEM2DPACK

I meant:
edge [1] is between nodes 1 and 2
edge [2] is between nodes 2 and 3
edge [3] is between nodes 3 and 4
edge [4] is between nodes 4 and 1

SEM2DPACK has no limit on the value of the boundary tags, these can be
larger than 4.
Your example is actually hitting a limitation of the FTQ format. This mesh
format does not have boundary tags, only node tags. SEM2DPACK figures out
the boundaries from the node tags. However this cannot work unambiguously
for elements that have more than 2 boundaries. This is the case for the
elements with material tag #3 in your mesh.

I recommend you the new format "MESH2D" introduced in SEM2DPACK 2.3.5. It
defines the boundaries explicitly. The format is described in the reference
for the input block MESH_MESH2D in the user's manual. See also the matlab
functions in PRE/mesh2d/.
The following example defines a boundary with tag #13, with 2 boundary
elements corresponding to the edges #1 and #3 of the bulk elements #23 and
#52, respectively:

BCTAG NBEL
13 2
BID EID EDGE
1 23 1
2 52 3

The edges inside each element are numbered with the following convention
(edge index in [brackets], node indices in the same counterclockwise order
as they appear in the list of nodes for this element):

4 --[3]-- 3
| |
[4] [2]
| |
1 --[1]-- 2

SEM2DPACK output to STDOUT for included mesh and Par.inp file

***********************************************
* I n i t i a l i z a t i o n p h a s e *
***********************************************


Defining the FEM mesh ... EMC2_build: unexpected configuration
FATAL ERROR, aborting.

The attached graphic shows a mesh where the left boundary has been labeled
by COMSOL with index=14. The upper boundary has multiple elements with
designations 3, 6, and 13. For the case where the upper boundary is
continuous (i.e. is labeled by a single index), COMSOL may or may not label
it within the limit of 1 to 4 (so all external boundaries may not be within
1-4 even if the boundary is not subdivided by internal edges or elements.