In POINT, we use POSITION, which is defined as shape 3 in cuba.yml. This is a single position (no shape specified), and the position is 3-dimensional. This is also ok.
521 POINT:
522 definition: A point in a 3D space system
523 parent: CUBA.CUDS_ITEM
524 CUBA.POSITION:
525 default: [0, 0, 0]
The problem is however in usages of VECTOR, which is defined as shape 3 in cuba.yml. The specification of shape: (3,3) means 3x3 entries of vectors (each vector holding 3 values). I doubt this is what was intended.
510 BOX:
511 definition: A simple hexahedron (with six faces) simulation box defined by the three vectors and three directions. The condition should be specified for each direction (two faces at a time).
512 parent: CUBA.BOUNDARY
513 CUBA.VECTOR:
514 shape: (3,3)
515 default: [[0, 0, 0], [0, 0, 0], [0, 0, 0]]
516 scope: CUBA.USER
Therefore I suspect the intention was to have shape 3 here. We also need to check if this is an issue somewhere else.
shape in BOX for VECTOR is not correct, in the context of a BOX we need to define three vectors, each of shape 3. So you are right, it should be shape (3).
The "shape" entry in some context is arbitrary and deceiving. For example, in this context:
Implies a list of PARTICLE entities of any length. This is ok.
Similarly, this entry specifies a list of three sizes, each of shape 1 as from cuba.yml
In POINT, we use POSITION, which is defined as shape 3 in cuba.yml. This is a single position (no shape specified), and the position is 3-dimensional. This is also ok.
The problem is however in usages of VECTOR, which is defined as shape 3 in cuba.yml. The specification of shape: (3,3) means 3x3 entries of vectors (each vector holding 3 values). I doubt this is what was intended.
Therefore I suspect the intention was to have shape 3 here. We also need to check if this is an issue somewhere else.