Ensuring NEURON 3d() functions target the correct section.

[aaberbach]

I was creating a cell model and came across an error in the following code:

bmtk/bmtk/simulator/bionet/morphology.py

Lines 51 to 57 in 022c24f

	for sec in self.hobj.soma:
	n3d = int(h.n3d()) # get number of n3d points in each section
	r3d = np.zeros((3, n3d)) # to hold locations of 3D morphology for the current section
	n3dsoma += n3d
	for i in range(n3d):
	r3dsoma[0] += h.x3d(i, sec=sec)

where the h.x3d(i, sec=sec) goes out of bounds. This was caused by the h.n3d() not accessing the correct section. When no sec is provided, NEURON uses a default section, and in this case, it was incorrect. Therefore, I went through bmtk and filled in sec=sec for these situations. This may not be necessary in all cases, but I think this is a situation where it is better to be safe than sorry.