Describe the bug
Setting periodic boundary conditions misses neighbors for some lattices.

To Reproduce
See, for example, the hexagonal lattice

import lattpy as lp
import matplotlib.pyplot as plt

latt = lp.Lattice.hexagonal()
latt.add_atom()
latt.add_connections()

latt.build((3, 3, ), primitive=True)
latt.set_periodic([0, ], primitive=True)

latt.plot()
plt.show()

The top (12) and bottom (3) sites are each missing one neighbor (site 1 and 14, respectively)

Environment

• lattpy version: 0.7.4
• OS and Python version: All

I just discovered this package and used it to generate some graphics for my masters thesis (graphene, but with the basis rotated in comparison to the predefined one to be in line with my definition) . It absolutely saved me a lot of work doing things myself, but I struggled a bit with the documentation, so I would like to contribute to that a bit.

I can imagine adding the following:

• My code as an example somewhere, to illustrate how to create lattice and BZ graphics
• API Documentation where its missing
• Typehints

Also, I couldn't really figure out how to use the things provided in lattpy.disptools, so I did plotting of bands myself. If you have any hints, I can also add that to the documentation.

Describe the bug
Setting periodic boundary conditions for small lattices in higher dimensions fails due a broadcasting error and raises a ValueError.

To Reproduce
Steps to reproduce the behavior:

import lattpy as lp

latt = lp.finite_hypercubic((2, 2), periodic=True)

The resulting error is:

Traceback (most recent call last):
File "D:\Dropbox\Dev\Physics\lattpy\issue.py", line 16, in <module>
  main()
File "D:\Dropbox\Dev\Physics\lattpy\issue.py", line 12, in main
  latt = lp.finite_hypercubic((2, 2), periodic=True)
File "D:\Dropbox\Dev\Physics\lattpy\lattpy\__init__.py", line 451, in finite_hypercubic
  latt.build(s, primitive=primitive, periodic=periodic)
File "D:\Dropbox\Dev\Physics\lattpy\lattpy\lattice.py", line 431, in build
  self.set_periodic(periodic, primitive)
File "D:\Dropbox\Dev\Physics\lattpy\lattpy\lattice.py", line 620, in set_periodic
  self.data.set_periodic(pidx, pdists, pnvecs, paxs)
File "D:\Dropbox\Dev\Physics\lattpy\lattpy\data.py", line 467, in set_periodic
  self.neighbors[i, i0:i1] = pidx
ValueError: could not broadcast input array from shape (2,) into shape (1,)

Expected behavior
Set periodic boundary conditions if possible. In the example above this is not necessary since the sites are already neighbors.

Environment

• lattpy version: 0.7.4
• OS and Python version: All

Describe the bug
See below, site 5 is found for site 3 as nearest neighbor, but site 3 is not found for site 5 as nearest neighbor,

To Reproduce
Steps to reproduce the behavior:

import lattpy as lp
import matplotlib.pyplot as plt

latt = lp.Lattice.hexagonal()
latt.add_atom()
latt.add_connections(2)

latt.build((3-0.1, 3-0.1, ), primitive=True)
latt.set_periodic([1, ], primitive=True)

latt.plot(show_indices=True)
plt.show()
print(latt.neighbors(3,distidx=0))
print(latt.neighbors(5,distidx=0))

The resulting error is:

[1 0 4 6 5 8]
[7 4 2 8 0]

Expected behavior
[1 0 4 6 5 8]
[7 4 2 8 0 3]

Environment

• lattpy version: 0.7.7
• OS and Python version: MacOs, python3.8

Additional context
Add any other context about the problem here.