update numpy matrices to numpy ndarray

[mec07]

We're getting some warnings about numpy deprecating matrices. We need to update to ndarray:

tests/pylato/test_hamiltonian.py::TestHamiltonian::test_total_energy_happy_path
  /Users/mcoury/development/PyLATO/pylato/electronic.py:41: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    self.rho = np.matrix(np.zeros((self.Job.Hamilton.HSOsize, self.Job.Hamilton.HSOsize), dtype='complex'))
  /Users/mcoury/development/PyLATO/pylato/electronic.py:42: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    self.rhotot = np.matrix(np.zeros((self.Job.Hamilton.HSOsize, self.Job.Hamilton.HSOsize), dtype='complex'))
  /Users/mcoury/development/PyLATO/pylato/electronic.py:94: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    self.rho = np.matrix(self.Job.psi)*np.diag(self.occ)*np.matrix(self.Job.psi).H
  /Users/mcoury/.virtualenvs/PyLATO/lib/python2.7/site-packages/numpy/matrixlib/defmatrix.py:68: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    return matrix(data, dtype=dtype, copy=False)
  /Users/mcoury/development/PyLATO/pylato/electronic.py:94: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    self.rho = np.matrix(self.Job.psi)*np.diag(self.occ)*np.matrix(self.Job.psi).H
  /Users/mcoury/.virtualenvs/PyLATO/lib/python2.7/site-packages/numpy/matrixlib/defmatrix.py:68: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    return matrix(data, dtype=dtype, copy=False)