def test_match_degree(self):
"""Test match proper degree for random given values."""
# test array 1
num_list1 = [3, 4, 5, 6, 7, 8, 9, 10]
result1 = match_degree(num_list1)
assert_array_equal(result1, [3, 5, 5, 7, 7, 9, 9, 11])
# test array 2
num_list2 = [33, 34, 35, 36, 37, 38, 39, 40]
result2 = match_degree(num_list2)
assert_array_equal(result2, [35, 35, 35, 41, 41, 41, 41, 41])
def __init__(self,
radial_grid,
atomic_rad,
*,
scales,
degs,
center=np.array([0.0, 0.0, 0.0])):
"""Construct atomic grid for given arguments.
Parameters
----------
radial_grid : Grid
Radial grid for x in xrange(1,10):
pass each unit spherical shell
atomic_rad : float
Atomic radium for targit atom
scales : np.ndarray(N,), keyword-only argument
Scales for selecting different spherical grids.
degs : np.ndarray(N+1, dtype=int), keyword-only argument
Different magic number for each section of atomic radium region
center : np.ndarray(3,), default to [0., 0., 0.], keyword-only argument
Central cartesian coordinates of atomic grid
Raises
------
TypeError
Radial_grid need to ba an instance of Grid class
ValueError
Length of degs should be one more than scales
"""
scales = np.array(scales)
degs = np.array(degs)
# check stage
if not isinstance(radial_grid, Grid):
raise TypeError(
f"Radial_grid is not an instance of Grid, got {type(radial_grid)}."
)
if len(degs) == 0:
raise ValueError("rad_list can't be empty.")
if len(degs) - len(scales) != 1:
raise ValueError(
"degs should have only one more element than scales.")
if not isinstance(center, np.ndarray):
raise TypeError(
f"Center should be a numpy array with 3 entries, got {type(center)}."
)
if len(center) != 3:
raise ValueError(
f"Center should only have 3 entries, got {len(center)}.")
# assign stage
self._center = center
self._radial_grid = radial_grid
# initiate atomic grid property as None
rad_degs = self._find_l_for_rad_list(self._radial_grid.points,
atomic_rad, scales, degs)
# set real degree to each rad point
self._rad_degs = match_degree(rad_degs)
self._points, self._weights, self._indices = self._generate_atomic_grid(
self._radial_grid, self._rad_degs, center)
self._size = len(self._weights)
def _generate_degree_from_radius(radial_grid, radius, scales, degs):
"""Generate proper degrees for radius."""
scales = np.array(scales)
degs = np.array(degs)
if len(degs) == 0:
raise ValueError("rad_list can't be empty.")
if len(degs) - len(scales) != 1:
raise ValueError(
"degs should have only one more element than scales.")
rad_degs = AtomicGrid._find_l_for_rad_list(radial_grid.points, radius,
scales, degs)
return match_degree(rad_degs)
def _generate_degree_from_radius(rgrid, radius, r_sectors, degs):
"""Generate proper degrees for radius.
Parameters
----------
rgrid : RadialGrid
A radialgrid instance
radius : float
radius of interested atom
r_sectors : list or np.ndarray
a list of r_sectors number
degs : list or np.ndarray
a list of degs for each radius section
Returns
-------
np.ndarray
a numpy array of L degree value for each radial point
Raises
------
ValueError
Description
"""
r_sectors = np.array(r_sectors)
degs = np.array(degs)
if len(degs) == 0:
raise ValueError("rad_list can't be empty.")
if len(degs) - len(r_sectors) != 1:
raise ValueError(
"degs should have only one more element than r_sectors.")
matched_deg = match_degree(degs)
rad_degs = AtomGrid._find_l_for_rad_list(rgrid.points,
radius * r_sectors,
matched_deg)
return rad_degs