def test_agspec_string():
agspec = AtomicGridSpec('power:0.001:10.0:20:26')
for number in 1, 4, 10:
rgrid, nlls = agspec.get(number, number)
assert isinstance(rgrid.rtransform, PowerRTransform)
assert rgrid.rtransform.rmin == 0.001 * angstrom
assert rgrid.rtransform.rmax == 10.0 * angstrom
assert rgrid.size == 20
assert (nlls == [26] * 20).all()
def test_atgrid_medium_contents():
for agspec in AtomicGridSpec('medium'), AtomicGridSpec():
rgrid, nlls = agspec.get(1, 1)
assert rgrid.rtransform.to_string(
) == 'PowerRTransform 3.69705074304963e-06 19.279558946793685 24'
assert (nlls == np.array([
6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 26, 38, 50, 86, 110, 110, 110, 110,
86, 50, 50, 14, 6, 6
])).all()
def test_agspec_tuple2():
rtf = ExpRTransform(0.1, 1e1, 4)
rgrid = RadialGrid(rtf)
agspec = AtomicGridSpec((rgrid, [6, 14, 26, 6]))
rgrid0, nlls0 = agspec.get(1, 1)
assert rgrid is rgrid0
assert (nlls0 == [6, 14, 26, 6]).all()
with assert_raises(ValueError):
AtomicGridSpec((rgrid, [6, 14, 26, 6, 6]))
def test_agspec_tuple1():
rtf = ExpRTransform(0.1, 1e1, 4)
rgrid = RadialGrid(rtf)
agspec = AtomicGridSpec((rgrid, 6))
rgrid0, nlls0 = agspec.get(1, 1)
assert rgrid is rgrid0
assert (nlls0 == [6, 6, 6, 6]).all()
rgrid0, nlls0 = agspec.get(2, 2)
assert rgrid is rgrid0
assert (nlls0 == [6, 6, 6, 6]).all()
def test_agspec_list():
agspec = AtomicGridSpec([
(1, 1, RadialGrid(ExpRTransform(0.1, 1e1, 4)), [6, 14, 26, 6]),
(2, 2, RadialGrid(ExpRTransform(0.2, 1e1, 4)), [6, 14, 26, 14]),
(10, 8, RadialGrid(ExpRTransform(0.3, 1e1, 4)), [6, 14, 26, 26]),
(10, 10, RadialGrid(ExpRTransform(0.4, 1e1, 4)), [6, 14, 26, 38]),
])
rgrid, nlls = agspec.get(1, 1)
assert rgrid.rtransform.rmin == 0.1
assert (nlls == [6, 14, 26, 6]).all()
rgrid, nlls = agspec.get(2, 2)
assert rgrid.rtransform.rmin == 0.2
assert (nlls == [6, 14, 26, 14]).all()
rgrid, nlls = agspec.get(10, 8)
assert rgrid.rtransform.rmin == 0.3
assert (nlls == [6, 14, 26, 26]).all()
rgrid, nlls = agspec.get(10, 10)
assert rgrid.rtransform.rmin == 0.4
assert (nlls == [6, 14, 26, 38]).all()
rgrid, nlls = agspec.get(10, 6)
assert rgrid.rtransform.rmin == 0.3
assert (nlls == [6, 14, 26, 26]).all()
rgrid, nlls = agspec.get(2, 1)
assert rgrid.rtransform.rmin == 0.2
assert (nlls == [6, 14, 26, 14]).all()
def test_agspec_local_file():
with tmpdir('grid.scripts.test.test_espfit.test_scripts_symmetry') as dn:
fn_dest = os.path.join(dn, 'mygrid.txt')
shutil.copy(
pkg_resources.resource_filename('grid.grid.data', 'tv-13.7-4.txt'),
fn_dest)
agspec = AtomicGridSpec(fn_dest)
rgrid, nlls = agspec.get(1, 1)
assert rgrid.rtransform.to_string(
) == 'PowerRTransform 3.69705074304963e-06 19.279558946793685 24'
assert (nlls == np.array([
6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 26, 38, 50, 86, 110, 110, 110, 110,
86, 50, 50, 14, 6, 6
])).all()
def test_agspec_coarse_contents():
rgrid, nlls = AtomicGridSpec('coarse').get(1, 1)
assert rgrid.rtransform.to_string(
) == 'PowerRTransform 7.0879993828935345e-06 16.05937640019924 20'
assert (nlls == np.array([
6, 6, 6, 6, 6, 6, 6, 14, 14, 26, 38, 50, 86, 86, 86, 86, 50, 14, 6, 6
])).all()
def test_agspec_get_size():
agspec = AtomicGridSpec()
assert agspec.get_size(1, 1) == 928
assert agspec.get_size(8, 8) == 3754
def test_agspec_load_names():
nrads = [20, 24, 34, 41, 49, 59]
for name in 'tv-13.7-3', 'tv-13.7-4', 'tv-13.7-5', 'tv-13.7-6', 'tv-13.7-7', 'tv-13.7-8':
agspec = AtomicGridSpec(name)
assert len(agspec.get(1, 1)[1]) == nrads.pop(0)
def test_agspec_load_simple_names():
nrads = [20, 24, 34, 41, 49, 59]
for name in 'coarse', 'medium', 'fine', 'veryfine', 'ultrafine', 'insane':
agspec = AtomicGridSpec(name)
assert len(agspec.get(1, 1)[1]) == nrads.pop(0)
def test_agspec_wrong_string():
with assert_raises(ValueError):
AtomicGridSpec('power:0.001:10.0:20')
def __init__(self,
centers,
numbers,
pseudo_numbers=None,
agspec='medium',
k=3,
random_rotate=True,
mode='discard'):
"""
**Arguments:**
centers
An array (N, 3) with centers for the atom-centered grids.
numbers
An array (N,) with atomic numbers.
**Optional arguments:**
pseudo_numbers
An array (N,) with effective core charges. When not given, this
defaults to ``numbers``.
agspec
A specifications of the atomic grid. This can either be an
instance of the AtomicGridSpec object, or the first argument
of its constructor.
k
The order of the switching function in Becke's weighting scheme.
random_rotate
Flag to control random rotation of spherical grids.
mode
Select one of the following options regarding atomic subgrids:
* ``'discard'`` (the default) means that all information about
subgrids gets discarded.
* ``'keep'`` means that a list of subgrids is kept, including
the integration weights of the local grids.
* ``'only'`` means that only the subgrids are constructed and
that the computation of the molecular integration weights
(based on the Becke partitioning) is skipped.
"""
natom, centers, numbers, pseudo_numbers = typecheck_geo(
centers, numbers, pseudo_numbers)
self._centers = centers
self._numbers = numbers
self._pseudo_numbers = pseudo_numbers
# check if the mode argument is valid
if mode not in ['discard', 'keep', 'only']:
raise ValueError(
'The mode argument must be \'discard\', \'keep\' or \'only\'.')
# transform agspec into a usable format
if not isinstance(agspec, AtomicGridSpec):
agspec = AtomicGridSpec(agspec)
self._agspec = agspec
# assign attributes
self._k = k
self._random_rotate = random_rotate
self._mode = mode
# allocate memory for the grid
size = sum(
agspec.get_size(self.numbers[i], self.pseudo_numbers[i])
for i in range(natom))
points = np.zeros((size, 3), float)
weights = np.zeros(size, float)
self._becke_weights = np.ones(size, float)
# construct the atomic grids
if mode != 'discard':
atgrids = []
else:
atgrids = None
offset = 0
if mode != 'only':
# More recent covalent radii are used than in the original work of Becke.
# No covalent radius is defined for elements heavier than Curium and a
# default value of 3.0 Bohr is used for heavier elements.
cov_radii = np.array([(periodic[n].cov_radius or 3.0)
for n in self.numbers])
# The actual work:
logging.info('Preparing Becke-Lebedev molecular integration grid.')
for i in range(natom):
atsize = agspec.get_size(self.numbers[i], self.pseudo_numbers[i])
atgrid = AtomicGrid(self.numbers[i], self.pseudo_numbers[i],
self.centers[i], agspec, random_rotate,
points[offset:offset + atsize])
if mode != 'only':
atbecke_weights = self._becke_weights[offset:offset + atsize]
becke_helper_atom(points[offset:offset + atsize],
atbecke_weights, cov_radii, self.centers, i,
self._k)
weights[offset:offset +
atsize] = atgrid.weights * atbecke_weights
if mode != 'discard':
atgrids.append(atgrid)
offset += atsize
# finish
IntGrid.__init__(self, points, weights, atgrids)
# Some screen info
self._log_init()