def test_good_init(self):
if (self.__dnacc):
fail = False
try:
potential.DNACC(**self.__params)
except:
fail = True
self.assertFalse(fail)
def test_reduce(self):
if (self.__dnacc):
res = potential.DNACC(**self.__params)
red = res.__reduce__()
x = dict(zip(res.__pnames__(), red[1]))
red[0](**x)
fail = False
try:
red[0](**x)
except:
fail = True
self.assertFalse(fail)
def test_potential_1(self):
if (self.__dnacc):
try:
import dnacc
from dnacc.units import nm
except:
pass
else:
self.__params = {
"r1": 500,
"r2": 500,
"lengths": {
"A": 20,
"B": 20
},
"sigma1": {
"A": 1 / 20.**2
},
"sigma2": {
"B": 1 / 20.**2
},
"beta_DeltaG0": {
("A", "A"): 0,
("A", "B"): -8,
("B", "B"): 0
}
}
res = potential.DNACC(**self.__params)
r = numpy.linspace(41 / 1000., 41, 1000) + 500. + 500.
u, f = res.evaluate_array(r)
# Example from documentation
plates = dnacc.PlatesMeanField()
plates.add_tether_type(plate='lower',
sticky_end='alpha',
L=20 * nm,
sigma=1 / (20 * nm)**2)
plates.add_tether_type(plate='upper',
sticky_end='alphap',
L=20 * nm,
sigma=1 / (20 * nm)**2)
plates.beta_DeltaG0['alpha', 'alphap'] = -8
plates.at(41 * nm).set_reference_now()
V_plate_arr = [
plates.at(rv - 1000.).free_energy_density for rv in r
]
R = 500 * nm
V_sphere_arr = dnacc.calc_spheres_potential(
r - 1000., V_plate_arr, R)
# Compare results over the domain of the theory
self.assertTrue(numpy.allclose(V_sphere_arr, u))
# Check that potential is zero beyond cutoff
self.assertEqual(res.evaluate(r[-1] + 0.00001), (0.0, 0.0))
# Check that WCA-esque potential wall is used at contact and below
rep_wallu, rep_wallf = res.evaluate_array(
numpy.linspace(0, r[0], 1000))
# Wall is monotonically decreasing
self.assertEqual(res.evaluate(0), (numpy.inf, numpy.inf))
self.assertTrue(
numpy.all(rep_wallu[1:] < numpy.inf)
and numpy.all(rep_wallu[1:] > 0))
self.assertTrue(
numpy.all(x > y for x, y in zip(rep_wallu, rep_wallu[1:])))
self.assertTrue(
numpy.all(rep_wallf[1:] < numpy.inf)
and numpy.all(rep_wallf[1:] > 0))
self.assertTrue(
numpy.all(x > y for x, y in zip(rep_wallf, rep_wallf[1:])))
# Wall connects continuously
self.assertTrue(numpy.isclose(rep_wallu[-1], u[0]))
self.assertTrue(numpy.isclose(rep_wallf[-1], f[0]))
def test_bad_init_beta(self):
if (self.__dnacc):
self.__params["beta"] = -1.0
with self.assertRaises(ValueError) as result:
potential.DNACC(**self.__params)
def test_bad_init_beta_DeltaG0_excess(self):
if (self.__dnacc):
self.__params["beta_DeltaG0"][("A", "C")] = -1.0
with self.assertRaises(Exception) as result:
potential.DNACC(**self.__params)
def test_bad_init_beta_DeltaG0_symm(self):
if (self.__dnacc):
self.__params["beta_DeltaG0"][("B", "A")] = -4.0
with self.assertRaises(ValueError) as result:
potential.DNACC(**self.__params)
def test_bad_init_sigma2_construct(self):
if (self.__dnacc):
self.__params["sigma2"]["C"] = 1.0
with self.assertRaises(Exception) as result:
potential.DNACC(**self.__params)
def test_bad_init_sigma2(self):
if (self.__dnacc):
self.__params["sigma2"]["A"] = -1
with self.assertRaises(ValueError) as result:
potential.DNACC(**self.__params)