def test_error01(self):
box = create(StaCustom({"foo": 0, "bar": 1}))
atoms = create(StaDumpAtoms("dumps_bead/bead.2990000.dump", 2990000))
atoms.append_updater(AddWrappedPosition(box))
check_error_msg(
self,
"RuntimeError: Missing key(s) 'hi_x', 'hi_y', 'hi_z', 'lo_x', 'lo_y', 'lo_z' in AddWrappedPosition",
atoms.get_data)
def _test_2way_molecules(self, arguments, mol_ids):
atoms = create(StaDumpAtoms(*arguments))
mols1 = create(StaMolecules(atoms))
mols2 = create(StaCustom([{"id": i} for i in mol_ids]))
mols2.append_updater(AddChildIDs(atoms, "atom", "mol"))
self.assertEqual(mols1.get_data(), mols2.get_data())
def test_error01(self):
atoms = create(StaDumpAtoms("dumps_bead/bead.2990000.dump", 2990000))
molecules = create(StaMolecules(atoms))
molecules.append_updater(AddCoMPosition(atoms))
check_error_msg(
self, "RuntimeError: Missing key(s) 'mass' in AddCoMPosition",
molecules.get_data)
def test_for_beads(self):
n_samples = 50
interval = 1000
atomses = [
create(StaDumpAtoms("dumps_atom/atom.{}.dump".format(i), i))
for i in range(0, n_samples * interval + 1, interval)
]
boxes = [
create(StaDumpBox("dumps_atom/atom.{}.dump".format(i), i))
for i in range(0, n_samples * interval + 1, interval)
]
molses = [create(StaMolecules(atoms)) for atoms in atomses]
mappings = [[0, 1, 2, 12, 13, 14, 15, 16, 17, 18],
[3, 4, 5, 19, 20, 21, 22, 23, 24],
[6, 7, 8, 25, 26, 27, 28, 29, 30],
[9, 10, 11, 31, 32, 33, 34, 35, 36, 37]]
abst_beads = [{
"type": 1,
"indices-in-mol": mapping
} for mapping in mappings]
beadses = [
create(StaBeads(mols, abst_beads)).append_updater(
AddCoMPosition(atoms)).append_updater(
AddInertiaMoment(atoms)).append_updater(
AddWrappedPosition(box))
for atoms, box, mols in zip(atomses, boxes, molses)
]
pro = ProRDFWD(list(zip(beadses, boxes)))
num_bins = 150
bin_width = 0.1
pro.set_bin(bin_width, num_bins)
pro.set_margin(2.0)
execute_omp(pro)
Rg2s = pro.get_squared_gyration_radius()
self.assertTrue(
np.allclose(Rg2s["isotropic"], (1 / 3) * Rg2s["parallel"] +
(2 / 3) * Rg2s["perpendicular"]))
Rg2s_traj = pro.get_squared_gyration_radius_traj()
self.assertTrue(
np.allclose(np.array(Rg2s_traj["isotropic"]),
(1 / 3) * np.array(Rg2s_traj["parallel"]) +
(2 / 3) * np.array(Rg2s_traj["perpendicular"])))
def test_error01(self):
atoms = create(StaDumpAtoms("dumps_atom/atom.0.dump", 0))
moles = create(StaMolecules(atoms))
check_error_msg(
self,
"RuntimeError: Mapping to Beads must be specified by 'indices-in-mol'",
create, StaBeads(moles, [{
"foo": [1, 2, 3]
}]))
def _test_get_2d_float(self, arguments, keys):
atoms = create(StaDumpAtoms(*arguments))
data = atoms.get_data()
arr = atoms.get_2d_float(*keys)
for i in range(10):
idx = randrange(len(data))
d = data[idx]
self.assertTrue(
np.allclose(np.array([d[k] for k in keys]), arr[idx]))
def test_error02(self):
atoms = create(StaDumpAtoms("dumps_atom/atom.0.dump", 0))
moles = create(StaMolecules(atoms))
self.check_error_msg(
"RuntimeError: The numbers of elements in 'indices-in-mol' and 'weights' are inconsistent",
create,
StaBeads(moles, [{
"indices-in-mol": [1, 2, 3, 4],
"weights": [1.0, 1.0, 1.0]
}]))
def _test_equivalent_filter(self, arguments, filter1, filter2):
atoms = create(StaDumpAtoms(*arguments))
filtered_atoms1 = create(StaCopy(atoms)).append_updater(
FilSet(filter1))
filtered_atoms2 = create(StaCopy(atoms)).append_updater(
FilSet(filter2))
self.assertEqual(filtered_atoms1.get_data(),
filtered_atoms2.get_data())
self.assertEqual(filtered_atoms1.get_keys(),
filtered_atoms2.get_keys())
def _test_get_1d_float(self, arguments, key):
atoms = create(StaDumpAtoms(*arguments))
data = atoms.get_data()
vec = atoms.get_1d_float(key)
for i in range(10):
idx = randrange(len(data))
d = data[idx][key]
self.assertEqual(d, vec[idx])
self.assertTrue(isinstance(d, float))
def test_error03(self):
atoms = create(StaDumpAtoms("dumps_atom/atom.0.dump", 0))
moles = create(StaMolecules(atoms))
check_error_msg(
self, "RuntimeError: The number of 'type' is invalid", create,
StaBeads(moles, [{
"indices-in-mol": [1, 2],
"weights": [1.0, 1.0]
}, {
"indices-in-mol": [3, 4],
"type": 1,
"weights": [1.0, 1.0]
}]))
def _test_wrapping(self, arguments):
box = create(StaDumpBox(*arguments))
atoms = create(StaDumpAtoms(*arguments))
atoms.append_updater(AddWrappedPosition(box))
wrapped = atoms.get_2d_float("x", "y", "z")
unwrapped = atoms.get_2d_float("xu", "yu", "zu")
box_data = box.get_data()
diff = unwrapped - wrapped
diff_x = diff.T[0] / (box_data["hi_x"] - box_data["lo_x"])
diff_y = diff.T[1] / (box_data["hi_y"] - box_data["lo_y"])
diff_z = diff.T[2] / (box_data["hi_z"] - box_data["lo_z"])
self.assertTrue(np.all(diff_x.round() == diff_x))
self.assertTrue(np.all(diff_y.round() == diff_y))
self.assertTrue(np.all(diff_z.round() == diff_z))
def test_error04(self):
atoms = create(StaDumpAtoms("dumps_atom/atom.0.dump", 0))
moles = create(StaMolecules(atoms))
check_error_msg(
self, "RuntimeError: The number of 'weights' is invalid", create,
StaBeads(
moles, {
1: [{
"indices-in-mol": [1, 2]
}, {
"indices-in-mol": [3, 4, 5]
}],
2: [{
"indices-in-mol": [1, 2, 3],
"weights": [1.0, 1.0, 1.0]
}, {
"indices-in-mol": [3, 4],
"weights": [1.0, 1.0]
}]
}))
def _test_remaining_number(self, arguments, filterset, num):
atoms = create(StaDumpAtoms(*arguments))
atoms.append_updater(FilSet(filterset))
self.assertEqual(len(atoms.get_data()), num)
def _test_get_keys(self, arguments, expectation):
molecules = create(StaMolecules(create(StaDumpAtoms(*arguments))))
self.assertEqual(molecules.get_keys(), expectation)
def _test_get_data(self, arguments, indices, expectation):
atoms = create(StaDumpAtoms(*arguments))
data = atoms.get_data()
self.assertEqual([data[i] for i in indices], expectation)
def test_error01(self):
atoms = create(StaDumpAtoms("dummy.file", 0))
check_error_msg(self, "RuntimeError: No such a file 'dummy.file'",
atoms.get_data)
def _test_get_keys(self, arguments, expectation):
atoms = create(StaDumpAtoms(*arguments))
self.assertEqual(atoms.get_keys(), expectation)
