def test_atom_id(self):
atoms = create(StaDumpAtoms("dumps_atom/atom.0.dump", 0))
moles = create(StaMolecules(atoms))
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,
"weights": [1.0] * len(mapping)
} for mapping in mappings]
beads = create(StaBeads(moles, abst_beads))
self.assertEqual(beads.get_keys(),
{"id", "mol", "type", "atom-ids", "atom-weights"})
data = beads.get_data()
for d in data:
offset = (d["mol"] - 1) * 38
in_mol = (d["id"] - 1) % 4
self.assertEqual(d["atom-ids"],
[offset + i + 1 for i in mappings[in_mol]])
def test_error01(self):
atoms = create(StaDumpAtoms("dumps_atom/atom.0.dump", 0))
moles = create(StaMolecules(atoms))
self.check_error_msg(
"RuntimeError: Mapping to beads must be specified by 'indices-in-mol'",
create, StaBeads(moles, [{
"foo": [1, 2, 3]
}]))
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_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_beads(self):
abst_atoms = []
atom_id = 0
for imol in range(10):
for iatom in range(20):
atom_id += 1
abst_atoms.append({
"id": atom_id,
"mol": imol + 1,
"mass": 1.0,
"xu": float(iatom // 4)
})
if iatom % 4 == 0:
abst_atoms[-1]["yu"] = 1.0
abst_atoms[-1]["zu"] = float(imol) * 10
elif iatom % 4 == 1:
abst_atoms[-1]["yu"] = 0.0
abst_atoms[-1]["zu"] = -1.0 + float(imol) * 10
elif iatom % 4 == 2:
abst_atoms[-1]["yu"] = -1.0
abst_atoms[-1]["zu"] = float(imol) * 10
elif iatom % 4 == 3:
abst_atoms[-1]["yu"] = 0.0
abst_atoms[-1]["zu"] = 1.0 + float(imol) * 10
atoms = create(StaCustom(abst_atoms))
moles = create(StaMolecules(atoms))
beads = create(
StaBeads(moles, [{
"indices-in-mol": list(range(4 * i, 4 * (i + 1)))
} for i in range(5)]))
beads.append_updater(AddCoMPosition(atoms))
rs = beads.get_2d_float("xu", "yu", "zu")
expected_rs = []
for imol in range(10):
for ibead in range(5):
expected_rs.append([float(ibead), 0.0, 10.0 * imol])
self.assertTrue(np.allclose(rs, np.array(expected_rs)))
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_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]
}]
}))