def test_squared(self):
custom_data = deepcopy(self.custom_data)
custom_data[0]["xu"] = 3.0
custom_data[1]["xu"] = -1.0
atoms = create(StaCustom(custom_data))
molecules = create(StaMolecules(atoms))
molecules.append_updater(AddCoMPosition(atoms))
molecules.append_updater(AddInertiaMoment(atoms))
molecules.append_updater(AddGyrationRadius())
data = molecules.get_data()[0]
self.assertAlmostEqual(data["Rg^2"], 2.0)
self.assertAlmostEqual(data["Rg^2(x+y)"], 5/3)
self.assertAlmostEqual(data["Rg^2(y+z)"], 2/3)
self.assertAlmostEqual(data["Rg^2(z+x)"], 5/3)
self.assertAlmostEqual(data["Rg^2(x)"], 4/3)
self.assertAlmostEqual(data["Rg^2(y)"], 1/3)
self.assertAlmostEqual(data["Rg^2(z)"], 1/3)
self.assertEqual(
molecules.get_keys(), {
"id", "atom-ids", "mass", "xu", "yu", "zu",
"I_xx", "I_yy", "I_zz", "I_xy", "I_xz", "I_yz",
"Rg^2", "Rg^2(y+z)", "Rg^2(z+x)", "Rg^2(x+y)",
"Rg^2(x)", "Rg^2(y)", "Rg^2(z)"})
def _test_positions(self, atoms):
mols = create(StaMolecules(atoms))
mols.append_updater(AddCoMPosition(atoms))
mol_data = mols.get_data()
target = mol_data[randrange(len(mol_data))]
atom_ids = set(target["atom-ids"])
atom_data = atoms.get_data()
tmpm = 0.0
tmpx = 0.0
tmpy = 0.0
tmpz = 0.0
for atom in atom_data:
if atom["id"] in atom_ids:
m = atom["mass"]
tmpm += m
tmpx += m * atom["xu"]
tmpy += m * atom["yu"]
tmpz += m * atom["zu"]
tmpx /= tmpm
tmpy /= tmpm
tmpz /= tmpm
self.assertEqual(target["xu"], tmpx)
self.assertEqual(target["yu"], tmpy)
self.assertEqual(target["zu"], tmpz)
def test_sqrted(self):
atoms = create(StaCustom(self.custom_data))
molecules = create(StaMolecules(atoms))
molecules.append_updater(AddCoMPosition(atoms))
molecules.append_updater(AddInertiaMoment(atoms))
molecules.append_updater(AddGyrationRadius().with_sqrted())
data = molecules.get_data()[0]
self.assertAlmostEqual(data["Rg"], 1.0)
self.assertAlmostEqual(data["Rg(x+y)"], sqrt(2/3))
self.assertAlmostEqual(data["Rg(x)"], sqrt(1/3))
self.assertEqual(data["Rg(x+y)"], data["Rg(y+z)"])
self.assertEqual(data["Rg(x+y)"], data["Rg(z+x)"])
self.assertEqual(data["Rg(x)"], data["Rg(y)"])
self.assertEqual(data["Rg(x)"], data["Rg(z)"])
self.assertEqual(
molecules.get_keys(), {
"id", "atom-ids", "mass", "xu", "yu", "zu",
"I_xx", "I_yy", "I_zz", "I_xy", "I_xz", "I_yz",
"Rg^2", "Rg^2(y+z)", "Rg^2(z+x)", "Rg^2(x+y)",
"Rg^2(x)", "Rg^2(y)", "Rg^2(z)",
"Rg", "Rg(y+z)", "Rg(z+x)", "Rg(x+y)",
"Rg(x)", "Rg(y)", "Rg(z)"})
def test_gyration_radius(self):
n_samples = 2000
rs = 100*np.random.random_sample((n_samples, 3)) - 50
abst_atoms = [
{
"id": i+1,
"mol": i//20 + 1,
"mass": 12.011,
"xu": rs[i,0],
"yu": rs[i,1],
"zu": rs[i,2]
}
for i in range(2000)]
atoms = create(StaCustom(abst_atoms))
moles = create(StaMolecules(atoms))
moles.append_updater(AddCoMPosition(atoms))
moles.append_updater(AddChildPositions(atoms, "atom"))
moles.append_updater(AddInertiaMoment(atoms))
moles.append_updater(AddGyrationRadius())
data = moles.get_data()
for d in data:
xyzs = d["atom-xs"] + d["atom-ys"] + d["atom-zs"]
self.assertAlmostEqual(
d["Rg^2"], sum([a*a for a in xyzs])/len(d["atom-ids"]))
def test_cubic_isotropic(self):
abst_atoms = []
mol_id = 0
for ix in range(10):
for iy in range(10):
for iz in range(10):
mol_id += 1
abst_atoms.extend(
self.create_rotated_abst_atoms_in_mol(
uniform(-0.5, 0.5), 6*(mol_id-1)+1, mol_id,
1.0*ix, 1.0*iy, 1.0*iz))
atoms = create(StaCustom(abst_atoms))
mols = create(StaMolecules(atoms))
mols.append_updater(AddCoMPosition(atoms))
mols.append_updater(AddInertiaMoment(atoms))
box = create(StaCustom({
"lo_x": 0.0, "hi_x": 10.0, "pbc_x": True,
"lo_y": 0.0, "hi_y": 10.0, "pbc_y": True,
"lo_z": 0.0, "hi_z": 10.0, "pbc_z": True}))
mols.append_updater(AddWrappedPosition(box))
pro = ProRDFWD(mols, box)
num_bins = 20
bin_width = 0.1
pro.set_bin(bin_width, num_bins)
execute_omp(pro)
self.assertTrue(np.allclose(
pro.get_r_axis(), np.arange(0.0, num_bins*bin_width, bin_width)))
expected_rdf = np.zeros(num_bins)
data = [
{"index": 10, "num": 6},
{"index": 14, "num": 12},
{"index": 17, "num": 8}]
for d in data:
r_inner = (d["index"]-0.5) * bin_width
r_outer = (d["index"]+0.5) * bin_width
dV = (4.0*np.pi/3.0) * (
np.power(r_outer, 3) - np.power(r_inner, 3))
expected_rdf[d["index"]] = (d["num"]/dV)/1.0
self.assertTrue(np.allclose(pro.get_rdf(), expected_rdf))
def test_with_and_without_modification(self):
n_traj = 100
n_mols = 100
abst_atoms_traj = []
mol_id = 0
for i in range(n_traj):
abst_atoms = []
mol_id = 0
for i in range(n_mols):
mol_id += 1
abst_atoms.extend(
self.create_rotated_abst_atoms_in_mol(
uniform(-1.0, 1.0), 6*(mol_id-1)+1, mol_id,
uniform(-50.0, 50.0),
uniform(-50.0, 50.0),
uniform(-50.0, 50.0)))
abst_atoms_traj.append(abst_atoms)
atomses = [
create(StaCustom(abst_atoms)) for abst_atoms in abst_atoms_traj]
boxes = [
create(StaCustom({
"lo_x": 0.0, "hi_x": 10.0, "pbc_x": True,
"lo_y": 0.0, "hi_y": 10.0, "pbc_y": True,
"lo_z": 0.0, "hi_z": 10.0, "pbc_z": True
})) for i in range(n_traj)]
molses = [
create(StaMolecules(atoms))
.append_updater(AddCoMPosition(atoms))
.append_updater(AddInertiaMoment(atoms))
.append_updater(AddWrappedPosition(box))
for atoms, box in zip(atomses, boxes)]
pro_with_modify = ProRDFWD(list(zip(molses, boxes)))
pro_without_modify = ProRDF(list(zip(molses, boxes)))
num_bins = 20
bin_width = 0.1
pro_with_modify.set_bin(bin_width, num_bins)
pro_without_modify.set_bin(bin_width, num_bins)
execute_omp([pro_with_modify, pro_without_modify])
self.assertTrue(np.allclose(
pro_with_modify.get_rdf(), pro_without_modify.get_rdf()))
self.assertTrue(np.allclose(
np.array(pro_with_modify.get_rdf_traj()),
np.array(pro_without_modify.get_rdf_traj())))
def test_error01(self):
atoms = create(StaDumpAtoms("dumps_bead/bead.2990000.dump", 2990000))
molecules = create(StaMolecules(atoms))
molecules.append_updater(AddCoMPosition(atoms))
self.check_error_msg(
"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(StaCustom(self.custom_data))
molecules = create(StaMolecules(atoms))
molecules.append_updater(AddCoMPosition(atoms))
molecules.append_updater(
AddInertiaMoment(create(StaCustom({"foo": 0, "bar": 1}))))
check_error_msg(
self, "RuntimeError: Missing key(s) 'id', 'mass', 'xu', 'yu', 'zu' in AddInertiaMoment", molecules.get_data)
def test_isotropic(self):
atoms = create(StaCustom(self.custom_data))
molecules = create(StaMolecules(atoms))
molecules.append_updater(AddCoMPosition(atoms))
molecules.append_updater(AddInertiaMoment(atoms))
data = molecules.get_data()[0]
self.assertEqual(data["I_xx"], data["I_yy"])
self.assertEqual(data["I_yy"], data["I_zz"])
self.assertEqual(data["I_xy"], data["I_xz"])
self.assertEqual(data["I_xy"], data["I_yz"])
def test_random(self):
rs = 10*np.random.random_sample((10, 3)) - 5
ms = np.random.random_sample(10) + 1
com = (rs.T*ms).T.sum(axis=0)/ms.sum()
expected = rs - com
abst_atoms_in_mol = [
{
"id": i+1,
"mol": 1,
"mass": ms[i],
"xu": rs[i,0],
"yu": rs[i,1],
"zu": rs[i,2]
}
for i in range(10)]
abst_atoms = []
for imol in range(100):
tmp = deepcopy(abst_atoms_in_mol)
shift_x = uniform(-100.0, 100.0)
shift_y = uniform(-100.0, 100.0)
shift_z = uniform(-100.0, 100.0)
for atom in tmp:
atom["id"] += 10*imol
atom["mol"] += imol
atom["xu"] += shift_x
atom["yu"] += shift_y
atom["zu"] += shift_z
abst_atoms.extend(tmp)
atoms = create(StaCustom(abst_atoms))
moles = create(StaMolecules(atoms))
moles.append_updater(AddCoMPosition(atoms))
moles.append_updater(AddChildPositions(atoms, "atom"))
data = moles.get_data()
for d in data:
self.assertTrue(np.allclose(expected, np.array(
[d["atom-xs"], d["atom-ys"], d["atom-zs"]]).T))
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_isotropic(self):
atoms = create(StaCustom(self.custom_data))
molecules = create(StaMolecules(atoms))
molecules.append_updater(AddCoMPosition(atoms))
molecules.append_updater(AddInertiaMoment(atoms))
molecules.append_updater(AddMolecularOrientation())
data = molecules.get_data()[0]
evals = data["I_values"]
self.assertEqual(evals[0], evals[1])
self.assertEqual(evals[0], evals[2])
evecs = data["I_vectors"]
self.assertTrue(np.allclose(np.array(evecs), np.identity(3)))
def test_x_oriented(self):
atoms = create(
StaCustom([
{
"id": 1,
"mol": 1,
"mass": 1.0,
"xu": 1.0,
"yu": 1.0,
"zu": 1.0
},
{
"id": 2,
"mol": 1,
"mass": 1.0,
"xu": 2.0,
"yu": 1.0,
"zu": 1.0
},
{
"id": 3,
"mol": 1,
"mass": 1.0,
"xu": 4.0,
"yu": 1.0,
"zu": 1.0
},
{
"id": 4,
"mol": 1,
"mass": 1.0,
"xu": 8.0,
"yu": 1.0,
"zu": 1.0
},
]))
molecules = create(StaMolecules(atoms))
molecules.append_updater(AddCoMPosition(atoms))
molecules.append_updater(AddInertiaMoment(atoms))
molecules.append_updater(AddMolecularOrientation())
data = molecules.get_data()[0]
self.assertEqual(data["S_x"], 1.0)
self.assertEqual(data["S_y"], -0.5)
self.assertEqual(data["S_z"], -0.5)