def test_error01(self):
atoms = create(StaDumpAtoms("dumps_bead/bead.2990000.dump", 2990000))
atoms.append_updater(FilSet({"dummy": {1, 2, 3}}))
check_error_msg(self, "RuntimeError: Missing key(s) 'dummy' in FilSet",
atoms.get_data)
def test_error02(self):
elem = create(StaCustom({"foo": 0, "bar": 1}))
elem.append_updater(AddRename("foo", "bar"))
check_error_msg(
self, "RuntimeError: Key 'bar' already exists", elem.get_data)
def test_error03(self):
elem = create(StaCustom({"foo": 0, "bar": 1}))
elem.append_updater(AddRename("foo", "id"))
check_error_msg(
self, "RuntimeError: Adder cannot add 'id'", elem.get_data)
def test_error03(self):
atoms_traj = []
base_atoms = deepcopy(self.base_data)
for i in range(2, 12):
atoms_tmp = []
for j in range(1, i):
for k, atom in enumerate(base_atoms):
atom["id"] = (j-1) * len(base_atoms) + k + 1
atom["mol"] = j
atoms_tmp.extend(deepcopy(base_atoms))
atoms_traj.append(create(StaCustom(atoms_tmp)))
mols_traj = [create(StaMolecules(atoms)) for atoms in atoms_traj]
pro = ProTimeCorrelationInMolecule(list(zip(mols_traj, atoms_traj)))
check_error_msg(
self, "RuntimeError: Number of molecules and molecular types must be unchanged", execute_omp, pro)
def test_error01(self):
elem = create(StaCustom({"foo": 0, "bar": 1}))
elem.append_updater(AddRename("dummy", "new"))
check_error_msg(
self, "RuntimeError: Missing key(s) 'dummy' in AddRename", elem.get_data)
def test_error02(self):
atoms = create(StaCustom(self.custom_data))
molecules = create(StaMolecules(atoms))
molecules.append_updater(AddInertiaMoment(atoms))
check_error_msg(
self, "RuntimeError: Missing key(s) 'xu', 'yu', 'zu' in AddInertiaMoment", molecules.get_data)
def test_error02(self):
atoms = create(
StaDumpAtoms("dumps_bead/bead.2990000.dump", 2990000))
atoms.append_updater(FilComparison([("mol", "dummy", 10)]))
check_error_msg(
self, "RuntimeError: Supported operators for comparison are '<', '>', '<=', '>=', '==' and '!='", atoms.get_data)
def test_error01(self):
elems = [create(StaCustom({"A": i, "B": i * i})) for i in range(1000)]
pro = ProData(elems)
pro.select("C")
check_error_msg(self, "RuntimeError: Missing key(s) 'C' in ProData",
execute_omp, pro)
def test_error01(self):
atoms = create(
StaDumpAtoms("dumps_bead/bead.2990000.dump", 2990000))
atoms.append_updater(FilComparison([("dummy", "<", 0)]))
check_error_msg(
self, "RuntimeError: Missing key(s) 'dummy' in FilComparison", atoms.get_data)
def test_error02(self):
atomses = [create(StaCustom(self.base_data)) for i in range(10)]
molses = [create(StaCustom([{"id": 1}])) for i in range(10)]
pro = ProTimeCorrelationInMolecule(list(zip(molses, atomses)))
check_error_msg(
self, "RuntimeError: Missing key(s) 'atom-ids' in ProTimeCorrelationInMolecule", execute_omp, pro)
def test_error01(self):
elems = [
create(StaCustom({"id": i, "A": i*i})) for i in range(1000)]
pro = ProValueArray(elems)
check_error_msg(
self, "RuntimeError: Selected value(s) for ProValueArray", execute_omp, pro)
def test_error01(self):
atoms = create(StaCustom(self.custom_data))
molecules = create(StaMolecules(atoms))
molecules.append_updater(AddGyrationRadius())
check_error_msg(
self,
"RuntimeError: Missing key(s) 'I_xx', 'I_yy', 'I_zz', 'mass' in AddGyrationRadius",
molecules.get_data)
def test_error02(self):
box = create(StaDumpBox("dumps_bead/bead.2990000.dump", 2990000))
atoms = create(StaCustom([{"A": i, "B": i * i} for i in range(1000)]))
atoms.append_updater(AddWrappedPosition(box))
check_error_msg(
self,
"RuntimeError: Missing key(s) 'xu', 'yu', 'zu' in AddWrappedPosition",
atoms.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_error01(self):
atoms = create(StaCustom(self.custom_data))
molecules = create(StaMolecules(atoms))
molecules.append_updater(AddMolecularOrientation())
check_error_msg(
self,
"RuntimeError: Missing key(s) 'I_xx', 'I_xy', 'I_xz', 'I_yy', 'I_yz', 'I_zz' in AddMolecularOrientation",
molecules.get_data)
def test_error02(self):
elems = [
create(StaCustom({"id": i, "A": i*i})) for i in range(1000)]
pro = ProValueArray(elems)
pro.select("B")
check_error_msg(
self, "RuntimeError: Missing key(s) 'B' in ProValueArray", execute_omp, pro)
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_error02(self):
atoms = create(StaCustom(self.base_data))
mols = create(StaCustom([{"id": 1, "foo": "var"}]))
pro = ProDistanceInMolecule(mols, atoms)
check_error_msg(
self,
"RuntimeError: Missing key(s) 'atom-ids' in ProDistanceInMolecule",
execute_omp, pro)
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_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_error03(self):
data = [
[{"id": j, "A": float(i*j)} for j in range(10*i+1)]
for i in range(100)]
elems = [create(StaCustom(d)) for d in data]
pro = ProValueArray(elems)
pro.select("A")
check_error_msg(
self, "RuntimeError: Data sizes must be the same", execute_omp, pro)
def test_error02(self):
atoms = create(StaDumpAtoms("dumps_atom/atom.0.dump", 0))
moles = create(StaMolecules(atoms))
check_error_msg(
self,
"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_error01(self):
dummy_data = deepcopy(self.base_data)
for i in range(len(dummy_data)):
del dummy_data[i]["xu"]
atomses = [create(StaCustom(dummy_data)) for i in range(10)]
molses = [create(StaMolecules(atoms)) for atoms in atomses]
pro = ProTimeCorrelationInMolecule(list(zip(molses, atomses)))
check_error_msg(
self, "RuntimeError: Missing key(s) 'xu' in ProTimeCorrelationInMolecule", execute_omp, pro)
def test_error02(self):
atoms = create(
StaCustom([{
"id": i,
"mol": i // 10
} for i in range(100)]))
moles = create(StaCustom([{"index": i} for i in range(10)]))
moles.append_updater(AddChildIDs(atoms, "atom", "mol"))
check_error_msg(self,
"RuntimeError: Missing key(s) 'id' in AddChildIDs",
moles.get_data)
def test_error01(self):
dummy_data = deepcopy(self.base_data)
for i in range(len(dummy_data)):
del dummy_data[i]["xu"]
atoms = create(StaCustom(dummy_data))
mols = create(StaMolecules(atoms))
pro = ProDistanceInMolecule(mols, atoms)
check_error_msg(
self, "RuntimeError: Missing key(s) 'xu' in ProDistanceInMolecule",
execute_omp, pro)
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_error01(self):
atoms = create(
StaCustom([{
"id": i,
"mol": i // 10
} for i in range(100)]))
moles = create(StaMolecules(atoms))
moles.append_updater(AddChildPositions(atoms, "child"))
check_error_msg(
self,
"RuntimeError: Missing key(s) 'child-ids', 'xu', 'yu', 'zu' in AddChildPositions",
moles.get_data)
def test_error01(self):
dummy_data = deepcopy(self.abst_atoms)
for i in range(len(dummy_data)):
del dummy_data[i]["mass"]
atoms = create(StaCustom(dummy_data))
pro = ProMeanSquareDisplacement([atoms])
check_error_msg(
self,
"RuntimeError: Missing key(s) 'mass' in ProMeanSquareDisplacement",
execute_omp, pro)
def test_error01(self):
atoms = create(
StaCustom([{
"x": 1.0 * i,
"y": 1.0 * i,
"z": 1.0 * i
} for i in range(100)]))
box = create(StaCustom({"foo": 0.0, "bar": 1.0}))
pro = ProThicknessProfile(atoms, box)
check_error_msg(
self,
"RuntimeError: Missing key(s) 'radius' in ProThicknessProfile",
execute_omp, pro)
def test_error01(self):
atoms = create(
StaCustom([{
"x": 1.0 * i,
"y": 1.0 * i,
"z": 1.0 * i
} for i in range(100)]))
box = create(StaCustom({"foo": 0.0, "bar": 1.0}))
pro = ProRDFWD(atoms, box)
check_error_msg(
self,
"RuntimeError: Missing key(s) 'I_xx', 'I_xy', 'I_xz', 'I_yy', 'I_yz', 'I_zz', 'id', 'mass' in ProRadialDistributionFunctionWithDeformation",
execute_omp, pro)
