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)