def test_atoms_bohr(): Mol = Molecule() Mol.setCellDim(2) Mol.newAtom() Mol.newAtom('H', (1, 1, 1), 1, [True, False], True) assert Mol.nat == 2 assert Mol.ntyp == 2 assert Mol.getTypes() == ['H', 'C'] assert Mol.getCellDim() == 2 assert atom_equal(Mol.getAtom(0, charge=True, fix=True, hidden=True), ['C', (0, 0, 0), 0., [False, False, False], False]) assert atom_equal(Mol.getAtom(1, charge=True, fix=True, hidden=True), ['H', (1, 1, 1), 1., [True, False, False], True]) assert list(map(len, Mol.getBonds(1.1))) == [1, 1, 1, 1, 1, 1, 1, 1] Mol.delAtom(1) assert Mol.nat == 1 assert Mol.getTypes() == ['C'] Mol.newAtoms(2) assert Mol.getTypes() == ['X', 'C'] Mol.setAtom(1, 'O', (0.5, 0.5, 0.5), 2, [False, True], False) Mol.setAtom(2, 'U', (1, 1, 1), 2, [True], False) assert atom_equal(Mol.getAtom(1, charge=True, fix=True, hidden=True), ['O', (0.5, 0.5, 0.5), 2., [False, True, False], False]) assert atom_equal(Mol.getAtom(2, charge=True, fix=True, hidden=True), ['U', (1, 1, 1), 2., [True, False, False], False]) assert Mol.getTypes() == ['C', 'O', 'U'] target = (['C', (0, 0, 0), 0., [False, False, False], False], ['O', (0.5, 0.5, 0.5), 2., [False, True, False], False], ['U', (1, 1, 1), 2., [True, False, False], False]) for a, t in zip(Mol.getAtoms(True, True, True), target): assert atom_equal(a, t)
def test_scripting(): Mol = Molecule() Mol.setFmt('angstrom') Mol.newAtom('C', (0, 0, 0)) Mol.newAtom('O', (1, 1, 0)) Mol.newAtom('B', (2, 2, 0)) Mol.newAtom('U', (0, 2, 0)) Mol.evalScript("def g all tU\n" "shi g 1-3 2") assert atom_equal(Mol.getAtom(3), ('U', (2, 0, 0))) Mol.undo() Mol.evalScript("rot 3 90 2-0 1") assert atom_equal(Mol.getAtom(3), ('U', (1, 1, np.sqrt(2)))) Mol.undo() Mol.evalScript("rot 3 90 2-0\n" "mir 3 (1,0,0) (0,0,1,'angstrom') (1,0,0)") assert atom_equal(Mol.getAtom(3), ('U', (1, -1, np.sqrt(2)))) Mol = Molecule() Mol.setFmt('angstrom') Mol.setCellDim(15) Mol.newAtom('C1', (0, 0, 0)) Mol.newAtom('C1', (1, 0, 0)) Mol.newAtom('C1', (1, 0, 0)) Mol.newAtom('C2', (0, 0, 3)) Mol.newAtom('C2', (1, 0, 3)) Mol.newAtom('C2', (1, 0, 3)) Mol.evalScript("rot [2, 5] 60 (0, 0, 1)") Mol.evalScript("rot 3-5 90 (1, 0, 0) 3") assert len(Mol.getBonds(1.1)[0]) == 6 Mol.evalScript("sel all tC2\npar sel sel 0-2") atoms = Mol.getAtoms() assert vec_equal(atoms[0][1], atoms[3][1]-(0,0,3)) assert vec_equal(atoms[1][1], atoms[4][1]-(0,0,3)) assert vec_equal(atoms[2][1], atoms[5][1]-(0,0,3)) Mol.evalScript("rot sel 45 (1, 0, 0) 3") Mol.evalScript("pshift 0-2 (0,0,1) sel") assert atom_equal(Mol.getAtom(0), ['C1', (0, np.sqrt(2)/2, -np.sqrt(2)/2)]) assert atom_equal(Mol.getAtom(1), ['C1', (1, np.sqrt(2)/2, -np.sqrt(2)/2)]) assert atom_equal(Mol.getAtom(2), ['C1', (0.5, (np.sqrt(3)+np.sqrt(2))/2, -np.sqrt(2)/2)])
def test_atoms_fmt(): Mol = Molecule() # standard: bohr: assert Mol.getFmt() == 'bohr' assert float_equal(Mol.getCellDim(), 1) assert vec_equal(Mol.getVec(), ((1, 0, 0), (0, 1, 0), (0, 0, 1))) Mol.newAtom('C', (1, 1, 1)) assert atom_equal(Mol.getAtom(0), ('C', (1, 1, 1))) # transition to angstrom: Mol.setFmt("angstrom", scale=True) assert Mol.getFmt() == 'angstrom' Mol.setCellDim(1) assert float_equal(Mol.getCellDim(), 1) assert atom_equal(Mol.getAtom(0, fmt="angstrom"), ('C', (1, 1, 1))) Mol.setCellDim(2.5, scale=True, fmt='angstrom') Mol.newAtom('C', (2.5, 2.5, 2.5), fmt='angstrom') for at in Mol.getAtoms(): assert atom_equal(at, ('C', (2.5, 2.5, 2.5))) Mol.setVec(((2, 0, 0), (0, 2, 0), (0, 0, 2)), scale=True) assert vec_equal(Mol.getVec(), ((2, 0, 0), (0, 2, 0), (0, 0, 2))) Mol.newAtom('C', (5, 5, 5), fmt='angstrom') Mol.newAtom('C', (2, 2, 2), fmt='alat') Mol.newAtom('C', (1, 1, 1), fmt='crystal') for at in Mol.getAtoms(): assert atom_equal(at, ('C', (5, 5, 5))) for at in Mol.getAtoms(fmt='alat'): assert atom_equal(at, ('C', (2, 2, 2))) for at in Mol.getAtoms(fmt='crystal'): assert atom_equal(at, ('C', (1, 1, 1))) # scale back down to bohr Mol.setCellDim(2.5, scale=True, fmt='bohr') for at in Mol.getAtoms(fmt='bohr'): assert atom_equal(at, ('C', (5, 5, 5))) Mol.setFmt('alat', scale=True) for at in Mol.getAtoms(fmt='bohr'): assert atom_equal(at, ('C', (12.5, 12.5, 12.5))) Mol.setFmt('crystal', scale=True) for at in Mol.getAtoms(fmt='bohr'): assert atom_equal(at, ('C', (62.5, 62.5, 62.5))) assert vec_equal(Mol.getCenter(), (2.5, 2.5, 2.5)) assert vec_equal(Mol.getCenter(com=True), (62.5, 62.5, 62.5))