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_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))
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_modify():
Mol = Molecule()
assert Mol.getUndo() == None
Mol.undo()
Mol.setVec(((5, 0, 0), (0, 5, 0), (0, 0, 5)))
Mol.newAtom('C', (0.5, 0.5, 0.5), fmt='crystal')
assert vec_equal(Mol.getVec(), ((5, 0, 0), (0, 5, 0), (0, 0, 5)))
assert Mol.nat == 1
Mol.mult(2, 1, 1)
assert vec_equal(Mol.getVec(), ((10, 0, 0), (0, 5, 0), (0, 0, 5)))
assert Mol.nat == 2
Mol.mult(1, 2, 2)
assert vec_equal(Mol.getVec(), ((10, 0, 0), (0, 10, 0), (0, 0, 10)))
assert Mol.nat == 8
Mol.setVec(((5, 0, 0), (0, 5, 0), (0, 0, 5)))
Mol.crop()
assert Mol.nat == 1
Mol.mult(2, 2, 2)
assert vec_equal(Mol.getVec(), ((10, 0, 0), (0, 10, 0), (0, 0, 10)))
assert Mol.nat == 8
Mol.setVec(((7, 0, 0), (0, 7, 0), (0, 0, 7)))
Mol.wrap()
assert Mol.nat == 8
assert list(map(len, Mol.getBonds(1.1))) == [24, 0, 0, 0, 0, 0, 0, 0]
assert Mol.getUndo() == 'wrap atoms'
Mol.undo()
assert list(map(len, Mol.getBonds(1.1))) == [0, 4, 4, 4, 4, 4, 4, 0]
Mol.wrap()
Mol.reshape(((14, 7, 0), (0, 7, 0), (0, 0, 7)))
assert list(map(len, Mol.getBonds(1.1))) == [38, 0, 10, 0, 0, 0, 0, 0]
assert vec_equal(Mol.getVec(), ((14, 7, 0), (0, 7, 0), (0, 0, 7)))
Mol.undo()
Mol.setVec(((5, 0, 0), (0, 5, 0), (0, 0, 5)))
assert atom_equal(Mol.getAtom(1, fmt="crystal"), ('C', (0.1, 0.5, 0.5)))
Mol.align(1, 'x')
assert vec_equal(Mol.getVec(), ((0, -5, 0), (5, 0, 0), (0, 0, 5)))
Mol.undo()
Mol.align(1, 'y')
assert vec_equal(Mol.getVec(), ((5, 0, 0), (0, 5, 0), (0, 0, 5)))
Mol.align(1, 'z')
assert vec_equal(Mol.getVec(), ((5, 0, 0), (0, 0, 5), (0, -5, 0)))
Mol.undo()
try:
Mol.align(0, 1)
except ValueError:
assert True
except:
assert False, "Wrong error"
else:
assert False, "Error missing"
def test_molecule():
Mol = Molecule(name="Test Mol", steps=0)
assert Mol.name == "Test Mol"
assert len(Mol) == 0
Mol.newStep()
assert len(Mol) == 1
Mol.newAtom('C', (1, 1, 1))
assert Mol.nat == 1
assert atom_equal(Mol.getAtom(0, fmt='crystal'), ['C', (1, 1, 1)])
Mol.copyStep()
assert len(Mol) == 2
for s in Mol.steps:
assert s.nat == 1
assert s.getCellDim() == 1
assert Mol.curStep == 1
Mol.changeStep(0)
assert Mol.curStep == 0
Mol.setCellDimAll(1, fmt='angstrom', scale=True)
for s in Mol.steps:
assert float_equal(s.getCellDim(fmt='angstrom'), 1)
assert vec_equal(s.getVec(), ((1, 0, 0), (0, 1, 0), (0, 0, 1)))
assert atom_equal(s.getAtom(0, fmt='angstrom'), ['C', (1, 1, 1)])
Mol.setVecAll(((2, 0, 0), (0, 2, 0), (0, 0, 2)), scale=True)
for s in Mol.steps:
assert float_equal(s.getCellDim(fmt='angstrom'), 1)
assert vec_equal(s.getVec(), ((2, 0, 0), (0, 2, 0), (0, 0, 2)))
assert atom_equal(s.getAtom(0, fmt='angstrom'), ['C', (2, 2, 2)])
Mol.setVecAll(((1, 0, 0), (0, 1, 0), (0, 0, 1)))
for s in Mol.steps:
assert float_equal(s.getCellDim(fmt='angstrom'), 1)
assert vec_equal(s.getVec(), ((1, 0, 0), (0, 1, 0), (0, 0, 1)))
assert atom_equal(s.getAtom(0, fmt='crystal'), ['C', (2, 2, 2)])
assert Mol.getKpoints('active') == 'gamma'
assert Mol.getKpoints('mpg') == ['1', '1', '1', '0', '0', '0']
assert Mol.getKpoints('discrete') == []
assert Mol.getKpoints('options') == {'crystal': False, 'bands': False}
Mol.setKpoints('active', 'mpg')
assert Mol.getKpoints('active') == 'mpg'
Mol1 = Mol.copy()
assert len(Mol1) == 1
assert Mol1.name == "Copy of Test Mol"
Mol2 = Mol.copyAll()
assert len(Mol2) == 2
assert Mol2.name == "Copy of Test Mol"
