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_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"
