def test_ortho_PBC(self):
from MDAnalysis.core.distances import applyPBC
U = MDAnalysis.Universe(PSF, DCD)
atoms = U.atoms.coordinates()
box1 = np.array([2.5, 2.5, 3.5], dtype=np.float32)
box2 = np.array([2.5, 2.5, 3.5, 90., 90., 90.], dtype=np.float32)
cyth1 = applyPBC(atoms, box1)
cyth2 = applyPBC(atoms, box2)
reference = atoms - np.floor(atoms / box1) * box1
assert_almost_equal(cyth1, reference, self.prec, err_msg="Ortho applyPBC #1 failed comparison with np")
assert_almost_equal(cyth2, reference, self.prec, err_msg="Ortho applyPBC #2 failed comparison with np")
def test_tric_PBC(self):
from MDAnalysis.core.distances import applyPBC
U = MDAnalysis.Universe(TRIC)
atoms = U.atoms.coordinates()
box1 = U.dimensions
box2 = MDAnalysis.coordinates.core.triclinic_vectors(box1)
print box2
print box2.shape
def numpy_PBC(coords, box):
coords -= np.array([box[2] * val for val in np.floor(coords[:, 2] / box[2][2])])
coords -= np.array([box[1] * val for val in np.floor(coords[:, 1] / box[1][1])])
coords -= np.array([box[0] * val for val in np.floor(coords[:, 0] / box[0][0])])
return coords
cyth1 = applyPBC(atoms, box1)
cyth2 = applyPBC(atoms, box2)
reference = numpy_PBC(atoms, box2)
assert_almost_equal(cyth1, reference, self.prec, err_msg="Triclinic applyPBC failed comparison with np")
assert_almost_equal(cyth2, reference, self.prec, err_msg="Trlclinic applyPBC failed comparison with np")