def calc_angle(self, d, h, a):
"""Calculate the angle (in degrees) between two atoms with H at apex."""
v1 = h.pos-d.pos
v2 = h.pos-a.pos
if numpy.all(v1 == v2):
return 0.0
return numpy.rad2deg(angle(v1, v2))
def calculateangles(centeratom, atomlist, coordinates, k, boxvector, normvecmatrix):
vectors = []
real1 = []
imag1 = []
for atom in atomlist:
# print "coordinates",coordinates[centeratom],coordinates[atom]
distancevector = coordinates[centeratom] - coordinates[atom]
# print distancevector
if all(coordinates[centeratom] == coordinates[atom]):
print coordinates[centeratom], coordinates[atom]
distancevectorpbc = np.where(distancevector > 0.5 * boxvector, distancevector - boxvector, distancevector)
distancevectorpbc = np.where(
distancevectorpbc < -0.5 * boxvector, distancevectorpbc + boxvector, distancevectorpbc
)
# print "distances",distancevector,distancevectorpbc,boxvector
vectors.append(np.dot(distancevectorpbc, normvecmatrix))
# vectors.append(distancevectorpbc)
# print vectors
vec0 = vectors.pop()
for vec in vectors:
angleij = angle(vec0, vec)
if np.isnan(angleij):
print angleij, vec0, vec
real1.append(np.cos(k * angleij))
imag1.append(np.sin(k * angleij))
real1 = np.array(real1)
imag1 = np.array(imag1)
# sys.exit()
return real1, imag1
def calc_angle(self, d, h, a):
"""Calculate the angle (in degrees) between two atoms with H at apex."""
v1 = h.pos - d.pos
v2 = h.pos - a.pos
if numpy.all(v1 == v2):
return 0.0
return numpy.rad2deg(angle(v1, v2))
def calculateangles(centeratom, atomlist, coordinates, k, boxvector,
normvecmatrix):
vectors = []
real1 = []
imag1 = []
for atom in atomlist:
#print "coordinates",coordinates[centeratom],coordinates[atom]
distancevector = coordinates[centeratom] - coordinates[atom]
#print distancevector
if all(coordinates[centeratom] == coordinates[atom]):
print coordinates[centeratom], coordinates[atom]
distancevectorpbc = np.where(distancevector > 0.5 * boxvector,
distancevector - boxvector,
distancevector)
distancevectorpbc = np.where(distancevectorpbc < -0.5 * boxvector,
distancevectorpbc + boxvector,
distancevectorpbc)
#print "distances",distancevector,distancevectorpbc,boxvector
vectors.append(np.dot(distancevectorpbc, normvecmatrix))
#vectors.append(distancevectorpbc)
#print vectors
vec0 = vectors.pop()
for vec in vectors:
angleij = angle(vec0, vec)
if np.isnan(angleij):
print angleij, vec0, vec
real1.append(np.cos(k * angleij))
imag1.append(np.sin(k * angleij))
real1 = np.array(real1)
imag1 = np.array(imag1)
#sys.exit()
return real1, imag1
def testAngleRandom(self):
for x in numpy.random.uniform(0, pi, 20):
r = numpy.random.uniform(0, 1000)
v = r * numpy.array([cos(x), sin(x), 0])
assert_almost_equal(util.angle(self.e1, v), x, 6)
def testAnglePi(self):
assert_almost_equal(util.angle(-2.3456e7 * self.e1, 3.4567e-6 * self.e1), pi)
assert_almost_equal(util.angle(2.3456e7 * self.e1, 3.4567e-6 * self.e1), 0.0)
def testAngleColinear(self):
assert_equal(util.angle(self.a, self.a), 0.0)
def testAngleNullVector(self):
assert_equal(util.angle(self.e1, self.null), numpy.nan)
def testAngleVectors(self):
assert_equal(util.angle(2 * self.e1, self.e2), pi / 2)
assert_equal(util.angle(-2 * self.e1, self.e2), pi - pi / 2)
assert_equal(util.angle(23.3 * self.e1, self.a), pi / 3)
def testAngleUnitvectors(self):
assert_equal(util.angle(self.e1, self.e2), pi / 2)
assert_equal(util.angle(self.e1, self.a), pi / 3)