def calc_q(r_o, r_op, r_h, box):
"""
Calculates the 3-body term, keeping the pbc in mind
@param r_o: x,y,z position of one oxygen donor/acceptor
@param r_op: x,y,z position of the other oxygen donor/acceptor
@param r_h: x,y,z position of the reactive H
@param box: the dimensions of the periodic box (assumed 90 degree angles)
@return: the dot-product of the vector q
"""
# pbc_vector_avg
q_vec = np.subtract(pbc_vector_avg(r_o, r_op, box), r_h)
# would an average be faster?
# q_vec = np.average(r_o, r_op) - r_h
return np.dot(q_vec, q_vec)
def calc_q(r_o, r_op, r_h, box):
"""
Calculates the 3-body term, keeping the pbc in mind
Per Wu et al. 2008 (http://pubs.acs.org/doi/abs/10.1021/jp076658h), eq. in text just below eq. 12
@param r_o: x,y,z position of one oxygen donor/acceptor (water or hydronium)
@param r_op: x,y,z position of the other oxygen donor/acceptor (glu)
@param r_h: x,y,z position of the reactive H
@param box: the dimensions of the periodic box (assumed 90 degree angles)
@return: the dot-product of the vector q (note: it really is the dot, not norm; it is written as q^2)
"""
# pbc_vector_avg
q_vec = np.subtract(pbc_vector_avg(r_o, r_op, box), r_h)
# would an average be faster?
# q_vec = np.average(r_o, r_op) - r_h
return np.dot(q_vec, q_vec)
def testAvgInDiffImages(self):
self.assertTrue(
np.allclose(pbc_vector_avg(A_VEC, C_VEC, PBC_BOX), GOOD_A_C_AVG))
def testAvgInSameImage(self):
self.assertTrue(
np.allclose(pbc_vector_avg(A_VEC, B_VEC, PBC_BOX), GOOD_A_B_AVG))
def testAvgInDiffImages(self):
self.assertTrue(np.allclose(pbc_vector_avg(A_VEC, C_VEC, PBC_BOX), GOOD_A_C_AVG))
def testAvgInSameImage(self):
self.assertTrue(np.allclose(pbc_vector_avg(A_VEC, B_VEC, PBC_BOX), GOOD_A_B_AVG))