def test_compile_2nd_matrix_rotor_point1(self):
"""Check the operation of the compile_2nd_matrix_rotor() function."""
# The simulated in frame rotor 2nd degree frame order matrix (1e7 ensembles).
real = array(
[[ 7.06775425e-01, 1.36710179e-04, 0.00000000e+00, 1.36710179e-04, 2.93224575e-01, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
[ -1.36710179e-04, 7.06775425e-01, 0.00000000e+00, -2.93224575e-01, 1.36710179e-04, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
[ 0.00000000e+00, 0.00000000e+00, 8.27014112e-01, 0.00000000e+00, 0.00000000e+00, 2.19539417e-04, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
[ -1.36710179e-04, -2.93224575e-01, 0.00000000e+00, 7.06775425e-01, 1.36710179e-04, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
[ 2.93224575e-01, -1.36710179e-04, 0.00000000e+00, -1.36710179e-04, 7.06775425e-01, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
[ 0.00000000e+00, 0.00000000e+00, -2.19539417e-04, 0.00000000e+00, 0.00000000e+00, 8.27014112e-01, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
[ 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 8.27014112e-01, 2.19539417e-04, 0.00000000e+00],
[ 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, -2.19539417e-04, 8.27014112e-01, 0.00000000e+00],
[ 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 1.00000000e+00]])
# Init.
sigma_max = 60.0 / 180.0 * pi
# The Kronecker product of the eigenframe rotation.
Rx2_eigen = self.calc_Rx2_eigen_axis(0.0, 0.0)
# Calculate the matrix.
f2 = compile_2nd_matrix_rotor(self.f2_temp, Rx2_eigen, sigma_max)
# Print out.
print_frame_order_2nd_degree(real, "real")
print_frame_order_2nd_degree(f2, "calculated")
print_frame_order_2nd_degree(real-f2, "difference")
# Check the values.
for i in range(9):
for j in range(9):
print("Element %s, %s." % (i, j))
self.assert_(abs(f2[i, j] - real[i, j]) < 1e-3)
def test_compile_2nd_matrix_rotor_point1(self):
"""Check the operation of the compile_2nd_matrix_rotor() function."""
# The simulated in frame rotor 2nd degree frame order matrix (1e7 ensembles).
real = array(
[[ 7.06775425e-01, 1.36710179e-04, 0.00000000e+00, 1.36710179e-04, 2.93224575e-01, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
[ -1.36710179e-04, 7.06775425e-01, 0.00000000e+00, -2.93224575e-01, 1.36710179e-04, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
[ 0.00000000e+00, 0.00000000e+00, 8.27014112e-01, 0.00000000e+00, 0.00000000e+00, 2.19539417e-04, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
[ -1.36710179e-04, -2.93224575e-01, 0.00000000e+00, 7.06775425e-01, 1.36710179e-04, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
[ 2.93224575e-01, -1.36710179e-04, 0.00000000e+00, -1.36710179e-04, 7.06775425e-01, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
[ 0.00000000e+00, 0.00000000e+00, -2.19539417e-04, 0.00000000e+00, 0.00000000e+00, 8.27014112e-01, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00],
[ 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 8.27014112e-01, 2.19539417e-04, 0.00000000e+00],
[ 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, -2.19539417e-04, 8.27014112e-01, 0.00000000e+00],
[ 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 1.00000000e+00]])
# Init.
sigma_max = 60.0 / 180.0 * pi
# The Kronecker product of the eigenframe rotation.
Rx2_eigen = self.calc_Rx2_eigen_axis(0.0, 0.0)
# Calculate the matrix.
f2 = compile_2nd_matrix_rotor(self.f2_temp, Rx2_eigen, sigma_max)
# Print out.
print_frame_order_2nd_degree(real, "real")
print_frame_order_2nd_degree(f2, "calculated")
print_frame_order_2nd_degree(real-f2, "difference")
# Check the values.
for i in range(9):
for j in range(9):
print("Element %s, %s." % (i, j))
self.assert_(abs(f2[i, j] - real[i, j]) < 1e-3)
def __init__(self):
"""Calculate the frame order at infinity.
This is when the starting positions are random.
"""
# Loop over the models.
for model_index in range(len(MODELS)):
# Aliases.
model = MODELS[model_index]
model_text = MODEL_TEXT[model_index]
# Loop over the tags.
for tag in TAGS:
# Set up the variables to loop over.
if model in ['rotor', 'free_rotor']:
vars = ['Z']
elif model in ['iso_cone_free_rotor', 'iso_cone_torsionless']:
vars = ['X']
elif model in ['iso_cone']:
vars = ['X', 'Z']
elif model in ['double_rotor', 'pseudo-ellipse_free_rotor', 'pseudo-ellipse_torsionless']:
vars = ['X', 'Y']
elif model in ['pseudo-ellipse']:
vars = ['X', 'Y', 'Z']
else:
raise RelaxError("Unknown model '%s'." % model)
# Loop over the variables.
for var in vars:
# The file name.
file_name = '_%s_%s_theta_%s_calc.agr' % (model, tag, lower(var))
print("Creating the '*%s' files." % file_name)
# Set up the eigenframe.
self.setup_eigenframe(tag=tag)
# The Kronecker product of the eigenframe rotation.
Rx2_eigen = kron_prod(self.eigenframe, self.eigenframe)
# Set the initial storage structures.
self.init_storage()
# Loop over the angle incs.
for i in range(INC+1):
# Get the angle for the increment.
theta = self.get_angle(i-1, model=model, var=var)
# Vary X.
if var == 'X':
theta_x = theta
theta_y = THETA_Y
theta_z = THETA_Z
# Vary Y.
elif var == 'Y':
theta_x = THETA_X
theta_y = theta
theta_z = THETA_Z
# Vary Z.
elif var == 'Z':
theta_x = THETA_X
theta_y = THETA_Y
theta_z = theta
# Calculate the frame order matrices.
if model == 'rotor':
self.first_frame_order[i] = rotor.compile_1st_matrix_rotor(self.first_frame_order[i], self.eigenframe, theta_z)
self.second_frame_order[i] = rotor.compile_2nd_matrix_rotor(self.second_frame_order[i], Rx2_eigen, theta_z)
elif model == 'free_rotor':
self.first_frame_order[i] = free_rotor.compile_1st_matrix_free_rotor(self.first_frame_order[i], self.eigenframe)
self.second_frame_order[i] = free_rotor.compile_2nd_matrix_free_rotor(self.second_frame_order[i], Rx2_eigen)
elif model == 'iso_cone':
self.first_frame_order[i] = iso_cone.compile_1st_matrix_iso_cone(self.first_frame_order[i], self.eigenframe, theta_x, theta_z)
self.second_frame_order[i] = iso_cone.compile_2nd_matrix_iso_cone(self.second_frame_order[i], Rx2_eigen, theta_x, theta_z)
elif model == 'iso_cone_free_rotor':
self.first_frame_order[i] = iso_cone_free_rotor.compile_1st_matrix_iso_cone_free_rotor(self.first_frame_order[i], self.eigenframe, theta_x)
self.second_frame_order[i] = iso_cone_free_rotor.compile_2nd_matrix_iso_cone_free_rotor(self.second_frame_order[i], Rx2_eigen, theta_x)
elif model == 'iso_cone_torsionless':
self.first_frame_order[i] = iso_cone_torsionless.compile_1st_matrix_iso_cone_torsionless(self.first_frame_order[i], self.eigenframe, theta_x)
self.second_frame_order[i] = iso_cone_torsionless.compile_2nd_matrix_iso_cone_torsionless(self.second_frame_order[i], Rx2_eigen, theta_x)
elif model == 'pseudo-ellipse':
self.first_frame_order[i] = pseudo_ellipse.compile_1st_matrix_pseudo_ellipse(self.first_frame_order[i], self.eigenframe, theta_x, theta_y, theta_z)
self.second_frame_order[i] = pseudo_ellipse.compile_2nd_matrix_pseudo_ellipse(self.second_frame_order[i], Rx2_eigen, theta_x, theta_y, theta_z)
elif model == 'pseudo-ellipse_free_rotor':
self.first_frame_order[i] = pseudo_ellipse_free_rotor.compile_1st_matrix_pseudo_ellipse_free_rotor(self.first_frame_order[i], self.eigenframe, theta_x, theta_y)
self.second_frame_order[i] = pseudo_ellipse_free_rotor.compile_2nd_matrix_pseudo_ellipse_free_rotor(self.second_frame_order[i], Rx2_eigen, theta_x, theta_y)
elif model == 'pseudo-ellipse_torsionless':
self.first_frame_order[i] = pseudo_ellipse_torsionless.compile_1st_matrix_pseudo_ellipse_torsionless(self.first_frame_order[i], self.eigenframe, theta_x, theta_y)
self.second_frame_order[i] = pseudo_ellipse_torsionless.compile_2nd_matrix_pseudo_ellipse_torsionless(self.second_frame_order[i], Rx2_eigen, theta_x, theta_y)
elif model == 'double_rotor':
self.first_frame_order[i] = double_rotor.compile_1st_matrix_double_rotor(self.first_frame_order[i], self.eigenframe, theta_y, theta_x)
self.second_frame_order[i] = double_rotor.compile_2nd_matrix_double_rotor(self.second_frame_order[i], Rx2_eigen, theta_y, theta_x)
else:
raise RelaxError("Unknown model '%s'." % model)
# Write the data.
self.write_data(file_name=file_name, model=model, model_text=model_text, var=var)
def __init__(self):
"""Calculate the frame order at infinity.
This is when the starting positions are random.
"""
# Loop over the models.
for model_index in range(len(MODELS)):
# Aliases.
model = MODELS[model_index]
model_text = MODEL_TEXT[model_index]
# Loop over the tags.
for tag in TAGS:
# Set up the variables to loop over.
if model in ['rotor', 'free_rotor']:
vars = ['Z']
elif model in ['iso_cone_free_rotor', 'iso_cone_torsionless']:
vars = ['X']
elif model in ['iso_cone']:
vars = ['X', 'Z']
elif model in [
'double_rotor', 'pseudo-ellipse_free_rotor',
'pseudo-ellipse_torsionless'
]:
vars = ['X', 'Y']
elif model in ['pseudo-ellipse']:
vars = ['X', 'Y', 'Z']
else:
raise RelaxError("Unknown model '%s'." % model)
# Loop over the variables.
for var in vars:
# The file name.
file_name = '_%s_%s_theta_%s_calc.agr' % (model, tag,
lower(var))
print("Creating the '*%s' files." % file_name)
# Set up the eigenframe.
self.setup_eigenframe(tag=tag)
# The Kronecker product of the eigenframe rotation.
Rx2_eigen = kron_prod(self.eigenframe, self.eigenframe)
# Set the initial storage structures.
self.init_storage()
# Loop over the angle incs.
for i in range(INC + 1):
# Get the angle for the increment.
theta = self.get_angle(i - 1, model=model, var=var)
# Vary X.
if var == 'X':
theta_x = theta
theta_y = THETA_Y
theta_z = THETA_Z
# Vary Y.
elif var == 'Y':
theta_x = THETA_X
theta_y = theta
theta_z = THETA_Z
# Vary Z.
elif var == 'Z':
theta_x = THETA_X
theta_y = THETA_Y
theta_z = theta
# Calculate the frame order matrices.
if model == 'rotor':
self.first_frame_order[
i] = rotor.compile_1st_matrix_rotor(
self.first_frame_order[i], self.eigenframe,
theta_z)
self.second_frame_order[
i] = rotor.compile_2nd_matrix_rotor(
self.second_frame_order[i], Rx2_eigen,
theta_z)
elif model == 'free_rotor':
self.first_frame_order[
i] = free_rotor.compile_1st_matrix_free_rotor(
self.first_frame_order[i], self.eigenframe)
self.second_frame_order[
i] = free_rotor.compile_2nd_matrix_free_rotor(
self.second_frame_order[i], Rx2_eigen)
elif model == 'iso_cone':
self.first_frame_order[
i] = iso_cone.compile_1st_matrix_iso_cone(
self.first_frame_order[i], self.eigenframe,
theta_x, theta_z)
self.second_frame_order[
i] = iso_cone.compile_2nd_matrix_iso_cone(
self.second_frame_order[i], Rx2_eigen,
theta_x, theta_z)
elif model == 'iso_cone_free_rotor':
self.first_frame_order[
i] = iso_cone_free_rotor.compile_1st_matrix_iso_cone_free_rotor(
self.first_frame_order[i], self.eigenframe,
theta_x)
self.second_frame_order[
i] = iso_cone_free_rotor.compile_2nd_matrix_iso_cone_free_rotor(
self.second_frame_order[i], Rx2_eigen,
theta_x)
elif model == 'iso_cone_torsionless':
self.first_frame_order[
i] = iso_cone_torsionless.compile_1st_matrix_iso_cone_torsionless(
self.first_frame_order[i], self.eigenframe,
theta_x)
self.second_frame_order[
i] = iso_cone_torsionless.compile_2nd_matrix_iso_cone_torsionless(
self.second_frame_order[i], Rx2_eigen,
theta_x)
elif model == 'pseudo-ellipse':
self.first_frame_order[
i] = pseudo_ellipse.compile_1st_matrix_pseudo_ellipse(
self.first_frame_order[i], self.eigenframe,
theta_x, theta_y, theta_z)
self.second_frame_order[
i] = pseudo_ellipse.compile_2nd_matrix_pseudo_ellipse(
self.second_frame_order[i], Rx2_eigen,
theta_x, theta_y, theta_z)
elif model == 'pseudo-ellipse_free_rotor':
self.first_frame_order[
i] = pseudo_ellipse_free_rotor.compile_1st_matrix_pseudo_ellipse_free_rotor(
self.first_frame_order[i], self.eigenframe,
theta_x, theta_y)
self.second_frame_order[
i] = pseudo_ellipse_free_rotor.compile_2nd_matrix_pseudo_ellipse_free_rotor(
self.second_frame_order[i], Rx2_eigen,
theta_x, theta_y)
elif model == 'pseudo-ellipse_torsionless':
self.first_frame_order[
i] = pseudo_ellipse_torsionless.compile_1st_matrix_pseudo_ellipse_torsionless(
self.first_frame_order[i], self.eigenframe,
theta_x, theta_y)
self.second_frame_order[
i] = pseudo_ellipse_torsionless.compile_2nd_matrix_pseudo_ellipse_torsionless(
self.second_frame_order[i], Rx2_eigen,
theta_x, theta_y)
elif model == 'double_rotor':
self.first_frame_order[
i] = double_rotor.compile_1st_matrix_double_rotor(
self.first_frame_order[i], self.eigenframe,
theta_y, theta_x)
self.second_frame_order[
i] = double_rotor.compile_2nd_matrix_double_rotor(
self.second_frame_order[i], Rx2_eigen,
theta_y, theta_x)
else:
raise RelaxError("Unknown model '%s'." % model)
# Write the data.
self.write_data(file_name=file_name,
model=model,
model_text=model_text,
var=var)
