Author: bugman
Date: Fri Mar 22 16:51:35 2013
New Revision: 18983
URL: http://svn.gna.org/viewcvs/relax?rev=18983&view=rev
Log:
Next block of the manual merger of the frame_order_testing branch.
The commands used were:
svn merge -r17950:17951
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r17951:17952
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r17952:17953
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r17953:17954
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r17955:17956
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r17956:17957
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r17957:17958
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r17958:17959
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
The console messages were:
[edau@localhost relax-trunk]$ svn merge -r17950:17951
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r17951 into '.':
U maths_fns/frame_order/matrix_ops.py
[edau@localhost relax-trunk]$ svn merge -r17951:17952
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r17952 into '.':
U maths_fns/frame_order/pseudo_ellipse.py
U maths_fns/frame_order/__init__.py
[edau@localhost relax-trunk]$ svn merge -r17952:17953
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r17953 into '.':
G maths_fns/frame_order/matrix_ops.py
[edau@localhost relax-trunk]$ svn merge -r17953:17954
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r17954 into '.':
G maths_fns/frame_order/__init__.py
G maths_fns/frame_order/matrix_ops.py
[edau@localhost relax-trunk]$ svn merge -r17955:17956
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r17956 into '.':
U
test_suite/shared_data/frame_order/cam/pseudo_ellipse/multi_processor_test.py
A test_suite/shared_data/frame_order/cam/pseudo_ellipse/pcs_dy_subset.txt
A test_suite/shared_data/frame_order/cam/pseudo_ellipse/pcs_tm_subset.txt
A test_suite/shared_data/frame_order/cam/pseudo_ellipse/pcs_tb_subset.txt
A test_suite/shared_data/frame_order/cam/pseudo_ellipse/pcs_er_subset.txt
[edau@localhost relax-trunk]$ svn merge -r17956:17957
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r17957 into '.':
G maths_fns/frame_order/matrix_ops.py
[edau@localhost relax-trunk]$ svn merge -r17957:17958
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r17958 into '.':
G maths_fns/frame_order/pseudo_ellipse.py
[edau@localhost relax-trunk]$ svn merge -r17958:17959
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
Conflict discovered in 'auto_analyses/dauvergne_protocol.py'.
Select: (p) postpone, (df) diff-full, (e) edit,
(mc) mine-conflict, (tc) theirs-conflict,
(s) show all options: p
--- Merging r17959 into '.':
C auto_analyses/dauvergne_protocol.py
Summary of conflicts:
Text conflicts: 1
[edau@localhost relax-trunk]$
Added:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/pcs_dy_subset.txt
- copied unchanged from r17956,
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/pseudo_ellipse/pcs_dy_subset.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/pcs_er_subset.txt
- copied unchanged from r17956,
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/pseudo_ellipse/pcs_er_subset.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/pcs_tb_subset.txt
- copied unchanged from r17956,
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/pseudo_ellipse/pcs_tb_subset.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/pcs_tm_subset.txt
- copied unchanged from r17956,
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/pseudo_ellipse/pcs_tm_subset.txt
Modified:
trunk/maths_fns/frame_order/__init__.py
trunk/maths_fns/frame_order/matrix_ops.py
trunk/maths_fns/frame_order/pseudo_ellipse.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/multi_processor_test.py
Modified: trunk/maths_fns/frame_order/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/maths_fns/frame_order/__init__.py?rev=18983&r1=18982&r2=18983&view=diff
==============================================================================
--- trunk/maths_fns/frame_order/__init__.py (original)
+++ trunk/maths_fns/frame_order/__init__.py Fri Mar 22 16:51:35 2013
@@ -51,8 +51,7 @@
from maths_fns.kronecker_product import kron_prod
from maths_fns import order_parameters
from maths_fns.pcs import pcs_tensor
-from maths_fns.rotation_matrix import euler_to_R_zyz
-from maths_fns.rotation_matrix import two_vect_to_R
+from maths_fns.rotation_matrix import euler_to_R_zyz, tilt_torsion_to_R,
two_vect_to_R
from maths_fns.rdc import rdc_tensor
from multi import fetch_data, Processor_box
from physical_constants import pcs_constant
@@ -334,15 +333,28 @@
self.create_sobol_data(n=self.num_int_pts, dims=['sigma'])
self.func = self.func_free_rotor_qrint
+ # Pre-calculate the rotation matrices Ri_prime from the Sobol'
angles.
+ for i in range(self.num_int_pts):
+ # Unpack the angles.
+ theta, phi, sigma = self.sobol_angles[i]
+
+ # The rotation matrix.
+ tilt_torsion_to_R(phi, theta, sigma, self.Ri_prime[i])
+
# Subdivide the Sobol' data points for the slave processors.
- blocks = []
+ blocks_sobol = []
for block in self.subdivide(self.sobol_angles,
self.processor.processor_size()):
- blocks.append(block)
+ blocks_sobol.append(block)
+
+ # Subdivide the Ri prime data.
+ blocks_Ri_prime = []
+ for block in self.subdivide(self.Ri_prime,
self.processor.processor_size()):
+ blocks_Ri_prime.append(block)
# Set up the slave processors.
self.slaves = []
for i in range(self.processor.processor_size()):
-
self.slaves.append(Slave_command_pcs_pseudo_ellipse_qrint(blocks[i],
full_in_ref_frame=self.full_in_ref_frame, r_ln_pivot=self.r_ln_pivot,
A=self.A_3D, Ri_prime=self.Ri_prime, pcs_theta=self.pcs_theta,
pcs_theta_err=self.pcs_theta_err, missing_pcs=self.missing_pcs))
+
self.slaves.append(Slave_command_pcs_pseudo_ellipse_qrint(blocks_sobol[i],
full_in_ref_frame=self.full_in_ref_frame, r_ln_pivot=self.r_ln_pivot,
A=self.A_3D, Ri_prime=blocks_Ri_prime[i], pcs_theta=self.pcs_theta,
pcs_theta_err=self.pcs_theta_err, missing_pcs=self.missing_pcs))
# The target function aliases (Scipy numerical integration).
else:
@@ -390,7 +402,7 @@
# The rotation to the Frame Order eigenframe.
self.R_eigen = zeros((3, 3), float64)
self.R_ave = zeros((3, 3), float64)
- self.Ri_prime = zeros((3, 3), float64)
+ self.Ri_prime = zeros((self.num_int_pts, 3, 3), float64)
self.tensor_3D = zeros((3, 3), float64)
# The cone axis storage and molecular frame z-axis.
Modified: trunk/maths_fns/frame_order/matrix_ops.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/maths_fns/frame_order/matrix_ops.py?rev=18983&r1=18982&r2=18983&view=diff
==============================================================================
--- trunk/maths_fns/frame_order/matrix_ops.py (original)
+++ trunk/maths_fns/frame_order/matrix_ops.py Fri Mar 22 16:51:35 2013
@@ -24,7 +24,7 @@
# Python module imports.
from math import cos, sin, sqrt
-from numpy import dot, float64, inner, transpose, zeros
+from numpy import dot, inner, transpose
from numpy.linalg import norm
# relax module imports.
@@ -152,15 +152,9 @@
return pcs
-def pcs_pivot_motion_full_qrint(theta_i=None, phi_i=None, sigma_i=None,
full_in_ref_frame=None, r_pivot_atom=None, r_pivot_atom_rev=None,
r_ln_pivot=None, A=None, R_eigen=None, RT_eigen=None, Ri_prime=None,
pcs_theta=None, pcs_theta_err=None, missing_pcs=None, error_flag=False):
+def pcs_pivot_motion_full_qrint(full_in_ref_frame=None, r_pivot_atom=None,
r_pivot_atom_rev=None, r_ln_pivot=None, A=None, R_eigen=None, RT_eigen=None,
Ri_prime=None, pcs_theta=None, pcs_theta_err=None, missing_pcs=None,
error_flag=False):
"""Calculate the PCS value after a pivoted motion for the isotropic cone
model.
- @keyword theta_i: The half cone opening angle (polar angle).
- @type theta_i: float
- @keyword phi_i: The cone azimuthal angle.
- @type phi_i: float
- @keyword sigma_i: The torsion angle for state i.
- @type sigma_i: float
@keyword full_in_ref_frame: An array of flags specifying if the tensor
in the reference frame is the full or reduced tensor.
@type full_in_ref_frame: numpy rank-1 array
@keyword r_pivot_atom: The pivot point to atom vector.
@@ -187,11 +181,19 @@
@type error_flag: bool
"""
- # The vectors.
- rot_vect, rot_vect_rev, length, length_rev =
vectors_pivot_motion_full(theta_i=theta_i, phi_i=phi_i, sigma_i=sigma_i,
r_pivot_atom=r_pivot_atom, r_pivot_atom_rev=r_pivot_atom_rev,
r_ln_pivot=r_ln_pivot, R_eigen=R_eigen, RT_eigen=RT_eigen, Ri_prime=Ri_prime)
+ # The rotation.
+ R_i = dot(R_eigen, dot(Ri_prime, RT_eigen))
+
+ # Pre-calculate all the new vectors (forwards and reverse).
+ rot_vect_rev = transpose(dot(R_i, r_pivot_atom_rev) + r_ln_pivot)
+ rot_vect = transpose(dot(R_i, r_pivot_atom) + r_ln_pivot)
# Loop over the atoms.
for j in range(len(r_pivot_atom[0])):
+ # The vector length (to the 5th power).
+ length_rev = 1.0 / sqrt(inner(rot_vect_rev[j], rot_vect_rev[j]))**5
+ length = 1.0 / sqrt(inner(rot_vect[j], rot_vect[j]))**5
+
# Loop over the alignments.
for i in range(len(pcs_theta)):
# Skip missing data.
@@ -201,10 +203,10 @@
# The projection.
if full_in_ref_frame[i]:
proj = dot(rot_vect_rev[j], dot(A[i], rot_vect_rev[j]))
- length_i = length_rev[j]
+ length_i = length_rev
else:
proj = dot(rot_vect[j], dot(A[i], rot_vect[j]))
- length_i = length[j]
+ length_i = length
# The PCS.
pcs_theta[i, j] += proj * length_i
@@ -449,70 +451,5 @@
return matrix_rot
-def vectors_pivot_motion_full(theta_i=None, phi_i=None, sigma_i=None,
r_pivot_atom=None, r_pivot_atom_rev=None, r_ln_pivot=None, R_eigen=None,
RT_eigen=None, Ri_prime=None):
- """Calculate the lanthanide to atom vectors.
-
- @keyword theta_i: The half cone opening angle (polar angle).
- @type theta_i: float
- @keyword phi_i: The cone azimuthal angle.
- @type phi_i: float
- @keyword sigma_i: The torsion angle for state i.
- @type sigma_i: float
- @keyword r_pivot_atom: The pivot point to atom vector.
- @type r_pivot_atom: numpy rank-2, 3D array
- @keyword r_pivot_atom_rev: The reversed pivot point to atom vector.
- @type r_pivot_atom_rev: numpy rank-2, 3D array
- @keyword r_ln_pivot: The lanthanide position to pivot point
vector.
- @type r_ln_pivot: numpy rank-2, 3D array
- @keyword R_eigen: The eigenframe rotation matrix.
- @type R_eigen: numpy rank-2, 3D array
- @keyword RT_eigen: The transpose of the eigenframe rotation
matrix (for faster calculations).
- @type RT_eigen: numpy rank-2, 3D array
- @keyword Ri_prime: The empty rotation matrix for the in-frame
isotropic cone motion for state i.
- @type Ri_prime: numpy rank-2, 3D array
- @return: The vectors, reverse vectors, vector
lengths, and reverse vector lengths.
- @rtype: tuple of numpy rank-2, 3D array
- """
-
- # The rotation matrix.
- c_theta = cos(theta_i)
- s_theta = sin(theta_i)
- c_phi = cos(phi_i)
- s_phi = sin(phi_i)
- c_sigma_phi = cos(sigma_i - phi_i)
- s_sigma_phi = sin(sigma_i - phi_i)
- c_phi_c_theta = c_phi * c_theta
- s_phi_c_theta = s_phi * c_theta
- Ri_prime[0, 0] = c_phi_c_theta*c_sigma_phi - s_phi*s_sigma_phi
- Ri_prime[0, 1] = -c_phi_c_theta*s_sigma_phi - s_phi*c_sigma_phi
- Ri_prime[0, 2] = c_phi*s_theta
- Ri_prime[1, 0] = s_phi_c_theta*c_sigma_phi + c_phi*s_sigma_phi
- Ri_prime[1, 1] = -s_phi_c_theta*s_sigma_phi + c_phi*c_sigma_phi
- Ri_prime[1, 2] = s_phi*s_theta
- Ri_prime[2, 0] = -s_theta*c_sigma_phi
- Ri_prime[2, 1] = s_theta*s_sigma_phi
- Ri_prime[2, 2] = c_theta
-
- # The rotation.
- R_i = dot(R_eigen, dot(Ri_prime, RT_eigen))
-
- # Pre-calculate all the new vectors (forwards and reverse).
- rot_vect_rev = transpose(dot(R_i, r_pivot_atom_rev) + r_ln_pivot)
- rot_vect = transpose(dot(R_i, r_pivot_atom) + r_ln_pivot)
-
- # Initialise the lengths.
- length = zeros(len(r_pivot_atom[0]), float64)
- length_rev = zeros(len(r_pivot_atom[0]), float64)
-
- # Loop over the atoms.
- for j in range(len(r_pivot_atom[0])):
- # The vector length (to the 5th power).
- length[j] = 1.0 / sqrt(inner(rot_vect[j], rot_vect[j]))**5
- length_rev[j] = 1.0 / sqrt(inner(rot_vect_rev[j],
rot_vect_rev[j]))**5
-
- # Return the data.
- return rot_vect, rot_vect_rev, length, length_rev
-
-
class Data:
"""A data container stored in the memo objects for use by the
Result_command class."""
Modified: trunk/maths_fns/frame_order/pseudo_ellipse.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/maths_fns/frame_order/pseudo_ellipse.py?rev=18983&r1=18982&r2=18983&view=diff
==============================================================================
--- trunk/maths_fns/frame_order/pseudo_ellipse.py (original)
+++ trunk/maths_fns/frame_order/pseudo_ellipse.py Fri Mar 22 16:51:35 2013
@@ -733,7 +733,7 @@
@type r_ln_pivot: numpy rank-2, 3D array
@keyword A: The full alignment tensor of the
non-moving domain.
@type A: numpy rank-2, 3D array
- @keyword Ri_prime: The empty rotation matrix for the
in-frame isotropic cone motion, used to calculate the PCS for each state i in
the numerical integration.
+ @keyword Ri_prime: The subdivision of rotation matrices
used to calculate the PCS for each state i in the numerical integration.
@type Ri_prime: numpy rank-2, 3D array
@keyword pcs_theta: The storage structure for the
back-calculated PCS values.
@type pcs_theta: numpy rank-2 array
@@ -808,7 +808,7 @@
continue
# Calculate the PCSs for this state.
- pcs_pivot_motion_full_qrint(theta_i=theta, phi_i=phi,
sigma_i=sigma, full_in_ref_frame=self.full_in_ref_frame,
r_pivot_atom=self.r_pivot_atom, r_pivot_atom_rev=self.r_pivot_atom_rev,
r_ln_pivot=self.r_ln_pivot, A=self.A, R_eigen=self.R_eigen,
RT_eigen=self.RT_eigen, Ri_prime=self.Ri_prime, pcs_theta=self.pcs_theta,
pcs_theta_err=self.pcs_theta_err, missing_pcs=self.missing_pcs)
+
pcs_pivot_motion_full_qrint(full_in_ref_frame=self.full_in_ref_frame,
r_pivot_atom=self.r_pivot_atom, r_pivot_atom_rev=self.r_pivot_atom_rev,
r_ln_pivot=self.r_ln_pivot, A=self.A, R_eigen=self.R_eigen,
RT_eigen=self.RT_eigen, Ri_prime=self.Ri_prime[i], pcs_theta=self.pcs_theta,
pcs_theta_err=self.pcs_theta_err, missing_pcs=self.missing_pcs)
# Increment the number of points.
num += 1
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/multi_processor_test.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/multi_processor_test.py?rev=18983&r1=18982&r2=18983&view=diff
==============================================================================
---
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/multi_processor_test.py
(original)
+++
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/multi_processor_test.py
Fri Mar 22 16:51:35 2013
@@ -37,7 +37,7 @@
ln = ['dy', 'tb', 'tm', 'er']
for i in range(len(ln)):
# Load the RDCs.
- #rdc.read(align_id=ln[i], file='rdc_%s.txt'%ln[i], spin_id1_col=1,
spin_id2_col=2, data_col=3, error_col=4)
+ rdc.read(align_id=ln[i], file='rdc_%s.txt'%ln[i], spin_id1_col=1,
spin_id2_col=2, data_col=3, error_col=4)
# The PCS.
pcs.read(align_id=ln[i], file='pcs_%s.txt'%ln[i], mol_name_col=1,
res_num_col=2, spin_name_col=5, data_col=6, error_col=7)
@@ -92,9 +92,9 @@
value.set(param='eigen_alpha', val=3.14159265358979311600+0.1)
value.set(param='eigen_beta', val=0.96007997859534310869+0.1)
value.set(param='eigen_gamma', val=4.03227550621962294031+0.1)
-value.set(param='cone_theta_x', val=30.0 * 2.0 * pi / 360.0+0.1)
-value.set(param='cone_theta_y', val=50.0 * 2.0 * pi / 360.0+0.1)
-value.set(param='cone_sigma_max', val=60.0 * 2.0 * pi / 360.0+0.1)
+value.set(param='cone_theta_x', val=30.0 * 2.0 * pi / 360.0+0.5)
+value.set(param='cone_theta_y', val=50.0 * 2.0 * pi / 360.0+0.5)
+value.set(param='cone_sigma_max', val=60.0 * 2.0 * pi / 360.0+0.5)
calc()
print("\nchi2: %s" % repr(cdp.chi2))
r18983 - in /trunk: maths_fns/frame_order/ test_suite/shared_data/frame_order/cam/pseudo_ellipse/