Author: bugman
Date: Mon Jun 16 17:39:25 2014
New Revision: 23979
URL: http://svn.gna.org/viewcvs/relax?rev=23979&view=rev
Log:
Fixes for all PCS numeric integration for all frame order models in the rigid
case.
The exact PCS values for the rigid state are now correctly calculated when no
Sobol' points lie
within the motional model. The identity matrix is used to set the rotation
to zero, and the PCS
values are now multiplied by the constant.
Modified:
branches/frame_order_cleanup/lib/frame_order/double_rotor.py
branches/frame_order_cleanup/lib/frame_order/iso_cone.py
branches/frame_order_cleanup/lib/frame_order/iso_cone_torsionless.py
branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse.py
branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse_torsionless.py
branches/frame_order_cleanup/lib/frame_order/rotor.py
Modified: branches/frame_order_cleanup/lib/frame_order/double_rotor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/frame_order/double_rotor.py?rev=23979&r1=23978&r2=23979&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/double_rotor.py
(original)
+++ branches/frame_order_cleanup/lib/frame_order/double_rotor.py Mon
Jun 16 17:39:25 2014
@@ -136,11 +136,16 @@
# Default to the rigid state if no points lie in the distribution.
if num == 0:
- # Fast frame shift.
- Ri = dot(R_eigen, tensordot(R_eigen, RT_eigen, axes=1))
+ # Fast identity frame shift.
+ Ri_prime = eye(3, dtype=float64)
+ Ri = dot(R_eigen, tensordot(Ri_prime, RT_eigen, axes=1))
+ Ri = swapaxes(Ri, 0, 1)
# Calculate the PCSs for this state.
pcs_pivot_motion_double_rotor(full_in_ref_frame=full_in_ref_frame,
r_pivot_atom=r_pivot_atom, r_pivot_atom_rev=r_pivot_atom_rev,
r_ln_pivot=r_ln_pivot, A=A, Ri=Ri, pcs_theta=pcs_theta,
pcs_theta_err=pcs_theta_err, missing_pcs=missing_pcs)
+
+ # Multiply the constant.
+ multiply(c, pcs_theta, pcs_theta)
# Average the PCS.
else:
Modified: branches/frame_order_cleanup/lib/frame_order/iso_cone.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/frame_order/iso_cone.py?rev=23979&r1=23978&r2=23979&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/iso_cone.py (original)
+++ branches/frame_order_cleanup/lib/frame_order/iso_cone.py Mon Jun 16
17:39:25 2014
@@ -24,7 +24,7 @@
# Python module imports.
from math import cos, pi, sqrt
-from numpy import divide, dot, multiply, sinc, swapaxes, tensordot
+from numpy import divide, dot, eye, float64, multiply, sinc, swapaxes,
tensordot
# relax module imports.
from lib.frame_order.matrix_ops import pcs_pivot_motion_full_qrint,
rotate_daeg
@@ -115,11 +115,16 @@
# Default to the rigid state if no points lie in the distribution.
if num == 0:
- # Fast frame shift.
- Ri = dot(R_eigen, tensordot(R_eigen, RT_eigen, axes=1))
+ # Fast identity frame shift.
+ Ri_prime = eye(3, dtype=float64)
+ Ri = dot(R_eigen, tensordot(Ri_prime, RT_eigen, axes=1))
+ Ri = swapaxes(Ri, 0, 1)
# Calculate the PCSs for this state.
pcs_pivot_motion_full_qrint(full_in_ref_frame=full_in_ref_frame,
r_pivot_atom=r_pivot_atom, r_pivot_atom_rev=r_pivot_atom_rev,
r_ln_pivot=r_ln_pivot, A=A, Ri=Ri, pcs_theta=pcs_theta,
pcs_theta_err=pcs_theta_err, missing_pcs=missing_pcs)
+
+ # Multiply the constant.
+ multiply(c, pcs_theta, pcs_theta)
# Average the PCS.
else:
Modified: branches/frame_order_cleanup/lib/frame_order/iso_cone_torsionless.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/frame_order/iso_cone_torsionless.py?rev=23979&r1=23978&r2=23979&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/iso_cone_torsionless.py
(original)
+++ branches/frame_order_cleanup/lib/frame_order/iso_cone_torsionless.py
Mon Jun 16 17:39:25 2014
@@ -24,7 +24,7 @@
# Python module imports.
from math import cos, sqrt
-from numpy import divide, dot, multiply, swapaxes, tensordot
+from numpy import divide, dot, eye, float64, multiply, swapaxes, tensordot
# relax module imports.
from lib.frame_order.matrix_ops import pcs_pivot_motion_torsionless_qrint,
rotate_daeg
@@ -135,11 +135,16 @@
# Default to the rigid state if no points lie in the distribution.
if num == 0:
- # Fast frame shift.
- Ri = dot(R_eigen, tensordot(R_eigen, RT_eigen, axes=1))
+ # Fast identity frame shift.
+ Ri_prime = eye(3, dtype=float64)
+ Ri = dot(R_eigen, tensordot(Ri_prime, RT_eigen, axes=1))
+ Ri = swapaxes(Ri, 0, 1)
# Calculate the PCSs for this state.
pcs_pivot_motion_torsionless_qrint(full_in_ref_frame=full_in_ref_frame,
r_pivot_atom=r_pivot_atom, r_pivot_atom_rev=r_pivot_atom_rev,
r_ln_pivot=r_ln_pivot, A=A, Ri=Ri, pcs_theta=pcs_theta,
pcs_theta_err=pcs_theta_err, missing_pcs=missing_pcs)
+
+ # Multiply the constant.
+ multiply(c, pcs_theta, pcs_theta)
# Average the PCS.
else:
Modified: branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse.py?rev=23979&r1=23978&r2=23979&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse.py
(original)
+++ branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse.py Mon
Jun 16 17:39:25 2014
@@ -24,7 +24,7 @@
# Python module imports.
from math import cos, pi, sin, sqrt
-from numpy import divide, dot, multiply, repeat, sinc, swapaxes, tensordot,
tile
+from numpy import divide, dot, eye, float64, multiply, repeat, sinc,
swapaxes, tensordot, tile
try:
from scipy.integrate import quad
except ImportError:
@@ -659,11 +659,16 @@
# Default to the rigid state if no points lie in the distribution.
if num == 0:
- # Fast frame shift.
- Ri = dot(R_eigen, tensordot(R_eigen, RT_eigen, axes=1))
+ # Fast identity frame shift.
+ Ri_prime = eye(3, dtype=float64)
+ Ri = dot(R_eigen, tensordot(Ri_prime, RT_eigen, axes=1))
+ Ri = swapaxes(Ri, 0, 1)
# Calculate the PCSs for this state.
pcs_pivot_motion_full_qrint(full_in_ref_frame=full_in_ref_frame,
r_pivot_atom=r_pivot_atom, r_pivot_atom_rev=r_pivot_atom_rev,
r_ln_pivot=r_ln_pivot, A=A, Ri=Ri, pcs_theta=pcs_theta,
pcs_theta_err=pcs_theta_err, missing_pcs=missing_pcs)
+
+ # Multiply the constant.
+ multiply(c, pcs_theta, pcs_theta)
# Average the PCS.
else:
Modified:
branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse_torsionless.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse_torsionless.py?rev=23979&r1=23978&r2=23979&view=diff
==============================================================================
---
branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse_torsionless.py
(original)
+++
branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse_torsionless.py
Mon Jun 16 17:39:25 2014
@@ -24,7 +24,7 @@
# Python module imports.
from math import cos, pi, sin, sqrt
-from numpy import divide, dot, multiply, swapaxes, tensordot
+from numpy import divide, dot, eye, float64, multiply, swapaxes, tensordot
try:
from scipy.integrate import quad
except ImportError:
@@ -328,11 +328,16 @@
# Default to the rigid state if no points lie in the distribution.
if num == 0:
- # Fast frame shift.
- Ri = dot(R_eigen, tensordot(R_eigen, RT_eigen, axes=1))
+ # Fast identity frame shift.
+ Ri_prime = eye(3, dtype=float64)
+ Ri = dot(R_eigen, tensordot(Ri_prime, RT_eigen, axes=1))
+ Ri = swapaxes(Ri, 0, 1)
# Calculate the PCSs for this state.
pcs_pivot_motion_torsionless_qrint(full_in_ref_frame=full_in_ref_frame,
r_pivot_atom=r_pivot_atom, r_pivot_atom_rev=r_pivot_atom_rev,
r_ln_pivot=r_ln_pivot, A=A, Ri=Ri, pcs_theta=pcs_theta,
pcs_theta_err=pcs_theta_err, missing_pcs=missing_pcs)
+
+ # Multiply the constant.
+ multiply(c, pcs_theta, pcs_theta)
# Average the PCS.
else:
Modified: branches/frame_order_cleanup/lib/frame_order/rotor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/frame_order/rotor.py?rev=23979&r1=23978&r2=23979&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/rotor.py (original)
+++ branches/frame_order_cleanup/lib/frame_order/rotor.py Mon Jun 16
17:39:25 2014
@@ -136,11 +136,16 @@
# Default to the rigid state if no points lie in the distribution.
if num == 0:
- # Fast frame shift.
- Ri = dot(R_eigen, tensordot(R_eigen, RT_eigen, axes=1))
+ # Fast identity frame shift.
+ Ri_prime = eye(3, dtype=float64)
+ Ri = dot(R_eigen, tensordot(Ri_prime, RT_eigen, axes=1))
+ Ri = swapaxes(Ri, 0, 1)
# Calculate the PCSs for this state.
pcs_pivot_motion_rotor_qrint(full_in_ref_frame=full_in_ref_frame,
r_pivot_atom=r_pivot_atom, r_pivot_atom_rev=r_pivot_atom_rev,
r_ln_pivot=r_ln_pivot, A=A, Ri=Ri, pcs_theta=pcs_theta,
pcs_theta_err=pcs_theta_err, missing_pcs=missing_pcs)
+
+ # Multiply the constant.
+ multiply(c, pcs_theta, pcs_theta)
# Average the PCS.
else:
r23979 - /branches/frame_order_cleanup/lib/frame_order/