Author: bugman
Date: Tue Jun 3 09:16:09 2014
New Revision: 23615
URL: http://svn.gna.org/viewcvs/relax?rev=23615&view=rev
Log:
Proper edge case handling and slight speed up of the frame order PCS
integration functions.
The case whereby no Sobol' points in the numerical integration lie within the
motional distribution
is now caught and the rotation matrix set to the motional eigenframe to
simulate the rigid state.
As the code for averaging the PCS was changed, it was also simplified by
removing an unnecessary
loop over all spins. This should speed up the PCS integration by a tiny
amount.
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=23615&r1=23614&r2=23615&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/double_rotor.py
(original)
+++ branches/frame_order_cleanup/lib/frame_order/double_rotor.py Tue
Jun 3 09:16:09 2014
@@ -129,11 +129,14 @@
# Increment the number of points.
num += 1
- # Calculate the PCS and error.
- for i in range(len(pcs_theta)):
- for j in range(len(pcs_theta[i])):
- # The average PCS.
- pcs_theta[i, j] = c[i] * pcs_theta[i, j] / float(num)
+ # Default to the rigid state if no points lie in the distribution.
+ if num == 0:
+ 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, R_eigen=R_eigen, RT_eigen=RT_eigen,
Ri_prime=R_eigen, pcs_theta=pcs_theta, pcs_theta_err=pcs_theta_err,
missing_pcs=missing_pcs)
+
+ # Average the PCS.
+ else:
+ for i in range(len(pcs_theta)):
+ pcs_theta[i] = c[i] * pcs_theta[i] / float(num)
def pcs_pivot_motion_double_rotor(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):
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=23615&r1=23614&r2=23615&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/iso_cone.py (original)
+++ branches/frame_order_cleanup/lib/frame_order/iso_cone.py Tue Jun 3
09:16:09 2014
@@ -109,11 +109,14 @@
# Increment the number of points.
num += 1
- # Calculate the PCS and error.
- for i in range(len(pcs_theta)):
- for j in range(len(pcs_theta[i])):
- # The average PCS.
- pcs_theta[i, j] = c[i] * pcs_theta[i, j] / float(num)
+ # Default to the rigid state if no points lie in the distribution.
+ if num == 0:
+ 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, R_eigen=R_eigen, RT_eigen=RT_eigen,
Ri_prime=R_eigen, pcs_theta=pcs_theta, pcs_theta_err=pcs_theta_err,
missing_pcs=missing_pcs)
+
+ # Average the PCS.
+ else:
+ for i in range(len(pcs_theta)):
+ pcs_theta[i] = c[i] * pcs_theta[i] / float(num)
def populate_1st_eigenframe_iso_cone(matrix, angle):
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=23615&r1=23614&r2=23615&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
Tue Jun 3 09:16:09 2014
@@ -128,8 +128,11 @@
# Increment the number of points.
num += 1
- # Calculate the PCS and error.
- for i in range(len(pcs_theta)):
- for j in range(len(pcs_theta[i])):
- # The average PCS.
- pcs_theta[i, j] = c[i] * pcs_theta[i, j] / float(num)
+ # Default to the rigid state if no points lie in the distribution.
+ if num == 0:
+
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, R_eigen=R_eigen, RT_eigen=RT_eigen,
Ri_prime=R_eigen, pcs_theta=pcs_theta, pcs_theta_err=pcs_theta_err,
missing_pcs=missing_pcs)
+
+ # Average the PCS.
+ else:
+ for i in range(len(pcs_theta)):
+ pcs_theta[i] = c[i] * pcs_theta[i] / float(num)
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=23615&r1=23614&r2=23615&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse.py
(original)
+++ branches/frame_order_cleanup/lib/frame_order/pseudo_ellipse.py Tue
Jun 3 09:16:09 2014
@@ -653,11 +653,14 @@
# Increment the number of points.
num += 1
- # Calculate the PCS and error.
- for i in range(len(pcs_theta)):
- for j in range(len(pcs_theta[i])):
- # The average PCS.
- pcs_theta[i, j] = c[i] * pcs_theta[i, j] / float(num)
+ # Default to the rigid state if no points lie in the distribution.
+ if num == 0:
+ 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, R_eigen=R_eigen, RT_eigen=RT_eigen,
Ri_prime=R_eigen, pcs_theta=pcs_theta, pcs_theta_err=pcs_theta_err,
missing_pcs=missing_pcs)
+
+ # Average the PCS.
+ else:
+ for i in range(len(pcs_theta)):
+ pcs_theta[i] = c[i] * pcs_theta[i] / float(num)
def tmax_pseudo_ellipse(phi, theta_x, theta_y):
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=23615&r1=23614&r2=23615&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
Tue Jun 3 09:16:09 2014
@@ -314,8 +314,11 @@
# Increment the number of points.
num += 1
- # Calculate the PCS and error.
- for i in range(len(pcs_theta)):
- for j in range(len(pcs_theta[i])):
- # The average PCS.
- pcs_theta[i, j] = c[i] * pcs_theta[i, j] / float(num)
+ # Default to the rigid state if no points lie in the distribution.
+ if num == 0:
+
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, R_eigen=R_eigen, RT_eigen=RT_eigen,
Ri_prime=R_eigen, pcs_theta=pcs_theta, pcs_theta_err=pcs_theta_err,
missing_pcs=missing_pcs)
+
+ # Average the PCS.
+ else:
+ for i in range(len(pcs_theta)):
+ pcs_theta[i] = c[i] * pcs_theta[i] / float(num)
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=23615&r1=23614&r2=23615&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/frame_order/rotor.py (original)
+++ branches/frame_order_cleanup/lib/frame_order/rotor.py Tue Jun 3
09:16:09 2014
@@ -130,14 +130,14 @@
# Increment the number of points.
num += 1
- # Calculate the PCS and error.
- for i in range(len(pcs_theta)):
- for j in range(len(pcs_theta[i])):
- if num == 0:
- continue
+ # Default to the rigid state if no points lie in the distribution.
+ if num == 0:
+ 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, R_eigen=R_eigen, RT_eigen=RT_eigen,
Ri_prime=R_eigen, pcs_theta=pcs_theta, pcs_theta_err=pcs_theta_err,
missing_pcs=missing_pcs)
- # The average PCS.
- pcs_theta[i, j] = c[i] * pcs_theta[i, j] / float(num)
+ # Average the PCS.
+ else:
+ for i in range(len(pcs_theta)):
+ pcs_theta[i] = c[i] * pcs_theta[i] / float(num)
def pcs_pivot_motion_rotor_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):
r23615 - /branches/frame_order_cleanup/lib/frame_order/