Author: bugman
Date: Fri Jun 14 18:35:34 2013
New Revision: 20130
URL: http://svn.gna.org/viewcvs/relax?rev=20130&view=rev
Log:
Fixes for the N-state model target functions for the lib.alignment.rdc
changes.
The absolute value is now calculated within the target function rather than
when back calculating
the RDCs.
Modified:
trunk/target_functions/n_state_model.py
Modified: trunk/target_functions/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/n_state_model.py?rev=20130&r1=20129&r2=20130&view=diff
==============================================================================
--- trunk/target_functions/n_state_model.py (original)
+++ trunk/target_functions/n_state_model.py Fri Jun 14 18:35:34 2013
@@ -675,11 +675,15 @@
for j in range(self.num_interatom):
# Calculate the average RDC.
if not self.missing_rdc[align_index, j]:
- self.rdc_theta[align_index, j] =
ave_rdc_tensor(self.dip_const[j], self.dip_vect[j], self.N,
self.A[align_index], weights=self.probs,
absolute=self.absolute_rdc[align_index, j])
+ self.rdc_theta[align_index, j] =
ave_rdc_tensor(self.dip_const[j], self.dip_vect[j], self.N,
self.A[align_index], weights=self.probs)
# Add the J coupling to convert into the
back-calculated T = J+D value.
if self.j_flag:
self.rdc_theta[align_index, j] +=
self.j_couplings[j]
+
+ # Take the absolute value.
+ if self.absolute_rdc[align_index, j]:
+ self.rdc_theta[align_index, j] =
abs(self.rdc_theta[align_index, j])
# The back calculated PCS.
if self.pcs_flag[align_index]:
@@ -929,11 +933,11 @@
if not self.fixed_tensors[align_index]:
for j in range(self.num_interatom):
if self.rdc_flag[align_index] and not
self.missing_rdc[align_index, j]:
- self.drdc_theta[align_index*5, align_index, j] =
ave_rdc_tensor_dDij_dAmn(self.dip_const[j], self.dip_vect[j], self.N,
self.dA[0], weights=self.probs, absolute=self.absolute_rdc[align_index, j])
- self.drdc_theta[align_index*5+1, align_index, j] =
ave_rdc_tensor_dDij_dAmn(self.dip_const[j], self.dip_vect[j], self.N,
self.dA[1], weights=self.probs, absolute=self.absolute_rdc[align_index, j])
- self.drdc_theta[align_index*5+2, align_index, j] =
ave_rdc_tensor_dDij_dAmn(self.dip_const[j], self.dip_vect[j], self.N,
self.dA[2], weights=self.probs, absolute=self.absolute_rdc[align_index, j])
- self.drdc_theta[align_index*5+3, align_index, j] =
ave_rdc_tensor_dDij_dAmn(self.dip_const[j], self.dip_vect[j], self.N,
self.dA[3], weights=self.probs, absolute=self.absolute_rdc[align_index, j])
- self.drdc_theta[align_index*5+4, align_index, j] =
ave_rdc_tensor_dDij_dAmn(self.dip_const[j], self.dip_vect[j], self.N,
self.dA[4], weights=self.probs, absolute=self.absolute_rdc[align_index, j])
+ self.drdc_theta[align_index*5, align_index, j] =
ave_rdc_tensor_dDij_dAmn(self.dip_const[j], self.dip_vect[j], self.N,
self.dA[0], weights=self.probs)
+ self.drdc_theta[align_index*5+1, align_index, j] =
ave_rdc_tensor_dDij_dAmn(self.dip_const[j], self.dip_vect[j], self.N,
self.dA[1], weights=self.probs)
+ self.drdc_theta[align_index*5+2, align_index, j] =
ave_rdc_tensor_dDij_dAmn(self.dip_const[j], self.dip_vect[j], self.N,
self.dA[2], weights=self.probs)
+ self.drdc_theta[align_index*5+3, align_index, j] =
ave_rdc_tensor_dDij_dAmn(self.dip_const[j], self.dip_vect[j], self.N,
self.dA[3], weights=self.probs)
+ self.drdc_theta[align_index*5+4, align_index, j] =
ave_rdc_tensor_dDij_dAmn(self.dip_const[j], self.dip_vect[j], self.N,
self.dA[4], weights=self.probs)
# Construct the Amn partial derivative components for the PCS.
if not self.fixed_tensors[align_index]:
@@ -960,7 +964,7 @@
# Calculate the RDC for state c (this is the pc partial
derivative).
for j in range(self.num_interatom):
if self.rdc_flag[align_index] and not
self.missing_rdc[align_index, j]:
- self.drdc_theta[param_index, align_index, j] =
rdc_tensor(self.dip_const[j], self.dip_vect[j, c], self.A[align_index],
absolute=self.absolute_rdc[align_index, j])
+ self.drdc_theta[param_index, align_index, j] =
rdc_tensor(self.dip_const[j], self.dip_vect[j, c], self.A[align_index])
# Calculate the PCS for state c (this is the pc partial
derivative).
for j in range(self.num_spins):
@@ -1135,11 +1139,11 @@
# Calculate the RDC Hessian component.
for j in range(self.num_interatom):
if self.fixed_tensors[align_index] and
self.rdc_flag[align_index] and not self.missing_rdc[align_index, j]:
- self.d2rdc_theta[pc_index, align_index*5+0,
align_index, j] = self.d2rdc_theta[align_index*5+0, pc_index, align_index, j]
= rdc_tensor(self.dip_const[j], self.dip_vect[j, c], self.dA[0],
absolute=self.absolute_rdc[align_index, j])
- self.d2rdc_theta[pc_index, align_index*5+1,
align_index, j] = self.d2rdc_theta[align_index*5+1, pc_index, align_index, j]
= rdc_tensor(self.dip_const[j], self.dip_vect[j, c], self.dA[1],
absolute=self.absolute_rdc[align_index, j])
- self.d2rdc_theta[pc_index, align_index*5+2,
align_index, j] = self.d2rdc_theta[align_index*5+2, pc_index, align_index, j]
= rdc_tensor(self.dip_const[j], self.dip_vect[j, c], self.dA[2],
absolute=self.absolute_rdc[align_index, j])
- self.d2rdc_theta[pc_index, align_index*5+3,
align_index, j] = self.d2rdc_theta[align_index*5+3, pc_index, align_index, j]
= rdc_tensor(self.dip_const[j], self.dip_vect[j, c], self.dA[3],
absolute=self.absolute_rdc[align_index, j])
- self.d2rdc_theta[pc_index, align_index*5+4,
align_index, j] = self.d2rdc_theta[align_index*5+4, pc_index, align_index, j]
= rdc_tensor(self.dip_const[j], self.dip_vect[j, c], self.dA[4],
absolute=self.absolute_rdc[align_index, j])
+ self.d2rdc_theta[pc_index, align_index*5+0,
align_index, j] = self.d2rdc_theta[align_index*5+0, pc_index, align_index, j]
= rdc_tensor(self.dip_const[j], self.dip_vect[j, c], self.dA[0])
+ self.d2rdc_theta[pc_index, align_index*5+1,
align_index, j] = self.d2rdc_theta[align_index*5+1, pc_index, align_index, j]
= rdc_tensor(self.dip_const[j], self.dip_vect[j, c], self.dA[1])
+ self.d2rdc_theta[pc_index, align_index*5+2,
align_index, j] = self.d2rdc_theta[align_index*5+2, pc_index, align_index, j]
= rdc_tensor(self.dip_const[j], self.dip_vect[j, c], self.dA[2])
+ self.d2rdc_theta[pc_index, align_index*5+3,
align_index, j] = self.d2rdc_theta[align_index*5+3, pc_index, align_index, j]
= rdc_tensor(self.dip_const[j], self.dip_vect[j, c], self.dA[3])
+ self.d2rdc_theta[pc_index, align_index*5+4,
align_index, j] = self.d2rdc_theta[align_index*5+4, pc_index, align_index, j]
= rdc_tensor(self.dip_const[j], self.dip_vect[j, c], self.dA[4])
# Calculate the PCS Hessian component.
for j in range(self.num_spins):
r20130 - /trunk/target_functions/n_state_model.py