Author: bugman
Date: Tue Mar 1 13:30:20 2011
New Revision: 12644
URL: http://svn.gna.org/viewcvs/relax?rev=12644&view=rev
Log:
This change is related to the task #6397 (https://gna.org/task/?6397)
kada _at_ chemi _dot_ muni _dot_ cz
https://mail.gna.org/public/relax-devel/2011-03/msg00001.html
https://gna.org/task/download.php?file_id=12603
This patch includes change in the functions calc_(d,d2)noe in a file
maths_fns/ri.py, where
(d,d2)ri_prime was renamed to (d,d2)ri. This patch covers also the related
change of names in the
function init_res_r1_data (class Mf, maths_fns/mf.py), where the variables
are initialized.
Modified:
branches/cst/maths_fns/mf.py
branches/cst/maths_fns/ri.py
Modified: branches/cst/maths_fns/mf.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/maths_fns/mf.py?rev=12644&r1=12643&r2=12644&view=diff
==============================================================================
--- branches/cst/maths_fns/mf.py (original)
+++ branches/cst/maths_fns/mf.py Tue Mar 1 13:30:20 2011
@@ -1506,9 +1506,9 @@
r1_data.csa_jw_comps_hess = zeros(data.num_ri, float64)
# Initialise the transformed relaxation values, gradients, and
Hessians.
- r1_data.ri_prime = zeros(data.num_ri, float64)
- r1_data.dri_prime = zeros((data.num_ri, data.total_num_params),
float64)
- r1_data.d2ri_prime = zeros((data.num_ri, data.total_num_params,
data.total_num_params), float64)
+ r1_data.ri = zeros(data.num_ri, float64)
+ r1_data.dri = zeros((data.num_ri, data.total_num_params), float64)
+ r1_data.d2ri = zeros((data.num_ri, data.total_num_params,
data.total_num_params), float64)
# Place a few function arrays in the data class for the calculation
of the R1 value when an NOE data set exists but the R1 set does not.
r1_data.create_dri_prime = data.create_dri_prime
Modified: branches/cst/maths_fns/ri.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/maths_fns/ri.py?rev=12644&r1=12643&r2=12644&view=diff
==============================================================================
--- branches/cst/maths_fns/ri.py (original)
+++ branches/cst/maths_fns/ri.py Tue Mar 1 13:30:20 2011
@@ -35,16 +35,16 @@
Half this code needs to be shifted into the function initialisation code.
"""
- # Get the r1 value either from data.ri_prime or by calculation if the
value is not in data.ri_prime
+ # Get the r1 value either from data.ri or by calculation if the value is
not in data.ri
data.r1[i] = get_r1[i](data, i, frq_num, params)
# Calculate the NOE.
- if data.r1[i] == 0.0 and data.ri_prime[i] == 0.0:
+ if data.r1[i] == 0.0 and data.ri[i] == 0.0:
data.ri[i] = 1.0
elif data.r1[i] == 0.0:
data.ri[i] = 1e99
else:
- data.ri[i] = 1.0 + data.g_ratio*(data.ri_prime[i] / data.r1[i])
+ data.ri[i] = 1.0 + data.g_ratio*(data.ri[i] / data.r1[i])
def calc_dnoe(data, i, frq_num, get_dr1, params, j):
@@ -55,12 +55,12 @@
# Calculate the NOE derivative.
data.dr1[j, i] = get_dr1[i](data, i, frq_num, params, j)
- if data.r1[i] == 0.0 and data.ri_prime[i] == 0.0:
+ if data.r1[i] == 0.0 and data.ri[i] == 0.0:
data.dri[j, i] = 0.0
elif data.r1[i] == 0.0:
data.dri[j, i] = 1e99
else:
- data.dri[j, i] = data.g_ratio * (1.0 / data.r1[i]**2) * (data.r1[i]
* data.dri_prime[j, i] - data.ri_prime[i] * data.dr1[j, i])
+ data.dri[j, i] = data.g_ratio * (1.0 / data.r1[i]**2) * (data.r1[i]
* data.dri[j, i] - data.ri[i] * data.dr1[j, i])
def calc_d2noe(data, i, frq_num, get_d2r1, params, j, k):
@@ -71,13 +71,13 @@
# Calculate the NOE second derivative.
data.d2r1[j, k, i] = get_d2r1[i](data, i, frq_num, params, j, k)
- if data.r1[i] == 0.0 and data.ri_prime[i] == 0.0:
+ if data.r1[i] == 0.0 and data.ri[i] == 0.0:
data.d2ri[j, k, i] = 0.0
elif data.r1[i] == 0.0:
data.d2ri[j, k, i] = 1e99
else:
- a = data.ri_prime[i] * (2.0 * data.dr1[j, i] * data.dr1[k, i] -
data.r1[i] * data.d2r1[j, k, i])
- b = data.r1[i] * (data.dri_prime[j, i] * data.dr1[k, i] +
data.dr1[j, i] * data.dri_prime[k, i] - data.r1[i] * data.d2ri_prime[j, k, i])
+ a = data.ri[i] * (2.0 * data.dr1[j, i] * data.dr1[k, i] - data.r1[i]
* data.d2r1[j, k, i])
+ b = data.r1[i] * (data.dri[j, i] * data.dr1[k, i] + data.dr1[j, i] *
data.dri[k, i] - data.r1[i] * data.d2ri[j, k, i])
data.d2ri[j, k, i] = data.g_ratio * (1.0 / data.r1[i]**3) * (a - b)
r12644 - in /branches/cst/maths_fns: mf.py ri.py