Author: bugman
Date: Sat Mar 23 10:17:04 2013
New Revision: 19052
URL: http://svn.gna.org/viewcvs/relax?rev=19052&view=rev
Log:
Shifted the target_functions.ri module to lib.auto_relaxation.ri.
Added:
trunk/lib/auto_relaxation/ri.py
- copied unchanged from r19029, trunk/target_functions/ri.py
Removed:
trunk/target_functions/ri.py
Modified:
trunk/lib/auto_relaxation/__init__.py
trunk/target_functions/__init__.py
trunk/target_functions/mf.py
Modified: trunk/lib/auto_relaxation/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/auto_relaxation/__init__.py?rev=19052&r1=19051&r2=19052&view=diff
==============================================================================
--- trunk/lib/auto_relaxation/__init__.py (original)
+++ trunk/lib/auto_relaxation/__init__.py Sat Mar 23 10:17:04 2013
@@ -23,5 +23,5 @@
"""The relax-lib NMR package - a library of functions for auto-relaxation
rates."""
__all__ = [
- ''
+ 'ri'
]
Modified: trunk/target_functions/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/__init__.py?rev=19052&r1=19051&r2=19052&view=diff
==============================================================================
--- trunk/target_functions/__init__.py (original)
+++ trunk/target_functions/__init__.py Sat Mar 23 10:17:04 2013
@@ -36,6 +36,5 @@
'potential',
'ri_comps',
'ri_prime',
- 'ri',
'weights'
]
Modified: trunk/target_functions/mf.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/mf.py?rev=19052&r1=19051&r2=19052&view=diff
==============================================================================
--- trunk/target_functions/mf.py (original)
+++ trunk/target_functions/mf.py Sat Mar 23 10:17:04 2013
@@ -29,11 +29,11 @@
from lib.diffusion.direction_cosine import calc_ellipsoid_di,
calc_ellipsoid_ddi, calc_ellipsoid_d2di, calc_spheroid_di, calc_spheroid_ddi,
calc_spheroid_d2di
from target_functions.weights import *
from target_functions.correlation_time import *
+from lib.auto_relaxation.ri import calc_noe, calc_dnoe, calc_d2noe, calc_r1,
calc_dr1, calc_d2r1, extract_r1, extract_dr1, extract_d2r1
from lib.spectral_densities.model_free import calc_jw, calc_S2_jw,
calc_S2_te_jw, calc_S2f_S2_ts_jw, calc_S2f_tf_S2_ts_jw, calc_S2f_S2s_ts_jw,
calc_S2f_tf_S2s_ts_jw, calc_diff_djw_dGj, calc_ellipsoid_djw_dGj,
calc_diff_S2_djw_dGj, calc_ellipsoid_S2_djw_dGj, calc_diff_S2_te_djw_dGj,
calc_ellipsoid_S2_te_djw_dGj, calc_diff_djw_dOj, calc_diff_S2_djw_dOj,
calc_diff_S2_te_djw_dOj, calc_S2_djw_dS2, calc_S2_te_djw_dS2,
calc_S2_te_djw_dte, calc_diff_S2f_S2_ts_djw_dGj,
calc_ellipsoid_S2f_S2_ts_djw_dGj, calc_diff_S2f_tf_S2_ts_djw_dGj,
calc_ellipsoid_S2f_tf_S2_ts_djw_dGj, calc_diff_S2f_S2_ts_djw_dOj,
calc_diff_S2f_tf_S2_ts_djw_dOj, calc_S2f_S2_ts_djw_dS2,
calc_S2f_S2_ts_djw_dS2f, calc_S2f_tf_S2_ts_djw_dS2f,
calc_S2f_tf_S2_ts_djw_dtf, calc_S2f_S2_ts_djw_dts,
calc_diff_S2f_S2s_ts_djw_dGj, calc_ellipsoid_S2f_S2s_ts_djw_dGj,
calc_diff_S2f_tf_S2s_ts_djw_dGj, calc_ellipsoid_S2f_tf_S2s_ts_djw_dGj,
calc_diff_S2f_S2s_ts_djw_dOj, calc_diff_S2f_tf_S2s_ts_djw_dOj,
calc_S2f_S2s_ts_djw_dS2f, calc_S2f_tf_S2s_ts_djw_dS2f,
calc_S2f_tf_S2s_ts_djw_dS2s, calc_S2f_tf_S2s_ts_djw_dtf,
calc_S2f_S2s_ts_djw_dts, calc_diff_d2jw_dGjdGk, calc_ellipsoid_d2jw_dGjdGk,
calc_diff_S2_d2jw_dGjdGk, calc_ellipsoid_S2_d2jw_dGjdGk,
calc_diff_S2_te_d2jw_dGjdGk, calc_ellipsoid_S2_te_d2jw_dGjdGk,
calc_diff_d2jw_dGjdOj, calc_ellipsoid_d2jw_dGjdOj, calc_diff_S2_d2jw_dGjdOj,
calc_ellipsoid_S2_d2jw_dGjdOj, calc_diff_S2_te_d2jw_dGjdOj,
calc_ellipsoid_S2_te_d2jw_dGjdOj, calc_diff_S2_d2jw_dGjdS2,
calc_ellipsoid_S2_d2jw_dGjdS2, calc_diff_S2_te_d2jw_dGjdS2,
calc_ellipsoid_S2_te_d2jw_dGjdS2, calc_diff_S2_te_d2jw_dGjdte,
calc_ellipsoid_S2_te_d2jw_dGjdte, calc_diff_d2jw_dOjdOk,
calc_diff_S2_d2jw_dOjdOk, calc_diff_S2_te_d2jw_dOjdOk,
calc_diff_S2_d2jw_dOjdS2, calc_diff_S2_te_d2jw_dOjdS2,
calc_diff_S2_te_d2jw_dOjdte, calc_S2_te_d2jw_dS2dte, calc_S2_te_d2jw_dte2,
calc_diff_S2f_S2_ts_d2jw_dGjdGk, calc_ellipsoid_S2f_S2_ts_d2jw_dGjdGk,
calc_diff_S2f_tf_S2_ts_d2jw_dGjdGk, calc_ellipsoid_S2f_tf_S2_ts_d2jw_dGjdGk,
calc_diff_S2f_S2_ts_d2jw_dGjdOj, calc_ellipsoid_S2f_S2_ts_d2jw_dGjdOj,
calc_diff_S2f_tf_S2_ts_d2jw_dGjdOj, calc_ellipsoid_S2f_tf_S2_ts_d2jw_dGjdOj,
calc_diff_S2f_S2_ts_d2jw_dGjdS2, calc_ellipsoid_S2f_S2_ts_d2jw_dGjdS2,
calc_diff_S2f_S2_ts_d2jw_dGjdS2f, calc_ellipsoid_S2f_S2_ts_d2jw_dGjdS2f,
calc_diff_S2f_tf_S2_ts_d2jw_dGjdS2f,
calc_ellipsoid_S2f_tf_S2_ts_d2jw_dGjdS2f, calc_diff_S2f_tf_S2_ts_d2jw_dGjdtf,
calc_ellipsoid_S2f_tf_S2_ts_d2jw_dGjdtf, calc_diff_S2f_S2_ts_d2jw_dGjdts,
calc_ellipsoid_S2f_S2_ts_d2jw_dGjdts, calc_diff_S2f_S2_ts_d2jw_dOjdOk,
calc_diff_S2f_tf_S2_ts_d2jw_dOjdOk, calc_diff_S2f_S2_ts_d2jw_dOjdS2,
calc_diff_S2f_S2_ts_d2jw_dOjdS2f, calc_diff_S2f_tf_S2_ts_d2jw_dOjdS2f,
calc_diff_S2f_tf_S2_ts_d2jw_dOjdtf, calc_diff_S2f_S2_ts_d2jw_dOjdts,
calc_S2f_S2_ts_d2jw_dS2dts, calc_S2f_tf_S2_ts_d2jw_dS2fdtf,
calc_S2f_S2_ts_d2jw_dS2fdts, calc_S2f_tf_S2_ts_d2jw_dtf2,
calc_S2f_S2_ts_d2jw_dts2, calc_diff_S2f_S2s_ts_d2jw_dGjdGk,
calc_ellipsoid_S2f_S2s_ts_d2jw_dGjdGk, calc_diff_S2f_tf_S2s_ts_d2jw_dGjdGk,
calc_ellipsoid_S2f_tf_S2s_ts_d2jw_dGjdGk, calc_diff_S2f_S2s_ts_d2jw_dGjdOj,
calc_ellipsoid_S2f_S2s_ts_d2jw_dGjdOj, calc_diff_S2f_tf_S2s_ts_d2jw_dGjdOj,
calc_ellipsoid_S2f_tf_S2s_ts_d2jw_dGjdOj, calc_diff_S2f_S2s_ts_d2jw_dGjdS2f,
calc_ellipsoid_S2f_S2s_ts_d2jw_dGjdS2f, calc_diff_S2f_tf_S2s_ts_d2jw_dGjdS2f,
calc_ellipsoid_S2f_tf_S2s_ts_d2jw_dGjdS2f, calc_diff_S2f_S2s_ts_d2jw_dGjdS2s,
calc_ellipsoid_S2f_S2s_ts_d2jw_dGjdS2s, calc_diff_S2f_tf_S2s_ts_d2jw_dGjdtf,
calc_ellipsoid_S2f_tf_S2s_ts_d2jw_dGjdtf, calc_diff_S2f_S2s_ts_d2jw_dGjdts,
calc_ellipsoid_S2f_S2s_ts_d2jw_dGjdts, calc_diff_S2f_S2s_ts_d2jw_dOjdOk,
calc_diff_S2f_tf_S2s_ts_d2jw_dOjdOk, calc_diff_S2f_S2s_ts_d2jw_dOjdS2f,
calc_diff_S2f_tf_S2s_ts_d2jw_dOjdS2f, calc_diff_S2f_tf_S2s_ts_d2jw_dOjdtf,
calc_diff_S2f_S2s_ts_d2jw_dOjdts, calc_S2f_S2s_ts_d2jw_dS2fdS2s,
calc_S2f_tf_S2s_ts_d2jw_dS2fdtf, calc_S2f_S2s_ts_d2jw_dS2fdts,
calc_S2f_S2s_ts_d2jw_dS2sdts, calc_S2f_tf_S2s_ts_d2jw_dtf2,
calc_S2f_S2s_ts_d2jw_dts2
from lib.spectral_densities.model_free_components import
calc_S2_te_jw_comps, calc_S2f_S2_ts_jw_comps, calc_S2f_S2s_ts_jw_comps,
calc_S2f_tf_S2_ts_jw_comps, calc_S2f_tf_S2s_ts_jw_comps, calc_diff_djw_comps,
calc_S2_te_djw_comps, calc_diff_S2_te_djw_comps, calc_S2f_S2_ts_djw_comps,
calc_diff_S2f_S2_ts_djw_comps, calc_S2f_tf_S2_ts_djw_comps,
calc_diff_S2f_tf_S2_ts_djw_comps, calc_S2f_S2s_ts_djw_comps,
calc_diff_S2f_S2s_ts_djw_comps, calc_S2f_tf_S2s_ts_djw_comps,
calc_diff_S2f_tf_S2s_ts_djw_comps
from target_functions.ri_comps import *
from target_functions.ri_prime import *
-from target_functions.ri import *
from target_functions.chi2 import *
Removed: trunk/target_functions/ri.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/ri.py?rev=19051&view=auto
==============================================================================
--- trunk/target_functions/ri.py (original)
+++ trunk/target_functions/ri.py (removed)
@@ -1,183 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2003-2013 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax (http://www.nmr-relax.com).
#
-#
#
-# This program is free software: you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation, either version 3 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# This program is distributed in the hope that it will be useful,
#
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
-# GNU General Public License for more details.
#
-#
#
-# You should have received a copy of the GNU General Public License
#
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
-#
#
-###############################################################################
-
-
-# relax module imports.
-from target_functions.ri_comps import r1_comps, dr1_comps, d2r1_comps
-from target_functions.ri_prime import func_ri_prime
-
-
-# Calculate the NOE value.
-##########################
-
-def calc_noe(data, i, frq_num, get_r1, params):
- """Calculate the NOE value.
-
- 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
- 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:
- 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])
-
-
-def calc_dnoe(data, i, frq_num, get_dr1, params, j):
- """Calculate the derivative of the NOE value.
-
- Half this code needs to be shifted into the function initialisation code.
- """
-
- # 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:
- 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])
-
-
-def calc_d2noe(data, i, frq_num, get_d2r1, params, j, k):
- """Calculate the second partial derivative of the NOE value.
-
- Half this code needs to be shifted into the function initialisation code.
- """
-
- # 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:
- 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])
- data.d2ri[j, k, i] = data.g_ratio * (1.0 / data.r1[i]**3) * (a - b)
-
-
-
-# Calculate the R1 value.
-#########################
-
-def calc_r1(data, i, frq_num, params):
- """Calculate the R1 value if there is no R1 data corresponding to the
NOE data.
-
- R1() = dip_const_func . dip_Jw_R1_func + csa_const_func .
csa_Jw_R1_func
- """
-
- # Place data in the R1 data class.
- data.r1_data.remap_table = data.remap_table
- data.r1_data.jw = data.jw
- data.r1_data.dip_const_func = data.dip_const_func
- data.r1_data.csa_const_func = data.csa_const_func
-
- # Calculate the r1 components.
- r1_comps(data.r1_data, i, params)
-
- # Calculate the r1 value.
- ri = func_ri_prime(data.r1_data)
- return ri[i]
-
-
-def calc_dr1(data, i, frq_num, params, j):
- """Calculate the R1 value if there is no R1 data corresponding to the
NOE data.
-
- The equations are::
-
- dR1()
- ----- = dip_const_func . dip_Jw_R1_grad + csa_const_func .
csa_Jw_R1_grad
- dJw
-
- dR1()
- ----- = 0
- dRex
-
- dR1()
- ----- = dip_const_grad . dip_Jw_R1_func
- dr
-
- dR1()
- ----- = csa_const_grad . csa_Jw_R1_func
- dcsa
- """
-
- # Place data in the R1 data class.
- data.r1_data.remap_table = data.remap_table
- data.r1_data.djw = data.djw
- data.r1_data.dip_const_grad = data.dip_const_grad
- data.r1_data.csa_const_grad = data.csa_const_grad
-
- # Calculate the dr1 components.
- dr1_comps(data.r1_data, i, params)
-
- # Calculate the dr1 value.
- dri = data.r1_data.create_dri_prime[j](data.r1_data)
-
- return dri[i]
-
-
-def calc_d2r1(data, i, frq_num, params, j, k):
- """Calculate the R1 value if there is no R1 data corresponding to the
NOE data."""
-
- # Place data in the R1 data class.
- data.r1_data.remap_table = data.remap_table
- data.r1_data.d2jw = data.d2jw
- data.r1_data.dip_const_hess = data.dip_const_hess
- data.r1_data.csa_const_hess = data.csa_const_hess
-
- # Calculate the dr1 components.
- d2r1_comps(data.r1_data, i, params)
-
- # Calculate the dr1 value.
- if data.r1_data.create_d2ri_prime[j][k]:
- d2ri = data.r1_data.create_d2ri_prime[j][k](data.r1_data)
- return d2ri[i]
- else:
- return 0.0
-
-
-
-# Extract the R1 value.
-#######################
-
-def extract_r1(data, i, frq_num, params):
- """Get the R1 value from data.ri_prime"""
-
- return data.ri_prime[data.noe_r1_table[i]]
-
-
-def extract_dr1(data, i, frq_num, params, j):
- """Get the dR1 value from data.dri_prime"""
-
- return data.dri_prime[j, data.noe_r1_table[i]]
-
-
-def extract_d2r1(data, i, frq_num, params, j, k):
- """Get the d2R1 value from data.d2ri_prime"""
-
- return data.d2ri_prime[j, k, data.noe_r1_table[i]]
r19052 - in /trunk: lib/auto_relaxation/ target_functions/