Author: bugman
Date: Fri Jul 12 17:39:35 2013
New Revision: 20287
URL: http://svn.gna.org/viewcvs/relax?rev=20287&view=rev
Log:
Created the lib.dispersion.ns_matrices module.
This module contains a collection of functions for generating the relaxation
matrices for the
numerical solutions to the Bloch-McConnell equations for relaxation
dispersion.
The code comes from the 'fitting_main_kex.py' file attached to
https://gna.org/task/?7712#comment3
(https://gna.org/support/download.php?file_id=18263).
Added:
branches/relax_disp/lib/dispersion/ns_matrices.py
Modified:
branches/relax_disp/lib/dispersion/__init__.py
Modified: branches/relax_disp/lib/dispersion/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/__init__.py?rev=20287&r1=20286&r2=20287&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/__init__.py (original)
+++ branches/relax_disp/lib/dispersion/__init__.py Fri Jul 12 17:39:35 2013
@@ -30,5 +30,6 @@
'm61',
'm61b',
'ns_2site_star',
+ 'ns_matrices',
'two_point'
]
Added: branches/relax_disp/lib/dispersion/ns_matrices.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/ns_matrices.py?rev=20287&view=auto
==============================================================================
--- branches/relax_disp/lib/dispersion/ns_matrices.py (added)
+++ branches/relax_disp/lib/dispersion/ns_matrices.py Fri Jul 12 17:39:35 2013
@@ -1,0 +1,104 @@
+###############################################################################
+#
#
+# Copyright (C) 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/>.
#
+#
#
+###############################################################################
+
+# Module docstring.
+"""A collection of functions for generating the relaxation matrices for the
numerical solutions.
+
+These are for the numerical solutions to the Bloch-McConnell equations for
relaxation dispersion.
+"""
+
+# Python module imports.
+from numpy import matrix
+
+
+def rcpmg_2d(R2E=None, R2G=None, df=None, kGE=None, kEG=None):
+ """Definition of the 2D exchange matrix.
+
+ @keyword R2E: The transverse, spin-spin relaxation rate for state A.
+ @type R2E: float
+ @keyword R2G: The transverse, spin-spin relaxation rate for state B.
+ @type R2G: float
+ @keyword df: FIXME - add description.
+ @type df: float
+ @keyword kGE: The forward exchange rate from state A to state B.
+ @type kGE: float
+ @keyword kEG: The reverse exchange rate from state B to state A.
+ @type kEG: float
+ @return: The relaxation matrix.
+ @rtype: numpy rank-2, 7D array
+ """
+
+ # Parameter conversions.
+ fG = 0
+ fE = fG + df
+
+ # Create the matrix.
+ temp = matrix([
+ [-R2G-kGE, -fG, kEG, 0.0],
+ [ fG, -R2G-kGE, 0.0, kEG],
+ [ kGE, 0.0, -R2E-kEG, -fE],
+ [ 0.0, kGE, fE, -R2E-kEG]
+ ])
+
+ # Return the matrix.
+ return temp
+
+
+def rcpmg_3d(R1E=None, R1G=None, R2E=None, R2G=None, df=None, kGE=None,
kEG=None):
+ """Definition of the 3D exchange matrix.
+
+ @keyword R1E: The longitudinal, spin-lattice relaxation rate for state
A.
+ @type R1E: float
+ @keyword R1G: The longitudinal, spin-lattice relaxation rate for state
B.
+ @type R1G: float
+ @keyword R2E: The transverse, spin-spin relaxation rate for state A.
+ @type R2E: float
+ @keyword R2G: The transverse, spin-spin relaxation rate for state B.
+ @type R2G: float
+ @keyword df: FIXME - add description.
+ @type df: float
+ @keyword kGE: The forward exchange rate from state A to state B.
+ @type kGE: float
+ @keyword kEG: The reverse exchange rate from state B to state A.
+ @type kEG: float
+ @return: The relaxation matrix.
+ @rtype: numpy rank-2, 7D array
+ """
+
+ # Parameter conversions.
+ fG = 0.0
+ fE = df
+ IGeq = kEG / (kEG + kGE)
+ IEeq = kGE / (kEG + kGE)
+
+ # Create the matrix.
+ temp = matrix([
+ [ 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0],
+ [ 0.0, -R2G-kGE, -fG, 0.0, kEG,
0.0, 0.0],
+ [ 0.0, fG, -R2G-kGE, 0.0, 0.0,
kEG, 0.0],
+ [2.0*R1G*IGeq, 0.0, 0.0, -R1G-kGE, 0.0,
0.0, kEG],
+ [ 0.0, kGE, 0.0, 0.0, -R2E-kEG,
-fE, 0.0],
+ [ 0.0, 0.0, kGE, 0.0, fE,
-R2E-kEG, 0.0],
+ [2.0*R1E*IEeq, 0.0, 0.0, kGE, 0.0,
0.0, -R1E-kEG]
+ ])
+
+ # Return the matrix.
+ return temp
r20287 - in /branches/relax_disp/lib/dispersion: __init__.py ns_matrices.py