Author: bugman
Date: Wed Jul 31 16:56:29 2013
New Revision: 20486
URL: http://svn.gna.org/viewcvs/relax?rev=20486&view=rev
Log:
Added the 'TP02' R1rho' calculating function to the relax library.
This is the Trott and Palmer 2002 R1rho analytic model for 2-site exchange.
This commit follows step 3 of the relaxation dispersion model addition
tutorial
(http://thread.gmane.org/gmane.science.nmr.relax.devel/3907). The Matlab
code from Skrynnikov and
Tollinger has not been converted to Python code yet. This is to allow the
Matlab->Python conversion
to be followed.
Added:
branches/relax_disp/lib/dispersion/tp02.py
Added: branches/relax_disp/lib/dispersion/tp02.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/tp02.py?rev=20486&view=auto
==============================================================================
--- branches/relax_disp/lib/dispersion/tp02.py (added)
+++ branches/relax_disp/lib/dispersion/tp02.py Wed Jul 31 16:56:29 2013
@@ -1,0 +1,83 @@
+###############################################################################
+#
#
+# Copyright (C) 2000-2001 Nikolai Skrynnikov
#
+# Copyright (C) 2000-2001 Martin Tollinger
#
+# 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.
+"""This Trott and Palmer (2002) 2-site exchange R1rho model.
+
+The code originates as the funTrottPalmer.m Matlab file from the sim_all.tar
file attached to task #7712 (https://gna.org/task/?7712). This is code from
Nikolai Skrynnikov and Martin Tollinger.
+
+Links to the copyright licensing agreements from all authors are:
+
+ - Nikolai Skrynnikov,
http://article.gmane.org/gmane.science.nmr.relax.devel/4279
+ - Martin Tollinger,
http://article.gmane.org/gmane.science.nmr.relax.devel/4276
+"""
+
+function residual = funTrottPalmer(optpar)
+
+% TrottPalmer's equ. acc. to Korzhnev (JBiomolNMR, 26, 39-48, 2003)
+
+global nu_0 x y Rcalc rms nfields offset w1 R1_51 R1_81
+%keyboard
+Rcalc=zeros(nfields,size(w1,2));
+tau_ex=optpar(1);
+pb=optpar(2);
+pa=1-pb;
+kex=1/tau_ex;
+
+for k=1:nfields
+ % we assume that A resonates at 0 [s^-1], without loss of generality
+ dw=nu_0(k)*optpar(3)*2*pi; % [s^-1]
+ Wa=0*2*pi; % Larmor frequ. [s^-1]
+ Wb=dw; % Larmor frequ. [s^-1]
+ Wsl=offset*2*pi; % Larmor frequ. of spin lock
[s^-1]
+ W=pa*Wa+pb*Wb; % pop-averaged Larmor frequ. [s^-1]
+ da=Wa-Wsl; % offset of sl from A
+ db=Wb-Wsl; % offset of sl from B
+ d =W -Wsl; % offset of sl from
pop-average
+ waeff2=w1.^2+da.^2; % effective field at A
+ wbeff2=w1.^2+db.^2; % effective field at B
+ weff2=w1.^2+d.^2; % effective field at pop-average
+ theta=atan(w1/d);
+ theta_degrees=atan(w1/d)*360/(2*pi); % not used, just to check
+
+ Rinf=optpar(3+k);
+ xx=pa*pb*dw^2*kex;
+ yytrottpalmer=waeff2.*wbeff2./weff2+kex^2;
+
yytrottpalmer_extended=waeff2.*wbeff2./weff2+kex^2-2*(sin(theta).^2)*pa*pb*dw^2;
+
+ %keyboard
+ if k==1;
+
Rcalc(k,:)=(cos(theta).^2)*R1_51+(sin(theta).^2)*(Rinf)+(sin(theta).^2).*xx./yytrottpalmer_extended;
+ end
+ if k==2;
+
Rcalc(k,:)=(cos(theta).^2)*R1_81+(sin(theta).^2)*(Rinf)+(sin(theta).^2).*xx./yytrottpalmer_extended;
+ end
+
+
+end
+
+if (size(Rcalc)==size(y))
+ residual=sum(sum((y-Rcalc).^2));
+ rms=sqrt(residual/(size(y,1)*size(y,2)));
+end
+
r20486 - /branches/relax_disp/lib/dispersion/tp02.py