Author: bugman
Date: Wed Mar 27 18:04:24 2013
New Revision: 19266
URL: http://svn.gna.org/viewcvs/relax?rev=19266&view=rev
Log:
Created a very basic initial target function class for relaxation dispersion.
This code is a translation of Sebastien Morin's C code in the old relax_disp
branch. This old code
can be checked out with the commands:
$ svn co
http://svn.gna.org/svn/relax/branches/relax_disp/maths_fns/relax_disp.c@r18123
$ svn co
http://svn.gna.org/svn/relax/branches/relax_disp/maths_fns/relax_disp.h@r18123
Added:
branches/relax_disp/target_functions/relax_disp.py
Added: branches/relax_disp/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/target_functions/relax_disp.py?rev=19266&view=auto
==============================================================================
--- branches/relax_disp/target_functions/relax_disp.py (added)
+++ branches/relax_disp/target_functions/relax_disp.py Wed Mar 27 18:04:24
2013
@@ -1,0 +1,74 @@
+###############################################################################
+#
#
+# Copyright (C) 2013 Edward d'Auvergne
#
+# Copyright (C) 2009 Sebastien Morin
#
+#
#
+# 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.
+"""Target functions for relaxation dispersion."""
+
+# relax module imports.
+from target_functions.chi2 import chi2
+
+
+class Dispersion:
+ def __init__(self, num_params=None, num_times=None, values=None,
sd=None, cpmg_frqs=None, scaling_matrix=None):
+ """Relaxation dispersion target functions for optimisation.
+
+ @keyword num_param: The number of parameters in the model.
+ @type num_param: int
+ @keyword num_times: The number of relaxation times.
+ @type num_times: int
+ @keyword values: The peak intensities.
+ @type values: numpy rank-2 float array
+ @keyword sd: The peak intensity errors.
+ @type sd: numpy rank-2 float array
+ @keyword cpmg_frqs: The CPMG frequencies in Hertz.
+ @type cpmg_frqs: numpy rank-1 float array
+ @keyword scaling_matrix: The square and diagonal scaling matrix.
+ @type scaling_matrix: numpy rank-2 array
+ """
+
+ # Store the arguments.
+ self.num_params = num_params
+ self.num_times = num_times
+ self.values = values
+ self.sd = sd
+ self.cpmg_frqs = cpmg_frqs
+ self.scaling_matrix = scaling_matrix
+
+
+ def func_fast_2site(self, params):
+ """Target function for the fast 2-site exchange model.
+
+ @param params: The vector of parameter values.
+ @type params: numpy rank-1 float array
+ @return: The chi-squared value.
+ @rtype: float
+ """
+
+ # Scaling.
+ if self.scaling_flag:
+ params = dot(params, self.scaling_matrix)
+
+ # Back calculated the effective transversal relaxation rates.
+ dispersion(params=params, cpmg_frqs=self.cpmg_frqs,
back_calc=self.back_calc, num_times=self.num_times);
+
+ # Calculate and return the chi-squared value.
+ return chi2(values, back_calc, sd)
r19266 - /branches/relax_disp/target_functions/relax_disp.py