Hi, That'll be my next commit, which is coming very soon :) Just jump back to the previous commit if you need to have running code.
Cheers, Edward On 11 October 2013 13:46, Troels Emtekær Linnet <[email protected]> wrote: > Hi Edward. > > lib/dispersion/mq_ns_cpmg_2site.py is missing. > > Best > Troels > > > --------- > [software@tomat software_relax_disp]$ svnversion > 21067 > [software@tomat software_relax_disp]$ ./relax > Traceback (most recent call last): > File "./relax", line 4, in <module> > import relax > File "/sbinlab2/software/NMR-relax/relax_disp/relax.py", line 66, in > <module> > user_functions.initialise() > File "/sbinlab2/software/NMR-relax/relax_disp/user_functions/__init__.py", > line 97, in initialise > import user_functions.consistency_tests > File > "/sbinlab2/software/NMR-relax/relax_disp/user_functions/consistency_tests.py", > line 29, in <module> > from specific_analyses.setup import consistency_tests_obj > File "/sbinlab2/software/NMR-relax/relax_disp/specific_analyses/setup.py", > line 35, in <module> > from specific_analyses.relax_disp.api import Relax_disp > File > "/sbinlab2/software/NMR-relax/relax_disp/specific_analyses/relax_disp/api.py", > line 48, in <module> > from specific_analyses.relax_disp.optimisation import Disp_memo, > Disp_minimise_command, grid_search_setup > File > "/sbinlab2/software/NMR-relax/relax_disp/specific_analyses/relax_disp/optimisation.py", > line 40, in <module> > from target_functions.relax_disp import Dispersion > File > "/sbinlab2/software/NMR-relax/relax_disp/target_functions/relax_disp.py", > line 38, in <module> > from lib.dispersion.mq_ns_cpmg_2site import r2eff_mq_ns_cpmg_2site > ImportError: No module named mq_ns_cpmg_2site > > > Troels Emtekær Linnet > > > > ---------- Forwarded message ---------- > From: <[email protected]> > Date: 2013/10/11 > Subject: r21067 - /branches/relax_disp/target_functions/relax_disp.py > To: [email protected] > > > Author: bugman > Date: Fri Oct 11 09:43:11 2013 > New Revision: 21067 > > URL: http://svn.gna.org/viewcvs/relax?rev=21067&view=rev > Log: > This time properly created the 'MQ NS CPMG 2-site' model target function. > > This follows the tutorial for adding relaxation dispersion models at: > http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_target_function > > > Modified: > branches/relax_disp/target_functions/relax_disp.py > > Modified: branches/relax_disp/target_functions/relax_disp.py > URL: > http://svn.gna.org/viewcvs/relax/branches/relax_disp/target_functions/relax_disp.py?rev=21067&r1=21066&r2=21067&view=diff > ============================================================================== > --- branches/relax_disp/target_functions/relax_disp.py (original) > +++ branches/relax_disp/target_functions/relax_disp.py Fri Oct 11 09:43:11 > 2013 > @@ -35,6 +35,7 @@ > from lib.dispersion.lm63_3site import r2eff_LM63_3site > from lib.dispersion.m61 import r1rho_M61 > from lib.dispersion.m61b import r1rho_M61b > +from lib.dispersion.mq_ns_cpmg_2site import r2eff_mq_ns_cpmg_2site > from lib.dispersion.ns_cpmg_2site_3d import r2eff_ns_cpmg_2site_3D > from lib.dispersion.ns_cpmg_2site_expanded import > r2eff_ns_cpmg_2site_expanded > from lib.dispersion.ns_cpmg_2site_star import r2eff_ns_cpmg_2site_star > @@ -44,7 +45,7 @@ > from lib.dispersion.tsmfk01 import r2eff_TSMFK01 > from lib.errors import RelaxError > from target_functions.chi2 import chi2 > -from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG, > EXP_TYPE_MQ_CPMG, EXP_TYPE_MQ_R1RHO, EXP_TYPE_R1RHO, MODEL_CR72, > MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_CPMG, > MODEL_LIST_FULL, MODEL_LIST_MQ_CPMG, MODEL_LIST_MQ_R1RHO, > MODEL_LIST_R1RHO, MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B, > MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, > MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR, > MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_R1RHO_2SITE, MODEL_R2EFF, > MODEL_TP02, MODEL_TSMFK01 > +from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG, > EXP_TYPE_MQ_CPMG, EXP_TYPE_MQ_R1RHO, EXP_TYPE_R1RHO, MODEL_CR72, > MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_CPMG, > MODEL_LIST_FULL, MODEL_LIST_MQ_CPMG, MODEL_LIST_MQ_R1RHO, > MODEL_LIST_R1RHO, MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B, > MODEL_MQ_NS_CPMG_2SITE, MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D, > MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, > MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, > MODEL_NS_R1RHO_2SITE, MODEL_R2EFF, MODEL_TP02, MODEL_TSMFK01 > > > class Dispersion: > @@ -75,6 +76,7 @@ > - 'NS CPMG 2-site star': The reduced numerical solution > for the 2-site Bloch-McConnell equations for CPMG data using complex > conjugate matrices with R20A = R20B. > - 'NS CPMG 2-site star full': The full numerical > solution for the 2-site Bloch-McConnell equations for CPMG data using > complex conjugate matrices. > - 'NS CPMG 2-site expanded': The numerical solution for > the 2-site Bloch-McConnell equations for CPMG data expanded using > Maple by Nikolai Skrynnikov. > + - 'MQ NS CPMG 2-site': The reduced numerical solution > for the 2-site Bloch-McConnell equations for MQ CPMG data using 3D > magnetisation vectors with R20A = R20B. > > > @keyword model: The relaxation dispersion model to fit. > @@ -171,7 +173,7 @@ > > # The spin and dependent parameters (phi_ex, dw, padw2). > self.end_index.append(self.end_index[-1] + self.num_spins) > - if model in [MODEL_IT99, MODEL_LM63_3SITE]: > + if model in [MODEL_IT99, MODEL_LM63_3SITE, MODEL_MQ_NS_CPMG_2SITE]: > self.end_index.append(self.end_index[-1] + self.num_spins) > > # Set up the matrices for the numerical solutions. > @@ -193,7 +195,7 @@ > self.r180x = r180x_3d() > > # This is a vector that contains the initial magnetizations > corresponding to the A and B state transverse magnetizations. > - if model in [MODEL_NS_CPMG_2SITE_STAR, > MODEL_NS_CPMG_2SITE_STAR_FULL]: > + if model in [MODEL_MQ_NS_CPMG_2SITE, > MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL]: > self.M0 = zeros(2, float64) > if model in [MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL]: > self.M0 = zeros(7, float64) > @@ -202,14 +204,14 @@ > self.M0 = zeros(6, float64) > > # Some other data structures for the analytical and numerical > solutions. > - if model in [MODEL_NS_CPMG_2SITE_3D, > MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, > MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, > MODEL_TSMFK01]: > + if model in [MODEL_MQ_NS_CPMG_2SITE, MODEL_NS_CPMG_2SITE_3D, > MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, > MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, > MODEL_TSMFK01]: > # The tau_cpmg times. > self.tau_cpmg = zeros(self.num_disp_points, float64) > for i in range(self.num_disp_points): > self.tau_cpmg[i] = 0.25 / self.cpmg_frqs[i] > > # Some other data structures for the numerical solutions. > - if model in [MODEL_NS_CPMG_2SITE_3D, > MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, > MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL]: > + if model in [MODEL_MQ_NS_CPMG_2SITE, MODEL_NS_CPMG_2SITE_3D, > MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, > MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL]: > # The matrix exponential power array. > self.power = zeros(self.num_disp_points, int16) > for i in range(self.num_disp_points): > @@ -221,8 +223,13 @@ > self.spin_lock_omega1_squared = self.spin_lock_omega1 ** 2 > > # The inverted relaxation delay. > - if model in [MODEL_NS_CPMG_2SITE_3D, > MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, > MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, > MODEL_NS_R1RHO_2SITE]: > + if model in [MODEL_MQ_NS_CPMG_2SITE, MODEL_NS_CPMG_2SITE_3D, > MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, > MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, > MODEL_NS_R1RHO_2SITE]: > self.inv_relax_time = 1.0 / relax_time > + > + # Special matrices for the multi-quantum CPMG 2-site numerical model. > + if model == MODEL_MQ_NS_CPMG_2SITE: > + self.m1 = zeros((2, 2), complex64) > + self.m2 = zeros((2, 2), complex64) > > # Set up the model. > if model == MODEL_NOREX: > @@ -259,6 +266,8 @@ > self.func = self.func_TP02 > if model == MODEL_NS_R1RHO_2SITE: > self.func = self.func_ns_r1rho_2site > + if model == MODEL_MQ_NS_CPMG_2SITE: > + self.func = self.func_mq_ns_cpmg_2site > > > def calc_CR72_chi2(self, R20A=None, R20B=None, dw=None, pA=None, > kex=None): > @@ -786,6 +795,64 @@ > return chi2_sum > > > + def func_mq_ns_cpmg_2site(self, params): > + """Target function for the Ishima and Torchia (1999) 2-site > model for all timescales with pA >> pB. > + > + @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) > + > + # Unpack the parameter values. > + R20 = params[:self.end_index[0]] > + dw = params[self.end_index[0]:self.end_index[1]] > + dwH = params[self.end_index[1]:self.end_index[2]] > + pA = params[self.end_index[2]] > + kex = params[self.end_index[2]+1] > + > + # Once off parameter conversions. > + pB = 1.0 - pA > + k_BA = pA * kex > + k_AB = pB * kex > + > + # This is a vector that contains the initial magnetizations > corresponding to the A and B state transverse magnetizations. > + self.M0[0] = pA > + self.M0[1] = pB > + > + # Initialise. > + chi2_sum = 0.0 > + > + # Loop over the spins. > + for spin_index in range(self.num_spins): > + # Loop over the spectrometer frequencies. > + for frq_index in range(self.num_frq): > + # The R20 index. > + r20_index = frq_index + spin_index*self.num_frq > + > + # Convert dw from ppm to rad/s. > + dw_frq = dw[spin_index] * self.frqs[spin_index, frq_index] > + dwH_frq = dwH[spin_index] * self.frqs[spin_index, frq_index] > + > + # Back calculate the R2eff values. > + r2eff_mq_ns_cpmg_2site(M0=self.M0, m1=self.m1, > m2=self.m2, r20=R20[r20_index], pA=pA, pB=pB, dw=dw_frq, dwH=dwH_frq, > k_AB=k_AB, k_BA=k_BA, cpmg_frqs=self.cpmg_frqs, > back_calc=self.back_calc[spin_index, frq_index], > num_points=self.num_disp_points, power=self.power) > + > + # For all missing data points, set the > back-calculated value to the measured values so that it has no effect > on the chi-squared value. > + for point_index in range(self.num_disp_points): > + if self.missing[spin_index, frq_index, point_index]: > + self.back_calc[spin_index, frq_index, > point_index] = self.values[spin_index, frq_index, point_index] > + > + # Calculate and return the chi-squared value. > + chi2_sum += chi2(self.values[spin_index, frq_index], > self.back_calc[spin_index, frq_index], self.errors[spin_index, > frq_index]) > + > + # Return the total chi-squared value. > + return chi2_sum > + > + > def func_NOREX(self, params): > """Target function for no exchange. > > > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-commits mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-commits > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-devel mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-devel _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
