Ok, re-regenerating the statistics now ;) On 18 June 2014 15:58, <[email protected]> wrote: > Author: tlinnet > Date: Wed Jun 18 15:58:31 2014 > New Revision: 24092 > > URL: http://svn.gna.org/viewcvs/relax?rev=24092&view=rev > Log: > Modified profiling script for TSMK01, to use correct parameters k_AB and r20a. > > Or else, the lib functions is just calculating with zero? > > Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion > models for Clustered analysis. > > Modified: > > branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tsmfk01.py > > Modified: > branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tsmfk01.py > URL: > http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tsmfk01.py?rev=24092&r1=24091&r2=24092&view=diff > ============================================================================== > --- > branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tsmfk01.py > (original) > +++ > branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tsmfk01.py > Wed Jun 18 15:58:31 2014 > @@ -110,7 +110,7 @@ > Class Profile inherits the Dispersion container class object. > """ > > - def __init__(self, num_spins=1, model=None, r2=None, r2a=None, r2b=None, > dw=None, pA=None, kex=None, spins_params=None): > + def __init__(self, num_spins=1, model=None, r2=None, r2a=None, r2b=None, > dw=None, pA=None, kex=None, k_AB=None, spins_params=None): > """ > Special method __init__() is called first (acts as Constructor). > It brings in data from outside the class like the variable num_spins. > @@ -136,6 +136,8 @@ > @type pA: float > @keyword kex: The rate of exchange. > @type kex: float > + @keyword k_AB: The exchange rate from state A to state B > + @type k_AB: float > @keyword spins_params: List of parameter strings used in dispersion > model. > @type spins_params: array of strings > """ > @@ -172,7 +174,7 @@ > self.error.append([1.0]*len(cpmg_point)) > > # Assemble param vector. > - self.params = self.assemble_param_vector(r2=r2, r2a=r2a, r2b=r2b, > dw=dw, pA=pA, kex=kex, spins_params=spins_params) > + self.params = self.assemble_param_vector(r2=r2, r2a=r2a, r2b=r2b, > dw=dw, pA=pA, kex=kex, k_AB=k_AB, spins_params=spins_params) > > # Make nested list arrays of data. And return them. > values, errors, cpmg_frqs, missing, frqs, exp_types, relax_times, > offsets = self.return_r2eff_arrays() > @@ -316,7 +318,7 @@ > return values, errors, cpmg_frqs, missing, frqs, exp_types, > relax_times, offsets > > > - def assemble_param_vector(self, r2=None, r2a=None, r2b=None, dw=None, > pA=None, kex=None, spins_params=None): > + def assemble_param_vector(self, r2=None, r2a=None, r2b=None, dw=None, > pA=None, kex=None, k_AB=None, spins_params=None): > """Assemble the dispersion relaxation dispersion curve fitting > parameter vector. > > @keyword r2: The transversal relaxation rate. > @@ -331,6 +333,8 @@ > @type pA: float > @keyword kex: The rate of exchange. > @type kex: float > + @keyword k_AB: The exchange rate from state A to state B > + @type k_AB: float > @keyword spins_params: List of parameter strings used in dispersion > model. > @type spins_params: array of strings > @return: An array of the parameter values of the > dispersion relaxation model. > @@ -357,6 +361,8 @@ > value = pA > elif param_name == 'kex': > value = kex > + elif param_name == 'k_AB': > + value = k_AB > > # Add to the vector. > param_vector.append(value) > @@ -411,6 +417,8 @@ > yield 'pA', 0, 0 > elif param == 'kex': > yield 'kex', 0, 0 > + elif param == 'k_AB': > + yield 'k_AB', 0, 0 > > > def calc(self, params): > @@ -441,7 +449,7 @@ > """ > > # Instantiate class > - C1 = Profile(num_spins=num_spins, model=model, r2a=5.0, r2b=10.0, > dw=3.0, pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex']) > + C1 = Profile(num_spins=num_spins, model=model, r2a=5.0, dw=3.0, > k_AB=10.0, spins_params=['r2a', 'dw', 'k_AB']) > > # Loop 100 times for each spin in the clustered analysis (to make the > timing numbers equivalent). > for spin_index in xrange(100): > @@ -465,7 +473,7 @@ > """ > > # Instantiate class > - C1 = Profile(num_spins=num_spins, model=model, r2a=5.0, r2b=10.0, > dw=3.0, pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex']) > + C1 = Profile(num_spins=num_spins, model=model, r2a=5.0, dw=3.0, > k_AB=10.0, spins_params=['r2a', 'dw', 'k_AB']) > > # Repeat the function call, to simulate minimisation. > for i in xrange(iter): > @@ -476,38 +484,3 @@ > # Execute main function. > if __name__ == "__main__": > main() > - > -def test_reshape(): > - C1 = Profile(num_spins=1, model=MODEL_TSMFK01, r2a=5.0, r2b=10.0, > dw=3.0, pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex']) > - end_index = C1.model.end_index > - #print("end_index:", end_index) > - num_spins = C1.model.num_spins > - #print("num_spins:", num_spins) > - num_frq = C1.model.num_frq > - #print("num_frq:", num_frq) > - params = C1.params > - #print("params", params) > - > - R20 = params[:end_index[1]].reshape(num_spins*2, num_frq) > - R20A = R20[::2].flatten() > - R20B = R20[1::2].flatten() > - dw = params[end_index[1]:end_index[2]] > - pA = params[end_index[2]] > - kex = params[end_index[2]+1] > - print("R20A", R20A, len(R20A)) > - print("R20B", R20B, len(R20B)) > - print("dw", dw, len(dw)) > - print("dw", pA) > - print("kex", kex) > - > - for si in range(num_spins): > - for mi in range(num_frq): > - r20_index = mi + si*num_frq > - r20a=R20A[r20_index] > - r20b=R20B[r20_index] > - print("r20a", r20a, "r20b", r20b) > - > - model = C1.calc(params) > - print(model) > - > -#test_reshape() > > > _______________________________________________ > 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
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