Hi Troels, For this script, you do not need to import the unused MODEL_NS_R1RHO_3SITE_LINEAR variable. Eliminating these unused imports helps in running the scripts on older relax versions.
Cheers, Edward On 24 June 2014 10:43, <[email protected]> wrote: > Author: tlinnet > Date: Tue Jun 24 10:43:06 2014 > New Revision: 24265 > > URL: http://svn.gna.org/viewcvs/relax?rev=24265&view=rev > Log: > Modified profiling script for NS R1rho 3site, to be functional. > > 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_ns_r1rho_3site.py > > Modified: > branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_3site.py > URL: > http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_3site.py?rev=24265&r1=24264&r2=24265&view=diff > ============================================================================== > --- > branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_3site.py > (original) > +++ > branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_3site.py > Tue Jun 24 10:43:06 2014 > @@ -54,7 +54,7 @@ > # relax module imports. > from lib.physical_constants import g1H, g15N > from target_functions.relax_disp import Dispersion > -from specific_analyses.relax_disp.variables import EXP_TYPE_R1RHO, > MODEL_NS_R1RHO_3SITE > +from specific_analyses.relax_disp.variables import EXP_TYPE_R1RHO, > MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR > > > # Alter setup. > @@ -109,7 +109,7 @@ > Class Profile inherits the Dispersion container class object. > """ > > - def __init__(self, num_spins=1, model=None, r2=None, r2a=None, r2b=None, > phi_ex=None, dw=None, pA=None, kex=None, spins_params=None): > + def __init__(self, num_spins=1, model=None, r2=None, r2a=None, r2b=None, > phi_ex=None, dw=None, dw_AB=None, dw_BC=None, pA=None, kex=None, kex_AB=None, > pB=None, kex_BC=None, kex_AC=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. > @@ -172,7 +172,7 @@ > self.chemical_shift = 1.0 > > # Assemble param vector. > - self.params = self.assemble_param_vector(r2=r2, r2a=r2a, r2b=r2b, > phi_ex=phi_ex, dw=dw, pA=pA, kex=kex, spins_params=spins_params) > + self.params = self.assemble_param_vector(r2=r2, r2a=r2a, r2b=r2b, > phi_ex=phi_ex, dw=dw, dw_AB=dw_AB, dw_BC=dw_BC, pA=pA, kex=kex, > kex_AB=kex_AB, pB=pB, kex_BC=kex_BC, kex_AC=kex_AC, spins_params=spins_params) > > # Make nested list arrays of data. And return them. > values, errors, cpmg_frqs, missing, frqs, exp_types, relax_times, > offsets, spin_lock_nu1 = self.return_r2eff_arrays() > @@ -402,7 +402,7 @@ > return values, errors, None, missing, frqs, exp_types, relax_times, > offsets, asarray(spin_lock_nu1) > > > - def assemble_param_vector(self, r2=None, r2a=None, r2b=None, > phi_ex=None, dw=None, pA=None, kex=None, spins_params=None): > + def assemble_param_vector(self, r2=None, r2a=None, r2b=None, > phi_ex=None, dw=None, dw_AB=None, dw_BC=None, pA=None, kex=None, kex_AB=None, > pB=None, kex_BC=None, kex_AC=None, spins_params=None): > """Assemble the dispersion relaxation dispersion curve fitting > parameter vector. > > @keyword r2: The transversal relaxation rate. > @@ -443,10 +443,22 @@ > value = phi_ex + spin_index > elif param_name == 'dw': > value = dw + spin_index > + elif param_name == 'dw_AB': > + value = dw_AB + spin_index > + elif param_name == 'dw_BC': > + value = dw_BC + spin_index > elif param_name == 'pA': > value = pA > elif param_name == 'kex': > value = kex > + elif param_name == 'kex_AB': > + value = kex_AB > + elif param_name == 'pB': > + value = pB > + elif param_name == 'kex_BC': > + value = kex_BC > + elif param_name == 'kex_AC': > + value = kex_AC > > # Add to the vector. > param_vector.append(value) > @@ -502,15 +514,31 @@ > yield 'padw2', pspin_index, 0 > if 'dw' in spins_params: > yield 'dw', spin_index, 0 > + if 'dw_AB' in spins_params: > + yield 'dw_AB', spin_index, 0 > + if 'dw_BC' in spins_params: > + yield 'dw_BC', spin_index, 0 > > # All other parameters (one per spin cluster). > for param in spins_params: > if not param in ['r2', 'r2a', 'r2b', 'phi_ex', 'phi_ex_B', > 'phi_ex_C', 'padw2', 'dw', 'dw_AB', 'dw_BC', 'dw_AB', 'dwH', 'dwH_AB', > 'dwH_BC', 'dwH_AB']: > if param == 'pA': > yield 'pA', 0, 0 > + > elif param == 'kex': > yield 'kex', 0, 0 > > + elif param == 'kex_AB': > + yield 'kex_AB', 0, 0 > + > + elif param == 'pB': > + yield 'pB', 0, 0 > + > + elif param == 'kex_BC': > + yield 'kex_BC', 0, 0 > + > + elif param == 'kex_AC': > + yield 'kex_AC', 0, 0 > > def calc(self, params): > """Calculate chi2 values. > @@ -522,11 +550,11 @@ > """ > > # Return chi2 value. > - chi2 = self.model.func_ns_r1rho_2site(params) > + chi2 = self.model.func_ns_r1rho_3site(params) > return chi2 > > > -def single(num_spins=1, model=MODEL_NS_R1RHO_2SITE, iter=None): > +def single(num_spins=1, model=MODEL_NS_R1RHO_3SITE, iter=None): > """Calculate for a single spin. > > @keyword num_spins: Number of spins in the cluster. > @@ -540,7 +568,7 @@ > """ > > # Instantiate class > - C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=1.0, pA=0.9, > kex=5000.0, spins_params=['r2', 'dw', 'pA', 'kex']) > + C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw_AB=1.0, > dw_BC=2.0, pA=0.8, kex_AB=5000.0, pB=0.1, kex_BC=3000.0, kex_AC=1000.0, > spins_params=['r2', 'dw_AB', 'dw_BC', 'pA', 'kex_AB', 'pB', 'kex_BC', > 'kex_AC']) > > # Loop 100 times for each spin in the clustered analysis (to make the > timing numbers equivalent). > for spin_index in xrange(100): > @@ -550,7 +578,7 @@ > print("chi2 single:", chi2) > > > -def cluster(num_spins=100, model=MODEL_NS_R1RHO_2SITE, iter=None): > +def cluster(num_spins=100, model=MODEL_NS_R1RHO_3SITE, iter=None): > """Calculate for a number of clustered spins. > > @keyword num_spins: Number of spins in the cluster. > @@ -564,7 +592,7 @@ > """ > > # Instantiate class > - C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=1.0, pA=0.9, > kex=5000.0, spins_params=['r2', 'dw', 'pA', 'kex']) > + C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw_AB=1.0, > dw_BC=2.0, pA=0.8, kex_AB=5000.0, pB=0.1, kex_BC=3000.0, kex_AC=1000.0, > spins_params=['r2', 'dw_AB', 'dw_BC', 'pA', 'kex_AB', 'pB', 'kex_BC', > 'kex_AC']) > > # Repeat the function call, to simulate minimisation. > for i in xrange(iter): > > > _______________________________________________ > 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
