Re: CST branch -- October 19, 2010 - 13:49

Hi,

Sorry for the delay, I just came back from a 2 week holiday.  This is
correct, the func_mf, func_local_tm, etc. methods are working on a
single spin.  This is stored in self.data[0].  The other functions
work on multiple spin data located in self.data[0], self.data[1], etc.

Regards,

Edward



On 14 October 2010 19:38, Pavel Kaderavek <pavel.kaderavek@xxxxxxxxx> wrote:
> Hi,
>
> I would like to announce a small clarification of my previous mail about
> changes in functions func_mf, func_local_tm, func_diff, func_all, and their
> derivatives (class Mf, file maths_fns/mf.py). Loop suggested in my last
> post:
>
> https://mail.gna.org/public/relax-devel/2010-09/msg00020.html
>
> is valid just for the functions func_diff, func_all, and their equivalents
> for a first and second derivatives.
> While for the functions  func_mf, func_local_tm, and corresponding
> derivatives the index of self.num_interactions should be set to `0` instead
> of index `i`
>
>         for j in xrange(self.num_interactions[0]):
>
> (The rest of the loop remains the same)
> That comes from the fact that these functions (func_mf, func_local_tm, ...
> ) are called for each spin separately. As it is indicated by the preceding
> statement:
>
>         data = self.data[0]
>
> Regards,
> Pavel
>
> On 29 September 2010 10:53, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> > Hi,
> >
> > This is the perfect approach.  It will abstract the calculations so
> > that we will not need to touch many of maths_fns modules.  With this
> > code in place, I would aim at then making the test suite pass again by
> > having the correct data structures pass into maths_fns.mf.  The last
> > step would be to input CSA tensors and the multi-dipole interactions
> > via user functions.  If you make a patch for all of the func_*(),
> > dfunc_*(), and d2func_*() methods, I can check and apply it quickly.
> >
> > Regards,
> >
> > Edward
> >
> >
> > On 28 September 2010 12:07, Pavel Kaderavek <pavel.kaderavek@xxxxxxxxx>
> > wrote:
> > > Hi,
> > > we were thinking about next necessary changes in the CST branch.
> > >
> > > Now we need to break through the problem, which implies the fact we
> > > split
> > > the relaxation rate calculation into contributions of individual
> > > interactions. Each of them has its own data class to store its
> > > parameters
> > > (so far called data[i][j], where the [i] was a spin index and [j] was
> > > the
> > > interaction index).
> > >
> > > It seems to us, that it the best way to deal with it is to edit
> > > functions:
> > > func_mf, func_local_tm , func_diff, func_all and their equivalents for a
> > > first and second derivatives (defined in mf.py file).
> > >
> > > Within these functions the calculations of direction cosines, diffusion
> > > tensor weight calculations, components of the spectral densities and so
> > > on
> > > are performed. All these must be calculated for each interaction
> > > separately,
> > > because each interaction has its own data storage (which replaced
> > > previously
> > > used one data class container for the whole IS spin system).
> > >
> > > Instead of:
> > >
> > >
> > >         # Direction cosine calculations.
> > >         if self.diff_data.calc_di:
> > >             self.diff_data.calc_di(data, self.diff_data)
> > >
> > >         # Diffusion tensor weight calculations.
> > >         self.diff_data.calc_ci(data, self.diff_data)
> > >
> > >         # Diffusion tensor correlation times.
> > >         self.diff_data.calc_ti(data, self.diff_data)
> > >
> > >         # Calculate the components of the spectral densities.
> > >         if data.calc_jw_comps:
> > >             data.calc_jw_comps(data, params)
> > >
> > >         # Calculate the R1, R2, and sigma_noe values.
> > >         data.ri_prime = data.create_ri_prime(data)
> > >
> > >
> > > we would suggest to introduce a loop over interacations
> > >         for j in xrange(self.num_interactions[i]):
> > >             # Direction cosine calculations.
> > >             if self.diff_data.calc_di:
> > >                 self.diff_data.calc_di(data[j], self.diff_data)
> > >
> > >             # Diffusion tensor weight calculations.
> > >             self.diff_data.calc_ci(data[j], self.diff_data)
> > >
> > >             # Diffusion tensor correlation times.
> > >             self.diff_data.calc_ti(data[j], self.diff_data)
> > >
> > >             # Calculate the components of the spectral densities.
> > >             if data.calc_jw_comps:
> > >                 data.calc_jw_comps(data[j], params)
> > >
> > >             # Calculate the R1, R2, and sigma_noe components.
> > >             data.ri_prime = data.create_ri_prime(data[j])
> > >
> > >
> > > It must be accompanied in the next step by a change the ri_prime
> > > function so
> > > that it just calculate only a product of specific interaction constant
> > > and
> > > corresponding linear combination of spectral densities. While the final
> > > sumation over all interactions should be done in a separate step.
> > >
> > > Moreover it will be also necessary to distinguish within the function
> > > setup_equation the type of equation used for contribution of individual
> > > interactions according to their type.
> > >
> > > Best
> > > Pavel
> > >
> > >
> > > On 10 September 2010 15:43, Edward d'Auvergne <edward@xxxxxxxxxxxxx>
> > > wrote:
> > > > Hi Pavel,
> > > >
> > > > I missed it in the patches, but there were tab characters '\t' causing
> > > > problems.  These are now fixed.  relax requires that a tab is replaced
> > > > by 4 spaces.  I have also added you to the copyright notices
> > > > (http://svn.gna.org/viewcvs/relax?view=rev&revision=11543) of the
> > > > files you have modified.
> > > >
> > > > Regards,
> > > >
> > > > Edward
> > > >
> > > > On 10 September 2010 15:36, Edward d'Auvergne <edward@xxxxxxxxxxxxx>
> > > > wrote:
> > > > > Hi,
> > > > >
> > > > > I've carefully checked the patches and committed them with the
> > > > > messages you wrote.  Sorry again for the delays.  It should be faster
> > > > > now that I am no longer in the tropical wilderness of far north
> > > > > Australia.
> > > > >
> > > > > Regards,
> > > > >
> > > > > Edward
> > > > >
> > > > >
> > > > > On 6 September 2010 13:23, Edward d'Auvergne <edward@xxxxxxxxxxxxx>
> > > > > wrote:
> > > > > > Hi Pavel,
> > > > > >
> > > > > > Sorry for the delayed response.  I was at the ICMRBS conference in
> > > > > > Australia and then travelled through the tropical north end of
> > > > > > Australia afterwards.  I came back yesterday out of the remote
> > > > > > wilderness and can soon start looking at this patches.
> > > > > >
> > > > > > Regards,
> > > > > >
> > > > > > Edward
> > > > > >
> > > > > >
> > > > > > On 31 August 2010 18:00, Pavel Kaderavek <pavel.kaderavek@xxxxxxxxx>
> > > > > > wrote:
> > > > > > > Hi,
> > > > > > >
> > > > > > > some time ago, we submitted two patches regarding CST branch. We
> > > > > > > are
> > > > > > > not
> > > > > > > sure if we should wait for some additional comment from your side,
> > > > > > > or
> > > > > > > we can
> > > > > > > continue with introducing further changes in the code.
> > > > > > > Next step would be a splitting of the relaxation equation so that
> > > > > > > contribution to the relaxation due to the individual types of
> > > > > > > interaction
> > > > > > > (dipole-dipole, CSA) can be calculated separately.
> > > > > > >
> > > > > > >
> > > > > > > Regars,
> > > > > > >
> > > > > > > Pavel, Petr