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
>> >>>
>> >>
>> >
>
>
Re: CST branch