On 25 November 2010 19:25, Pavel Kaderavek <
pavel.kaderavek@xxxxxxxxx> wrote:
> Hi,
>
> We prepared another set of changes according to discussion in:
>
https://mail.gna.org/public/relax-devel/2010-11/msg00001.html
> and previous.
>
> Normally, we use command "svn diff" to create a patch by comparing new code
> and code of our branch in the repository. As the current changes are applied
> on the already patched version of the code (not present in the current
> repository revision of our branch obtained by "svn up"), we would like to
> ask you how the patch should be created.
>
> Regards,
> Pavel
>
>
> On 15 November 2010 19:21, Edward d'Auvergne <
edward@xxxxxxxxxxxxx> wrote:
>>
>> Hi,
>>
>> I'm now back from a few weeks holidays. This is correct, a double
>> looping will be required. I think this will still be efficient as the
>> "for k in xrange(self.num_interactions[0])" loops are not very
>> expensive. The alternative is to bring the "for j in
>> xrange(data.total_num_params):" loop, but this would duplicate
>> calculations and hence be even more expensive. This will also be
>> required in the d2func_* methods as well.
>>
>> On a different note, as the code is becoming more complex, I would
>> recommend for a future patch that "data = "" so that we
>> always use "self.data[0][k].dri_prime[j]" for each element rather than
>> "data..dri_prime[j]". This will help with debugging in the future as
>> we could end up mixing the self.data elements.
>>
>> Also for the Rex interaction, there are plans for the future to allow
>> for it to be non-quadratic for situations closer to slow exchange or
>> intermediate. For slow exchange the interaction is then linear with
>> field strength, and the value ranges from linear (alpha=1) to
>> quadratic (alpha=2). So the alpha value between 1 and 2 might become
>> an optimisable parameter and hence this interaction type will become
>> more complex and require its own code paths. So if this branch
>> separates out the Rex interaction, this would be of benefit to the
>> rest of relax. Though the separation might be essential for the
>> powerful code restructuring currently anyway.
>>
>> Cheers,
>>
>> Edward
>>
>>
>>
>>
>> On 27 October 2010 20:45, Pavel Kaderavek <
pavel.kaderavek@xxxxxxxxx>
>> wrote:
>> > Hi,
>> > sorry for a late response. Your suggestions seem reasonable. I would add
>> > just a two comments.
>> > 1) We should keep as before not only ri_prime but probably also chi2,
>> > dchi2
>> > and d2chi2 as well.
>> > .
>> > 2)The consideration of Rex as an additional interaction is a one of the
>> > suitable approaches and it fits the general idea. We have to consider
>> > that
>> > it requires to add new interaction into the list of the interactions (
>> > __init__ function in class Mf, file maths_fns/mf.py).
>> > It might be done just within the __init__ function (class Mf, file
>> > maths_fns/mf.py). It will be based on the presence of Rex term within
>> > the
>> > loaded variable param_types. The other possibility is to do it before
>> > calling this __init__ function (number of interactions is one of its
>> > arguments).
>> >
>> > Then I address to discussion one additional problem related to the patch
>> > in
>> > the preparation. Within the functions related to the derivations:
>> > dfunc_mf,
>> > dfunc_local_tm, dfunc_all, dfunc_diff (class Mf, maths_fns/mf.py) there
>> > is a
>> > small complication. It will be illustrated using "dfunc_mf" function as
>> > an
>> > example. The original code is following:
>> >
>> > data = "">
>> >
>> > # Calculate the spectral density gradient components.
>> > if data.calc_djw_comps:
>> > data.calc_djw_comps(data, params)
>> >
>> > # Diffusion tensor correlation times.
>> > self.diff_data.calc_dti(data, self.diff_data)
>> >
>> > # Loop over the gradient.
>> > for j in xrange(data.total_num_params):
>> > # Calculate the spectral density gradients.
>> > if data.calc_djw[j]:
>> > data.djw = data.calc_djw[j](data, params, j)
>> > else:
>> > data.djw = data.djw * 0.0
>> >
>> > # Calculate the relaxation gradient components.
>> > data.create_dri_comps(data, params)
>> >
>> > # Calculate the R1, R2, and sigma_noe gradients.
>> > data.dri_prime[j] = data.create_dri_prime[j](data)
>> >
>> > # Loop over the relaxation values and modify the NOE
>> > gradients.
>> > data.dri[j] = data.dri_prime[j]
>> > for m in xrange(data.num_ri):
>> > if data.create_dri[m]:
>> > data.create_dri[m](data, m, data.remap_table[m],
>> > data.get_dr1, params, j)
>> >
>> > # Calculate the chi-squared gradient.
>> > data.dchi2[j] = dchi2_element(data.relax_data, data.ri,
>> > data.dri[j], data.errors)
>> >
>> > If the loop over interactions is incorporated, it is necessary to do it
>> > before "data.calc_djw_comps" is calculated. However then we get into the
>> > conflict with calculation of "modification of NOE gradients" and also
>> > calculation of "dchi2". These quantities can be calculated only when
>> > contributions from all interactions has been already evaluated (it is
>> > similar to already discussed ri_prime). In this case it is complicated
>> > by
>> > the presence of loop over fitted parameters. The possible solution would
>> > be
>> > to make the loop over the interactions the inner one. However this seems
>> > to
>> > require repeating the loop over interactions twice within the code:
>> >
>> > data = "">
>> >
>> > # Loop over the interactions
>> > for k in xrange(self.num_interactions[0]):
>> > # Calculate the spectral density gradient components.
>> > if data[k].calc_djw_comps:
>> > data[k].calc_djw_comps(data[k], params)
>> >
>> > # Diffusion tensor correlation times.
>> > self.diff_data.calc_dti(data[k], self.diff_data)
>> >
>> > # Loop over the gradient.
>> > for j in xrange(data.total_num_params):
>> > # Loop over the interactions
>> > for k in xrange(self.num_interactions[0])
>> > # Calculate the spectral density gradients.
>> > if data[k].calc_djw[j]:
>> > data[k].djw = data[k].calc_djw[j](data[k], params,
>> > j)
>> > else:
>> > data[k].djw = data[k].djw * 0.0
>> >
>> > # Calculate the relaxation gradient components.
>> > data[k].create_dri_comps(data[k], params)
>> >
>> > # Calculate the R1, R2, and sigma_noe gradients.
>> > data[k].dri_prime[j] =
>> > data[k].create_dri_prime[j](data[k]) #
>> > later
>> > data[k].dri_prime[j] will be replaced by data.dri_prime[j]
>> >
>> > # but you suggest not
>> > to
>> > include both changes into the following patch together
>> >
>> >
>> > # Loop over the relaxation values and modify the NOE
>> > gradients.
>> > data.dri[j] = data.dri_prime[j]
>> > for m in xrange(data.num_ri):
>> > if data.create_dri[m]:
>> > data.create_dri[m](data, m, data.remap_table[m],
>> > data.get_dr1, params, j)
>> >
>> > # Calculate the chi-squared gradient.
>> > data.dchi2[j] = dchi2_element(data.relax_data, data.ri,
>> > data.dri[j], data.errors)
>> >
>> > Additionally I would notify that variable "total_num_params" needs to be
>> > kept at the position self.data[0] (similar to your suggestion in your
>> > last
>> > mail, concerning ri_prime)
>> > What do you think about this?
>> > Regards
>> > Pavel
>> >
>> > On 22 October 2010 19:46, Edward d'Auvergne <
edward@xxxxxxxxxxxxx>
>> > wrote:
>> >>
>> >> Hi,
>> >>
>> >> This is a good idea. First I would suggest putting this into 2
>> >> patches, as this is easier to check and apply. Don't worry about
>> >> breaking the code at this point - it is in your own special branch so
>> >> as long as it works in the end, you can smash it into a million pieces
>> >> and put it back together again if you like. Commits to the repository
>> >> are better when they are many small ones, as they can be more easily
>> >> managed. For example if something is found to be designed not
>> >> ideally, or there is a fatal bug, that patch/commit can be reverted
>> >> and then new code can be worked on. And small patches make it much
>> >> easier for the other relax developers to read and catch potential
>> >> hidden bugs or design issues.
>> >>
>> >> This is an intriguing problem, as the data flow hits a fork here.
>> >> ri_prime is the correct target for the merging of the data from all
>> >> the interactions, as this needs to occur before the calculation of the
>> >> NOE using sigma_noe and the R1. The relaxation rates R1, R2, and
>> >> sigma_noe add. However the NOE does not. I just thought I'd explain
>> >> the logic for others to follow ;)
>> >>
>> >> I would suggest we store ri_prime somewhere else. What I can do is to
>> >> apply a patch for the first change to accommodate for the multiple
>> >> relaxation interactions. Then I could make a change myself, creating
>> >> a special Python object for 'data[i]'. We can store the ri_prime data
>> >> this special object. Essentially, it will be like the current code
>> >> base. We could have specific interaction data in say:
>> >>
>> >> self.data[10][0].jw (or self.data[0].jw if data = "">
>> >>
>> >> This is new. But as before we could have:
>> >>
>> >> self.data[10].ri_prime (or data.ri_prime if data = "">
>> >>
>> >> So the forking can all be managed within the self.data[i] data
>> >> structures. What do you think? Also, we will have to work out how to
>> >> modify or replace func_ri_prime and func_ri_prime_rex in the
>> >> maths_fns.ri_prime module. This is where the merging of data streams
>> >> currently occurs. Maybe Rex needs to be considered as its own
>> >> interaction, as this is added to produce ri_prime?
>> >>
>> >> Regards,
>> >>
>> >> Edward
>> >>
>> >>
>> >> P. S. I just talked to Kathleen Hall and she seemed very interested
>> >> in what you are doing here!
>> >>
>> >>
>> >>
>> >> On 22 October 2010 18:26, Pavel Kaderavek <
pavel.kaderavek@xxxxxxxxx>
>> >> wrote:
>> >> > Hi,
>> >> > I am continuing in the discussion started in my post
>> >> >
https://mail.gna.org/public/relax-devel/2010-09/msg00020.html
>> >> > It covers changes of functions func_mf.py, func_local_tm , func_diff,
>> >> > func_all and their equivalents for a first and second derivatives
>> >> > (class
>> >> > Mf,
>> >> > file maths_fns/mf.py).
>> >> >
>> >> > I would like to include into next patch also treatment of the fact,
>> >> > that
>> >> > it
>> >> > is necessary to sum together contributions of all interactions. It
>> >> > seems
>> >> > to
>> >> > me that the most suitable way is to do that by the modification just
>> >> > revised
>> >> > functions (func_mf.py, func_local_tm ...)
>> >> > I would suggest to initialize ri_prime before loop over interactions
>> >> > and
>> >> > then step by step add the contributions into the ri_prime:
>> >> >
>> >> > data = "" # the
>> >> > cases
>> >> > when `i` is replaced by `0` were discussed in your last mail
>> >> > ri_prime=0
>> >> >
>> >> >
>> >> > for j in xrange(self.num_interactions[i]):
>> >> >
>> >> > ...
>> >> > ...
>> >> >
>> >> > # Calculate the R1, R2, and sigma_noe values.
>> >> > ri_prime = ri_prime + data[j].create_ri_prime(data[j])
>> >> >
>> >> > data[0].ri_prime = ri_prime
>> >> >
>> >> >
>> >> > When the loop over interactions is finished the accumulated
>> >> > relaxation
>> >> > rate
>> >> > is copied into the data storage of the first interaction. Then it is
>> >> > possible to call functions, where total ri_prime is needed:
>> >> >
>> >> > # Calculate the NOE values.
>> >> > data[0].ri = data[0].ri_prime * 1.0
>> >> > for m in xrange(data[0].num_ri):
>> >> > if data[0].create_ri[m]:
>> >> > data[0].create_ri[m](data[0], m,
>> >> > data[0].remap_table[m],
>> >> > data[0].get_r1, params)
>> >> >
>> >> > # Calculate the chi-squared value.
>> >> > data[0].chi2 = chi2(data[0].relax_data, data[0].ri,
>> >> > data[0].errors)
>> >> >
>> >> > Regards,
>> >> > Pavel
>> >> >
>> >> > On 19 October 2010 13:49, Edward d'Auvergne <
edward@xxxxxxxxxxxxx>
>> >> > wrote:
>> >> >>
>> >> >> 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 = "">
>> >> >> >
>> >> >> > 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
>> >> >> >> >> >>>
>> >> >> >> >> >>
>> >> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >
>> >> >> >
>> >> >
>> >> >
>> >
>> >
>
>
Re: CST branch