Hi, The Gna! infrastructure is finally back. It looks like nothing was cracked. So I can now apply your patch. However there is a problem:
[e...@localhost cst]$ patch -p0 < patch00003.bin patching file maths_fns/mf.py Reversed (or previously applied) patch detected! Assume -R? [n] y Hunk #1 succeeded at 40 (offset 1 line). Hunk #2 FAILED at 56. Hunk #3 FAILED at 253. 2 out of 3 hunks FAILED -- saving rejects to file maths_fns/mf.py.rej [e...@localhost cst]$ svn st ? patch00003.bin ? svnmerge-commit-message.txt ? .sconsign.dblite ? maths_fns/mf.py.orig ? maths_fns/relax_fit.so ? maths_fns/mf.py.rej M maths_fns/mf.py [e...@localhost cst]$ svn info Path: . URL: svn+ssh://bug...@svn.gna.org/svn/relax/branches/cst Repository Root: svn+ssh://bug...@svn.gna.org/svn/relax Repository UUID: b7916896-f9f9-0310-9fe5-b3996d8957d5 Revision: 11699 Node Kind: directory Schedule: normal Last Changed Author: bugman Last Changed Rev: 11695 Last Changed Date: 2010-11-23 11:30:42 +0100 (Tue, 23 Nov 2010) [e...@localhost cst]$ This looks like the patch is for an earlier revision of the branch. Would you be able to 'svn up' and attach a new patch to the task (https://gna.org/task/?6397). Cheers, Edward On 30 November 2010 18:21, Edward d'Auvergne <edw...@nmr-relax.com> wrote: > Hi, > > I'll have to look at this patch later. The Gna! website > (http://gna.org) looks like it has been hacked, so I can't reach the > task to download the patch :S Hopefully I can have it applied > tomorrow, but the next 2 days will be almost impossible for me due to > a day long meeting. > > Cheers, > > Edward > > > > On 29 November 2010 23:28, Pavel Kaderavek <pavel.kadera...@gmail.com> wrote: >> This change is related to the task #6397 (https://gna.org/task/?6397) >> >> kada _at_ chemi _dot_ muni _dot_ cz >> >> https://mail.gna.org/public/relax-devel/2010-11/msg00001.html >> https://gna.org/task/download.php?file_id=11449 >> >> This patch includes change in func_mf, func_local_tm, func_diff, func_all, >> dfunc_mf, dfunc_local_tm, dfunc_diff, dfunc_all, d2func_mf, d2func_local_tm, >> d2func_diff, d2func_all functions of class Mf in a file maths_fns/mf.py. >> Functions were modified in order to handle data for more interactions. >> >> On 27 November 2010 09:25, Edward d'Auvergne <edw...@nmr-relax.com> wrote: >>> >>> Hi, >>> >>> First make a backup copy just in case, then simply perform an 'svn up' >>> and then 'svn diff'. This should work without clashes. If there is a >>> clash, this is a normal part of software development. This really >>> shouldn't be necessary. But if you need to resolve a clash, you need >>> to edit the file and find the '<<<<<', '=====', and '>>>>>' marks. >>> This separates code from the old file and the new file for you to >>> manually edit and merge. If it's too confusing, just ask again. >>> >>> Cheers, >>> >>> Edward >>> >>> >>> On 25 November 2010 19:25, Pavel Kaderavek <pavel.kadera...@gmail.com> >>> 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 <edw...@nmr-relax.com> >>> > 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 = self.data[0]" 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.kadera...@gmail.com> >>> >> 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 = self.data[0] >>> >> > >>> >> > # 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 = self.data[0] >>> >> > >>> >> > # 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 <edw...@nmr-relax.com> >>> >> > 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 = self.data[i]) >>> >> >> >>> >> >> This is new. But as before we could have: >>> >> >> >>> >> >> self.data[10].ri_prime (or data.ri_prime if data = self.data[i]) >>> >> >> >>> >> >> 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.kadera...@gmail.com> >>> >> >> 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 = self.data[i] # 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 <edw...@nmr-relax.com> >>> >> >> > 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.kadera...@gmail.com> >>> >> >> >> 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 >>> >> >> >> > <edw...@nmr-relax.com> >>> >> >> >> > 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.kadera...@gmail.com> >>> >> >> >> >> 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 >>> >> >> >> >> > <edw...@nmr-relax.com> >>> >> >> >> >> > 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 >>> >> >> >> >> >> <edw...@nmr-relax.com> >>> >> >> >> >> >> 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 >>> >> >> >> >> >> > <edw...@nmr-relax.com> >>> >> >> >> >> >> > 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.kadera...@gmail.com> >>> >> >> >> >> >> >> 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 >>> >> >> >> >> >> >>> >>> >> >> >> >> >> >> >>> >> >> >> >> >> > >>> >> >> >> >> > >>> >> >> >> >> > >>> >> >> >> > >>> >> >> >> > >>> >> >> > >>> >> >> > >>> >> > >>> >> > >>> > >>> > >> >> > _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org 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
