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/2011-03/msg00027.html https://gna.org/task/download.php?file_id=13916 This patch includes the changes in setup_equations function of class Mf in a file maths_fns/mf.py. The selection of the equation was modified in order to select based on both type of relaxation rate and type of interaction. On 12 April 2011 17:06, Edward d'Auvergne <edw...@nmr-relax.com> wrote: > Hi, > > I think we should avoid optimising the bond length and the CSA tensor, > if the full tensor is used or if there are multiple bond lengths for > one spin, at least for now. This could be caught in the setup method > and a RelaxError thrown saying that the optimisation of these things > is not yet implemented. That will allow for the current models and > the new code to work together. Optimisation of the CSA tensor or > multiple dipole-dipole distances is too much effort for now, and there > probably isn't enough information in the current data to extract this. > What do you think? > > Cheers, > > Edward > > > On 12 April 2011 15:28, Pavel Kaderavek <pavel.kadera...@gmail.com> wrote: > > Hi, > > > > it seems possible, but I think that it means that there will be for each > > type of the interaction an unique (d,d2)ri_comps function. It will be > > defined in the setup_equation (mf.py, class Mf). Currently, the > > (d,d2)ri_comps function is selected just based on the fact whether the > > values of physical quantities (internuclei distance, csa) are optimized > or > > not. Now it will be selected again according to the same criteria and > > moreover according the type of interaction. This ensure that inside the > > function (d,d2)ri_comps the function create_(d,d2)ri_comps will be called > > with appropriate parameters. > > > > Generally, it is probably not very convenient to optimize all internuclei > > distances, but only the most crucial one (to the bonded hydrogen) would > be > > sufficient. However, the selection should be upon user. The > optimalization > > of CST will be also quite difficult, because 5 parameters would be needed > to > > optimize (3 euler angles + 2 csa values - corresponding to two pseudo > > chemical shielding tensors which stand for asymmetric chemical shielding > > tensor - hence I always mention csa1 and csa2 as well as the cross-term, > > because they are not independent). So far I would consider only the > > optimalization of the eigenvalues of the tensors, the optimalization of > the > > orientation might be added later. > > > > Best regards, > > Pavel > > > > On 22 March 2011 12:23, Edward d'Auvergne <edw...@nmr-relax.com> wrote: > >> > >> >> > At this point we would like to address a related question. > Currently > >> >> > the > >> >> > calculation of physical constant is done in a several steps. First, > >> >> > the > >> >> > physical constant is calculated and the value is stored in the > >> >> > data.dip_const_func or data.csa_const_func (grad, hess). Then, when > >> >> > the > >> >> > relaxation rates are calculated, the physical constant is > >> >> > recalculated > >> >> > by > >> >> > the function create_dip_func or create_csa_func (grad, hess) > (method > >> >> > setup_equations in class Mf, maths_fns/mf.py). > >> >> > > >> >> > comp_dip_const_func(data, data.bond_length) > >> >> > comp_csa_const_func(data, data.csa) > >> >> > for i in xrange(data.num_ri): > >> >> > data.dip_comps_func[i] = data.dip_const_func > >> >> > if data.create_dip_func[i]: > >> >> > data.dip_comps_func[i] = > >> >> > data.create_dip_func[i](data.dip_const_func) > >> >> > if data.create_csa_func[i]: > >> >> > data.csa_comps_func[i] = > >> >> > data.create_csa_func[i](data.csa_const_func[data.remap_table[i]]) > >> >> > > >> >> > There is one exception, the dipolar physical constant is not > >> >> > recalculated in > >> >> > the case of calculation R1 relaxation rate, because the function > >> >> > create_dip_func does not exist in this case. We do not see a reason > >> >> > for > >> >> > such > >> >> > a recalculation. > >> >> > >> >> The reason is because of the m10 to m39 models built into relax. I > >> >> have made it possible to optimise the bond length and CSA > information. > >> >> However these models are not stable with the current relaxation > data. > >> >> I do plan on working with these in the future though, so it would be > >> >> useful to keep them. Note that for models m0 to m9, the > >> >> data.create_dip_func[i] and data.create_csa_func[i] function pointers > >> >> are set to None. Therefore for normal model-free analysis the > >> >> constant is not recalculated. > >> >> > >> >> > >> >> > It seems better to us to just change the coefficient in the > >> >> > functions comp_r1_dip_jw, comp_r2_dip_jw, comp_r1_csa_jw, > >> >> > comp_r2_csa_jw > >> >> > (maths_fns/ri_comps.py). I guess, that this design was dedicated to > >> >> > avoid > >> >> > multiple calculation of the same interaction constant for each > >> >> > measured > >> >> > relaxation rate. We would suggest to reach the same effect by this > >> >> > construction: > >> >> > > >> >> > for i in xrange(data.num_ri): > >> >> > if data.const_func[0]: > >> >> > data.const_func[i] = data.const_func[0] > >> >> > else > >> >> > data.create_const_func(data) > >> >> > >> >> For models m10 to m39, this construct will not work. The constants > >> >> are already pre-calculated for models m0 to m9 so this is not needed. > >> >> > >> >> > >> >> > Note, the comp_dip_const_func and comp_csa_const_func should be > >> >> > change > >> >> > so > >> >> > that, it is possible to call them just with the argument data > >> >> > (maths_fns/ri_comps.py). Instead of: > >> >> > > >> >> > > >> >> > def comp_dip_const_func(data, bond_length): > >> >> > """Calculate the dipolar constant. > >> >> > > >> >> > ... > >> >> > > >> >> > if bond_length == 0.0: > >> >> > data.dip_const_func = 1e99 > >> >> > else: > >> >> > data.dip_const_func = 0.25 * data.dip_const_fixed * > >> >> > bond_length**-6 > >> >> > > >> >> > > >> >> > It should look like: > >> >> > > >> >> > def comp_dip_const_func(data): > >> >> > """Calculate the dipolar constant. > >> >> > > >> >> > ... > >> >> > > >> >> > if data.internuclei_distance == 0.0: > >> >> > data.const_func = 1e99 > >> >> > else: > >> >> > data.const_func = 0.25 * data.dip_const_fixed * > >> >> > data.internuclei_distance**-6 > >> >> > >> >> The bond_length arg was designed so that the bond length could either > >> >> come from a fixed value supplied by the user or from the parameter > >> >> vector when bond lengths or CSA values are optimised. This behaviour > >> >> might have to be preserved. > >> >> > >> >> > >> >> > data.dip_const_func were renamed to more general data.const_func > and > >> >> > instead > >> >> > of bond_length the function directly takes the internuclei > distance > >> >> > for > >> >> > the > >> >> > current dipole-dipole interaction. The change of > data.dip_const_func > >> >> > to > >> >> > data.const_func later simplify the code design in the > >> >> > maths_fns/ri_prime.py > >> >> > . It will be reduced just to a multiplication of constant and the > >> >> > linear > >> >> > combination of spectral density functions. > >> >> > >> >> For models m10 to m39, I'm not sure if this design would work. Could > >> >> we redesign this in another way in which these complex models are > >> >> still functional? > >> >> > >> > > >> > Then, we would suggest to call the function comp_dip_const_func, > >> > comp_csa_const_func ... with full set of possible parameters, i.e. > >> > comp_dip_const_func(data,internuclei_distance,csa1,csa2,rex) > >> > comp_csa_const_func(data,internuclei_distance,csa1,csa2,rex) > >> > ... > >> > If we would call the function with just physically relevant arguments > >> > then > >> > we would have to use yet another condition to decide the type of the > >> > interaction in the loop where individual interaction contributions are > >> > calculated. The physical quantities irrelevent for the given > interaction > >> > (for example csa1,csa2,rex for the dipole-dipole interaction) are None > >> > from > >> > the initialization and will not be used by the function anyway. > >> > >> It would be easier to have a different function for each physical > >> constant, as this is very specific code. For example > >> comp_dip_const_func is only called from functions which require the > >> dipolar constant. For the normal model-free models, this is only > >> called during setup. So there is no need to pass in the csa1 and csa2 > >> constants, or Rex for this specific function. For the CSA constants, > >> do you calculate 2 separate constants? For example would you use: > >> > >> comp_dip_const_func(data[i],internuclei_distance) > >> comp_csa_const_func(data[j],csa1) > >> comp_csa_const_func(data[k],csa2) > >> > >> where data[x] in each case is a different interaction? > >> > >> > >> >> > Moreover, there is an unanswered question about the NOE and the > >> >> > additional > >> >> > dipolar interaction. I am not sure if the suggested design is > >> >> > physically > >> >> > correct, rather not. During the NOE experiment, the protons are > >> >> > saturated in > >> >> > order to reach the steady state. Then a complete set cross > relaxation > >> >> > rates > >> >> > between all interacting spin pairs should be taken into the > account, > >> >> > not > >> >> > only between the spin of interest and all other interacting nuclei. > >> >> > On > >> >> > the > >> >> > other hand this is probably beyond the aim of the program relax. > What > >> >> > do > >> >> > you > >> >> > think about that? > >> >> > >> >> This is getting quite complex as you would need to take the > >> >> cross-correlated relaxation rates between the different relaxation > >> >> interactions into account, as well as the motion of all spins if they > >> >> are not directly bonded. Is this needed for the current work? Of > >> >> course anything is accepted into relax, especially if you would like > >> >> to probe this area (with a paper in mind), but it has to play nicely > >> >> with the rest of relax and not be a burden on the relax developers to > >> >> maintain in the future (as well as not make the current number > >> >> crunching code slower than it already is). The code would therefore > >> >> need to be designed in public. So if you would like to tackle such a > >> >> task, I would first recommend finishing off the cst branch, and then > >> >> make a new branch for this work. > >> > > >> > Then, I will design the code as I suggested. So, the sigma_noe will be > >> > calculated separately for all dipole-dipole interactions with the > >> > central > >> > spin (assuming they are isolated spin pairs). The total sigma_noe will > >> > be > >> > calculated as a sum of all individual sigma_noe contributions. > >> > >> This sounds the most reasonable for a first approximation. In reality > >> the cross rates will be important as well. > >> > >> Cheers, > >> > >> Edward > > > > >
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