Here is one more point. For the DPL94 model, the denominator is "kex**2 + spin_lock_fields**2". This can only be zero when kex is zero, and then there should be no exchange. Therefore we can add a kex == 0 check at the start to return R1_R2 and then delete the mask_denom_zero logic. This should slightly speed things up by removing one 'if' statement. Also, kex**2 is not a repetitive operation.
Cheers, Edward On 27 June 2014 17:33, Edward d'Auvergne <edw...@nmr-relax.com> wrote: > There are also a number of double spacing issues. You can find these > by running: > > $ ./devel_scripts/code_validator lib/dispersion/b14.py > $ ./devel_scripts/code_validator lib/dispersion/cr72.py > > Etc. Some things can be ignored, like the capitals in the function > name and double spacing or trailing spacing for equations in > docstrings. This script will identify most formatting problems > remaining. > > Cheers, > > Edward > > > > On 27 June 2014 17:28, Edward d'Auvergne <edw...@nmr-relax.com> wrote: >> Also the documentation in the get_back_calc() method of the target >> function needs a little polish - it is not a float that is returned. >> So, the running list: >> >> - Some modules have "=" operators outside of functions that need >> spaces around them. >> >> - Trailing whitespace, most of it is in the trunk, but there are some >> new ones. Just run: grep " $" lib/dispersion/* | grep -v "\\\\ " >> >> - There are some empty lines straight after a 'for' loop in many places. >> >> - Your copyright in the tsmfk01.py file needs to be extended to 2014. >> >> - There are some FIXME comments in the lib.dispersion package. >> >> - In some places, comment lines require empty lines before them (in >> target_functions.relax_disp and lib.dispersion). >> >> - Not very important, but the target function calc_ns_mmq_3site_chi2() >> can have the "Once off parameter conversions" shifted into the >> lib.dispersion module to simplify this. >> >> - The newline spacing between target function methods needs some fixes. >> >> - The 'chi2_sum' initialisation in func_ns_mmq_2site() should go. >> >> - The get_back_calc() method of the target function needs a little >> polish - it is not a float that is returned. >> >> Cheers, >> >> Edward >> >> >> >> On 27 June 2014 17:26, Edward d'Auvergne <edw...@nmr-relax.com> wrote: >>> To add to the list of trivialities to fix: >>> >>> - The 'chi2_sum' initialisation in func_ns_mmq_2site() should go. >>> >>> Cheers, >>> >>> Edward >>> >>> >>> >>> On 27 June 2014 17:23, Edward d'Auvergne <edw...@nmr-relax.com> wrote: >>>> Let me see. You've covered most of the running list, there's just one >>>> or two things left. I'll add a few more trivial things as well. >>>> >>>> - Some modules have "=" operators outside of functions that need >>>> spaces around them. >>>> >>>> - Trailing whitespace, most of it is in the trunk, but there are some >>>> new ones. Just run: grep " $" lib/dispersion/* | grep -v "\\\\ " >>>> >>>> - There are some empty lines straight after a 'for' loop in many places. >>>> >>>> - Your copyright in the tsmfk01.py file needs to be extended to 2014. >>>> >>>> - There are some FIXME comments in the lib.dispersion package. >>>> >>>> - In some places, comment lines require empty lines before them (in >>>> target_functions.relax_disp and lib.dispersion). >>>> >>>> - Not very important, but the target function calc_ns_mmq_3site_chi2() >>>> can have the "Once off parameter conversions" shifted into the >>>> lib.dispersion module to simplify this. >>>> >>>> - The newline spacing between target function methods needs some fixes. >>>> >>>> >>>> I'll keep looking. I'm guessing you will not be tackling the numeric >>>> models to speed them up to match 'NS CPMG 2-site expanded' model via >>>> the ultimate solution of brute-force expansion >>>> (http://www.mail-archive.com/relax-users@gna.org/msg01641.html) any >>>> time soon. This will have a similar effect as the ultimate speed up >>>> at http://www.mail-archive.com/relax-devel%40gna.org/msg05691.html >>>> which you have so successfully achieved in this branch. Can you >>>> remember if there were any other changes required? I will create a >>>> new timings file just before tagging the relax release. >>>> >>>> Cheers, >>>> >>>> Edward >>>> >>>> On 27 June 2014 16:53, Troels Emtekær Linnet <tlin...@nmr-relax.com> wrote: >>>>> This sounds good. >>>>> >>>>> What is needed to be done, to merge disp_spin_speed in trunk now? >>>>> >>>>> Best >>>>> Troels >>>>> >>>>> 2014-06-27 15:53 GMT+02:00 Edward d'Auvergne <edw...@nmr-relax.com>: >>>>>> Hmmm: >>>>>> >>>>>> $ grep -c "out=\|einsum" lib/dispersion/* >>>>>> lib/dispersion/b14.py:0 >>>>>> lib/dispersion/cr72.py:2 >>>>>> lib/dispersion/dpl94.py:0 >>>>>> lib/dispersion/__init__.py:0 >>>>>> lib/dispersion/it99.py:0 >>>>>> lib/dispersion/lm63_3site.py:0 >>>>>> lib/dispersion/lm63.py:0 >>>>>> lib/dispersion/m61b.py:0 >>>>>> lib/dispersion/m61.py:0 >>>>>> lib/dispersion/matrix_exponential.py:5 >>>>>> lib/dispersion/matrix_power.py:0 >>>>>> lib/dispersion/mmq_cr72.py:0 >>>>>> lib/dispersion/mp05.py:0 >>>>>> lib/dispersion/ns_cpmg_2site_3d.py:6 >>>>>> lib/dispersion/ns_cpmg_2site_expanded.py:0 >>>>>> lib/dispersion/ns_cpmg_2site_star.py:3 >>>>>> lib/dispersion/ns_matrices.py:0 >>>>>> lib/dispersion/ns_mmq_2site.py:12 >>>>>> lib/dispersion/ns_mmq_3site.py:12 >>>>>> lib/dispersion/ns_r1rho_2site.py:3 >>>>>> lib/dispersion/ns_r1rho_3site.py:3 >>>>>> lib/dispersion/tap03.py:0 >>>>>> lib/dispersion/tp02.py:0 >>>>>> lib/dispersion/tsmfk01.py:0 >>>>>> lib/dispersion/two_point.py:0 >>>>>> >>>>>> >>>>>> What do you think of the idea of making this a hard dependency: >>>>>> >>>>>> """ >>>>>> Index: dep_check.py >>>>>> =================================================================== >>>>>> --- dep_check.py (revision 24343) >>>>>> +++ dep_check.py (working copy) >>>>>> @@ -37,6 +37,9 @@ >>>>>> # numpy. >>>>>> try: >>>>>> import numpy >>>>>> + if float(numpy.version.version[:3]) < 1.6: >>>>>> + sys.stderr.write("Version %s of the 'numpy' dependency is not >>>>>> supported, numpy >= 1.6 is required.\n" % numpy.version.version) >>>>>> + sys.exit() >>>>>> except ImportError: >>>>>> sys.stderr.write("The dependency 'numpy' has not been installed.\n") >>>>>> sys.exit() >>>>>> """ >>>>>> >>>>>> This might be the easiest way, just forcing users to upgrade. I've >>>>>> used the out argument a lot with the frame order analysis as well and >>>>>> plan to use it more often, so maybe we just have to put our foot down >>>>>> and make this a hard dependency. That will make everyone's life >>>>>> easier, and simplify what we as developers have to do to handle this. >>>>>> I can apply this to the trunk and release relax 3.2.3 with all the >>>>>> current fixes and this hard numpy version dependency, and then in a >>>>>> few weeks when you are ready, merge the disp_spin_speed branch and >>>>>> release relax 3.2.4. What do you think? >>>>>> >>>>>> Regards, >>>>>> >>>>>> Edward >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 27 June 2014 14:40, Troels Emtekær Linnet <tlin...@nmr-relax.com> >>>>>> wrote: >>>>>>> Hi Ed. >>>>>>> >>>>>>> You can just grep for "out" or "einsum" in lib/dispersion. >>>>>>> >>>>>>> Best >>>>>>> Troels >>>>>>> >>>>>>> 2014-06-27 14:15 GMT+02:00 Edward d'Auvergne <edw...@nmr-relax.com>: >>>>>>>> Hi Troels, >>>>>>>> >>>>>>>> I think if would be better if we caught this earlier, specifically the >>>>>>>> select_model() method of the specific_analyses.relax_disp.uf module if >>>>>>>> the user chooses a model which is not supported by their numpy >>>>>>>> version. Such a check with a RelaxError would only be two lines of >>>>>>>> code, plus a comment (which could include the current version in >>>>>>>> numpy.version.version). It would be very useful to add the models to >>>>>>>> a list variable in specific_analyses.relax_disp.variables so that I >>>>>>>> can replicate the checks in the GUI. Even better would be to add the >>>>>>>> 2 line check to a function in specific_analyses.relax_disp.checks to >>>>>>>> allow for consistent checking in all user interfaces. There could >>>>>>>> even be two separate tests, one for the numpy.einsum and one for the >>>>>>>> numpy out argument, each with their own model lists, if you wish. >>>>>>>> >>>>>>>> Cheers, >>>>>>>> >>>>>>>> Edward >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 27 June 2014 12:58, <tlin...@nmr-relax.com> wrote: >>>>>>>>> Author: tlinnet >>>>>>>>> Date: Fri Jun 27 12:58:22 2014 >>>>>>>>> New Revision: 24336 >>>>>>>>> >>>>>>>>> URL: http://svn.gna.org/viewcvs/relax?rev=24336&view=rev >>>>>>>>> Log: >>>>>>>>> Added to target function that experiment_type_setup() should not be >>>>>>>>> initiated, if numpy.einsum is missing. >>>>>>>>> >>>>>>>>> Task #7807 (https://gna.org/task/index.php?7807): Speed-up of >>>>>>>>> dispersion models for Clustered analysis. >>>>>>>>> >>>>>>>>> Modified: >>>>>>>>> branches/disp_spin_speed/target_functions/relax_disp.py >>>>>>>>> >>>>>>>>> Modified: branches/disp_spin_speed/target_functions/relax_disp.py >>>>>>>>> URL: >>>>>>>>> http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24336&r1=24335&r2=24336&view=diff >>>>>>>>> ============================================================================== >>>>>>>>> --- branches/disp_spin_speed/target_functions/relax_disp.py >>>>>>>>> (original) >>>>>>>>> +++ branches/disp_spin_speed/target_functions/relax_disp.py Fri >>>>>>>>> Jun 27 12:58:22 2014 >>>>>>>>> @@ -365,8 +365,10 @@ >>>>>>>>> # This is to make sure, that the chi2 values is not affected >>>>>>>>> by missing values. >>>>>>>>> self.mask_replace_blank = masked_equal(self.missing, 1.0) >>>>>>>>> >>>>>>>>> - # Check the experiment types, simplifying the data >>>>>>>>> structures as needed. >>>>>>>>> - self.experiment_type_setup() >>>>>>>>> + # Check if eisum is available for numerical models. >>>>>>>>> + if dep_check.einsum_module: >>>>>>>>> + # Check the experiment types, simplifying the data >>>>>>>>> structures as needed. >>>>>>>>> + self.experiment_type_setup() >>>>>>>>> >>>>>>>>> # Scaling initialisation. >>>>>>>>> self.scaling_flag = False >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> relax (http://www.nmr-relax.com) >>>>>>>>> >>>>>>>>> This is the relax-commits mailing list >>>>>>>>> relax-comm...@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-commits >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> relax (http://www.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 _______________________________________________ relax (http://www.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
