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== Tutorial =={{tip|See the [https://mail.{{gna.org/public/mailing list link|url=relax-devel/2013-06/msg00016.html |text=mail archive] message}} for the original post.}}
Firstly This step is normally performed first. This is the model should be added to most important part that makes sure that the code not only works now, but will continue working for the lists entire lifetime of the specific_analyses.relax_disp.variables module. The model name is stored in a special variable which will be used throughout relaxproject.
==== Reference commits ====The idea is that real or synthetic data, for example as Sparky peak lists, is obtained or created for the model and added to the test suite directory <code>test_suite/shared_data/dispersion/</code>. This is then used in a system test to check that the code in relax can consistently reproduce the results.
* NS R1rho 2-site [http://article.gmane.org/gmane.science.nmr.relax.scm/18477]* The DPL94 model [http://article.gmane.org/gmane.science.nmr.relax.scm/17753]* The M61 skew model [http://article.gmane.org/gmane.science.nmr.relax.scm/17724]* The M61 model [http://article.gmane.org/gmane.science.nmr.relax.scm/17611]* No Rex [http://article.gmane.org/gmane.science.nmr.relax.scm/17592]=== Synthetic data ===
The next step An alternative is to add the model, its description, the equations for the analytic models, and all references to the relax_disp.select_model user function front enduse real measured relaxation dispersion data. When the relaxation This data should be added as peak lists containing peak intensities to <code>test_suite/shared_data/dispersion chapter of the relax [[manual]] is created (this will be the docs/latex</relax_dispcode>.tex file) As the real solution cannot be known a priori, then the same description should results from relax must be added there as wellcompared to results obtained from another software program (possibly directly from a publication). The steps required for using such data are:
==== Reference commits ====* Create a new directory name for the test data.
=== The * Add a script which performs the full analysis in relax library ===for the model. Also a script which performs the analysis using only the [[R2eff]] model. See the <code>test_suite/shared_data/dispersion/Hansen/*.py</code> scripts for reference - these scripts should be copied to your data directory and modified (using the <code>svn cp</code> command). Once the scripts are functional, they can be copied and modified for the truncated data (again using the <code>svn cp</code> command).
Now * Copy the dispersion function needs full analysis script to be added to the relax library <code>test_suite/system_tests/scripts/relax_disp/</code> with an appropriate name (in always using the lib.relax_disp package<code>svn cp</code> command). This should can then be designed as used in a simple Python function which takes new system test. Better still, the dispersion parameters and experimental variables, and calculates final save file from the R2eff<code>r2eff_calc.py</R1rho valuescode> script for the truncated data can be used to start the script. The module can contain auxiliary functions for This is again to save a lot of computation time in the calculationtest. Some auxiliary functions, if not specific to relaxation dispersion, may be better placed See the <code>test_tp02_data_to_ns_r1rho_2site()</code> system test in other locations within the relax library<code>test_suite/system_tests/relax_disp.py</code> file for a template.
The relaxation dispersion functions in the library currently take as an argument If you are not a relax developer, a data structure for the back[https://sourceforge.net/p/nmr-relax/tickets-calculated R2effsupport/R1rho values and populate this structuresupport request] can be [https://sourceforge. This design is not essential if the target function, described in the next point, handles the library function appropriatelynet/p/nmr-relax/tickets-support/new/ submitted]. Just look at the You can attach files in lib/dispersion and add comments to that request for a relax developer to get an idea of make the design usedchanges for you.
The dispersion code in the relax library must be robust. This involves identifying parameter values or combinations which would cause failures in the mathematical operations (numerical issues not present in the mathematics must be considered). Note that parameter values of 0 are common within a grid search. It should be decided if the R2eff/R1rho value should be set to zero, to another value, or to something large (e.g. 1e100). For example:=== Reference commits ===
Divisions * The [[MQ CR72]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18878 r21122]* The [[MQ NS CPMG 2- always catch zeros in the denominator with if statements, even if you believe that this will never be encounteredsite]] model at [http://article.gmane.org/gmane. Square roots science.nmr.relax.scm/18774 r21018] [http://article.gmane.org/gmane.science.nmr.relax.scm/18775 r21019] [http://article.gmane.org/gmane.science.nmr.relax.scm/18776 r21020] [http://article.gmane.org/gmane.science.nmr.relax.scm/18780 r21024] [http://article.gmane.org/gmane.science.nmr.relax.scm/18784 r21028] [http://article.gmane.org/gmane.science.nmr.relax.scm/18785 r21029] [http://article.gmane.org/gmane.science.nmr.relax.scm/18786 r21030] [http://article.gmane.org/gmane.science.nmr.relax.scm/18787 r21031]* The [[TSMFK01]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18538 r20782]* The [[NS R1rho 2- make sure that the value inside is always > 0site]] model at [http://article.gmane.org/gmane.science.nmr.relax. Trigonometric functions - these should be tested for where they are not defined or where the software implementation can no longer handle certain valuesscm/18485 r20729] [http://article.gmane.org/gmane.science.nmr.relax.scm/18486 r20739] [http://article.gmane.org/gmane.science.nmr.relax.scm/18488 r20732]* The [[TP02]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18256 r20500] [http://article.gmane.org/gmane.science.nmr.relax.scm/18293 r20538] [http://article.gmane.org/gmane.science.nmr.relax.scm/18295 r20541] [http://article.gmane.org/gmane.science.nmr.relax.scm/18297 r20537]* The [[M61]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17647 r19891] [http://article.gmane.org/gmane.science.nmr.relax.scm/17648 r19892] [http://article.gmane.org/gmane.science.nmr.relax.scm/17649 r19893] [http://article.gmane.org/gmane.science.nmr.relax.scm/17662 r19906] [http://article.gmane.org/gmane.science.nmr. For example try cosh(1000) in Pythonrelax.scm/17663 r19907]
In the reference example, the M61 model code was copied from the LM63 module and modified appropriately.== Creating a new experiment type ==
==== Reference commits ====If the model being added is for a completely new data type, then support for this must be added. In almost all cases, the experiment type will already be supported.
* NS R1rho 2-site [http://article.gmane.org/gmane.science.nmr.relax.scm/18479]* The DPL94 model [http://article.gmane.org/gmane.science.nmr.relax.scm/17756]* The M61 skew model [http://article.gmane.org/gmane.science.nmr.relax.scm/17729]* The M61 model [http://article.gmane.org/gmane.science.nmr.relax.scm/17615]* The CR72 model [http://article.gmane.org/gmane.science.nmr.relax.scm/17570] [http://article.gmane.org/gmane.science.nmr.relax.scm/17572] [http://article.gmane.org/gmane.science.nmr.relax.scm/17575] [http://article.gmane.org/gmane.science.nmr.relax.scm/17589]=== Reference commits ===
=== The target function ===
Again in this example, the code for the M61 is copied from the LM63 model and then modified.=== Reference commits ===
==== Reference commits ====* The [[MQ CR72]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18881 r21125]* The [[MQ NS CPMG 2-site]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18811 r21055]* The [[NS R1rho 2-site]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18482 r20726]* The [[TP02]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18249 r20493]* The [[DPL94]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17758 r20002]* The [[M61 skew]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17732 r19976]* The [[M61]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17622 r19866]* The [[No Rex]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17592 r19836]
* NS R1rho 2-site [http://article.gmane.org/gmane.science.nmr.relax.scm/18481]* The DPL94 model [http://article.gmane.org/gmane.science.nmr.relax.scm/17757]* The M61 skew model [http://article.gmane.org/gmane.science.nmr.relax.scm/17730]* The M61 model [http://article.gmane.org/gmane.science.nmr.relax.scm/17616] [http://article.gmane.org/gmane.science.nmr.relax.scm/17660] [http://article.gmane.org/gmane.science.nmr.relax.scm/17661]* No Rex [http://article.gmane.org/gmane.science.nmr.relax.scm/17592]* The CR72 model [http://article.gmane.org/gmane.science.nmr.relax.scm/17571]== Adding support for the parameters ==
This is needed to enable the * The [[MQ NS CPMG 2-site]] modelat [http://article. This example is for the gmane.org/gmane.science.nmr.relax.scm/18812 r21056]* The [[CR72 ]] model implementation as the parameters required for the M61 model match those of the preexisting LM63 modelat [http://article.gmane.org/gmane.science.nmr.relax.scm/17573 r19817]
* [http://articleThe target function is used in optimisation and is a class method which takes as a single argument the parameter vector.gmane This list is changed by the minimisation algorithm during optimisation.org/gmane.science.nmr The target function should then return a single floating point number - the chi-squared value.relax.scm/17573 The CR72 model]
Now the back end of the relax_disp* The [[MQ CR72]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18882 r21126]* The [[MQ NS CPMG 2-site]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18823 r21067]* The [[NS R1rho 2-site]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18481 r20725]* The [[TP02]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18248 r20492]* The [[DPL94]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17757 r20001]* The [[M61 skew]] model at [http://article.select_model user function for the gmane.org/gmane.science.nmr.relax.scm/17730 r19974]* The [[M61]] model can be addedat [http://article.gmane.org/gmane.science.nmr. This involved identifying the relax.scm/17616 r19860] [http://article.gmane.org/gmane.science.nmr.relax.scm/17660 r19904] [http://article.gmane.org/gmane.science.nmr.relax.scm/17661 r19905]* The [[No Rex]] model and constructing the parameter listat [http://article.gmane.org/gmane.science.nmr.relax.scm/17592 r19836]* The [[CR72]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17571 r19815]
* NS R1rho 2-site [http://articleNow the dispersion function needs to be added to the relax library (in the <code>lib.gmane.orgrelax_disp</gmanecode> package).science.nmr.relax.scm This should be designed as a simple Python function which takes the dispersion parameters and experimental variables, and calculates the {{:R2eff}}/18482]* The DPL94 model [http{{://article.gmaneR1rho}} values.org/gmane.science.nmr.relax.scm/17758]* The M61 skew model [http://article.gmane.org/gmane.science.nmrmodule can contain auxiliary functions for the calculation. Some auxiliary functions, if not specific to relaxation dispersion, may be better placed in other locations within the relaxlibrary.scm/17732]* The M61 model [http://article.gmane.org/gmane.science.nmr Remember to add all new modules to the <code>lib.relaxrelax_disp.scm__init__</17622]* No Rex [http:code> package <code>__all__<//articlecode> list.gmane.org/gmane.science.nmr.relax.scm/17592]
=== The test suite ===dispersion code in the relax library must be robust. This involves identifying parameter values or combinations which would cause failures in the mathematical operations (numerical issues not present in the mathematics must be considered). Note that parameter values of 0 are common within a grid search. It should be decided if the {{:R2eff}}/{{:R1rho}} value should be set to zero, to another value, or to something large (e.g. 1e100). For example:
This step is normally performed as step number 1Divisions - always catch zeros in the denominator with if statements, even if you believe that this will never be encountered. This is the most important part that makes Square roots - make sure that the code value inside is always > 0. Trigonometric functions - these should be tested for where they are not only works now, but will continue working for defined or where the entire lifetime of the relax projectsoftware implementation can no longer handle certain values. For example try <code>cosh(1000)</code> in Python.
The idea is that synthetic data (here for example as Sparky peak lists) is created for the model and added to the test suite directory test_suite/shared_data/dispersion/. This is then used in a system test to check that the code in relax can reproduce the data. It is very important that the code added to the relax library is not used to create the synthetic data!=== Reference commits ===
==== Reference commits ====* The [[MQ CR72]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18883 r21127]* The [[MQ NS CPMG 2-site]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18824 r21068]* The [[NS R1rho 2-site]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18479 r20723]* The [[TP02]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18241 r20486] [http://article.gmane.org/gmane.science.nmr.relax.scm/18246 r20490] [http://article.gmane.org/gmane.science.nmr.relax.scm/18280 r20524]* The [[DPL94]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17756 r20000]* The [[M61 skew]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17729 r19973]* The [[M61]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17615 r19859]* The [[CR72]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17570 r19814] [http://article.gmane.org/gmane.science.nmr.relax.scm/17572 r19816] [http://article.gmane.org/gmane.science.nmr.relax.scm/17575 r19819] [http://article.gmane.org/gmane.science.nmr.relax.scm/17589 r19833]
* NS R1rho 2-site [http://article.gmane.org/gmane.science.nmr.relax.scm/18485] [http://article.gmane.org/gmane.science.nmr.relax.scm/18486] [http://article.gmane.org/gmane.science.nmr.relax.scm/18488]* The M61 model [http://article.gmane.org/gmane.science.nmr.relax.scm/17647] [http://article.gmane.org/gmane.science.nmr.relax.scm/17648] [http://article.gmane.org/gmane.science.nmr.relax.scm/17649] [http://article.gmane.org/gmane.science.nmr.relax.scm/17662] [http://article.gmane.org/gmane.science.nmr.relax.scm/17663]== Comparing to other software ==
=== Comparing Once the relax code is able to other software ===find identical or better results than the dispersion softwares, then the values found in the test suite optimisation can be locked in. The <code>assertEqual()</code> and <code>assertAlmostEqual()</code> methods can be used to only allow the test to pass when the correct values are found.
It can happen that a bug present in the lib.dispersion package code is also replicated in the synthetic data. This is not uncommon. Therefore it is very useful to use other software with the test data from step 7 to see if the original parameters can be found. A good example can be seen in the test_suite/shared_data/dispersion/Hansen which contains Dr. Flemming Hansen's CPMG data (see the README file) and the results from different programs including NESSY, relax, CPMGFit, and ShereKhan. The comparison is in the file 'software_comparison'.== Debugging ==
Once the relax code is able to find identical or better results than the dispersion softwares, then the values found This step should not require an explanation. It goes hand-in -hand with the test suite optimisation can be locked in. The assertEqual() and assertAlmostEqual() methods can be used to only allow the test comparison to pass when the correct values are foundother software.
This step should not require an explanationThe model variable in <code>specific_analyses.relax_disp.variables</code> needs to be imported into the <code>auto_analyses.relax_disp</code> module. It goes hand-This is then used in-hand with steps 7the <code>write_results() </code> method to output text files and 8)Grace plots of the parameters. Be sure that the model variable is added to each part of this method corresponding to the parameters of the model.
=== * The auto[[MQ CR72]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18884 r21128]* The [[MQ NS CPMG 2-site]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18828 r21072]* The [[TP02]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18527 r20771]* The [[NS R1rho 2-site]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18526 r20770]* The [[LM63 3-analysis ===site]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18183 r20427] [http://article.gmane.org/gmane.science.nmr.relax.scm/18189 r20433]
=== For the model to be accessible via the GUI, it must be added to the <code>Disp_model_list_cpmg</code> or <code>Disp_model_list_r1rho</code> model list classes (at the bottom of the module). The GUI ===model variable should be added to the models list, and the list of parameters added to the params list.
The model needs to also be added to the graphical user interface (GUI). This is in the gui.analyses.auto_relax_disp module. The model variable should first be imported. In the __init__() method, it should be decided if the model should be selected by default or if the user should manually select the model during the analysis. If the former, then it should be added to the ds.relax_gui.analyses[data_index].disp_models list.=== Reference commits ===
For the * The [[MQ CR72]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18885 r21129]* The [[MQ NS CPMG 2-site]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18829 r21073]* The [[NS R1rho 2-site]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18511 r20755]* The [[TP02]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18511 r20755]* The [[LM63 3-site]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18212 r20456]* The [[IT99]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17762 r20006]* The [[DPL94]] model to be accessible via the GUI, it must be added to the Disp_model_list_cpmg or Disp_model_list_r1rho at [http://article.gmane.org/gmane.science.nmr.relax.scm/17762 r20006]* The [[M61B]] model list classes (at the bottom of the module)[http://article.gmane.org/gmane.science.nmr.relax. scm/17762 r20006]* The [[M61]] model variable should be added to the models list, and the list of parameters added to the params listat [http://article.gmane.org/gmane.science.nmr.relax.scm/17617 r19861]* The [[R2eff]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17617 r19861]* The [[No Rex]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17592 r19836] [http://article.gmane.org/gmane.science.nmr.relax.scm/17617 r19861]
* No Rex The next step is to add the model, its description, the equations for the analytic models, and all references to the relaxation dispersion chapter of the relax [http:[manual]] (the source is the <code>docs/latex/article.gmanedispersion.orgtex</gmane.sciencecode> file).nmr The model could also be included in the script section of the chapter.relax.scm/17592]
=== * The [[MQ CR72]] model at [http://article.gmane.org/gmane.science.nmr.relax manual ===.scm/18900 r21144]* The [[MQ NS CPMG 2-site]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18833 r21077]* The [[NS R1rho 2-site]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18483 r20727]* The [[TP02]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18242 r20485] [http://article.gmane.org/gmane.science.nmr.relax.scm/18247 r20491] [http://article.gmane.org/gmane.science.nmr.relax.scm/18296 r20540]* The [[LM63 3-site]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18165 r20409]* The [[NS CPMG 2-site expanded]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18122 r20366]* The [[NS CPMG 2-site star]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18071 r20315]* The [[M61]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18294 r20539]* The [[CR72]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18077 r20321]
==== Reference commits ====If the added model is to be presented to the user, it should also be added to the sample scripts. This includes all scripts in the <code>sample_scripts/relax_disp/</code> directory. For example it can be included in the <code>MODELS</code> list in the <code>cpmg_analysis.py</code> script.
* NS R1rho 2-site [http://article.gmane.org/gmane.science.nmr.relax.scm/18483]=== Reference commits ===
Replacement of dead Gna! links.
The following is a tutorial for adding new relaxation dispersion models for either CPMG-type or {{:R1rho}}-type experiments to the software relax. This includes both the models based on the analytic, closed-form expressions as well as the models involving numeric solutions of the Bloch-McConnell equations.
The tutorial will follow the example of the addition of the models already present within relax, pointing to the relevant commits for reference. To see the commit message and the code changes in colour, click on the links found within these commit messages. The models in the reference commits sections are in reverse chronological order and therefore the top links will be the most recent and relevant.
=== Adding the model to the list =The test suite ==
It is very important that the code added to the relax library is not used to create the synthetic data! This type of data is useful for checking that the known solution can be found by relax. The only issue is that the same mistake can be made in both relax and the script used to generated the synthetic data, in which case the buggy relax code will never be detected. To mitigate against this, testing against other software is recommended.
=== The relax_disp.select_model user function front end Measured data ===
* NS R1rho 2-site [http://articleAdd the original full peak lists to the directory.gmane.org/gmane.science.nmr.relax.scm/18478]* The DPL94 model [http://article.gmane.org/gmane.science.nmr.relax.scm/17754]* The M61 skew model [http://article.gmane.org/gmane.science.nmr.relax.scm/17725]* The M61 model [http://article.gmane.org/gmane.science.nmr.relax.scm/17612]* No Rex [http://article.gmane.org/gmane.science.nmr.relax.scm/17592]* The CR72 model [http://article.gmane.org/gmane.science.nmr.relax.scm/17568]
* Make truncated versions of these files (ending in <code>_trunc.*</code>) and add these as well. These will be used for the system test instead of the full data to allow the test to finish in a reasonable amount of time.
* The [[MQ NS CPMG 2-site]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18814 r21058] [http://article.gmane.org/gmane.science.nmr.relax.scm/18816 r21060] [http://article.gmane.org/gmane.science.nmr.relax.scm/18817 r21061] [http://article.gmane.org/gmane.science.nmr.relax.scm/18819 r21063] [http://article.gmane.org/gmane.science.nmr.relax.scm/18820 r21064]
== Adding the model to the list == Firstly the model should be added to the lists of the <code>specific_analyses.relax_disp.variables</code> module. The target function model name is used stored in optimisation and is a class method special variable which takes as a single argument the parameter vectorwill be used throughout relax. === Reference commits === * The [[MQ CR72]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18879 r21123]* The [[MQ NS CPMG 2-site]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18788 r21032]* The [[NS R1rho 2-site]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18477 r20721]* The [[TP02]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18239 r20483]* The [[DPL94]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17753 r19997]* The [[M61 skew]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17724 r19968]* The [[M61]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17611 r19855]* The [[No Rex]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17592 r19836] == The relax_disp. This list select_model user function front end == The next step is changed by to add the minimisation algorithm during optimisationmodel, its description, the equations for the analytic models, and all references to the {{uf|relax_disp.select_model}} user function front end. === Reference commits === * The [[MQ CR72]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18880 r21124]* The [[MQ NS CPMG 2-site]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18791 r21035]* The [[NS R1rho 2-site]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18478 r20722]* The [[TP02]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18240 r20484]* The [[DPL94]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17754 r19998]* The [[M61 skew]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17725 r19969]* The [[M61]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17612 r19856]* The [[No Rex]] model at [http://article.gmane.org/gmane. science.nmr.relax.scm/17592 r19836]* The [[CR72]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/17568 r19812] == The target relax_disp.select_model user function should then return a single floating point number - back end == Now the back end of the {{uf|relax_disp.select_model}} user function for the model can be added. This involved identifying the model and constructing the chi-squared valueparameter list.
This is needed to enable the model. It involves modifying many of the modules in the <code>specific_analyses.relax_disp</code> package.
=== Adding support for the parameters Reference commits ===
==== Reference commits ==The target function ==
Again in this example, the code for the [[M61]] is copied from the [[LM63]] model and then modified.
=== The relax_disp.select_model back end Reference commits ===
==== Reference commits ==The relax library ==
The relaxation dispersion functions in the library currently take as an argument a data structure for the back-calculated {{:R2eff}}/{{:R1rho}} values and populate this structure. This design is not essential if the target function, described in the next point, handles the library function appropriately. Just look at the files in <code>lib/dispersion</code> to get an idea of the design used.
It can happen that a bug present in the <code>lib.dispersion</code> package code is also replicated in the synthetic data. This is not uncommon. Therefore it is very useful to use other software with the test data from the test-suite step to see if the original parameters can be found. A good example can be seen in the <code>test_suite/shared_data/dispersion/Hansen</code> which contains Dr. Flemming Hansen's CPMG data (see the README file) and the results from different programs including NESSY, relax, CPMGFit, and ShereKhan. The comparison is in the file <code>software_comparison</code>.
=== Debugging =The auto-analysis ==
=== Reference commits ===
== The model variable in specific_analyses.relax_disp.variables needs to be imported into the auto_analyses.relax_disp module. This is then used in the write_results() method to output text files and Grace plots of the parameters. Be sure that the model variable is added to each part of this method corresponding to the parameters of the model.GUI ==
The model needs to also be added to the graphical user interface (GUI). This is in the <code>gui.analyses.auto_relax_disp</code> module. The model variable should first be imported. In the <code>__init__()</code> method, it should be decided if the model should be selected by default or if the user should manually select the model during the analysis. If the former, then it should be added to the <code>ds.relax_gui.analyses[data_index].disp_models</code> list.
==== Reference commits ==The relax manual ==
=== Reference commits ===
== The next step is to add the model, its description, the equations for the analytic models, and all references to the relaxation dispersion chapter of the relax [[manual]] (the source is the docs/latex/dispersion.tex file).sample scripts ==
* The [[NS CPMG 2-site expanded]] model at [http://article.gmane.org/gmane.science.nmr.relax.scm/18243 r20488]
== See also ==
[[Category:Tutorials]]
[[Category:Relaxation_dispersionRelaxation dispersion analysis]]