updated readme and license

ep2lab · Jul 17, 2018 · 21c92d1 · 21c92d1
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diff --git a/+dimagno/+postprocessor/fronts_to_arrays.m b/+dimagno/+postprocessor/fronts_to_arrays.m
@@ -4,7 +4,7 @@
 
 MMM20180522
 %}
-function solution = fronts_to_arrays(data,solution)
+% function solution = fronts_to_arrays(data,solution)
 
 frontfiles = dir(fullfile(data.dimagno.simdir,'fronts','*.mat'));
 

diff --git a/+dimagno/+postprocessor/induced_field.m b/+dimagno/+postprocessor/induced_field.m
@@ -8,7 +8,7 @@
 
 MMM20180522
 %}
-function solution = induced_field(data,solution)
+% function solution = induced_field(data,solution)
 
 %% Create and prepare induced field object
 solution.induced = magnetic_field.library_2d; % Field object (library_2d)
@@ -25,6 +25,7 @@
 I = scatteredInterpolant(solution.z(:),solution.r(:),solution.jtheta(:));
 JTHETA = I(solution.induced.ZZ,solution.induced.RR);
 JTHETA(data.applied.field_2d(solution.induced.ZZ,solution.induced.RR) > data.applied.field_2d(data.initialfront.front.z_(end),data.initialfront.front.r_(end)) ) = 0; % set to 0 the jtheta of points outside of the plasma.
+JTHETA(solution.induced.ZZ<=0 & solution.induced.RR>1) = 0; % set to 0 the jtheta of points outside of the plasma.
 clear I; % delete interpolant 
 
 % Generate temporary loop_2d object

diff --git a/+dimagno/+solver/dMoC_close_kernel.m b/+dimagno/+solver/dMoC_close_kernel.m
@@ -0,0 +1,33 @@
+%{
+
+This function receives a integration front_2d (Fold) and propagates it
+downstream once (Fnew).
+
+%} 
+function [Fnew] = dMoC_close_kernel(data,Fold)
+
+Fsub = dimagno.front;
+Fnew = dimagno.front;
+
+%% Subfront    
+for i = 1:Fold.n_points-1         
+    p = dimagno.solver.dMoC_inner(data,i+1,i,Fold);
+    Fsub.setpoint(p,i); clear p;   
+end
+
+%% Calculate inner
+for i = 1:Fsub.n_points-1 
+    p = dimagno.solver.dMoC_inner(data,i+1,i,Fsub);
+    Fnew.setpoint(p,i); clear p;   
+end
+
+%% Calculate axis       
+Fsub.setpoint(Fold.point(1),'prepend');
+p = dimagno.solver.dMoC_axis(data,2,1,Fsub);
+Fnew.setpoint(p,'prepend'); clear p;       
+
+%% Calculate border point    
+Fsub.setpoint(Fold.point(Fold.n_points),'append');
+p = dimagno.solver.dMoC_border(data,Fsub.n_points,Fsub.n_points-1,Fsub);
+Fnew.setpoint(p,'append'); clear p;
+
diff --git a/LICENSE.md b/LICENSE.md
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2018 Mario Merino
+Copyright (c) 2018 Mario Merino and Eduardo Ahedo
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -18,4 +18,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+SOFTWARE.
diff --git a/README.md b/README.md
@@ -9,34 +9,37 @@ DIMAGNO is a two-fluid code for the simulation of DIvergent MAgnetic NOzzles for
 It uses the method of characteristics to integrate the supersonic
 ion equations.
 
-The full version of DIMAGNO was developed since 2009 as part of my MSc and then my PhD theses, and has been used extensively to research the operation and the physics of the plasma flow in a magnetic nozzle. The version contained in this repository is a **refactored** version of that code, created recently with the purpose of making the code open source. As such, the code currently 
-only includes the basic functionality, and more features will be included gradually. If you are interested in any particular aspect of the code not yet included in the repository, feel free to contact me.
+The full version of DIMAGNO was developed since 2009 in the Space Propulsion and Plasmas Research Group
+at Universidad Carlos III de Madrid, by Mario Merino and Eduardo Ahedo,
+and has been used extensively to research the operation and the physics of the plasma flow in a magnetic nozzle. The version contained in this repository is a (still incomplete) **refactored** version of that code, created recently with the purpose of making the code open source. As such, the code currently
+only includes the basic functionality, and more features will be included gradually.
+ If you are interested in any particular aspect of the code not yet included in the repository, feel free to contact us.
 
 The full description of the model can be found in *E. Ahedo and M. Merino, "Two-dimensional supersonic plasma acceleration in a magnetic nozzle", Physics of Plasmas 17, 073501 (2010)*.
 
 ## Installation
 
-Installation requires simply that you 
-[download DIMAGNO](https://github.com/mariomerinomartinez/dimagno/archive/master.zip) 
-and add the base directory (the one that contains the `+dimagno` directory) 
+Installation requires simply that you
+[download DIMAGNO](https://github.com/mariomerinomartinez/dimagno/archive/master.zip)
+and add the base directory (the one that contains the `+dimagno` directory)
 to your Matlab path.
 
 ### Dependencies
 
-A recent version of Matlab is needed to run the code. 
-DIMAGNO has been developed in Matlab R2016b Academic version. 
+A recent version of Matlab is needed to run the code.
+DIMAGNO has been developed in Matlab R2016b Academic version.
 
 DIMAGNO depends on other Matlab packages that you can download from this
-GitHub account: 
+GitHub account:
 [magnetic_field](https://github.com/mariomerinomartinez/magnetic_field),
 [fluid_plasma](https://github.com/mariomerinomartinez/fluid_plasma),
 [utilities](https://github.com/mariomerinomartinez/utilities),
-[logger](https://github.com/mariomerinomartinez/logger). 
+[logger](https://github.com/mariomerinomartinez/logger).
 These packages must be installed and in your Matlab path to run DIMAGNO.
- 
+
 ## Quick usage guide
 
-All input parameters are configured in the `simrc` function included in the package. To use the code, copy this file as a template to the directory where you will run your simulation from, and edit it to your liking. 
+All input parameters are configured in the `simrc` function included in the package. To use the code, copy this file as a template to the directory where you will run your simulation from, and edit it to your liking.
 
 After creating a `magnetic_field` and a `fluid_plasma` object using the dependencies listed above, you need to create an initial condition `dimagno.ic`object. You can customize many aspects of these objects and the other parameters in your user `simrc` file, including the name of the folder where the output files will be generated and the type of postprocessing functions that will be run (currently limited to two until I finish refactoring the previous codebase).
 
@@ -49,7 +52,7 @@ To run DIMAGNO, pass the path to your `simrc` file to the main program:
 ```
 
 This will create a number of `.mat` files in the subfolder `fronts` with the raw results of the simulation, and two structures: `data` and `solution`.
-The output structure `data` contains all the actual preprocessed inputs used by the program; `solution` contains all the postprocessing results. 
+The output structure `data` contains all the actual preprocessed inputs used by the program; `solution` contains all the postprocessing results.
 
 *Unforturnately, the current version of DIMAGNO does not come with detailed documentation.*
 
@@ -67,23 +70,23 @@ There are also 4 subpackages:
 *  `preprocessor`: contains a function to perform some preprocessing of the input
 *  `postprocessor`: functions that the user can select, that will be run after the main simulation loop is completed.
 * `solver`: the functions that embody the method of characteristics and enable DIMAGNO to perform a simulation.
- 
+
 ### Testing
 
-The test suite of the refactored version of DIMAGNO is still quite minimal. 
-However, a few tests can be 
+The test suite of the refactored version of DIMAGNO is still quite minimal.
+However, a few tests can be
 found in the `/test` subdirectory. These tests can give you a feeling of how to run DIMAGNO on your own. After adding the package to
 your Matlab path, you can run all tests by executing `runtests` from this
 subdirectory.
 
 ## Contributing
 
-If you have any comments for improvement or 
-are interested in contributing to the continued 
-development of this or any of my other codes, you can contact us through 
+If you have any comments for improvement or
+are interested in contributing to the continued
+development of this or any of our other codes, you can contact us through
 [Mario's website](http://mariomerino.uc3m.es/).
 
-## Acknowledging 
+## Acknowledging
 
 This program is the result of substantial effort. It is released as open
 source in the hope that it will be useful to other people. If you find it
@@ -94,9 +97,9 @@ by citing the main article of the DIMAGNO model,
 
 and/or citing the code directly as:
 
-> Mario Merino (2018). DIMAGNO code: Divergent Magnetic Nozzle plasma flow integrator, [DOI: 10.5281/zenodo.1257295](https://doi.org/10.5281/zenodo.1257295)
-  
+> Mario Merino, Eduardo Ahedo (2018). DIMAGNO code: Divergent Magnetic Nozzle plasma flow integrator, [DOI: 10.5281/zenodo.1257295](https://doi.org/10.5281/zenodo.1257295)
+
 ## License
 
-Copyright (c) 2018 Mario Merino. 
+Copyright (c) 2018 Mario Merino and Eduardo Ahedo.
 The software is released as open source under the [MIT License](LICENSE.md).