Updates koliop to 0.0.20

Includes:

- some documentation improvements;
- toolchain typos;
- default to release unless set my user/parent project;
- the_ removal;
- tor1, tor2, tor3 support for the distribution function (some inputs are still in (theta, r) layout right !);
- a rewrite of the collision operator is setup, notably, the configuration is now explicit and dependent on the geometry. The user needs to provide the operator with geometry specific quantities.

See merge request gysela-developpers/gyselalibxx!809

--------------------------------------------

Co-authored-by: Etienne Malaboeuf <eti.malaboeuf@gmail.com>

docs/Adding_docs.md

@@ -107,7 +107,7 @@ The `README.md` file should begin with a title:
 ```markdown
 # <title>
 ```
-If the folder doesn't contain a `.private` file (indicating that the folder is not yet ready to be shared publically), the new page can be referenced from any enclosing page that may exist. For example if you create a new folder in `src/`, you should add the following line to the list of folders in `src/README.md`:
+If the folder doesn't contain a `.private` file (indicating that the folder is not yet ready to be shared publicly), the new page can be referenced from any enclosing page that may exist. For example if you create a new folder in `src/`, you should add the following line to the list of folders in `src/README.md`:
 ```markdown
 - [my_new_folder](./my_new_folder/README.md) : Short description of contents.
 ```
@@ -150,4 +150,4 @@ $$
 ```
 The first syntax can be used when the expression fits in one line and doesn't use markdown special characters. The second syntax can be used in all contexts.
 
-In C++ header files it should be blocked with Doxagen syntax, i.e. `@f$` instead of `$`, and `@f[` and `@f]` instead of `$$`.
+In C++ header files it should be blocked with Doxygen syntax, i.e. `@f$` instead of `$`, and `@f[` and `@f]` instead of `$$`.

simulations/geometryVparMu/collisions/CMakeLists.txt

@@ -8,6 +8,7 @@ target_link_libraries(test_collSpVparMu
   PDI::pdi
   gslx::collisions
   gslx::geometry_vparmu
+  gslx::geometry_collisions_vparmu
   gslx::initialization_vparmu
   gslx::io
   gslx::quadrature

simulations/geometryVparMu/collisions/coll_1specie_maxwellian.yaml

@@ -13,9 +13,9 @@ SpeciesInfo:
   temperature_eq: 1.
   mean_velocity_eq: 0.
 
-CollisionsInfo:
+Collisions:
   nustar0_rpeak: 1.
-  collisions_interspecies: false
+  interspecies: false
 
 Algorithm:
   deltat: 0.01  # Attention: must be < 1.e-2 because plays the role of nustar here

simulations/geometryVparMu/collisions/coll_2species_maxwellian_differentT.yaml

@@ -18,9 +18,9 @@ SpeciesInfo:
   temperature_eq: 1.1
   mean_velocity_eq: 0.
 
-CollisionsInfo:
+Collisions:
   nustar0_rpeak: 1.
-  collisions_interspecies: true
+  interspecies: true
 
 Algorithm:
   deltat: 0.0001    # Attention: must be < 1.e-2 because plays the role of nustar here

simulations/geometryVparMu/collisions/coll_2species_maxwellian_differentV.yaml

@@ -18,9 +18,9 @@ SpeciesInfo:
   temperature_eq: 1.
   mean_velocity_eq: 0.1
 
-CollisionsInfo:
+Collisions:
   nustar0_rpeak: 1.
-  collisions_interspecies: true
+  interspecies: true
 
 Algorithm:
   deltat: 0.0001    # Attention: must be < 1.e-2 because plays the role of nustar here

simulations/geometryVparMu/collisions/params.yaml.hpp

@@ -22,9 +22,9 @@ constexpr char const* const params_yaml = R"PDI_CFG(SplineMesh:
   temperature_eq: 1.1
   mean_velocity_eq: 0.
 
-CollisionsInfo:
+Collisions:
   nustar0_rpeak: 1.
-  collisions_interspecies: true
+  interspecies: true
 
 Algorithm:
   deltat: 0.01

simulations/geometryVparMu/collisions/test_collSpVparMu.cpp

@@ -11,8 +11,8 @@
 #include <paraconf.h>
 #include <pdi.h>
 
-#include "CollisionSpVparMu.hpp"
-#include "collisioninfo.hpp"
+#include "collision_configuration.hpp"
+#include "collision_operator.hpp"
 #include "ddc_alias_inline_functions.hpp"
 #include "geometry.hpp"
 #include "input.hpp"
@@ -67,7 +67,7 @@ int main(int argc, char** argv)
             = MaxwellianEquilibrium::init_from_input(idxrange_kinsp, conf_collision);
     init_fequilibrium(get_field(allfequilibrium));
 
-    // ---> Initialisation of the distribution function as a pertubed Maxwellian
+    // ---> Initialisation of the distribution function as a perturbed Maxwellian
     DFieldMemSpVparMu allfdistribu(idxrange_spvparmu);
     NoPerturbInitialization const init(get_const_field(allfequilibrium));
     init(get_field(allfdistribu));
@@ -98,14 +98,14 @@ int main(int argc, char** argv)
     SplineMuBuilder const builder_mu(idxrange_mu);
     DFieldMemMu const coeff_intdmu(simpson_trapezoid_quadrature_coefficients_1d<
                                    Kokkos::DefaultExecutionSpace>(idxrange_mu, Extremity::BACK));
-    CollisionInfo const collision_info(conf_collision);
-    CollisionSpVparMu<CollisionInfo, IdxRangeSpVparMu, GridVpar, GridMu, double> collision_operator(
-            collision_info,
+    CollisionConfiguration const collision_configuration(
+            conf_collision,
             idxrange_spvparmu,
             get_const_field(coeff_intdmu),
             get_const_field(coeff_intdvpar),
             B_norm,
             get_const_field(Bstar_s));
+    CollisionOperator collision_operator(collision_configuration);
 
     // --------- TIME ITERATION ---------
     // ---> Reading of algorithm info from input YAML file

src/collisions/CMakeLists.txt

@@ -1,7 +1,7 @@
 # SPDX-License-Identifier: MIT
 
 add_library("collisions" STATIC
-    koliop_interface.cpp
+    collision_operator.cpp
 )
 
 target_include_directories("collisions"