cleaning and doc

docs/source/run/parameters.rst

@@ -222,6 +222,28 @@ General parameters
     Background plasma density in SI units. Certain physical modules (collisions, ionization, radiation reactions) depend on the actual background density.
     Hence, in normalized units, they can only be included, if a background plasma density in SI units is provided using this input parameter.
 
+Binary collisions
+-----------------
+
+WARNING: this module is in development.
+
+HiPACE++ proposes an implementation of [Perez et al., Phys. Plasmas 19, 083104 (2012)], inherited from WarpX,
+for collisions between plasma-plasma and beam-plasma.
+As collisions depend on the physical density, in normalized units `hipace.background_density_SI` must be specified.
+
+* ``plasmas.collisions`` (list of `strings`) optional
+    List of names of binary Coulomb collisions.
+    Each will represent collisions between 2 species.
+
+* ``<collision name>.species`` (two `strings`) optional
+    The name of the two species for which collisions should be included.
+    This can either be plasma-plasma or beam-plasma collisions. For plasma-plasma collisions, the species can be the same to model collisions within a species.
+    The names must be in `plasmas.names` or `beams.names` (for beam-plasma collisions).
+
+* ``<collision name>.CoulombLog`` (`float`) optional (default `-1.`)
+    Coulomb logarithm used for this collision.
+    If not specified, the Coulomb logarithm is determined from the temperature in each cell.
+
 Field solver parameters
 -----------------------
 
@@ -410,25 +432,6 @@ When both are specified, the per-species value is used.
     making the opposite index type ideal. Since the normal deposition still requires the original index type,
     the compromise option ``2 2`` can be chosen. This will however require more memory in the binning process.
 
-Binary collisions for plasma species
-------------------------------------
-
-WARNING: this module is in development.
-
-HiPACE++ proposes an implementation of [Perez et al., Phys. Plasmas 19, 083104 (2012)], inherited from WarpX, between plasma species.
-As collisions depend on the physical density, in normalized units `hipace.background_density_SI` must be specified.
-
-* ``plasmas.collisions`` (list of `strings`) optional
-    List of names of types binary Coulomb collisions.
-    Each will represent collisions between 2 plasma species (potentially the same).
-
-* ``<collision name>.species`` (two `strings`) optional
-    The name of the two plasma species for which collisions should be included.
-
-* ``<collision name>.CoulombLog`` (`float`) optional (default `-1.`)
-    Coulomb logarithm used for this collision.
-    If not specified, the Coulomb logarithm is determined from the temperature in each cell.
-
 Beam parameters
 ---------------
 

src/particles/plasma/MultiPlasma.H

@@ -122,16 +122,6 @@ public:
     /** returns number of plasma species */
     int GetNPlasmas() const {return m_nplasmas;}
 
-    // /** Perform binary elastic Coulomb collision, inter- and/or intra-species.
-    //  *
-    //  * The algorithm implemented is that of [Perez et al., Phys. Plasmas 19, 083104 (2012)]
-    //  *
-    //  * \param[in] lev MR level
-    //  * \param[in] bx box on which plasma particles are sorted per-cell and collide together
-    //  * \param[in] geom Corresponding gemetry
-    //  */
-    // void doCoulombCollision (int lev, amrex::Box bx, amrex::Geometry geom);
-
     /** Reorder particles to speed-up current deposition
      * \param[in] islice zeta slice index
      */

src/particles/plasma/MultiPlasma.cpp

@@ -158,13 +158,6 @@ MultiPlasma::TileSort (amrex::Box bx, amrex::Geometry geom)
     }
 }
 
-// void
-// MultiPlasma::doCoulombCollision (int lev, amrex::Box bx, amrex::Geometry geom)
-// {
-//     HIPACE_PROFILE("MultiPlasma::doCoulombCollision()");
-//
-// }
-
 void
 MultiPlasma::ReorderParticles (const int islice)
 {