Clean up documentation (#3542)

* Fix comments for documentation

* More fixes to comments for documentation

* Fixes in the doc files

* Fix typo in parameters.rst

4 files changed, 13 insertions, 4 deletions

diff --git a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.H b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.H
index 142bb098d..63dadd127 100644
--- a/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.H
+++ b/Source/Diagnostics/ComputeDiagFunctors/BackTransformFunctor.H
@@ -42,6 +42,7 @@ public:
                         and store in destination multifab.
      * \param[in] num_buffers number of user-defined snapshots in the back-transformed lab-frame
      * \param[in] varnames names of the field-components as defined by the user for back-transformed diagnostics.
+     * \param[in] varnames_fields base names of field-components for the RZ modes
      * \param[in] crse_ratio the coarsening ratio for fields
      */
     BackTransformFunctor ( const amrex::MultiFab * const mf_src, const int lev,
diff --git a/Source/Diagnostics/ComputeDiagFunctors/BackTransformParticleFunctor.H b/Source/Diagnostics/ComputeDiagFunctors/BackTransformParticleFunctor.H
index 39c70553a..4bb1b0656 100644
--- a/Source/Diagnostics/ComputeDiagFunctors/BackTransformParticleFunctor.H
+++ b/Source/Diagnostics/ComputeDiagFunctors/BackTransformParticleFunctor.H
@@ -30,6 +30,7 @@ struct SelectParticles
      * @param[in] tmp_particle_data  temporary particle data
      * @param[in] current_z_boost    current z-position of the slice in boosted frame
      * @param[in] old_z_boost        previous z-position of the slice in boosted frame
+     * @param[in] a_offset           index offset for particles to be selected
      */
     SelectParticles( const WarpXParIter& a_pti, TmpParticles& tmp_particle_data,
                      amrex::Real current_z_boost, amrex::Real old_z_boost,
@@ -40,7 +41,8 @@ struct SelectParticles
      * for Lorentz transformation in obtaining the lab-frame data. The particles that
      * with positions that correspond to the specific z-slice in boosted frame are selected.
      *
-     * @param[in] SrcData particle tile data
+     * @tparam SrcData type of source data
+     * @param[in] src SrcData particle tile data
      * @param[in] i       particle index
      * @return 1 if particles is selected for transformation, else 0
      */
@@ -85,6 +87,7 @@ struct LorentzTransformParticles
      * @param[in] t_boost            time in boosted frame
      * @param[in] dt                 timestep in boosted-frame
      * @param[in] t_lab              time in lab-frame
+     * @param[in] a_offset           index offset for particles to be transformed
      */
     LorentzTransformParticles ( const WarpXParIter& a_pti, TmpParticles& tmp_particle_data,
                                 amrex::Real t_boost, amrex::Real dt,
@@ -94,8 +97,8 @@ struct LorentzTransformParticles
      * \brief Functor call. This method computes the Lorentz-transform for particle
      * attributes to obtain the lab-frame snapshot data.
      *
-     * @param[out] DstData particle tile data that stores the transformed particle data
-     * @param[in] SrcData particle tile data that is selected for transformation
+     * @param[out] dst DstData particle tile data that stores the transformed particle data
+     * @param[in] src SrcData particle tile data that is selected for transformation
      * @param[in] i_src particle index of the source particles
      * @param[in] i_dst particle index of the target particles (transformed data).
      */
@@ -206,6 +209,7 @@ public:
      * \param[in] z_slice_in_domain  if the z-slice at current_z_boost is within the bounds of
      *            the boosted-frame and lab-frame domain. The particles are transformed
      *            only if this value is true.
+     * \param[in] old_z_boost        previous z-position of the slice in boosted frame
      * \param[in] current_z_boost    z co-ordinate of the slice selected in boosted-frame.
      * \param[in] t_lab              current time in lab-frame for snapshot, i_buffer.
      * \param[in] snapshot_full      if the current snapshot, with index, i_buffer, is
diff --git a/Source/Diagnostics/ComputeDiagFunctors/ComputeParticleDiagFunctor.H b/Source/Diagnostics/ComputeDiagFunctors/ComputeParticleDiagFunctor.H
index a76cde936..e14e777e0 100644
--- a/Source/Diagnostics/ComputeDiagFunctors/ComputeParticleDiagFunctor.H
+++ b/Source/Diagnostics/ComputeDiagFunctors/ComputeParticleDiagFunctor.H
@@ -30,9 +30,10 @@ public:
      *         back-transformed diagnostics, that are unused for regular diagnostics.
      *
      * \param[in] i_buffer           index of the snapshot
-     * \param[in] z_slice_in_domain  if the z-slice at current_z_boost is within the bounds of
+     * \param[in] ZSliceInDomain     if the z-slice at current_z_boost is within the bounds of
      *            the boosted-frame and lab-frame domain. The particles are transformed
      *            only if this value is true.
+     * \param[in] old_z_boost        old z co-ordinate of the slice selected in boosted-frame.
      * \param[in] current_z_boost    z co-ordinate of the slice selected in boosted-frame.
      * \param[in] t_lab              current time in lab-frame for snapshot, i_buffer.
      * \param[in] snapshot_full      if the current snapshot, with index, i_buffer, is
@@ -50,6 +51,7 @@ public:
                                       }
     /** Compute particle attributes and store the result in pc_dst particle container.
      *  \param[out] pc_dst  output particle container where the result is stored.
+     *  \param[out] totalParticlesInBuffer total number of particles in the container
      *  \param[in] i_buffer snapshot index for which the particle buffer is processed
      */
     virtual void operator () (PinnedMemoryParticleContainer& pc_dst, int &totalParticlesInBuffer, int i_buffer = 0) const = 0;
diff --git a/Source/Diagnostics/ComputeDiagFunctors/DivBFunctor.H b/Source/Diagnostics/ComputeDiagFunctors/DivBFunctor.H
index ebc62808c..a76411bf3 100644
--- a/Source/Diagnostics/ComputeDiagFunctors/DivBFunctor.H
+++ b/Source/Diagnostics/ComputeDiagFunctors/DivBFunctor.H
@@ -19,6 +19,8 @@ public:
      * \param[in] lev level of multifab.
      * \param[in] crse_ratio for interpolating field values from simulation MultiFabs
                   to the output diagnostic MultiFab, mf_dst.
+     * \param[in] convertRZmodes2cartesian whether to generate the result in Cartesian coordinates
+     *            (summing over modes)
      * \param[in] ncomp Number of component of mf_src to cell-center in dst multifab.
      */
     DivBFunctor(const std::array<const amrex::MultiFab* const, 3> arr_mf_src, const int lev, amrex::IntVect crse_ratio,