Clean up documentation (#3542)

* Fix comments for documentation

* More fixes to comments for documentation

* Fixes in the doc files

* Fix typo in parameters.rst

31 files changed, 100 insertions, 92 deletions

diff --git a/Docs/source/developers/fields.rst b/Docs/source/developers/fields.rst
index b40bb750e..af834354d 100644
--- a/Docs/source/developers/fields.rst
+++ b/Docs/source/developers/fields.rst
@@ -112,7 +112,9 @@ Bilinear filter
 
 The multi-pass bilinear filter (applied on the current density) is implemented in ``Source/Filter/``, and class ``WarpX`` holds an instance of this class in member variable ``WarpX::bilinear_filter``. For performance reasons (to avoid creating too many guard cells), this filter is directly applied in communication routines, see ``WarpX::AddCurrentFromFineLevelandSumBoundary`` above and
 
-.. doxygenfunction:: WarpX::ApplyFilterandSumBoundaryJ
+.. doxygenfunction:: WarpX::ApplyFilterJ(const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>, 3>> &current, const int lev, const int idim)
+
+.. doxygenfunction:: WarpX::SumBoundaryJ(const amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>, 3>> &current, const int lev, const int idim, const amrex::Periodicity &period)
 
 Godfrey's anti-NCI filter for FDTD simulations
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/Docs/source/index.rst b/Docs/source/index.rst
index c1755f44f..ad9719d90 100644
--- a/Docs/source/index.rst
+++ b/Docs/source/index.rst
@@ -98,7 +98,6 @@ Data Analysis
    dataanalysis/visit
    dataanalysis/visualpic
    dataanalysis/picviewer
-   dataanalysis/backtransformed_diags
    dataanalysis/reduced_diags
 
 Theory
diff --git a/Docs/source/usage/parameters.rst b/Docs/source/usage/parameters.rst
index 36855a52d..22f01196a 100644
--- a/Docs/source/usage/parameters.rst
+++ b/Docs/source/usage/parameters.rst
@@ -766,7 +766,7 @@ Particle initialization
 
     * ``maxwell_boltzmann``: Maxwell-Boltzmann distribution that takes a dimensionless
       temperature parameter :math:`\theta` as an input, where :math:`\theta = \frac{k_\mathrm{B} \cdot T}{m \cdot c^2}`,
-      "math:`T` is the temperature in Kelvin, :math:`k_\mathrm{B}` is the Boltzmann constant, :math:`c` is the speed of light, and :math:`m` is the mass of the species.
+      :math:`T` is the temperature in Kelvin, :math:`k_\mathrm{B}` is the Boltzmann constant, :math:`c` is the speed of light, and :math:`m` is the mass of the species.
       Theta is specified by a combination of ``<species_name>.theta_distribution_type``, ``<species_name>.theta``, and ``<species_name>.theta_function(x,y,z)`` (see below).
       For values of :math:`\theta > 0.01`, errors due to ignored relativistic terms exceed 1%.
       Temperatures less than zero are not allowed.
diff --git a/Docs/source/usage/python.rst b/Docs/source/usage/python.rst
index f42a5cf57..d5af350b7 100644
--- a/Docs/source/usage/python.rst
+++ b/Docs/source/usage/python.rst
@@ -102,10 +102,6 @@ ElectrostaticFieldDiagnostic
 
 Lab-frame diagnostics diagnostics are used when running boosted-frame simulations.
 
-LabFrameParticleDiagnostic
-""""""""""""""""""""""""""
-.. autoclass:: pywarpx.picmi.LabFrameParticleDiagnostic
-
 LabFrameFieldDiagnostic
 """""""""""""""""""""""
 .. autoclass:: pywarpx.picmi.LabFrameFieldDiagnostic
@@ -258,12 +254,6 @@ simulation objects (particles, fields and memory buffers) as well as general pro
 
 .. autofunction:: pywarpx.picmi.Simulation.extension.finalize
 
-.. autofunction:: pywarpx.picmi.Simulation.extension.getistep
-
-.. autofunction:: pywarpx.picmi.Simulation.extension.gett_new
-
-.. autofunction:: pywarpx.picmi.Simulation.extension.evolve
-
 .. autofunction:: pywarpx.picmi.Simulation.extension.getProbLo
 
 .. autofunction:: pywarpx.picmi.Simulation.extension.getProbHi
@@ -309,8 +299,6 @@ with scraped particle data.
 
 .. autofunction:: pywarpx.picmi.Simulation.extension.get_particle_boundary_buffer_size
 
-.. autofunction:: pywarpx.picmi.Simulation.extension.get_particle_boundary_buffer_size
-
 .. autofunction:: pywarpx.picmi.Simulation.extension.get_particle_boundary_buffer_structs
 
 .. autofunction:: pywarpx.picmi.Simulation.extension.get_particle_boundary_buffer
diff --git a/Source/BoundaryConditions/WarpX_PEC.H b/Source/BoundaryConditions/WarpX_PEC.H
index 7fb9a8821..fe182feb7 100644
--- a/Source/BoundaryConditions/WarpX_PEC.H
+++ b/Source/BoundaryConditions/WarpX_PEC.H
@@ -26,7 +26,7 @@ using namespace amrex;
      * \param[in] fboundary  Value containing boundary type
      * \param[in] dir        direction
      *
-     * \param[out] 1 if the boundary type is PEC else 0
+     * \returns 1 if the boundary type is PEC else 0
      */
     AMREX_GPU_DEVICE AMREX_FORCE_INLINE
     bool is_boundary_PEC (amrex::GpuArray<int, 3> const& fboundary, int dir) {
diff --git a/Source/Diagnostics/BTD_Plotfile_Header_Impl.H b/Source/Diagnostics/BTD_Plotfile_Header_Impl.H
index a7fc9fd1e..c4f9d52b4 100644
--- a/Source/Diagnostics/BTD_Plotfile_Header_Impl.H
+++ b/Source/Diagnostics/BTD_Plotfile_Header_Impl.H
@@ -245,7 +245,8 @@ class BTDSpeciesHeaderImpl
 {
 public:
     /** Constructor.
-     * \param[in] string containing path of Headerfile
+     * \param[in] Headerfile_path string containing path of Headerfile
+     * \param[in] species_name string containing species name
      */
     BTDSpeciesHeaderImpl (std::string const& Headerfile_path, std::string const& species_name);
     ~BTDSpeciesHeaderImpl () = default;
@@ -256,7 +257,7 @@ public:
     /** Set data Index of the data-file, DATAXXXXX, that the particles belong to*/
     void set_DataIndex (const int lev, const int box_id, const int data_index);
     /** Add new_particles to existing to obtain the total number of particles of the species.
-        \param[in] new_particles, total particles in the new buffer
+        \param[in] new_particles total particles in the new buffer
      */
     void AddTotalParticles (const int new_particles) { m_total_particles += new_particles;}
     /** Increment number of boxes in a box array by 1, with every flush. */
@@ -310,7 +311,7 @@ class BTDParticleDataHeaderImpl
 {
 public:
     /** Constructor.
-     * \param[in] string containing path of Headerfile
+     * \param[in] Headerfile_path containing path of Headerfile
      */
     BTDParticleDataHeaderImpl (std::string const& Headerfile_path);
     /** Destructor */
@@ -326,14 +327,14 @@ public:
      */
     void IncreaseBoxArraySize ( const int add_size) { m_ba_size += add_size;}
     /** Returns box corresponding to the ith box in the BoxArray, m_ba.
-     *  \param[in] int ibox, index of the box in the BoxArray.
+     *  \param[in] ibox index of the box in the BoxArray.
      */
     amrex::Box ba_box (int ibox) {return m_ba[ibox]; }
     /** Resize boxArray, m_ba, to size, m_ba_size. */
     void ResizeBoxArray () { m_ba.resize(m_ba_size); }
     /** Set Box indices of the ith-box in Box Array, m_ba, to the new Box, ba_box.
-     *  \param[in] int ibox, index of the ith box in BoxArray, m_ba.
-     *  \param[in] amrex::Box box dimensions corresponding to the ith Fab.
+     *  \param[in] ibox index of the ith box in BoxArray, m_ba.
+     *  \param[in] ba_box dimensions corresponding to the ith Fab.
      */
     void SetBox (int ibox, amrex::Box ba_box) { m_ba.set(ibox, ba_box); }
     /** Size of BoxArray, m_ba*/
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,
diff --git a/Source/Diagnostics/FlushFormats/FlushFormatAscent.H b/Source/Diagnostics/FlushFormats/FlushFormatAscent.H
index 01b051373..cdf08eaf8 100644
--- a/Source/Diagnostics/FlushFormats/FlushFormatAscent.H
+++ b/Source/Diagnostics/FlushFormats/FlushFormatAscent.H
@@ -44,11 +44,12 @@ public:
         bool isLastBTDFlush = false,
         const amrex::Vector<int>& totalParticlesFlushedAlready = amrex::Vector<int>() ) const override;
 
+#ifdef AMREX_USE_ASCENT
     /** \brief Do in-situ visualization for particle data.
      * \param[in] particle_diags Each element of this vector handles output of 1 species.
+     * \param[out] a_bp_mesh blueprint mesh generated from the container
      * Only compile if AMREX_USE_ASCENT because we need to pass a conduit class
      */
-#ifdef AMREX_USE_ASCENT
     void WriteParticles(const amrex::Vector<ParticleDiag>& particle_diags, conduit::Node& a_bp_mesh) const;
 #endif
 
diff --git a/Source/Diagnostics/FlushFormats/FlushFormatPlotfile.H b/Source/Diagnostics/FlushFormats/FlushFormatPlotfile.H
index e773f8e2f..744ef2e4b 100644
--- a/Source/Diagnostics/FlushFormats/FlushFormatPlotfile.H
+++ b/Source/Diagnostics/FlushFormats/FlushFormatPlotfile.H
@@ -48,6 +48,7 @@ public:
     /** \brief Write particles data to file.
      * \param[in] filename name of output directory
      * \param[in] particle_diags Each element of this vector handles output of 1 species.
+     * \param[in] isBTD whether this is a back-transformed diagnostic
      */
     void WriteParticles(const std::string& filename,
                         const amrex::Vector<ParticleDiag>& particle_diags,
diff --git a/Source/Diagnostics/FullDiagnostics.H b/Source/Diagnostics/FullDiagnostics.H
index bf0b8b6a5..8620af75e 100644
--- a/Source/Diagnostics/FullDiagnostics.H
+++ b/Source/Diagnostics/FullDiagnostics.H
@@ -54,7 +54,7 @@ private:
       */
     void InitializeBufferData ( int i_buffer, int lev ) override;
     /** Initialize functors that store pointers to the RZ fields requested by the user.
-     * \parm[in] lev level on which the vector of unique_ptrs to field functors is initialized.
+     * \param[in] lev level on which the vector of unique_ptrs to field functors is initialized.
      */
     void InitializeFieldFunctorsRZopenPMD (int lev) override;
     /** Append m_all_field_functors[lev] with all modes of all components of E B and j
diff --git a/Source/Diagnostics/WarpXOpenPMD.H b/Source/Diagnostics/WarpXOpenPMD.H
index 4d22b2953..aaa0acba8 100644
--- a/Source/Diagnostics/WarpXOpenPMD.H
+++ b/Source/Diagnostics/WarpXOpenPMD.H
@@ -106,6 +106,8 @@ public:
    * @param filetype file backend, e.g. "bp" or "h5"
    * @param operator_type openPMD-api backend operator (compressor) for ADIOS2
    * @param operator_parameters openPMD-api backend operator parameters for ADIOS2
+   * @param engine_type ADIOS engine for output
+   * @param engine_parameters map of parameters for the engine
    * @param fieldPMLdirections PML field solver, @see WarpX::getPMLdirections()
    */
   WarpXOpenPMDPlot (openPMD::IterationEncoding ie,
@@ -143,7 +145,7 @@ public:
    *
    * @param varnames variable names in each multifab
    * @param mf multifab for each level
-   * @param geometry for each level
+   * @param geom for each level
    * @param output_levels the finest level to output, <= maxLevel
    * @param iteration the current iteration or reconstructed labframe station number
    * @param time the current simulation time in the lab frame
@@ -262,6 +264,7 @@ private:
    * @param[in] write_int_comp The int attribute ids, from WarpX
    * @param[in] int_comp_names The int attribute names, from WarpX
    * @param[in] np  Number of particles
+   * @param[in] isBTD whether this is a back-transformed diagnostic
    */
   void SetupRealProperties (ParticleContainer const * pc,
                openPMD::ParticleSpecies& currSpecies,
diff --git a/Source/Diagnostics/WarpXOpenPMD.cpp b/Source/Diagnostics/WarpXOpenPMD.cpp
index c5fdcc205..2cee7db21 100644
--- a/Source/Diagnostics/WarpXOpenPMD.cpp
+++ b/Source/Diagnostics/WarpXOpenPMD.cpp
@@ -1103,8 +1103,8 @@ WarpXOpenPMDPlot::SetConstParticleRecordsEDPIC (
 /*
  * Set up parameter for mesh container using the geometry (from level 0)
  *
- * @param [IN] meshes: openPMD-api mesh container
- * @param [IN] full_geom: field geometry
+ * @param [in] meshes: openPMD-api mesh container
+ * @param [in] full_geom: field geometry
  *
  */
 void
@@ -1177,9 +1177,9 @@ WarpXOpenPMDPlot::SetupFields ( openPMD::Container< openPMD::Mesh >& meshes,
 
 /*
  * Setup component properties  for a field mesh
- * @param [IN]: mesh          a mesh field
- * @param [IN]: full_geom     geometry for the mesh
- * @param [IN]: mesh_comp     a component for the mesh
+ * @param [in]: mesh          a mesh field
+ * @param [in]: full_geom     geometry for the mesh
+ * @param [in]: mesh_comp     a component for the mesh
  */
 void
 WarpXOpenPMDPlot::SetupMeshComp (openPMD::Mesh& mesh,
diff --git a/Source/FieldSolver/FiniteDifferenceSolver/FiniteDifferenceSolver.H b/Source/FieldSolver/FiniteDifferenceSolver/FiniteDifferenceSolver.H
index afa731734..ed6f918b3 100644
--- a/Source/FieldSolver/FiniteDifferenceSolver/FiniteDifferenceSolver.H
+++ b/Source/FieldSolver/FiniteDifferenceSolver/FiniteDifferenceSolver.H
@@ -101,10 +101,10 @@ class FiniteDifferenceSolver
           * \param[out] Efield  vector of electric field MultiFabs updated at a given level
           * \param[in] Bfield   vector of magnetic field MultiFabs at a given level
           * \param[in] Jfield   vector of current density MultiFabs at a given level
+          * \param[in] edge_lengths length of edges along embedded boundaries
           * \param[in] dt       timestep of the simulation
           * \param[in] macroscopic_properties contains user-defined properties of the medium.
           */
-
         void MacroscopicEvolveE ( std::array< std::unique_ptr<amrex::MultiFab>, 3>& Efield,
                       std::array< std::unique_ptr<amrex::MultiFab>, 3> const& Bfield,
                       std::array< std::unique_ptr<amrex::MultiFab>, 3 > const& Jfield,
diff --git a/Source/FieldSolver/SpectralSolver/SpectralFieldData.H b/Source/FieldSolver/SpectralSolver/SpectralFieldData.H
index c7848d731..e86348484 100644
--- a/Source/FieldSolver/SpectralSolver/SpectralFieldData.H
+++ b/Source/FieldSolver/SpectralSolver/SpectralFieldData.H
@@ -41,9 +41,12 @@ class SpectralFieldIndex
          *
          * \param[in] update_with_rho whether rho is used in the field update equations
          * \param[in] time_averaging  whether the time averaging algorithm is used
-         * \param[in] do_multi_J      whether the multi-J algorithm is used (hence two currents
+         * \param[in] J_in_time       the multi-J algorithm used (hence two currents
          *                            computed at the beginning and the end of the time interval
          *                            instead of one current computed at half time)
+         * \param[in] rho_in_time     the multi-rho algorithm used (hence two densities
+         *                            computed at the beginning and the end of the time interval
+         *                            instead of one density computed at half time)
          * \param[in] dive_cleaning   whether to use div(E) cleaning to account for errors in
          *                            Gauss law (new field F in the update equations)
          * \param[in] divb_cleaning   whether to use div(B) cleaning to account for errors in
diff --git a/Source/FieldSolver/SpectralSolver/SpectralSolver.H b/Source/FieldSolver/SpectralSolver/SpectralSolver.H
index da4b9687b..66fe1b816 100644
--- a/Source/FieldSolver/SpectralSolver/SpectralSolver.H
+++ b/Source/FieldSolver/SpectralSolver/SpectralSolver.H
@@ -143,10 +143,6 @@ class SpectralSolver
          * declared in the base class SpectralBaseAlgorithm and defined in its
          * derived classes, from objects of class SpectralSolver through the private
          * unique pointer \c algorithm.
-         *
-         * \param[in]     lev     The mesh refinement level
-         * \param[in,out] current Array of unique pointers to \c MultiFab storing
-         *                        the three components of the current density
          */
         void VayDeposition ()
         {
diff --git a/Source/Laser/LaserProfiles.H b/Source/Laser/LaserProfiles.H
index 8555b5187..098a48e8c 100644
--- a/Source/Laser/LaserProfiles.H
+++ b/Source/Laser/LaserProfiles.H
@@ -58,7 +58,6 @@ public:
      * member variables of the laser profile class.
      *
      * @param[in] ppl should be amrex::ParmParse(laser_name)
-     * @param[in] ppc should be amrex::ParmParse("my_constants")
      * @param[in] params common laser profile parameters
      */
     virtual void
diff --git a/Source/Parallelization/GuardCellManager.H b/Source/Parallelization/GuardCellManager.H
index 248a3dabf..35df85514 100644
--- a/Source/Parallelization/GuardCellManager.H
+++ b/Source/Parallelization/GuardCellManager.H
@@ -47,6 +47,8 @@ public:
      * \param do_pml_in_domain whether pml is done in the domain (only used by RZ PSATD)
      * \param pml_ncell number of cells on the pml layer (only used by RZ PSATD)
      * \param ref_ratios mesh refinement ratios between mesh-refinement levels
+     * \param use_filter whether filtering will be done
+     * \param bilinear_filter_stencil_length the size of the stencil for filtering
      */
     void Init(
         const amrex::Real dt,
diff --git a/Source/Particles/Collision/BinaryCollision/BinaryCollision.H b/Source/Particles/Collision/BinaryCollision/BinaryCollision.H
index 0c5ec182e..2c1cdc689 100644
--- a/Source/Particles/Collision/BinaryCollision/BinaryCollision.H
+++ b/Source/Particles/Collision/BinaryCollision/BinaryCollision.H
@@ -111,8 +111,9 @@ public:
      * @param mypc Container of species involved
      *
      */
-    void doCollisions (amrex::Real /*cur_time*/, amrex::Real dt, MultiParticleContainer* mypc) override
+    void doCollisions (amrex::Real cur_time, amrex::Real dt, MultiParticleContainer* mypc) override
     {
+        amrex::ignore_unused(cur_time);
 
         auto& species1 = mypc->GetParticleContainerFromName(m_species_names[0]);
         auto& species2 = mypc->GetParticleContainerFromName(m_species_names[1]);
@@ -192,6 +193,7 @@ public:
 
     /** Perform all binary collisions within a tile
      *
+     * \param[in] dt time step size
      * \param[in] lev the mesh-refinement level
      * \param[in] mfi iterator for multifab
      * \param species_1 first species container
diff --git a/Source/Particles/Collision/BinaryCollision/NuclearFusion/BoschHaleFusionCrossSection.H b/Source/Particles/Collision/BinaryCollision/NuclearFusion/BoschHaleFusionCrossSection.H
index 08af65ca6..e2a4fca25 100644
--- a/Source/Particles/Collision/BinaryCollision/NuclearFusion/BoschHaleFusionCrossSection.H
+++ b/Source/Particles/Collision/BinaryCollision/NuclearFusion/BoschHaleFusionCrossSection.H
@@ -21,6 +21,8 @@
  *
  * @param[in] E_kin_star the kinetic energy of the reactants in their center of mass frame, in SI units.
  * @param[in] fusion_type indicates which fusion reaction to calculate the cross-section for
+ * @param[in] m1 mass of the incoming particle
+ * @param[in] m2 mass of the target particle
  * @return The total cross section in SI units (square meters).
  */
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
diff --git a/Source/Particles/Collision/CollisionHandler.cpp b/Source/Particles/Collision/CollisionHandler.cpp
index cc8d8eb4a..e8f25a78b 100644
--- a/Source/Particles/Collision/CollisionHandler.cpp
+++ b/Source/Particles/Collision/CollisionHandler.cpp
@@ -68,6 +68,7 @@ CollisionHandler::CollisionHandler(MultiParticleContainer const * const mypc)
 /** Perform all collisions
  *
  * @param cur_time Current time
+ * @param dt time step size
  * @param mypc MultiParticleContainer calling this method
  *
  */
diff --git a/Source/Particles/Deposition/CurrentDeposition.H b/Source/Particles/Deposition/CurrentDeposition.H
index d478d838e..84d696ce4 100644
--- a/Source/Particles/Deposition/CurrentDeposition.H
+++ b/Source/Particles/Deposition/CurrentDeposition.H
@@ -36,7 +36,6 @@ using namespace amrex::literals;
                          ion_lev is a null pointer.
  * \param jx_fab,jy_fab,jz_fab FArrayBox of current density, either full array or tile.
  * \param np_to_depose Number of particles for which current is deposited.
- * \param dt           Time step for particle level
  * \param relative_time Time at which to deposit J, relative to the time of the
  *                      current positions of the particles. When different than 0,
  *                      the particle position will be temporarily modified to match
diff --git a/Source/Particles/Pusher/PushSelector.H b/Source/Particles/Pusher/PushSelector.H
index a56dda2b9..b1e590299 100644
--- a/Source/Particles/Pusher/PushSelector.H
+++ b/Source/Particles/Pusher/PushSelector.H
@@ -33,7 +33,7 @@
  * \param Bx, By, Bz                Magnetic field on particles.
  * \param ion_lev                   Ionization level of this particle (0 if ioniziation not on)
  * \param m                         Mass of this species.
- * \param q                         Charge of this species.
+ * \param a_q                       Charge of this species.
  * \param pusher_algo               0: Boris, 1: Vay, 2: HigueraCary
  * \param do_crr                    Whether to do the classical radiation reaction
  * \param do_copy                   Whether to copy the old x and u for the BTD
diff --git a/Source/Particles/WarpXParticleContainer.H b/Source/Particles/WarpXParticleContainer.H
index cb5542025..4f226fbf8 100644
--- a/Source/Particles/WarpXParticleContainer.H
+++ b/Source/Particles/WarpXParticleContainer.H
@@ -279,7 +279,7 @@ public:
      */
     void AddNParticles (int lev,
                         int n, const amrex::ParticleReal* x, const amrex::ParticleReal* y, const amrex::ParticleReal* z,
-                        const amrex::ParticleReal* vx, const amrex::ParticleReal* vy, const amrex::ParticleReal* vz,
+                        const amrex::ParticleReal* ux, const amrex::ParticleReal* uy, const amrex::ParticleReal* uz,
                         const int nattr_real, const amrex::ParticleReal* attr_real,
                         const int nattr_int, const int* attr_int,
                         int uniqueparticles, amrex::Long id=-1);
@@ -293,9 +293,6 @@ public:
     static void BackwardCompatibility ();
 
     /** \brief Apply particle BC.
-     *
-     * \param[in] boundary_conditions Type of boundary conditions. For now, only absorbing or none
-     * are supported
      */
     void ApplyBoundaryConditions ();
 
diff --git a/Source/Particles/WarpXParticleContainer.cpp b/Source/Particles/WarpXParticleContainer.cpp
index 6eae0d0b6..21ab1408c 100644
--- a/Source/Particles/WarpXParticleContainer.cpp
+++ b/Source/Particles/WarpXParticleContainer.cpp
@@ -144,9 +144,9 @@ WarpXParticleContainer::AddNParticles (int /*lev*/,
                                        int n, const amrex::ParticleReal* x,
                                        const amrex::ParticleReal* y,
                                        const amrex::ParticleReal* z,
-                                       const amrex::ParticleReal* vx,
-                                       const amrex::ParticleReal* vy,
-                                       const amrex::ParticleReal* vz,
+                                       const amrex::ParticleReal* ux,
+                                       const amrex::ParticleReal* uy,
+                                       const amrex::ParticleReal* uz,
                                        const int nattr_real, const amrex::ParticleReal* attr_real,
                                        const int nattr_int, const int* attr_int,
                                        int uniqueparticles, amrex::Long id)
@@ -226,9 +226,9 @@ WarpXParticleContainer::AddNParticles (int /*lev*/,
     if (np > 0)
     {
         pinned_tile.push_back_real(PIdx::w , weight.data(), weight.data() + np);
-        pinned_tile.push_back_real(PIdx::ux,     vx + ibegin,     vx + iend);
-        pinned_tile.push_back_real(PIdx::uy,     vy + ibegin,     vy + iend);
-        pinned_tile.push_back_real(PIdx::uz,     vz + ibegin,     vz + iend);
+        pinned_tile.push_back_real(PIdx::ux,     ux + ibegin,     ux + iend);
+        pinned_tile.push_back_real(PIdx::uy,     uy + ibegin,     uy + iend);
+        pinned_tile.push_back_real(PIdx::uz,     uz + ibegin,     uz + iend);
 
         if ( (NumRuntimeRealComps()>0) || (NumRuntimeIntComps()>0) ){
             DefineAndReturnParticleTile(0, 0, 0);
diff --git a/Source/Utils/Parser/IntervalsParser.H b/Source/Utils/Parser/IntervalsParser.H
index f590139b3..329e114bb 100644
--- a/Source/Utils/Parser/IntervalsParser.H
+++ b/Source/Utils/Parser/IntervalsParser.H
@@ -31,6 +31,7 @@ namespace utils::parser
         * Any of these integers may be omitted in which case it will be equal to their default value
         * (0 for the starting point, std::numeric_limits<int>::max() for the stopping point and 1 for
         * the period). For example SliceParser(":1000:") is equivalent to SliceParser("0:1000:1").
+        * @param[in] isBTD whether this is a back-transformed diagnostic
         */
         SliceParser (const std::string& instr, bool isBTD=false);
 
diff --git a/Source/Utils/ParticleUtils.H b/Source/Utils/ParticleUtils.H
index a997412f6..621f9725b 100644
--- a/Source/Utils/ParticleUtils.H
+++ b/Source/Utils/ParticleUtils.H
@@ -60,6 +60,7 @@ namespace ParticleUtils {
      *
      * @param[in] u2 square of particle speed (i.e. u dot u where u = gamma*v)
      * @param[in] m, M mass of projectile and target, respectively
+     * @param[out] gamma relativistic factor of the particle
      * @param[out] energy particle energy in eV
      */
     AMREX_GPU_HOST_DEVICE AMREX_INLINE
@@ -82,7 +83,7 @@ namespace ParticleUtils {
      * \brief Perform a Lorentz transformation of the given velocity
      * to a frame moving with velocity (Vx, Vy, Vz) relative to the present one.
      *
-     * @param[in/out] ux,uy,uz components of velocity vector in the current
+     * @param[in,out] ux,uy,uz components of velocity vector in the current
                       frame - importantly these quantities are gamma * velocity
      * @param[in] Vx,Vy,Vz velocity of the new frame relative to the current one,
                       NOT gamma*velocity!
@@ -150,7 +151,7 @@ namespace ParticleUtils {
      * random velocity vector with given magnitude. This is used in isotropic
      * collision events.
      *
-     * @param[in/out] ux, uy, uz colliding particle's velocity
+     * @param[in,out] ux, uy, uz colliding particle's velocity
      * @param[in] vp velocity magnitude of the colliding particle after collision.
      * @param[in] engine the random-engine
      */
diff --git a/Source/WarpX.H b/Source/WarpX.H
index 2d1124c06..5c25eb180 100644
--- a/Source/WarpX.H
+++ b/Source/WarpX.H
@@ -327,13 +327,13 @@ public:
      * to the map of MultiFabs (used to ease the access to MultiFabs from the Python
      * interface
      *
-     * \param mf[out] The MultiFab unique pointer to be allocated
-     * \param ba[in] The BoxArray describing the MultiFab
-     * \param dm[in] The DistributionMapping describing the MultiFab
-     * \param ncomp[in] The number of components in the MultiFab
-     * \param ngrow[in] The number of guard cells in the MultiFab
-     * \param name[in] The name of the MultiFab to use in the map
-     * \param initial_value[in] The optional initial value
+     * \param[out] mf The MultiFab unique pointer to be allocated
+     * \param[in] ba The BoxArray describing the MultiFab
+     * \param[in] dm The DistributionMapping describing the MultiFab
+     * \param[in] ncomp The number of components in the MultiFab
+     * \param[in] ngrow The number of guard cells in the MultiFab
+     * \param[in] name The name of the MultiFab to use in the map
+     * \param[in] initial_value The optional initial value
      */
     static void AllocInitMultiFab (
         std::unique_ptr<amrex::MultiFab>& mf,
@@ -350,13 +350,13 @@ public:
      * to the map of MultiFabs (used to ease the access to MultiFabs from the Python
      * interface
      *
-     * \param mf[out] The iMultiFab unique pointer to be allocated
-     * \param ba[in] The BoxArray describing the iMultiFab
-     * \param dm[in] The DistributionMapping describing the iMultiFab
-     * \param ncomp[in] The number of components in the iMultiFab
-     * \param ngrow[in] The number of guard cells in the iMultiFab
-     * \param name[in] The name of the iMultiFab to use in the map
-     * \param initial_value[in] The optional initial value
+     * \param[out] mf The iMultiFab unique pointer to be allocated
+     * \param[in] ba The BoxArray describing the iMultiFab
+     * \param[in] dm The DistributionMapping describing the iMultiFab
+     * \param[in] ncomp The number of components in the iMultiFab
+     * \param[in] ngrow The number of guard cells in the iMultiFab
+     * \param[in] name The name of the iMultiFab to use in the map
+     * \param[in] initial_value The optional initial value
      */
     static void AllocInitMultiFab (
         std::unique_ptr<amrex::iMultiFab>& mf,
@@ -370,11 +370,12 @@ public:
     /**
      * \brief
      * Create an alias of a MultiFab, adding the alias to the MultiFab map
-     * \param mf[out] The MultiFab to create
-     * \param mf_to_alias[in] The MultiFab to alias
-     * \param scomp[in] The starting component to be aliased
-     * \param ncomp[in] The number of components to alias
-     * \param name[in] The name of the MultiFab to use in the map
+     * \param[out] mf The MultiFab to create
+     * \param[in] mf_to_alias The MultiFab to alias
+     * \param[in] scomp The starting component to be aliased
+     * \param[in] ncomp The number of components to alias
+     * \param[in] name The name of the MultiFab to use in the map
+     * \param[in] initial_value optional initial value for MultiFab
      */
     static void AliasInitMultiFab (
         std::unique_ptr<amrex::MultiFab>& mf,
@@ -394,7 +395,7 @@ public:
      * \brief
      * Add the MultiFab to the map of MultiFabs
      * \param name The name of the MultiFab use to reference the MultiFab
-     * \parame mf The MultiFab to be added to the map (via a pointer to it)
+     * \param mf The MultiFab to be added to the map (via a pointer to it)
      */
     static void AddToMultiFabMap(const std::string name, const std::unique_ptr<amrex::MultiFab>& mf) {
         multifab_map[name] = mf.get();
@@ -404,7 +405,7 @@ public:
      * \brief
      * Add the iMultiFab to the map of MultiFabs
      * \param name The name of the iMultiFab use to reference the iMultiFab
-     * \parame mf The iMultiFab to be added to the map (via a pointer to it)
+     * \param mf The iMultiFab to be added to the map (via a pointer to it)
      */
     static void AddToMultiFabMap(const std::string name, const std::unique_ptr<amrex::iMultiFab>& mf) {
         imultifab_map[name] = mf.get();
@@ -593,7 +594,7 @@ public:
     /** apply QED correction on electric field for level lev and patch type patch_type
      *
      * \param lev mesh refinement level
-     * \param dt patch_type which MR patch: PatchType::fine or PatchType::coarse
+     * \param patch_type which MR patch: PatchType::fine or PatchType::coarse
      * \param dt time step
      */
     void Hybrid_QED_Push (int lev, PatchType patch_type, amrex::Real dt);
@@ -896,16 +897,16 @@ public:
      * on the staggered yee-grid or cell-centered grid, in the interior cells
      * and guard cells.
      *
-     * \param[in] mfx, x-component of the field to be initialized
-     * \param[in] mfy, y-component of the field to be initialized
-     * \param[in] mfz, z-component of the field to be initialized
-     * \param[in] xfield_parser, parser function to initialize x-field
-     * \param[in] yfield_parser, parser function to initialize y-field
-     * \param[in] zfield_parser, parser function to initialize z-field
-     * \param[in] edge_lengths, edge lengths information
-     * \param[in] face_areas, face areas information
-     * \param[in] field, flag indicating which field is being initialized ('E' for electric, 'B' for magnetic)
-     * \param[in] lev, level of the Multifabs that is initialized
+     * \param[in] mfx x-component of the field to be initialized
+     * \param[in] mfy y-component of the field to be initialized
+     * \param[in] mfz z-component of the field to be initialized
+     * \param[in] xfield_parser parser function to initialize x-field
+     * \param[in] yfield_parser parser function to initialize y-field
+     * \param[in] zfield_parser parser function to initialize z-field
+     * \param[in] edge_lengths edge lengths information
+     * \param[in] face_areas face areas information
+     * \param[in] field flag indicating which field is being initialized ('E' for electric, 'B' for magnetic)
+     * \param[in] lev level of the Multifabs that is initialized
      */
     void InitializeExternalFieldsOnGridUsingParser (
          amrex::MultiFab *mfx, amrex::MultiFab *mfy, amrex::MultiFab *mfz,
@@ -923,7 +924,7 @@ public:
      * EBs such as edge lengths, face areas, distance to EB, etc. It also
      * appropriately communicates EB data to guard cells.
      *
-     * \param[in] lev, level of the Multifabs that is initialized
+     * \param[in] lev level of the Multifabs that is initialized
      */
     void InitializeEBGridData(int lev);
 
@@ -1248,7 +1249,7 @@ private:
     amrex::Vector<std::array< std::unique_ptr<amrex::MultiFab>, 3 > > m_face_areas;
 
     /** EB: for every mesh face flag_info_face contains a:
-     *           * 0 if the face needs to be extended
+     *          * 0 if the face needs to be extended
      *          * 1 if the face is large enough to lend area to other faces
      *          * 2 if the face is actually intruded by other face
      * It is initialized in WarpX::MarkCells
diff --git a/Source/ablastr/constant.H b/Source/ablastr/constant.H
index 477f57f90..afa15e103 100644
--- a/Source/ablastr/constant.H
+++ b/Source/ablastr/constant.H
@@ -57,9 +57,9 @@ namespace ablastr::constant
 
         //! reduced Planck Constant = h / tau [J*s]
         static constexpr auto hbar = 1.054571817e-34_rt;
-        //! fine-structure constant = mu0/(4*MathConst::pi)*q_e*q_e*c/hbar [dimensionless]
+        //! fine-structure constant = mu0/(4*pi)*q_e*q_e*c/hbar [dimensionless]
         static constexpr auto alpha = 0.007297352573748943_rt;
-        //! classical electron radius = 1./(4*MathConst::pi*ep0) * q_e*q_e/(m_e*c*c) [m]
+        //! classical electron radius = 1./(4*pi*ep0) * q_e*q_e/(m_e*c*c) [m]
         static constexpr auto r_e = 2.817940326204929e-15_rt;
         //! xi: nonlinearity parameter of Heisenberg-Euler effective theory = (2.*alpha*alpha*ep0*ep0*hbar*hbar*hbar)/(45.*m_e*m_e*m_e*m_e*c*c*c*c*c)
         static constexpr double xi = 1.3050122447005176e-52;