diff --git a/Docs/sphinx_documentation/source/Basics.rst b/Docs/sphinx_documentation/source/Basics.rst
index 94987ad30b..5b9b137e30 100644
--- a/Docs/sphinx_documentation/source/Basics.rst
+++ b/Docs/sphinx_documentation/source/Basics.rst
@@ -1063,7 +1063,7 @@ an :cpp:`int` pointer or array specifying periodicity. If a :cpp:`RealBox` is no
 given in the first constructor, AMReX  will construct one based on :cpp:`ParmParse` parameters,
 ``geometry.prob_lo`` / ``geometry.prob_hi`` / ``geometry.prob_extent``,
 where each of the parameter is an array of ``AMREX_SPACEDIM`` real numbers.
-See the section on :ref:`sec:inputs:pd` for more details about how to specify these.
+See the section on :ref:`sec:inputs:geom` for more details about how to specify these.
 
 The argument for coordinate system is an integer type with
 valid values being 0 (Cartesian), or 1 (cylindrical), or 2 (spherical). If it
diff --git a/Docs/sphinx_documentation/source/RuntimeParameters.rst b/Docs/sphinx_documentation/source/RuntimeParameters.rst
index 87d7ec5834..d024238873 100644
--- a/Docs/sphinx_documentation/source/RuntimeParameters.rst
+++ b/Docs/sphinx_documentation/source/RuntimeParameters.rst
@@ -1,5 +1,5 @@
 
-.. _chap:runtime_parameters:
+.. _chap:inputs:
 
 Runtime Parameters
 ==================
@@ -17,7 +17,28 @@ to :cpp:`amrex::Initialize` and the function adds parameters to AMReX's
 .. important:: AMReX reserves the following prefixes in :cpp:`ParmParse`
                parameters: ``amr``, ``amrex``, ``blprofiler``, ``device``,
                ``DistributionMapping``, ``eb2``, ``fab``, ``fabarray``,
-               ``geometry``, ``vismf`` and ``tiny_profiler``.
+               ``geometry``, ``particles``, ``tiny_profiler``, and
+               ``vismf``.
+
+AMR
+---
+
+AMR Mesh
+^^^^^^^^
+
+AMR mesh
+
+..
+  AmrCore/AMReX_AmrMesh.cpp:    ParmParse pp("amr");
+
+Amr Class
+^^^^^^^^^
+
+AmrClass
+
+..
+  Amr/AMReX_Amr.cpp:    ParmParse pp("amr");
+  Amr/AMReX_AmrLevel.cpp:    ParmParse pp("amr");
 
 Basic Controls
 --------------
@@ -123,6 +144,16 @@ Distribution Mapping
    default strategy can also be set by calling
    :cpp:`DistributionMapping::strategy(DistributionMapping::Strategy)`.
 
+Embedded Boundary
+-----------------
+
+EB
+
+..
+  EB/AMReX_EB2.cpp:    ParmParse pp("eb2");
+  EB/AMReX_EB2_Level.H:        ParmParse pp("eb2");
+
+
 Error Handling
 --------------
 
@@ -224,6 +255,29 @@ for debugging.
     (i.e., the result is too large to be representable) trapping will be
     enabled. This flag has no effect on Windows.
 
+Extern
+------
+
+HDF5
+^^^^
+
+..
+  Extern/HDF5/AMReX_WriteBinaryParticleDataHDF5.H:    ParmParse  pp("particles");
+
+Hypre
+^^^^^
+
+..
+  pp.queryAdd("init_hypre", init_hypre);
+  pp.queryAdd("hypre_spgemm_use_vendor", hypre_spgemm_use_vendor);
+  pp.queryAdd("hypre_spmv_use_vendor", hypre_spmv_use_vendor);
+  pp.queryAdd("hypre_sptrans_use_vendor", hypre_sptrans_use_vendor);
+  Extern/HYPRE/AMReX_HypreIJIface.cpp:    amrex::ParmParse pp;
+  Extern/HYPRE/AMReX_HypreIJIface.cpp:    amrex::ParmParse pp(prefix);
+
+
+.. _sec:inputs:geom:
+
 Geometry
 --------
 
@@ -231,7 +285,7 @@ All these parameters are optional for constructing a :ref:`Geometry <sec:basics:
 object. There are only used if the information is not provided via function
 arguments.
 
-.. py:data:: geometry.coord
+.. py:data:: geometry.coord_sys
    :type: int
    :value: 0
 
@@ -409,6 +463,19 @@ Memory
    :cpp:`amrex::Gpu::ManagedVector`, etc. A smaller value can avoid wasting
    memory, but it may result in a performance penalty during resizing.
 
+Particles
+---------
+
+Particles
+
+..
+  Particle/AMReX_ParticleContainerBase.cpp:        ParmParse pp("particles");
+  Particle/AMReX_ParticleContainerI.H:        ParmParse pp("particles");
+  Particle/AMReX_ParticleIO.H:    ParmParse pp("particles");
+  Particle/AMReX_TracerParticles.cpp:    ParmParse pp("particles");
+  Particle/AMReX_WriteBinaryParticleData.H:    ParmParse pp("particles");
+
+
 Tiling
 ------
 
@@ -464,15 +531,3 @@ enabled.
   which are unnecessary for correctness, could potentially degrade the
   performance.
 
-..
-        pp.queryAdd("init_hypre", init_hypre);
-        pp.queryAdd("hypre_spgemm_use_vendor", hypre_spgemm_use_vendor);
-        pp.queryAdd("hypre_spmv_use_vendor", hypre_spmv_use_vendor);
-        pp.queryAdd("hypre_sptrans_use_vendor", hypre_sptrans_use_vendor);
-
-        /home/wqzhang/mygitrepo/amrex/Docs/sphinx_documentation/source/Basics.rst:908:
-        WARNING: undefined label: sec:inputs:pd
-
-        added in version for mathexpr
-
-        update FabArrayBase with queryArr for IntVect and RealVect