Commits

John Wise committed cbbfb34 Merge

Merged in mornkr/enzo-doc-mornkr (pull request #8)

  • Participants
  • Parent commits 085f629, f4ac3e5

Comments (0)

Files changed (17)

File doc/manual/source/parameters/bhform.rst

 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Following parameters are for the accretion and feedback from the
-massive black hole particle (``PARTICLE_TYPE_MBH``). More details
-will soon be described in Kim et al. (2010).
+massive black hole particle (``PARTICLE_TYPE_MBH``). Details
+are described in Kim, Wise, Alvarez, and Abel (2011).
 
 Accretion Physics
 ^^^^^^^^^^^^^^^^^

File doc/manual/source/parameters/cooling.rst

-Radiative Cooling Parameters
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. _cooling_parameters:
+
+Cooling Parameters
+~~~~~~~~~~~~~~~~~~
 
 Simple Cooling Options
 ^^^^^^^^^^^^^^^^^^^^^^
     six-species primordial gas (H, He, no H2 or D) in equilibrium, and
     is valid for temperatures greater than 10,000 K. This requires the
     file ``TREECOOL`` to execute. Default: 0
+``GadgetEquilibriumCooling`` (external)
+    An implementation of the ionization equilibrium cooling code used
+    in the GADGET code which includes both radiative cooling and a
+    uniform metagalactic UV background specified by the ``TREECOOL`` file
+    (in the ``amr_mpi/exe`` directory). When this parameter is turned on,
+    ``MultiSpecies`` and ``RadiationFieldType`` are forced to 0 and
+    ``RadiativeCooling`` is forced to 1.
+    [Not in public release version]
 ``MetalCooling`` (external)
     This flag (0 - off, 1 - metal cooling from Glover & Jappsen 2007,
     2 - Cen et al (1995), 3 - Cloudy cooling from Smith, Sigurdsson, &
     (Metal_Density) and two additional metal fields (Z_Field1 and
     Z_Field2). Acceptable values are 1 or 0, Default: 0 (off).
 ``ThreeBodyRate`` (external)
-    Which Three Body rate should be used for H2 formation: 0 = Abel, Bryan, Norman 2002, 1 = PSS83, 2= CW83, 3 = FH07, 4= G08.  (Turk et al 2011 covers these)
+    Which Three Body rate should be used for H2 formation?: 0 = Abel, Bryan, Norman 2002, 1 = PSS83, 2= CW83, 3 = FH07, 4= G08.  (Turk et al 2011 covers these)
 ``CIECooling`` (external)
-    Should CIE (Ripamonti & Abel 2004) cooling be included at high densities
+    Should CIE (Ripamonti & Abel 2004) cooling be included at high densities?
 ``H2OpticalDepthApproximation`` (external)
-    Should the H2 cooling be attenuated (RA04)
+    Should the H2 cooling be attenuated (RA04)?
 ``H2FormationOnDust`` (external)
     Turns on H2 formation on dust grains and gas-grain heat transfer following Omukai (2000). Default: 0 (OFF)
 ``NumberOfDustTemperatureBins`` (external)
 ``PhotoelectricHeatingRate`` (external)
     This is the parameter used as Gamma_pe for uniform photoelectric heating.
     Default: 8.5e-26 erg s^-1 cm^-3
-``GadgetEquilibriumCooling`` (external)
-    An implementation of the ionization equilibrium cooling code used
-    in the GADGET code which includes both radiative cooling and a
-    uniform metagalactic UV background specified by the ``TREECOOL`` file
-    (in the ``amr_mpi/exe`` directory). When this parameter is turned on,
-    ``MultiSpecies`` and ``RadiationFieldType`` are forced to 0 and
-    ``RadiativeCooling`` is forced to 1.
-    [Not in public release version]
 
 .. _cloudy_cooling:
 

File doc/manual/source/parameters/cosmology.rst

     This is the contribution of the cosmological constant to the energy
     density at the current epoch, in the same units as above. Default:
     0.721
+``CosmologyHubbleConstantNow`` (external)
+    The Hubble constant at z=0, in units of 100 km/s/Mpc. Default:
+    0.701
 ``CosmologyComovingBoxSize`` (external)
     The size of the volume to be simulated in Mpc/h (at z=0). Default:
     64.0
-``CosmologyHubbleConstantNow`` (external)
-    The Hubble constant at z=0, in units of 100 km/s/Mpc. Default:
-    0.701
 ``CosmologyInitialRedshift`` (external)
     The redshift for which the initial conditions are to be generated.
     Default: 20.0

File doc/manual/source/parameters/gravity.rst

     Number of iterations to solve the potential on the subgrids. Values
     less than 4 sometimes will result in slight overdensities on grid
     boundaries. Default: 4.
-``BaryonSelfGravityApproximation`` (external)
-    This flag indicates if baryon density is derived in a strange,
-    expensive but self-consistent way (0 - off), or by a completely
-    reasonable and much faster approximation (1 - on). This is an
-    experiment gone wrong; leave on. Well, actually, it's important for
-    very dense structures as when radiative cooling is turned on, so
-    set to 0 if using many levels and radiative cooling is on [ignored
-    in current version]. Default: 1
 ``MaximumGravityRefinementLevel`` (external)
     This is the lowest (most refined) depth that a gravitational
     acceleration field is computed. More refined levels interpolate
     completely baryon dominated. It is used to remove the discreteness
     effects of the few remaining dark matter particles. Not used if set
     to a value less than 0. Default: -1
+``BaryonSelfGravityApproximation`` (external)
+    This flag indicates if baryon density is derived in a strange,
+    expensive but self-consistent way (0 - off), or by a completely
+    reasonable and much faster approximation (1 - on). This is an
+    experiment gone wrong; leave on. Well, actually, it's important for
+    very dense structures as when radiative cooling is turned on, so
+    set to 0 if using many levels and radiative cooling is on [ignored
+    in current version]. Default: 1
 
 External Gravity Source
 ^^^^^^^^^^^^^^^^^^^^^^^
 
-These parameters set-up an external static background gravity source that is
+These parameters set up an external static background gravity source that is
 added to the acceleration field for the baryons and particles.
 
 ``PointSourceGravity`` (external)

File doc/manual/source/parameters/hierarchy.rst

 Hierarchy Control Parameters
-----------------------------
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 ``StaticHierarchy`` (external)
     A flag which indicates if the hierarchy is static (1) or dynamic
     detection. Default: 0.1
 ``MinimumShearForRefinement`` (external)
     It is the minimum shear above which a refinement occurs if the CellFlaggingMethod is appropriately set. Default: 0
+``MetallicityRefinementMinMetallicity`` (external)
+    This is the threshold metallicity (in units of solar metallicity)
+    above which cells must be refined to a minimum level of
+    ``MetallicityRefinementMinLevel``. Default: 1.0e-5
 ``MetallicityRefinementMinLevel`` (external)
     Sets the minimum level (maximum cell size) to which a cell enriched
     with metal above a level set by ``MetallicityRefinementMinMetallicity``
     will be refined. This can be set to any level up to and including
     ``MaximumRefinementLevel``. (No default setting)
-``MetallicityRefinementMinMetallicity`` (external)
-    This is the threshold metallicity (in units of solar metallicity)
-    above which cells must be refined to a minimum level of
-    ``MetallicityRefinementMinLevel``. Default: 1.0e-5
 ``MetallicityRefinementMinDensity`` (external)
     It is the minimum density above which a refinement occurs when the cells are refined on metallicity.  Default: FLOAT_UNDEFINED
 ``ShockwaveRefinementMinMach`` (external)
     The minimum shock velocity required to refine a level when using ShockwaveRefinement. Default: 1.0e7 (cm/s)
 ``ShockwaveRefinementMaxLevel`` (external)
     The maximum level to refine to using the ShockwaveRefinement criteria. Default: 0 (not used)
-``FindShocksOnlyOnOutput`` (external)
-    0: Finds shocks during Evolve Level and just before writing out data. 1: Only find shocks just before writing out data.  2: Only find shocks during EvolveLevel. Default: 0
-``MustRefineRegionMinRefinementLevel`` (external)
-    Minimum level to which the rectangular solid volume defined by
-    ``MustRefineRegionLeftEdge`` and ``MustRefineRegionRightEdge`` will be
-    refined to at all times. (No default setting)
-``MustRefineRegionLeftEdge`` (external)
-    Bottom-left corner of refinement region. Must be within the overall
-    refinement region. Default: 0.0 0.0 0.0
-``MustRefineRegionRightEdge`` (external)
-    Top-right corner of refinement region. Must be within the overall
-    refinement region. Default: 1.0 1.0 1.0
+``RefineByJeansLengthSafetyFactor`` (external)
+    If the Jeans length refinement criterion (see ``CellFlaggingMethod``)
+    is being used, then this parameter specifies the number of cells
+    which must cover one Jeans length. Default: 4
+``JeansRefinementColdTemperature`` (external)
+    If the Jeans length refinement criterion (see ``CellFlaggingMethod``)
+    is being used, and this parameter is greater than zero, it will be
+    used in place of the temperature in all cells. Default: -1.0
+``RefineByResistiveLengthSafetyFactor`` (external)
+    Resistive length is defined as the curl of the magnetic field over
+    the magnitude of the magnetic field. We make sure this length is
+    covered by this number of cells. i.w. The resistive length in a MHD simulation should not be smaller than CellWidth * RefineByResistiveLengthSafetyFactor.  Default: 2.0
 ``MustRefineParticlesRefineToLevel`` (external)
     The maximum level on which ``MustRefineParticles`` are required to
     refine to. Currently sink particles and MBH particles are required
     ``MustRefineParticlesRefineToLevel`` using the boxsize and redshift
     information. Default: 0 (FALSE)
 ``MustRefineParticlesMinimumMass`` (external)
-    This was an experimental parameter to set a minimum for MustRefineParticles.  Default: 0.0
-``FluxCorrection`` (external)
-    This flag indicates if the flux fix-up step should be carried out
-    around the boundaries of the sub-grid to preserve conservation (1 -
-    on, 0 - off). Strictly speaking this should always be used, but we
-    have found it to lead to a less accurate solution for cosmological
-    simulations because of the relatively sharp density gradients
-    involved. However, it does appear to be important when radiative
-    cooling is turned on and very dense structures are created.
-    It does work with the ZEUS
-    hydro method, but since velocity is face-centered, momentum flux is
-    not corrected. Species quantities are not flux corrected directly
-    but are modified to keep the fraction constant based on the density
-    change. Default: 1
-``InterpolationMethod`` (external)
-    There should be a whole section devoted to the interpolation
-    method, which is used to generate new sub-grids and to fill in the
-    boundary zones of old sub-grids, but a brief summary must suffice.
-    The possible values of this integer flag are shown in the table
-    below. The names specify (in at least a rough sense) the order of
-    the leading error term for a spatial Taylor expansion, as well as a
-    letter for possible variants within that order. The basic problem
-    is that you would like your interpolation method to be:
-    multi-dimensional, accurate, monotonic and conservative. There
-    doesn't appear to be much literature on this, so I've had to
-    experiment. The first one (ThirdOrderA) is time-consuming and
-    probably not all that accurate. The second one (SecondOrderA) is
-    the workhorse: it's only problem is that it is not always
-    symmetric. The next one (SecondOrderB) is a failed experiment, and
-    SecondOrderC is not conservative. FirstOrderA is everything except
-    for accurate. If HydroMethod = 2 (ZEUS), this flag is ignored, and
-    the code automatically uses SecondOrderC for velocities and
-    FirstOrderA for cell-centered quantities. Default: 1
-    ::
-
-              0 - ThirdOrderA     3 - SecondOrderC
-              1 - SecondOrderA    4 - FirstOrderA
-              2 - SecondOrderB  
-
-
-``ConservativeInterpolation`` (external)
-    This flag (1 - on, 0 - off) indicates if the interpolation should
-    be done in the conserved quantities (e.g. momentum rather than
-    velocity). Ideally, this should be done, but it can cause problems
-    when strong density gradients occur. This must(!) be set off for
-    ZEUS hydro (the code does it automatically). Default: 1
-``MinimumEfficiency`` (external)
-    When new grids are created during the rebuilding process, each grid
-    is split up by a recursive bisection process that continues until a
-    subgrid is either of a minimum size or has an efficiency higher
-    than this value. The efficiency is the ratio of flagged zones
-    (those requiring refinement) to the total number of zones in the
-    grid. This is a number between 0 and 1 and should probably by
-    around 0.4 for standard three-dimensional runs. Default: 0.2
-``NumberOfBufferZones`` (external)
-    Each flagged cell, during the regridding process, is surrounded by
-    a number of zones to prevent the phenomenon of interest from
-    leaving the refined region before the next regrid. This integer
-    parameter controls the number required, which should almost always
-    be one. Default: 1
-``JeansRefinementColdTemperature`` (external)
-    If the Jeans length refinement criterion (see ``CellFlaggingMethod``)
-    is being used, and this parameter is greater than zero, it will be
-    used in place of the temperature in all cells. Default: -1.0
-``RefineByJeansLengthSafetyFactor`` (external)
-    If the Jeans length refinement criterion (see ``CellFlaggingMethod``)
-    is being used, then this parameter specifies the number of cells
-    which must cover one Jeans length. Default: 4
-``RefineByResistiveLength`` (external)
-    Resistive length is defined as the curl of the magnetic field over
-    the magnitude of the magnetic field. We make sure this length is
-    covered by this number of cells. Default: 2
-``RefineByResistiveLengthSafetyFactor`` (external)
-    The resistive length in a MHD simulation should not be smaller than CellWidth * RefineByResistiveLengthSafetyFactor, if the CellFlaggingMethod is appropriately set.  Default: 2.0
+    This was an experimental parameter to set a minimum for ``MustRefineParticles``.  Default: 0.0
+``MustRefineRegionMinRefinementLevel`` (external)
+    Minimum level to which the rectangular solid volume defined by
+    ``MustRefineRegionLeftEdge`` and ``MustRefineRegionRightEdge`` will be
+    refined to at all times. (No default setting)
+``MustRefineRegionLeftEdge`` (external)
+    Bottom-left corner of refinement region. Must be within the overall
+    refinement region. Default: 0.0 0.0 0.0
+``MustRefineRegionRightEdge`` (external)
+    Top-right corner of refinement region. Must be within the overall
+    refinement region. Default: 1.0 1.0 1.0
 ``StaticRefineRegionLevel[#]`` (external)
     This parameter is used to specify regions of the problem that are
     to be statically refined, regardless of other parameters. This is mostly
     These two parameters specify the two corners of a region that
     limits refinement to a certain level (see the previous
     parameter). Default: none
+``MinimumEfficiency`` (external)
+    When new grids are created during the rebuilding process, each grid
+    is split up by a recursive bisection process that continues until a
+    subgrid is either of a minimum size or has an efficiency higher
+    than this value. The efficiency is the ratio of flagged zones
+    (those requiring refinement) to the total number of zones in the
+    grid. This is a number between 0 and 1 and should probably by
+    around 0.4 for standard three-dimensional runs. Default: 0.2
+``NumberOfBufferZones`` (external)
+    Each flagged cell, during the regridding process, is surrounded by
+    a number of zones to prevent the phenomenon of interest from
+    leaving the refined region before the next regrid. This integer
+    parameter controls the number required, which should almost always
+    be one. Default: 1
 ``MinimumSubgridEdge`` (external)
     The minimum length of the edge of a subgrid.  See :ref:`running_large_simulations`. Default: 6
 ``MaximumSubgridSize`` (external)

File doc/manual/source/parameters/hydro.rst

+.. _hydrodynamics_parameters:
+
 Hydrodynamics Parameters
 ~~~~~~~~~~~~~~~~~~~~~~~~
 
     This integer specifies the hydrodynamics method that will be used.
     Currently implemented are
 
-    ============ =============================
-    Hydro method Description
-    ============ =============================
-    0            PPM DE (a direct-Eulerian version of PPM)
-    1            [reserved]
-    2            ZEUS (a Cartesian, 3D version of Stone & Norman). Note that if ZEUS is selected, it automatically turns off ``ConservativeInterpolation`` and the ``DualEnergyFormalism`` flags.
-    3            Runge Kutta second-order based MUSCL solvers.
-    4            Same as 3 but including Dedner MHD (Wang & Abel 2008). For 3 and 4 there are the additional parameters ``RiemannSolver`` and ``ReconstructionMethod`` you want to set.
-    ============ =============================
+    ============== =============================
+    Hydro method   Description
+    ============== =============================
+    0              PPM DE (a direct-Eulerian version of PPM)
+    1              [reserved]
+    2              ZEUS (a Cartesian, 3D version of Stone & Norman). Note that if ZEUS is selected, it automatically turns off ``ConservativeInterpolation`` and the ``DualEnergyFormalism`` flags.
+    3              Runge Kutta second-order based MUSCL solvers.
+    4              Same as 3 but including Dedner MHD (Wang & Abel 2008). For 3 and 4 there are the additional parameters ``RiemannSolver`` and ``ReconstructionMethod`` you want to set.
+    ============== =============================
 
     Default: 0
 
     More details on each of the above methods can be found at :ref:`hydro_methods`.
+``FluxCorrection`` (external)
+    This flag indicates if the flux fix-up step should be carried out
+    around the boundaries of the sub-grid to preserve conservation (1 -
+    on, 0 - off). Strictly speaking this should always be used, but we
+    have found it to lead to a less accurate solution for cosmological
+    simulations because of the relatively sharp density gradients
+    involved. However, it does appear to be important when radiative
+    cooling is turned on and very dense structures are created.
+    It does work with the ZEUS
+    hydro method, but since velocity is face-centered, momentum flux is
+    not corrected. Species quantities are not flux corrected directly
+    but are modified to keep the fraction constant based on the density
+    change. Default: 1
+``InterpolationMethod`` (external)
+    There should be a whole section devoted to the interpolation
+    method, which is used to generate new sub-grids and to fill in the
+    boundary zones of old sub-grids, but a brief summary must suffice.
+    The possible values of this integer flag are shown in the table
+    below. The names specify (in at least a rough sense) the order of
+    the leading error term for a spatial Taylor expansion, as well as a
+    letter for possible variants within that order. The basic problem
+    is that you would like your interpolation method to be:
+    multi-dimensional, accurate, monotonic and conservative. There
+    doesn't appear to be much literature on this, so I've had to
+    experiment. The first one (ThirdOrderA) is time-consuming and
+    probably not all that accurate. The second one (SecondOrderA) is
+    the workhorse: it's only problem is that it is not always
+    symmetric. The next one (SecondOrderB) is a failed experiment, and
+    SecondOrderC is not conservative. FirstOrderA is everything except
+    for accurate. If HydroMethod = 2 (ZEUS), this flag is ignored, and
+    the code automatically uses SecondOrderC for velocities and
+    FirstOrderA for cell-centered quantities. Default: 1
+    ::
+
+              0 - ThirdOrderA     3 - SecondOrderC
+              1 - SecondOrderA    4 - FirstOrderA
+              2 - SecondOrderB  
+
+``ConservativeInterpolation`` (external)
+    This flag (1 - on, 0 - off) indicates if the interpolation should
+    be done in the conserved quantities (e.g. momentum rather than
+    velocity). Ideally, this should be done, but it can cause problems
+    when strong density gradients occur. This must(!) be set off for
+    ZEUS hydro (the code does it automatically). Default: 1
 ``RiemannSolver`` (external; only if ``HydroMethod`` is 3 or 4)
     This integer specifies the Riemann solver used by the MUSCL solver. Choice of
 
-    ============== ===========================
-    Riemann solver Description
-    ============== ===========================
-    0              [reserved]
-    1              HLL (Harten-Lax-van Leer) a two-wave, three-state solver with no resolution of contact waves
-    2              [reserved]
-    3              LLF (Local Lax-Friedrichs)
-    4              HLLC (Harten-Lax-van Leer with Contact) a three-wave, four-state solver with better resolution of contacts
-    5              TwoShock
-    ============== ===========================
+    ================ ===========================
+    Riemann solver   Description
+    ================ ===========================
+    0                [reserved]
+    1                HLL (Harten-Lax-van Leer) a two-wave, three-state solver with no resolution of contact waves
+    2                [reserved]
+    3                LLF (Local Lax-Friedrichs)
+    4                HLLC (Harten-Lax-van Leer with Contact) a three-wave, four-state solver with better resolution of contacts
+    5                TwoShock
+    ================ ===========================
 
     Default: 1 (HLL) for ``HydroMethod`` = 3; 5 (TwoShock) for
     ``HydroMethod`` = 0
-
-``RiemannSolverFallback`` (external)
+``RiemannSolverFallback`` (external; only if ``HydroMethod`` is 3 or 4)
     If the euler update results in a negative density or energy, the
     solver will fallback to the HLL Riemann solver that is more
     diffusive only for the failing cell.  Only active when using the
     ===================== ====================
 
     Default: 0 (PLM) for ``HydroMethod`` = 3; 1 (PPM) for ``HydroMethod`` = 0
-
+``ConservativeReconstruction`` (external; only if ``HydroMethod`` is 3 or 4)
+    Experimental.  This option turns on the reconstruction of the
+    left/right interfaces in the Riemann problem in the conserved
+    variables (density, momentum, and energy) instead of the primitive
+    variables (density, velocity, and pressure).  This generally gives
+    better results in constant-mesh problems has been problematic in
+    AMR simulations.  Default: OFF
+``PositiveReconstruction`` (external; only if ``HydroMethod`` is 3 or 4)
+    Experimental and not working.  This forces the Riemann solver to
+    restrict the fluxes to always give positive pressure.  Attempts to
+    use the Waagan (2009), JCP, 228, 8609 method.  Default: OFF
 ``Gamma`` (external)
     The ratio of specific heats for an ideal gas (used by all hydro
     methods). If using multiple species (i.e. ``MultiSpecies`` > 0), then
     PPM LR) Default: 5/3.
 ``Mu`` (external)
     The molecular weight. Default: 0.6.
-``ConservativeReconstruction`` (external)
-    Experimental.  This option turns on the reconstruction of the
-    left/right interfaces in the Riemann problem in the conserved
-    variables (density, momentum, and energy) instead of the primitive
-    variables (density, velocity, and pressure).  This generally gives
-    better results in constant-mesh problems has been problematic in
-    AMR simulations.  Default: OFF
-``PositiveReconstruction`` (external)
-    Experimental and not working.  This forces the Riemann solver to
-    restrict the fluxes to always give positive pressure.  Attempts to
-    use the Waagan (2009), JCP, 228, 8609 method.  Default: OFF
 ``CourantSafetyNumber`` (external)
     This is the maximum fraction of the CFL-implied timestep that will
     be used to advance any grid. A value greater than 1 is unstable
 Magnetohydrodynamics (Dedner) Parameters
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
+The following parameters are considered only when ``HydroMethod`` is 3 or 4 (and occasionally only in some test problems).  
+Because many of the following parameters are not actively being tested and maintained, users are encouraged to carefully examine the code before using it.
+
 ``UseDivergenceCleaning`` (external)
     Method 1 and 2 are a failed experiment to do divergence cleaning
     using successive over relaxation. Method 3 uses conjugate gradient

File doc/manual/source/parameters/initialization.rst

+.. _initialization_parameters:
+
 Initialization Parameters
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 
 ``Initialdt`` (internal)
     The timestep, in code units, for the current step. For cosmology
     the units are in free-fall times at the initial epoch (see :ref:`EnzoOutputFormats`). Default: generally 0, depending on problem
+``Unigrid`` (external)
+    This parameter should be set to 1 (TRUE) for large cases--AMR as
+    well as non-AMR--where the root grid is 512\ :sup:`3`\  or larger.
+    This prevents initialization under subgrids at start up, which is
+    unnecessary in cases with simple non-nested initial conditions.
+    Unigrid must be set to 0 (FALSE) for cases with nested initial
+    conditions. Default: 0 (FALSE). See also ``ParallelRootGridIO`` in :ref:`io_parameters`.
+``UnigridTranspose`` (external)
+    This parameter governs the fast FFT bookkeeping for Unigrid runs.
+    Does not work with isolated gravity. Default: 0 (FALSE). See also
+    ``Unigrid`` above.
 ``MaximumTopGridTimeStep`` (external)
     This parameter limits the maximum timestep on the root grid.  Default: huge_number.
 ``ShearingVelocityDirection`` (external)
 ``TemperatureEnd`` (external)
     Do NOT change this parameter unless you know exactly what you are doing. Default: 1e8
 ``ExternalBoundaryIO`` (external)
-    not recommended for use at this point. Only works if compiled with oc-boundary-yes.  Default: 0
+    not recommended for use at this point. Only works if compiled with ``ooc-boundary-yes``.  Default: 0
 ``ExternalBoundaryTypeIO`` (external)
     not recommended for use at this point. Default: 0
 ``ExternalBoundaryValueIO`` (external)

File doc/manual/source/parameters/io.rst

+.. _io_parameters:
+
 I/O Parameters
 --------------
 
     every level thereafter. Default is 0 (off). User can usefully
     specify anything up to the maximum number of levels in a given
     simulation.
-``XrayLowerCutoffkeV``, ``XrayUpperCutoffkeV``, ``XrayTableFileName`` (external)
-    These parameters are used in 2D projections (``enzo -p ...``). The
-    first two specify the X-ray band (observed at z=0) to be used, and
-    the last gives the name of an ascii file that contains the X-ray
-    spectral information. A gzipped version of this file good for
-    bands within the 0.1 - 20 keV range is provided in the
-    distribution in ``input/lookup_metal0.3.data``. If these
-    parameters are specified, then the second field is replaced with
-    integrated emissivity along the line of sight in units of 10\
-    :sup:`-23` erg/cm\ :sup:`2`/s. Default: ``XrayLowerCutoffkeV =
-    0.5``, ``XrayUpperCutoffkeV = 2.5``.
-``ExtractFieldsOnly`` (external)
-    Used for extractions (enzo -x ...) when only field data are needed
-    instead of field + particle data. Default is 1 (TRUE).
 ``ParallelRootGridIO`` (external)
     Normally for the mpi version, the root grid is read into the root
     processor and then partitioned to separate processors using communication.
     root grid. More I/O is required (to split up the grids and
     particles), but it is more balanced in terms of memory.
     ``ParallelRootGridIO`` and ``ParallelParticleIO`` MUST be set to 1 (TRUE)
-    for runs involving > 64 cpus! Default: 0 (FALSE). See also ``Unigrid``
-    below.
-``Unigrid`` (external)
-    This parameter should be set to 1 (TRUE) for large cases--AMR as
-    well as non-AMR--where the root grid is 512\ :sup:`3`\  or larger.
-    This prevents initialization under subgrids at start up, which is
-    unnecessary in cases with simple non-nested initial conditions.
-    Unigrid must be set to 0 (FALSE) for cases with nested initial
-    conditions. Default: 0 (FALSE). See also ``ParallelRootGridIO`` above.
-``UnigridTranspose`` (external)
-    This parameter governs the fast FFT bookkeeping for Unigrid runs.
-    Does not work with isolated gravity. Default: 0 (FALSE). See also
-    ``Unigrid`` above.
+    for runs involving > 64 cpus! Default: 0 (FALSE). 
+    See ``ParallelParticleIO`` in :ref:`particle_parameters`.    
+    See also ``Unigrid`` in :ref:`initialization_parameters`.
 ``OutputTemperature`` (external)
     Set to 1 if you want to output a temperature field in the datasets.
     Always 1 for cosmology simulations. Default: 0.
 ``BAnyl`` (external)
     Set to 1 if you want to output the divergence and vorticity of
     ``Bfield``. Works in 2D and 3D.
+``ExtractFieldsOnly`` (external)
+    Used for extractions (enzo -x ...) when only field data are needed
+    instead of field + particle data. Default is 1 (TRUE).
+``XrayLowerCutoffkeV``, ``XrayUpperCutoffkeV``, ``XrayTableFileName`` (external)
+    These parameters are used in 2D projections (``enzo -p ...``). The
+    first two specify the X-ray band (observed at z=0) to be used, and
+    the last gives the name of an ascii file that contains the X-ray
+    spectral information. A gzipped version of this file good for
+    bands within the 0.1 - 20 keV range is provided in the
+    distribution in ``input/lookup_metal0.3.data``. If these
+    parameters are specified, then the second field is replaced with
+    integrated emissivity along the line of sight in units of 10\
+    :sup:`-23` erg/cm\ :sup:`2`/s. Default: ``XrayLowerCutoffkeV =
+    0.5``, ``XrayUpperCutoffkeV = 2.5``.
 ``ParticleTypeInFile`` (external)    
     Output ParticleType to disk?  Default: 1
 ``OutputParticleTypeGrouping`` (external) 	

File doc/manual/source/parameters/particles.rst

+.. _particle_parameters:
+
 Particle Parameters
 ~~~~~~~~~~~~~~~~~~~
 
 ``NumberOfParticleAttributes`` (internal)
     It is set to 3 if either ``StarParticleCreation`` or
     ``StarParticleFeedback`` is set to 1 (TRUE). Default: 0
-``AddParticleAttributes`` (internal)
+``AddParticleAttributes`` (external)
     If set to 1, additional particle attributes will be added and
     zeroed. This is handy when restarting a run, and the user wants to
     use star formation afterwards. Default: 0.
     its own part of the particle data. More I/O is required, but it is
     more balanced in terms of memory. ``ParallelRootGridIO`` and
     ``ParallelParticleIO`` MUST be set for runs involving > 64 cpus!
+    See also ``ParallelRootGridIO`` in :ref:`io_parameters`.
     Default: 0 (FALSE).
 ``ParticleSplitterIterations`` (external)
     Set to 1 to split particles into 13 particles (= 12 children+1

File doc/manual/source/parameters/radiation.rst

 
    ::
   
-     1. Haardt & Madau spectrum with q_alpha=1.5
-     2. Haardt & Madau spectrum with q_alpha = 1.8
-     3. Modified Haardt & Madau spectrum to match observations
-     	(Kirkman & Tytler 2005).
-     4. H&M spectrum (q_alpha=1.5. supplemented with an X-ray Compton heating
-        background from Madau & Efstathiou (see astro-ph/9902080)
-     9. a constant molecular H2 photo-dissociation rate
-     10. internally computed radiation field using the algorithm of Cen & Ostriker
-     11. same as previous, but with very, very simple optical shielding fudge
-     12. Haardt & Madau spectrum with q_alpha=1.57
+     1  - Haardt & Madau spectrum with q_alpha = 1.5
+     2  - Haardt & Madau spectrum with q_alpha = 1.8
+     3  - Modified Haardt & Madau spectrum to match observations
+     	  (Kirkman & Tytler 2005).
+     4  - Haardt & Madau spectrum with q_alpha = 1.5 supplemented with an X-ray Compton heating
+          background from Madau & Efstathiou (see astro-ph/9902080)
+     9  - Constant molecular H2 photo-dissociation rate
+     10 - Internally computed radiation field using the algorithm of Cen & Ostriker
+     11 - Same as previous, but with very, very simple optical shielding fudge
+     12 - Haardt & Madau spectrum with q_alpha = 1.57
 
 ``RadiationFieldLevelRecompute`` (external)
     This integer parameter is used only if the previous parameter is
     hydrogen (H2) dissociation rate. There a normalization is performed
     on the rate by multiplying it with ``RadiationSpectrumNormalization``.
     Default: 1e-21
-``RadiationFieldRedshift`` (external)
-    This parameter specifies the redshift at which the radiation field
-    is calculated.  Default: 0
 ``RadiationShield`` (external)
     This parameter specifies whether the user wants to employ
     approximate radiative-shielding. This parameter will be
     automatically turned on when RadiationFieldType is set to 11. See
     ``calc_photo_rates.src``. Default: 0
+``RadiationFieldRedshift`` (external)
+    This parameter specifies the redshift at which the radiation field
+    is calculated.  Default: 0
 ``RadiationRedshiftOn`` (external) 
     The redshift at which the UV 
     background turns on. Default: 7.0.
 ``RadiationSpectrumSlope`` (external)
     Add description. Default: 1.5.
 
+.. _radiative_transfer_ray_tracing:
+
 Radiative Transfer (Ray Tracing) Parameters
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 ``RadiativeTransferRadiationPressure`` (external)
     Set to 1 to turn on radiation pressure created from absorbed photon
     packages. Default: 0
-``RadiativeTransferInitialHEALPixLevel`` (internal)
+``RadiativeTransferInitialHEALPixLevel`` (external)
     Chooses how many rays are emitted from radiation sources. The
     number of rays in Healpix are given through # =
     12x4\ :sup:`level`\ . Default: 3.
 ``RadiativeTransferSourceRadius`` (external)
     The radius at which the photons originate from the radiation
     source. A positive value results in a radiating sphere. Default: 0.
-``RadiativeTransferPropagationRadius`` (internal)
+``RadiativeTransferPropagationRadius`` (external)
     The maximum distance a photon package can travel in one timestep.
     Currently unused. Default: 0.
-``RadiativeTransferPropagationSpeed`` (internal)
+``RadiativeTransferPropagationSpeed`` (external)
     The fraction of the speed of light at which the photons travel.
     Default: 1.
-``RadiativeTransferCoupledRateSolver`` (internal)
+``RadiativeTransferCoupledRateSolver`` (external)
     Set to 1 to calculate the new ionization fractions and gas energies
     after every radiative transfer timestep. This option is highly
     recommended to be kept on. If not, ionization fronts will propagate too
     (Lyman-Werner) radiation field. Only used if ``MultiSpecies`` > 1. If
     ``MultiSpecies`` > 1 and this option is off, the Lyman-Werner radiation
     field will be calculated with ray tracing. Default: 1.
-``RadiativeTransferSplitPhotonPackage`` (internal)
+``RadiativeTransferSplitPhotonPackage`` (external)
     Once photons are past this radius, they can no longer split. In
     units of kpc. If this value is negative (by default), photons can
     always split. Default: ``FLOAT_UNDEFINED``.
-``RadiativeTransferPhotonEscapeRadius`` (internal)
+``RadiativeTransferPhotonEscapeRadius`` (external)
     The number of photons that pass this distance from its source are
     summed into the global variable ``EscapedPhotonCount[]``. This variable
     also keeps track of the number of photons passing this radius
     multiplied by 0.5, 1, and 2. Units are in kpc. Not used if set to
     0. Default: 0.
-``RadiativeTransferSourceClustering`` (internal)
+``RadiativeTransferSourceClustering`` (external)
     Set to 1 to turn on ray merging from combined virtual sources on a
     binary tree. Default: 0.
-``RadiativeTransferPhotonMergeRadius`` (internal)
+``RadiativeTransferPhotonMergeRadius`` (external)
     The radius at which the rays will merge from their SuperSource,
     which is the luminosity weighted center of two sources. This radius
     is in units of the separation of two sources associated with one
     SuperSource. If set too small, there will be angular artifacts in
     the radiation field. Default: 2.5
+``RadiativeTransferSourceBeamAngle`` (external)
+    Rays will be emitted within this angle in degrees of the poles from sources with "Beamed" types.  Default: 30
+``RadiativeTransferPeriodicBoundary`` (external)
+    Set to 1 to turn on periodic boundary conditions for photon
+    packages. Default: 0.
 ``RadiativeTransferTimestepVelocityLimit`` (external)
     Limits the radiative transfer timestep to a minimum value that is
     determined by the cell width at the finest level divided by this
     velocity. Units are in km/s. Default: 100.
-``RadiativeTransferPeriodicBoundary`` (external)
-    Set to 1 to turn on periodic boundary conditions for photon
-    packages. Default: 0.
-``RadiativeTransferSourceBeamAngle`` (external)
-    Rays will be emitted within this angle in degrees of the poles from sources with "Beamed" types.  Default: 30
 ``RadiativeTransferHIIRestrictedTimestep`` (external)
     Adaptive ray tracing timesteps will be restricted by a maximum change of 10% in neutral fraction if this parameter is set to 1.  If set to 2, then the incident flux can change by a maximum of 0.5 between cells.  See Wise & Abel (2011) in Sections 3.4.1 and 3.4.4 for more details.  Default: 0
 ``RadiativeTransferAdaptiveTimestep`` (external)
     Must be 1 when RadiativeTransferHIIRestrictedTimestep is non-zero.  When RadiativeTransferHIIRestrictedTimestep is 0, then the radiative transfer timestep is set to the timestep of the finest AMR level.  Default: 0
+``RadiativeTransferLoadBalance`` (external)
+    When turned on, the grids are load balanced based on the number of ray segments traced.  The grids are moved to different processors only for the radiative transfer solver.  Default: 0
 ``RadiativeTransferHydrogenOnly`` (external)
     When turned on, the photo-ionization fields are only created for hydrogen.  Default: 0
-``RadiativeTransferLoadBalance`` (external)
-    When turned on, the grids are load balanced based on the number of ray segments traced.  The grids are moved to different processors only for the radiative transfer solver.  Default: 0
 ``RadiationXRaySecondaryIon`` (external)
     Set to 1 to turn on secondary ionizations and reduce heating from
     X-ray radiation (Shull & van Steenberg 1985). Currently only BH and
     Ionizing photon luminosity of a "simple radiating source" that is independent of mass.  In units of photons per second.  Default: 1e50
 ``SimpleRampTime`` (external)
     Time to exponential ramp up the luminosity of a simple radiating source.  In units of 1e6 years.  Default: 0.1
-``RadiativeTransferTraceSpectrum`` (external)
-    reserved for experimentation. Default: 0.
-``RadiativeTransferTraceSpectrumTable`` (external)
-    reserved for experimentation. Default: ``spectrum_table.dat``
+``RadiativeTransferTraceSpectrum`` (reserved)
+    reserved for future experimentation. Default: 0.
+``RadiativeTransferTraceSpectrumTable`` (reserved)
+    reserved for future experimentation. Default: ``spectrum_table.dat``
+
+.. _radiative_transfer_fld:
 
 Radiative Transfer (FLD) Parameters
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
     hypre-yes``. Note that if FLD is turned on, it will force
     ``RadiativeCooling = 0``, ``GadgetEquilibriumCooling = 0``, and
     ``RadiationFieldType = 0`` to prevent conflicts. Default: 0.
-    IMPORTANT: Set ``RadiativeTransfer = 0`` to avoid conflicts with the ray tracing solver above.
+
+    *IMPORTANT*: Set ``RadiativeTransfer = 0`` to avoid conflicts with the ray tracing solver above.
+    Set ``RadiativeTransferOpticallyThinH2 = 0`` to avoid conflicts with the built-in optically-thin H_2 dissociating field from the ray-tracing solver. 
 ``ImplicitProblem`` (external)
     Set to 1 to turn on the implicit FLD solver, or 3 to turn on the
     split FLD solver. Default: 0.
     The level in the static AMR hierarchy where the unigrid FLD solver
     should be called. Currently only works for 0 (the root grid).
     Default: 0.
-``RadiativeTransferOpticallyThinH2`` (external)
-    Set to 0 to avoid conflicts with the built-in optically-thin H_2
-    dissociating field from the ray-tracing solver. Default: 1.
 ``StarMakerEmissivityField`` (external)
     When compiled with the FLD radiation transfer >make emissivity-yes; make hypre-yes, setting this to 1 turns on the emissivity field to source the gray radiation. Default: 0
 ``uv_param`` (external)

File doc/manual/source/parameters/shocks.rst

+.. _shock_finding_parameters:
+
 Shock Finding Parameters
 ~~~~~~~~~~~~~~~~~~~~~~~~
 
 
 ``StorePreShockFields`` (external)
     Optionally store the Pre-shock Density and Temperature during data output.
+
+``FindShocksOnlyOnOutput`` (external)
+    0: Finds shocks during Evolve Level and just before writing out data. 1: Only find shocks just before writing out data.  2: Only find shocks during EvolveLevel. Default: 0

File doc/manual/source/parameters/starform.rst

     
     ::
 
-	0 - Cen & Ostriker (1992)
-	1 - Cen & Ostriker (1992) with stocastic star formation
-	2 - Global Schmidt Law / Kravstov et al. (2003)
-	3 - Population III stars / Abel, Wise & Bryan (2007)
-	4 - Sink particles: Pure sink particle or star particle with wind feedback depending on 
-	    choice for HydroMethod / Wang et al. (2009)
-	5 - Radiative star clusters  / Wise & Cen (2009)
-	6 - [reserved]
-	7 - Cen & Ostriker (1992) with no delay in formation
-	8 - Springel & Hernquist (2003)
-	9 - Massive Black Hole (MBH) particles insertion by hand / Kim et al. (2010)
+	0  - Cen & Ostriker (1992)
+	1  - Cen & Ostriker (1992) with stocastic star formation
+	2  - Global Schmidt Law / Kravstov et al. (2003)
+	3  - Population III stars / Abel, Wise & Bryan (2007)
+	4  - Sink particles: Pure sink particle or star particle with wind feedback depending on 
+	     choice for HydroMethod / Wang et al. (2009)
+	5  - Radiative star clusters  / Wise & Cen (2009)
+	6  - [reserved for future use]
+	7  - Cen & Ostriker (1992) with no delay in formation
+	8  - Springel & Hernquist (2003)
+	9  - Massive Black Hole (MBH) particles insertion by hand / Kim et al. (2010)
 	10 - Population III stellar tracers  
+	11 - Molecular hydrogen regulated star formation
 
 ``StarParticleFeedback`` (external)
     This parameter works the same way as ``StarParticleCreation`` but only
-    is valid for ``StarParticleCreation`` = 0, 1, 2, 7 and 8 because methods 3, 5 and 9
+    is valid for ``StarParticleCreation`` method = 0, 1, 2, 7 and 8 because methods 3, 5 and 9
     use the radiation transport module and ``Star_*.C`` routines to
     calculate the feedback, 4 has explicit feedback and 10 does not use feedback. Default: 0.
 
     radius.  This results in feedback being distributed to a cube with
     a side of ``StarFeedbackDistRadius+1``. It is in units of cell
     widths of the finest grid which hosts the star particle.  Only
-    implemented for ``StarFeedbackCreation`` = 0 or 1 with ``StarParticleFeedback`` =  1. (If ``StarParticleFeedback`` = 0, stellar feedback is only deposited into the cell in which the star particle lives).  Default: 0.
+    implemented for ``StarParticleCreation`` method = 0 or 1 with ``StarParticleFeedback`` method =  1. (If ``StarParticleFeedback`` = 0, stellar feedback is only deposited into the cell in which the star particle lives).  Default: 0.
 
 ``StarFeedbackDistCellStep`` (external)
     In essence, this parameter controls the shape of the volume where
     that are within ``StarFeedbackDistCellSteps`` cells from the host
     cell, counted in steps in Cartesian directions, are injected with
     stellar feedback.  Its maximum value is ``StarFeedbackDistRadius``
-    * ``TopGridRank``.  Only implemented for ``StarFeedbackCreation`` = 0
-    or 1.  See :ref:`distributed_feedback` for an illustration.
+    * ``TopGridRank``.  Only implemented for ``StarParticleCreation`` method = 0
+    or 1  with ``StarParticleFeedback`` method =  1.  See :ref:`distributed_feedback` for an illustration.
     Default: 0.
 
 ``StarMakerTypeIaSNe`` (external)
     traced in a separate species field, ``MetalSNIa_Density``.  The
     metallicity of star particles that comes from this ejecta is
     stored in the particle attribute ``typeia_fraction``.  Can be used
-    with ``StarParticleCreation`` = 0, 1, 2, 5, 7, and 8.  Default:
+    with ``StarParticleCreation`` method = 0, 1, 2, 5, 7, and 8.  Default:
     0.
 
 ``StarMakerPlanetaryNebulae`` (external) 
     feedback injects gas with the same metallicity as the star
     particle, and the thermal feedback equates to a 10 km/s wind.  The
     ejecta are not stored in its own species field.  Can be used
-    with ``StarParticleCreation`` = 0, 1, 2, 5, 7, and 8.  Default: 0.
+    with ``StarParticleCreation`` method = 0, 1, 2, 5, 7, and 8.  Default: 0.
 
 Normal Star Formation
 ^^^^^^^^^^^^^^^^^^^^^
 ``StarMakerOverDensityThreshold`` (external)
     The overdensity threshold in code units (for cosmological simulations, note that code units are relative to the total mean density, not
     just the dark matter mean density) before star formation will be
-    considered. For ``StarParticleCreation`` = 7 in cosmological
+    considered. For ``StarParticleCreation`` method = 7 in cosmological
     simulations, however, ``StarMakerOverDensityThreshold`` should be in
     particles/cc, so it is not the ratio with respect to the
     ``DensityUnits`` (unlike most other
 ``StarMakerSHDensityThreshold`` (external)
     The critical density of gas used in Springel & Hernquist star
     formation ( \\rho_{th} in the paper) used to determine the star
-    formation timescale in units of g cm\ :sup:`-3`\ . Only valid for ``StarParticleCreation`` = 8. Default: 7e-26.
+    formation timescale in units of g cm\ :sup:`-3`\ . Only valid for ``StarParticleCreation`` method = 8. Default: 7e-26.
 ``StarMakerMassEfficiency`` (external)
     The fraction of identified baryonic mass in a cell
     (Mass\*dt/t_dyn) that is converted into a star particle. Default:
     returned as UV radiation with a quasar spectrum. This is used when
     calculating the radiation background. Default: 5e-6
 
+Molecular Hydrogen Regulated Star Formation
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The parameters below are considered in ``StarParticleCreation`` method 11.
+
+``H2StarMakerEfficiency`` (external)
+    See :ref:`molecular_hydrogen_regulated_star_formation`.
+``H2StarMakerNumberDensityThreshold`` (external)
+    See :ref:`molecular_hydrogen_regulated_star_formation`.
+``H2StarMakerMinimumMass`` (external)
+    See :ref:`molecular_hydrogen_regulated_star_formation`.
+``H2StarMakerMinimumH2FractionForStarFormation`` (external)
+    See :ref:`molecular_hydrogen_regulated_star_formation`.
+``H2StarMakerStochastic`` (external)
+    See :ref:`molecular_hydrogen_regulated_star_formation`.
+``H2StarMakerUseSobolevColumn`` (external)
+    See :ref:`molecular_hydrogen_regulated_star_formation`.
+``H2StarMakerSigmaOverR`` (external)
+    See :ref:`molecular_hydrogen_regulated_star_formation`.
+``H2StarMakerAssumeColdWarmPressureBalance`` (external)
+    See :ref:`molecular_hydrogen_regulated_star_formation`.
+``H2StarMakerH2DissociationFlux_MW`` (external)
+    See :ref:`molecular_hydrogen_regulated_star_formation`.
+``H2StarMakerH2FloorInColdGas`` (external)
+    See :ref:`molecular_hydrogen_regulated_star_formation`.
+``H2StarMakerColdGasTemperature`` (external)
+    See :ref:`molecular_hydrogen_regulated_star_formation`.
+``StarFormationOncePerRootGridTimeStep`` (external)
+    See :ref:`molecular_hydrogen_regulated_star_formation`.
+
 Population III Star Formation
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 ``PopIIIColorMass`` (external)
     A Pop III "color" particle will populate the surrounding region with a mass of PopIIIColorMass.  Units: solar masses.  Default: 1e6
 
-Radiative Star Cluster Star Formation
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Radiative Star Cluster Formation
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The parameters below are considered in ``StarParticleCreation`` method 5.
 
-``StarClusterUseMetalField`` (external)
-    Set to 1 to trace ejecta from supernovae. Default: 0.
 ``StarClusterMinDynamicalTime`` (external)
     When determining the size of a star forming region, one method is
     to look for the sphere with an enclosed average density that
     if ray merging is used. Originally this was developed to reduce the
     amount of ray tracing involved from galaxies with hundreds of these
     radiating particles. Default: 10.
+``StarClusterUseMetalField`` (external)
+    Set to 1 to trace ejecta from supernovae. Default: 0.
 ``StarClusterHeliumIonization`` (external)
     When turned on, stellar clusters will emit helium singly- and doubly-ionizing radiation.  Default: 0
 ``StarClusterRegionLeftEdge`` (external)
 ``StarClusterUnresolvedModel`` (external)
     Regular star clusters live for 20 Myr, but this is only valid when molecular clouds are resolved.  When this parameter is on, the star formation rate is the same as the Cen & Ostriker exponential rate.  Default: 0
 
-Molecular Hydrogen Regulated Star Formation
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-``H2StarMakerEfficiency`` (external)
-    See :ref:`molecular_hydrogen_regulated_star_formation`.
-``H2StarMakerNumberDensityThreshold`` (external)
-    See :ref:`molecular_hydrogen_regulated_star_formation`.
-``H2StarMakerMinimumMass`` (external)
-    See :ref:`molecular_hydrogen_regulated_star_formation`.
-``H2StarMakerMinimumH2FractionForStarFormation`` (external)
-    See :ref:`molecular_hydrogen_regulated_star_formation`.
-``H2StarMakerStochastic`` (external)
-    See :ref:`molecular_hydrogen_regulated_star_formation`.
-``H2StarMakerUseSobolevColumn`` (external)
-    See :ref:`molecular_hydrogen_regulated_star_formation`.
-``H2StarMakerSigmaOverR`` (external)
-    See :ref:`molecular_hydrogen_regulated_star_formation`.
-``H2StarMakerAssumeColdWarmPressureBalance`` (external)
-    See :ref:`molecular_hydrogen_regulated_star_formation`.
-``H2StarMakerH2DissociationFlux_MW`` (external)
-    See :ref:`molecular_hydrogen_regulated_star_formation`.
-``H2StarMakerH2FloorInColdGas`` (external)
-    See :ref:`molecular_hydrogen_regulated_star_formation`.
-``H2StarMakerColdGasTemperature`` (external)
-    See :ref:`molecular_hydrogen_regulated_star_formation`.
-``StarFormationOncePerRootGridTimeStep`` (external)
-    See :ref:`molecular_hydrogen_regulated_star_formation`.
-
 Massive Black Hole Particle Formation
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The parameters below are considered in StarParticleCreation method 9.
+The parameters below are considered in ``StarParticleCreation`` method 9.
 
 ``MBHInsertLocationFilename`` (external)
     The mass and location of the MBH particle that has to be inserted.
 Sink Formation and Feedback
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The parameters below are considered in sink creation routines: sink_maker, star_maker8, star_maker9.
+The parameters below are considered in sink creation routines: sink_maker, star_maker8, star_maker9 (and occasionally only in certain set-ups).  
+Because many of the following parameters are not actively being tested and maintained, users are encouraged to carefully examine the code before using it.
 
 ``AccretionKernal`` (external)
     While this parameter is used to determine the accretion kernel in star_maker8.C, there is no choice other than 1 at the moment: Ruffert, ApJ (1994) 427 342 (a typo in the parameter name...).  Default: 0

File doc/manual/source/physics/cooling.rst

 these methods require the parameter ``RadiativeCooling`` be set to 1.
 Other parameters are required for using the various methods, which are
 described below.
+For relevant parameters, please also see :ref:`cooling_parameters`.
 
 MultiSpecies = 0: Sarazin & White
 ---------------------------------

File doc/manual/source/physics/hydro_methods.rst

 There are four available methods in Enzo for calculating the evolution
 of the gas with and without magnetic fields. Below is a brief
 description of each method, including the parameters associated with
-each one and a link to further reading.
+each one and a link to further reading. 
+For relevant parameters please also see :ref:`hydrodynamics_parameters`.
+
 
 Method 0: Piecewise Parabolic Method (PPM)
 ------------------------------------------

File doc/manual/source/physics/radiative_transfer.rst

 .. sectionauthor:: John Wise <jwise@physics.gatech.edu>
 .. versionadded:: 2.0
 
+For relevant parameters, please also see :ref:`radiative_transfer_ray_tracing` and :ref:`radiative_transfer_fld`.
+
+
 Adaptive Ray Tracing
 --------------------
 

File doc/manual/source/physics/shock_finding.rst

 ==================
 .. sectionauthor:: Sam Skillman <samskillman@gmail.com>
 .. versionadded:: 2.1
+
+For relevant parameters, please also see :ref:`shock_finding_parameters`.
+
 *Source: Grid_FindShocks.C*
 
 Shock finding is accomplished using one of four methods.  The primary

File doc/manual/source/physics/star_particles.rst

 in Enzo.  There are also methods that include routines for black hole,
 sink, and Pop III stellar tracer formation.  Here we give the details
 of each implementation and the parameters that control them.
-
+For relevant parameters please also see :ref:`StarParticleParameters`.
 
 
 Method 0: Cen & Ostriker