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Merged in mornkr/enzo-doc-mornkr (pull request #6)

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

 ``HaloFinderTimestep`` (external)
     Find halos every dt = (this parameter). Only evaluated at each
     top-level timestep. Not used if negative. Default: -99999.0
+``HaloFinderRunAfterOutput`` (external)
+    When turned on, the inline halo finder is run after an output is written.  Default: 0
 ``HaloFinderLastTime`` (internal)
     Last time of a halo find. Default: 0.
 
 Inline Python
 ^^^^^^^^^^^^^
 
+``PythonTopGridSkip`` (external)
+    How many top grid cycles should we skip between calling python at the top of the hierarchy?  Only works with python-yes in compile settings.
 ``PythonSubcycleSkip`` (external)
-    The number of times Enzo should reach the bottom of the hierarchy
-    before exposing its data and calling Python. Only works with
-    python-yes in compile settings.
-
+    How many subgrid cycles should we skip between calling python at the bottom of the hierarchy?
+``PythonReloadScript`` (external)
+    Should "user_script.py" be reloaded in between Python calls?
+``NumberOfPythonCalls`` (internal)
+    Internal parameter tracked by Enzo
+``NumberOfPythonTopGridCalls`` (internal)
+    Internal parameter tracked by Enzo
+``NumberOfPythonSubcycleCalls`` (internal)
+    Internal parameter tracked by Enzo

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

        from the Hercules code written by Peter Anninos and Yu Zhang,
        featuring rates from Tom Abel. Other varieties of cooling are
        controlled by the ``MetalCooling`` parameter, as discused below.
-
+``RadiativeCoolingModel`` (external)
+    This switches between the tabular look up cooling that is standard (RadiativeCoolingModel=1) and an analytic fit to the Wolfire et al 2003, ApJ, 587, 278 made by Koyama and Inutsuka 2006 (RadiativeCoolingModel = 3, arXiv:astro-ph/0605528).  Default: 1
 ``GadgetCooling`` (external)
     This flag (1 - on, 0 - off) turns on (when set to 1) a set of
     routines that calculate cooling rates based on the assumption of a
     [Not in public release version]
 ``PhotoelectricHeating`` (external)
     If set to be 1, the following parameter will be added uniformly
-    to the gas without any shielding (Tasker & Bryan 2008). At the
-    moment this is still experimental. Default: 0
+    to the gas without any shielding (Tasker & Bryan 2008). Default: 0
 ``PhotoelectricHeatingRate`` (external)
     This is the parameter used as Gamma_pe for uniform photoelectric heating.
     Default: 8.5e-26 erg s^-1 cm^-3
     metal fields - currently there is the standard metallicity field
     (Metal_Density) and two additional metal fields (Z_Field1 and
     Z_Field2). Acceptable values are 1 or 0, Default: 0 (off).
+``H2FormationOnDust`` (external)
+    Turns on H2 formation on dust grains and gas-grain heat transfer following Omukai (2000). Default: 0 (OFF)
+``NumberOfDustTemperatureBins`` (external)
+    Number of dust temperature bins for the dust cooling and H2 formation rates.  Default: 250
+``DustTemperatureStart`` (external)
+    Minimum dust temperature for dust rates.  Default: 1.0
+``DustTemperatureEnd`` (external)
+    Maximum dust temperature for dust rates.  Default: 1500
+``OutputDustTemperature`` (external)
+    Flag to write out the dust temperature field.  Default: 0
 
 .. _cloudy_cooling:
 

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

 ``SelfGravity`` (external)
     This flag (1 - on, 0 - off) indicates if the baryons and particles
     undergo self-gravity.
+``SelfGravityGasOff`` (external)
+    This parameter is used in conjuction with SelfGravity so that only particles contribute to potential, not gas. Default = False (i.e. gas does contribute)
 ``GravitationalConstant`` (external)
     This is the gravitational constant to be used in code units. For cgs units it
     should be 4\*pi\*G. For cosmology, this value must be 1 for the

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

     shock-detection, this is an extra filter which removes weak shocks
     (or noise in the dual energy fields) from triggering the shock
     detection. Default: 0.1
+``MinimumShearForRefinement`` (external)
+    It is the minimum shear above which a refinement occurs if the CellFlaggingMethod is appropriately set. Default: 0
 ``MetallicityRefinementMinLevel`` (external)
     Sets the minimum level (maximum cell size) to which a cell enriched
     with metal above a level set by ``MetallicityRefinementMinMetallicity``
     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 Mach number required to refine a level when using ShockwaveRefinement. Default: 1.3
+``ShockwaveRefinementMinVelocity`` (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
     = 128 (pc), then the code will automatically calculate
     ``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 -
     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
-``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
+``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
 ``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
-``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
+``MinimumSubgridEdge`` (external)
+    The minimum length of the edge of a subgrid.  See :ref:`running_large_simulations`. Default: 6
+``MaximumSubgridSize`` (external)
+    The maximum size (volume) of a subgrid.  See :ref:`running_large_simulations`. Default: 32768
+``SubgridSizeAutoAdjust`` (external)
+    See :ref:`running_large_simulations`.  Default: 1 (TRUE)
+``OptimalSubgridsPerProcessor`` (external)
+    See :ref:`running_large_simulations`.  Default: 16
 ``LoadBalancing`` (external)
     Set to 0 to keep child grids on the same processor as their
     parents. Set to 1 to balance the work on one level over all
     = (01234567) reside on node (00112233) if there are 4 nodes. Option
     3 assumes round-robin scheduling (proc = (01234567) -> node =
     (01230123)). Set to 4 for load balancing along a Hilbert
-    space-filling curve on each level. Default: 1
+    space-filling curve on each level. See :ref:`running_large_simulations`. Default: 1
 ``LoadBalancingCycleSkip`` (external)
     This sets how many cycles pass before we load balance the root
     grids. Only works with LoadBalancing set to 2 or 3. NOT RECOMMENDED
     for nested grid calculations. Default: 10
+``LoadBalancingMinLevel`` (external)
+    Load balance the grids in levels greater than this parameter.  Default: 0
+``LoadBalancingMaxLevel`` (external)
+    Load balance the grids in levels less than this parameter.  Default: MAX_DEPTH_OF_HIERARCHY
+``ResetLoadBalancing`` (external)
+    When restarting a simulation, this parameter resets the processor number of each root grid to be sequential.  All child grids are assigned to the processor of their parent grid.  Only implemented for LoadBalancing = 1.  Default = 0
+``NumberOfRootGridTilesPerDimensionPerProcessor`` (external)
+    Splits the root grid into 2^(dimensions*this parameter) grids per MPI process.  Default: 1
+``FastSiblingLocatorEntireDomain`` (external)
+    In zoom-in calculations, the fast sibling locator doesn't need to search the entire domain.  Turning this parameter on restricts the finder to the inner nested grid.  Currently broken.  Default: 0
+``MoveParticlesBetweenSiblings`` (external)
+    During RebuildHierarchy, particles that have moved beyond the grid boundaries are moved to the correct grid.  Default: 1
+``RebuildHierarchyCycleSkip`` (external)
+    Set the number of cycles at a given level before rebuilding the hierarchy.  Example: RebuildHierarchyCycleSkip[1] = 4

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

 ``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
+``MaximumTopGridTimeStep`` (external)
+    This parameter limits the maximum timestep on the root grid.  Default: huge_number.
 ``ShearingVelocityDirection`` (external)
     Select direction of shearing boundary. Default is x direction. Changing this is probably not a good idea.
 ``AngularVelocity`` (external)
     in the shearing boundary. Default: 1.0
 ``GridVelocity`` (external)
     The whole computational domain will have this velocity.  Experimental.  Default: 0 0 0
-``MaximumTopGridTimeStep`` (external)
-    This parameter limits the maximum timestep on the root grid.  Default: huge_number.
 ``StringKick`` (external)
     While this parameter was initially designed to describe the kick by cosmic strings in CosmologySimulation, it can be used to model the velocity (in km/s) that the baryons should move relative to dark matter at the initial redshift, in order to study the effect discussed by Tseliakhovich & Hirata (astro-ph:1005.2416). Default: 0
 ``StringKickDimension`` (external)
-    This parameter is used to control the orthogonal direction of the flow.  Default: 0 (x-axis)
+    This parameter is used to control the orthogonal direction of the flow.  Default: 0 (x-axis)
+``MemoryLimit`` (external)
+    If the memory usage on a single MPI process exceeds this number, then the simulation will halt after outputting.  Only used when the compile-time define MEM_TRACE is used. Default: 4e9
+``HydrogenFractionByMass`` (external)
+    This parameter is used to set up initial conditions in some test problems.  Default: 0.76
+``DeuteriumToHydrogenRatio`` (external)
+    This parameter is used to set up initial conditions in some test problems.  Default: 2.0*3.4e-5 (Burles & Tytler 1998, the parameter here is by mass, so multiply by 2)
+``SolarMetalFractionByMass`` (external)
+    This parameter is used to set up initial conditions in some test problems. Do NOT change this parameter unless you know exactly what you are doing. Default: 0.02041
+``CoolDataIh2co`` (external)
+    Whether to include molecular hydrogen cooling.  Do NOT change this parameter unless you know exactly what you are doing.  Default: 1
+``CoolDataIpiht`` (external)
+    Whether to include photoionization heating.  Do NOT change this parameter unless you know exactly what you are doing.  Default: 1
+``CoolDataCompXray`` (external)
+    Do NOT change this parameter unless you know exactly what you are doing.  Saved to CoolData.comp_xray. Default: 0
+``CoolDataTempXray`` (external)
+    Do NOT change this parameter unless you know exactly what you are doing.  Saved to CoolData.temp_xray. Default: 0
+``NumberOfTemperatureBins`` (external)
+    Do NOT change this parameter unless you know exactly what you are doing. Default: 600
+``TemperatureStart`` (external)
+    Do NOT change this parameter unless you know exactly what you are doing. Default: 10
+``TemperatureEnd`` (external)
+    Do NOT change this parameter unless you know exactly what you are doing. Default: 1e8

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

     ``star_particle_density``; and 2 will dump
     ``actively_forming_stellar_mass_density``, ``SFR_density``, etc.
     Default: 0.
+``ComputePotential`` (external)
+    When turned on, the gravitational potential is computed and stored in memory.  Always done when SelfGravity is on.  Default: 0
+``WritePotential`` (external)
+    When turned on, the gravitational potential is written to file.  Default: 0
 ``VelAnyl`` (external)
     Set to 1 if you want to output the divergence and vorticity of
     velocity. Works in 2D and 3D.
 ``BAnyl`` (external)
     Set to 1 if you want to output the divergence and vorticity of
     ``Bfield``. Works in 2D and 3D.
+``TimingCycleSkip`` (external)
+    Controls how many cycles to skip when timing information is collected, reduced, and written out to performance.out.  Default: 1
+``OutputParticleTypeGrouping`` (external) 	
+    In the grid HDF5 groups, particles are sorted by type, and a reference is created to indicate which particle index range corresponds to each type.  Default: 0
+``HierarchyFileInputFormat`` (external) 
+    See :ref:`controlling_the_hierarhcy_file_output`.
+``HierarchyFileOutputFormat`` (external) 
+    See :ref:`controlling_the_hierarhcy_file_output`.
+``LocalDir`` (external) 
+    See :ref:`controlling_data_output`.
+``GlobalDir`` (external) 
+    See :ref:`controlling_data_output`.
 
 Stopping Parameters
 ^^^^^^^^^^^^^^^^^^^

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

     Reserved for future use.
 ``TimeActionType[#]``
     Reserved for future use.
+``StopSteps``
+    Reserved for future use
+``CoolDataf0to3``
+    Reserved for future use
+``StageInput``
+    Reserved for future use
+``LocalPath``
+    Reserved for future use
+``GlobalPath``
+    Reserved for future use
 
 Other Internal Parameters
 ^^^^^^^^^^^^^^^^^^^^^^^^^
     Reserved for future use.
 ``InitialCycleNumber`` (internal)
     The current cycle
-``DataLabel[#]`` (internal)
-    These are printed out into the restart dump parameter file. One
-    Label is produced per baryon field with the name of that baryon
-    field. The same labels are used to name data sets in HDF files.
-``DataUnits[#]`` 
-    Reserved for future use.
 ``SubcycleNumber`` (internal)
     The current subcycle
 ``DataDumpNumber`` (internal)
     Reserved for future use.
 ``HistoryDumpNumber``
     Reserved for future use.
+``DataLabel[#]`` (internal)
+    These are printed out into the restart dump parameter file. One
+    Label is produced per baryon field with the name of that baryon
+    field. The same labels are used to name data sets in HDF files.
+``DataUnits[#]`` 
+    Reserved for future use.
 ``VersionNumber`` (internal)
     Sets the version number of the code which is written out to restart
     dumps.

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

 ``TurbulenceSimulationGridLevel[]`` (external)
 ``TurbulenceSimulationInitialMagneticField[i]`` (external)
      Initial magnetic field strength in the ith direction. Default: 5.0 (all)
+``RandomForcing`` (external)
+    This parameter is used to add random forcing field to create turbulence; see Mac Low 1999, ApJ 524, 169. Default: 0
+``RandomForcingEdot`` (external)
+    This parameter is used to define the value of such field; see TurbulenceSimulationInitialize.C and ComputeRandomForcingNormalization.C. Default: -1.0
+``RandomForcingMachNumber`` (external)
+    This parameter is used to define the value of such field; see Grid_TurbulenceSimulationInitialize.C and Grid_ComputeRandomForcingFields.C. Default: 0.0
+``CycleSkipGlobalDataDump`` (external)
+    Cycles to skip before global data (defined in ComputeRandomForcingNormalization.C) is dumped.
 
 .. _protostellar_param:
 

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

     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.
 ``ImplicitProblem`` (external)
     Set to 1 to turn on the implicit FLD solver, or 3 to turn on the
     split FLD solver. Default: 0.
     solver options for the FLD-based solvers. These are described in
     the relevant User Guides, located in ``doc/implicit_fld`` and
     ``doc/split_fld``. Default: NULL.
-``RadiativeTransfer`` (external)
-    Set to 0 to avoid conflicts with the ray tracing solver above.
-    Default: 0.
 ``RadiativeTransferFLDCallOnLevel`` (reserved)
     The level in the static AMR hierarchy where the unigrid FLD solver
     should be called. Currently only works for 0 (the root grid).
 ``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)
+    When using the FLD radiation transfer and StarMakerEmissivityFIeld = 1, this is the efficiency of mass to UV light ratio. Default: 0
 
 Radiative Transfer (FLD) Implicit Solver Parameters
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

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

     Set to 1 to create black hole particles that radiate in X-rays for
     stars that do not go supernova (< 140 solar masses and > 260 solar
     masses). Default: 0.
-``PopIIIBHLuminosityEfficiency`` (internal)
+``PopIIIBHLuminosityEfficiency`` (external)
     The radiative efficiency in which the black holes convert accretion
     to luminosity. Default: 0.1.
-``PopIIIOverDensityThreshold`` (internal)
+``PopIIIOverDensityThreshold`` (external)
     The overdensity threshold (relative to the total mean density)
     before Pop III star formation will be considered. Default: 1e6.
-``PopIIIH2CriticalFraction`` (internal)
+``PopIIIH2CriticalFraction`` (external)
     The H_2 fraction threshold before Pop III star formation will be
     considered. Default: 5e-4.
-``PopIIIMetalCriticalFraction`` (internal)
+``PopIIIMetalCriticalFraction`` (external)
     The metallicity threshold (relative to gas density, not solar)
     before Pop III star formation will be considered. Note: this should
     be changed to be relative to solar! Default: 1e-4.
-``PopIIISupernovaRadius`` (internal)
+``PopIIISupernovaRadius`` (external)
     If the Population III star will go supernova (140<M<260 solar
     masses), this is the radius of the sphere to inject the supernova
     thermal energy at the end of the star's life. Units are in parsecs.
     Default: 1.
-``PopIIISupernovaUseColour`` (internal)
+``PopIIISupernovaUseColour`` (external)
     Set to 1 to trace the metals expelled from supernovae. Default: 0.
+``PopIIIInitialMassFunction`` (external)
+    When turned on, each Pop III stellar mass is randomly drawn from an IMF that is Salpeter above some characteristic mass and exponentially cutoff below this mass.  Default: 0
+``PopIIIInitialMassFunctionSeed`` (external)
+    Random initial seed for the Pop III stellar mass randomizer.  Default: INT_UNDEFINED
+``PopIIILowerMassCutoff`` (external)
+    Lower limit of the Pop III IMF.  Default: 1
+``PopIIIUpperMassCutoff`` (external)
+    Upper limit of the Pop III IMF.  Default: 300
+``PopIIIInitialMassFunctionSlope`` (external)
+    Slope of the Salpeter (high-mass) portion of the Pop III IMF.  Default: -1.3
+``PopIIIInitialMassFunctionCalls`` (internal) 
+    Number of times a Pop III mass has been drawn from the IMF.  Used for restarts and reproducibility.  Default: 0
+``PopIIISupernovaMustRefine`` (external)
+    When turned on, the region around a star about to go supernova is refined to the maximum AMR level.  Experimental.  Default: 0
+``PopIIISupernovaMustRefineResolution`` (external)
+    Used with PopIIISupernovaMustRefine.  Minimum number of cells across the blastwave.  Default: 32
+``PopIIIHeliumIonization`` (external)
+    When turned on, Pop III stars will emit helium singly- and doubly-ionizing radiation.  Default: 0
+``PopIIIColorDensityThreshold`` (external)
+    Above this density, a Pop III "color" particle forms, and it will populate the surrounding region with a color field.  Units: mean density. Default: 1e6
+``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
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The parameters below are considered in ``StarParticleCreation`` method 5.
 
-``StarClusterUseMetalField`` (internal)
+``StarClusterUseMetalField`` (external)
     Set to 1 to trace ejecta from supernovae. Default: 0.
-``StarClusterMinDynamicalTime`` (internal)
+``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
     corresponds to some minimum dynamical time. Observations hint that
     this value should be a few million years. Units are in years.
     Default: 1e7.
-``StarClusterIonizingLuminosity`` (internal)
+``StarClusterIonizingLuminosity`` (external)
     The specific luminosity of the stellar clusters. In units of
     ionizing photons per solar mass. Default: 1e47.
-``StarClusterSNEnergy`` (internal)
+``StarClusterSNEnergy`` (external)
     The specific energy injected into the gas from supernovae in the
     stellar clusters. In units of ergs per solar mass. Default: 6.8e48
     (Woosley & Weaver 1986).
-``StarClusterSNRadius`` (internal)
+``StarClusterSNRadius`` (external)
     This is the radius of the sphere to inject the supernova thermal
     energy in stellar clusters. Units are in parsecs. Default: 10.
-``StarClusterFormEfficiency`` (internal)
+``StarClusterFormEfficiency`` (external)
     Fraction of gas in the sphere to transfer from the grid to the star
     particle. Recall that this sphere has a minimum dynamical time set
     by ``StarClusterMinDynamicalTime``. Default: 0.1.
-``StarClusterMinimumMass`` (internal)
+``StarClusterMinimumMass`` (external)
     The minimum mass of a star cluster particle before the formation is
     considered. Units in solar masses. Default: 1000.
-``StarClusterCombineRadius`` (internal)
+``StarClusterCombineRadius`` (external)
     It is possible to merge star cluster particles together within this
     specified radius. Units in parsecs. This is probably not necessary
     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.
+``StarClusterHeliumIonization`` (external)
+    When turned on, stellar clusters will emit helium singly- and doubly-ionizing radiation.  Default: 0
+``StarClusterRegionLeftEdge`` (external)
+    Can restrict the region in which star clusters can form.  Origin of this region.  Default: 0 0 0
+``StarClusterRegionRightEdge`` (external)
+    Can restrict the region in which star clusters can form.  Right corner of this region.  Default: 1 1 1
+``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
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 ``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
-
 ``StellarWindFeedback`` (external)
     This parameter is used to turn on sink particle creation by star_maker8.C and also its feedback.  Currently implemented are: 1 - protostellar jets along the magnetic fields, 2 - protostellar jets along random directions, 3 - isotropic main sequence stellar wind, 4 - not implemented, 5 - not implemented, 6 - methods 2 and 3 combined.  Default: 0
-
 ``StellarWindTurnOnMass`` (external)
     This parameter is used to decide whether mass increase reached the ejection threshold for StellarWindFeedback=1, 2, or 6 in star_maker8.C. Default: 0.1
-
 ``MSStellarWindTurnOnMass`` (external)
     This parameter is used to decide whether mass increase reached the ejection threshold for StellarWindFeedback = 3 or 6 in star_maker8.C. Default: 10.0
-
 ``BigStarFormation`` (external)
     This parameter is used to turn on sink particle creation by star_maker9.C.  
-
 ``BigStarFormationDone`` (external)
     In star_maker9.C, this parameter is used when we do not want to form BigStars any more.
-
 ``BigStarSeparation`` (external)
     In star_maker[89].C, if the newly-created sink particle is within a certain distance from the closest pre-existing sink, then add to it rather than creating a new one.
-
 ``SinkMergeDistance``
     [not used]
-
 ``SinkMergeMass``
     [not used]

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

 *Source: pop3_color_maker.F*
 
 
+.. _molecular_hydrogen_regulated_star_formation:
+
 Method 11: Molecular Hydrogen Regulated Star Formation
 ------------------------------------------------------
 Select this method by setting ``StarParticleCreation = 2048``.

File doc/manual/source/user_guide/HierarchyFile.rst

      >>> <ExternalLink to "Grid00000002" in file "./RD0007/RedshiftOutput0007.cpu0000"
 
 
+.. _controlling_the_hierarhcy_file_output: 
+
 Controlling the Hierarchy File Output Format
 --------------------------------------------