Ji-hoon Kim avatar Ji-hoon Kim committed dcba0ff

All done! all 175 parameters are in; people should be able to add new parameters to here as they push new features!

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doc/manual/source/parameters/cooling.rst

     a 12 species model is followed, including D, D+ and HD. This
     routine, like the last one, is based on work done by Abel, Zhang
     and Anninos. 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]
-``PhotoelectricHeating`` (external)
-    If set to be 1, the following parameter will be added uniformly
-    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
 ``MultiMetals`` (external)
     This was added so that the user could turn on or off additional
     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).
+``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)
+``CIECooling`` (external)
+    Should CIE (Ripamonti & Abel 2004) cooling be included at high densities
+``H2OpticalDepthApproximation`` (external)
+    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)
     Maximum dust temperature for dust rates.  Default: 1500
 ``OutputDustTemperature`` (external)
     Flag to write out the dust temperature field.  Default: 0
+``PhotoelectricHeating`` (external)
+    If set to be 1, the following parameter will be added uniformly
+    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
+``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:
 
 
 ``CloudyCoolingGridFile`` (external)
     A string specifying the path to the Cloudy cooling dataset.
-
 ``IncludeCloudyHeating`` (external)
     An integer (0 or 1) specifying whether the heating rates are to be
     included in the calculation of the cooling. Some Cloudy datasets
     are made with the intention that only the cooling rates are to be
     used. Default: 0 (off).
-
 ``CMBTemperatureFloor`` (external)
     An integer (0 or 1) specifying whether a temperature floor is
     created at the temperature of the cosmic microwave background
     (T\ :sub:`CMB`\  = 2.72 (1 + z) K). This is accomplished in the
     code by subtracting the cooling rate at T\ :sub:`CMB`\  such that
     Cooling = Cooling(T) - Cooling(T\ :sub:`CMB`\ ). Default: 1 (on).
-
 ``CloudyElectronFractionFactor`` (external)
     A float value to account for additional electrons contributed by
     metals. This is only used with Cloudy datasets with dimension

doc/manual/source/parameters/initialization.rst

 ``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
+    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
+``ExternalBoundaryTypeIO`` (external)
+    not recommended for use at this point. Default: 0
+``ExternalBoundaryValueIO`` (external)
+    not recommended for use at this point. Default: 0
+``SimpleConstantBoundary`` (external)
+    not recommended for use at this point. Default: 0

doc/manual/source/parameters/io.rst

     ``star_particle_density``; and 2 will dump
     ``actively_forming_stellar_mass_density``, ``SFR_density``, etc.
     Default: 0.
+``OutputOnDensity`` (external)
+    Should interpolated outputs be generated at varying peak density?  Default: 0
+``StartDensityOutput`` (external)
+    The first density (in log g/cc) at which to output.
+``CurrentDensityOutput`` (external)
+    The most recent density at which output was generated.
+``IncrementDensityOutput`` (external)
+    After a density-directed output, how much should the density be increased by?  Default: 999
 ``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
+``WriteGhostZones`` (external)
+    Should ghost zones be written to disk?  Default: 0 
+``ReadGhostZones`` (external)
+    Are ghost zones present in the files on disk?  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
+``ParticleTypeInFile`` (external)    
+    Output ParticleType to disk?  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`.
+``TimingCycleSkip`` (external)
+    Controls how many cycles to skip when timing information is collected, reduced, and written out to performance.out.  Default: 1
+``DatabaseLocation`` (external)
+    (Not recommended for use at this point)  Where should the SQLite database of outputs be placed?
+``CubeDumpEnabled`` (external)
+    not recommended for use at this point. Default: 0
+``CubeDump[]`` (external)
+    not recommended for use at this point
 ``LocalDir`` (external) 
     See :ref:`controlling_data_output`.
 ``GlobalDir`` (external) 

doc/manual/source/parameters/radiation.rst

     approximate radiative-shielding. This parameter will be
     automatically turned on when RadiationFieldType is set to 11. See
     ``calc_photo_rates.src``. Default: 0
-``RadiationRedshiftOn`` (external) The redshift at which the UV 
+``RadiationRedshiftOn`` (external) 
+    The redshift at which the UV 
     background turns on. Default: 7.0.
-``RadiationRedshiftFullOn`` (external) The redshift at which the UV
+``RadiationRedshiftFullOn`` (external) 
+    The redshift at which the UV
     background is at full strength.  Between z =
     ``RadiationRedshiftOn`` and z = ``RadiationRedshiftFullOn``, the 
     background is gradually ramped up to full strength. Default: 6.0.
-``RadiationRedshiftDropOff`` (external) The redshift at which the 
+``RadiationRedshiftDropOff`` (external) 
+    The redshift at which the 
     strength of the UV background is begins to gradually reduce,
     reaching zero by ``RadiationRedshiftOff``. Default: 0.0.
-``RadiationRedshiftOff`` (external) The redshift at which the UV 
+``RadiationRedshiftOff`` (external) 
+    The redshift at which the UV 
     background is fully off. Default: 0.0.
+``TabulatedLWBackground`` (external)
+    When on, the amplitude of the Lyman-Werner background is read from the file LW_J21.in as a function of redshift.  Each line should have the redshift and LW background in units of 1e-21 erg/cm^3/s/Hz/sr.  Default: 0
 ``AdjustUVBackground`` (external)
     Add description. Default: 1.
+``AdjustUVBackgroundHighRedshift`` (external)
+    Add description. Default: 0.
 ``SetUVAmplitude`` (external)
     Add description. Default: 1.0.
 ``SetHeIIHeatingScale`` (external)
     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.
-``RadiativeTransferInterpolateField`` (obsolete)
-    A failed experiment in which we evaluate the density at the
-    midpoint of the ray segment in each cell to calculate the optical
-    depth. To interpolate, we need to calculate the vertex interpolated
-    density fields. Default: 0.
 ``RadiativeTransferSourceClustering`` (internal)
     Set to 1 to turn on ray merging from combined virtual sources on a
     binary tree. Default: 0.
     Set to 1 to turn on Compton heating on electrons from X-ray
     radiation (Ciotti & Ostriker 2001). Currently only BH and MBH
     particles emit X-rays. Default: 0.
+``RadiativeTransferInterpolateField`` (obsolete)
+    A failed experiment in which we evaluate the density at the
+    midpoint of the ray segment in each cell to calculate the optical
+    depth. To interpolate, we need to calculate the vertex interpolated
+    density fields. Default: 0.
+``SimpleQ`` (external)
+    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)
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