Commits

John Wise committed 6eb247f Merge

Merged in mornkr/enzo-doc-mornkr (pull request #5)

  • Participants
  • Parent commits de968bd, 960116f

Comments (0)

Files changed (24)

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

+Inline Analysis
+~~~~~~~~~~~~~~~
+
 Inline Halo Finding
-~~~~~~~~~~~~~~~~~~~
+^^^^^^^^^^^^^^^^^^^
 
 Enzo can find dark matter (sub)halos on the fly with a
 friends-of-friends (FOF) halo finder and a subfind method,
     Last time of a halo find. Default: 0.
 
 Inline Python
-~~~~~~~~~~~~~
+^^^^^^^^^^^^^
 
 ``PythonSubcycleSkip`` (external)
     The number of times Enzo should reach the bottom of the hierarchy

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

 Conduction
-~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~
 
 Isotropic and anisotropic thermal conduction are implemented using the
 method of Parrish and Stone: namely, using an explicit, forward

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

 Radiative Cooling Parameters
-----------------------------
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Simple Cooling Options
+^^^^^^^^^^^^^^^^^^^^^^
 
 ``RadiativeCooling`` (external)
     This flag (1 - on, 0 - off) controls whether or not a radiative
 .. _cloudy_cooling:
 
 Cloudy Cooling
-~~~~~~~~~~~~~~
+^^^^^^^^^^^^^^
 
 Cloudy cooling from Smith, Sigurdsson, & Abel (2008) interpolates
 over tables of precomputed cooling data. Cloudy cooling is turned

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

 Cosmology Parameters
---------------------
+~~~~~~~~~~~~~~~~~~~~
 
 ``ComovingCoordinates`` (external)
     Flag (1 - on, 0 - off) that determines if comoving coordinates are

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

 Gravity Parameters
-------------------
+~~~~~~~~~~~~~~~~~~
+
+General
+^^^^^^^
 
 ``TopGridGravityBoundary`` (external)
     A single integer which specified the type of gravitational boundary
     to a value less than 0. Default: -1
 
 External Gravity Source
-~~~~~~~~~~~~~~~~~~~~~~~~
+^^^^^^^^^^^^^^^^^^^^^^^
 
 These parameters set-up an external static background gravity source that is
 added to the acceleration field for the baryons and particles.

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

     :: 
 
        1 - refine by slope		       9 - refine by shear
-       2 - refine by baryon mass	       10 - refine by optical depth (in radiation calculation)
+       2 - refine by baryon mass	       10 - refine by optical depth (in RT calculation)
        3 - refine by shocks 		       11 - refine by resistive length (in MHD calculation)
        4 - refine by particle mass	       12 - refine by defined region "MustRefineRegion"
        5 - refine by baryon overdensity	       13 - refine by metallicity

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

-Hydrodynamic Parameters
------------------------
+Hydrodynamics Parameters
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+General
+^^^^^^^
 
 ``UseHydro`` (external)
     This flag (1 - on, 0 - off) controls whether a hydro solver is used.  
     Norman. Default: 0.0
 
 Minimum Pressure Support Parameters
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 ``UseMinimumPressureSupport`` (external)
     When radiative cooling is turned on, and objects are allowed to
 ``MinimumPressureSupportParameter`` (external)
     This is the numerical parameter discussed above. Default: 100
 
+Magnetohydrodynamics (CT) Parameters
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Coming very soon...!
+
+Magnetohydrodynamics (Dedner) Parameters
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+``UseDivergenceCleaning`` (external)
+    Method 1 and 2 are a failed experiment to do divergence cleaning
+    using successive over relaxation. Method 3 uses conjugate gradient
+    with a 2 cell stencil and Method 4 uses a 4 cell stencil. 4 is more
+    accurate but can lead to aliasing effects. Default: 0
+``DivergenceCleaningBoundaryBuffer`` (external)
+    Choose to *not* correct in the active zone of a grid by a
+    boundary of cells this thick. Default: 0
+``DivergenceCleaningThreshold`` (external)
+    Calls divergence cleaning on a grid when magnetic field divergence
+    is above this threshold. Default: 0.001
+``PoissonApproximateThreshold`` (external)
+    Controls the accuracy of the resulting solution for divergence
+    cleaning Poisson solver. Default: 0.001
+``UseDrivingField`` (external)
+    This parameter is used to add external driving force as a source term in some test problems; see hydro_rk/Grid_(MHD)SourceTerms.C. Default: 0
+``DrivingEfficiency`` (external)
+    This parameter is used to define the efficiency of such driving force; see hydro_rk/Grid_(MHD)SourceTerms.C. Default: 1.0
+``UseConstantAcceleration`` (external)
+    This parameter is used to add constant acceleration as a source term in some set-ups; see hydro_rk/Grid_(MHD)SourceTerms.C. Default: 0
+``ConstantAcceleration[]`` (external)
+    This parameter is used to define the value of such acceleration; see hydro_rk/Grid_(MHD)SourceTerms.C. 
+``UseViscosity`` (external)
+    This parameter is used to add viscosity and thereby update velocity in some set-ups (1 - constant viscosity, 2 - alpha viscosity); see ComputeViscosity in hydro_rk/Grid_AddViscosity.C.  Default: 0
+``ViscosityCoefficient`` (external)
+    This parameter is used to define the value of such viscosity for UseViscosity = 1; see ComputeViscosity in hydro_rk/Grid_AddViscosity.C. Default: 0.0
+``UseGasDrag`` (external)
+    This parameter is used to calculate velocity decrease caused by gas drag as a source term in some set-ups; see hydro_rk/Grid_(MHD)SourceTerms.C. Default: 0
+``GasDragCoefficient`` (external)
+    This parameter is used to define the value of such gas drag; see hydro_rk/Grid_(MHD)SourceTerms.C. Default: 0.0
+``UseFloor`` (external)
+    This parameter is used to impose the minimum energy based on MaximumAlvenSpeed in some set-ups; see hydro_rk/Grid_SetFloor.C. Default: 0
+``MaximumAlvenSpeed`` (external)
+    This parameter is used to define the value of such minimum; see hydro_rk/Grid_SetFloor.C. Default: 1e30
+``UseAmbipolarDiffusion`` (external)
+    This parameter is used to update magnetic fields by ambipolar diffusion in some set-ups; see hydro_rk/Grid_AddAmbipolarDiffusion.C. Default: 0
+``UseResistivity`` (external)
+    This parameter is used to add resistivity and thereby update magnetic fields in some set-ups; see ComputeResistivity in hydro_rk/Grid_AddResistivity.C.  Default: 0
+``UsePhysicalUnit`` (external)
+    For some test problems (mostly in hydro_rk), the relevant parameters could be defined in physical CGS units.  Default: 0
+``SmallRho`` (external)
+    Minimum value for density in hydro_rk/EvolveLevel_RK.C.  Default: 1e-30 (note that the default value assumes UsePhysicalUnit = 1)
+``SmallT`` (external)
+    Minimum value for temperature in hydro_rk/EvolveLevel_RK.C.  Default: 1e-10 (note that the default value assumes UsePhysicalUnit = 1)
+``SmallP``
+    [not used]
+``RKOrder``
+    [not used]
+``Theta_Limiter`` (external)
+    Flux limiter in the minmod Van Leer formulation.  Must be between 1 (most dissipative) and 2 (least dissipative). Default: 1.5
+``Coordinate`` (external)
+    Coordinate systems to be used in hydro_rk/EvolveLevel_RK.C.  Currently implemented are Cartesian and Spherical for HD_RK, and Cartesian and Cylindrical for MHD_RK.  See Grid_(MHD)SourceTerms.C.  Default: Cartesian
+``EOSType`` (external)
+    Types of Equation of State used in hydro_rk/EvolveLevel_RK.C (0 - ideal gas, 1 - polytropic EOS, 2 - another polytropic EOS, 3 - isothermal, 4 - pseudo cooling, 5 - another pseudo cooling, 6 - minimum pressure); see hydro_rk/EOS.h. Default: 0
+``EOSSoundSpeed`` (external)
+    Sound speed to be used in EOS.h for EOSType = 1, 2, 3, 4, 5.  Default: 2.65e4
+``EOSCriticalDensity`` (external)
+    Critical density to be used in EOS.h for EOSType = 1, 2, 4, 6. Default: 1e-13
+``EOSGamma`` (external)
+    Polytropic gamma to be used in EOS.h for EOSType = 1. Default: 1.667
+``DivBDampingLength`` (external)
+    From C_h (the Dedner wave speeds at which the div*B error is isotropically transferred; as defined in e.g. Matsumoto, PASJ, 2007, 59, 905) and this parameter, C_p (the decay rate of the wave) is calculated; see ComputeDednerWaveSpeeds.C  Default: 1.0
+``UseCUDA`` (external)
+    Set to 1 to use the CUDA-accelerated (M)HD solver.  Only works if compiled with cuda-yes. Default: 0
+``ResetMagneticField`` (external)
+    Set to 1 to reset the magnetic field in the regions that are denser
+    than the critical matter density. Very handy when you want to
+    re-simulate or restart the dumps with MHD. Default: 0
+``ResetMagneticFieldAmplitude`` (external)
+    The magnetic field values (in Gauss) that will be used for the
+    above parameter. Default: 0.0 0.0 0.0
+``CoolingCutOffDensity1``
+    Reserved for future use
+``CoolingCutOffDensity2``
+    Reserved for future use
+``CoolingCutOffTemperature``
+    Reserved for future use
+``CoolingPowerCutOffDensity1``
+    Reserved for future use
+``CoolingPowerCutOffDensity2``
+    Reserved for future use
+

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

-Simulation Identifiers and UUIDs
---------------------------------
-
-These parameters help to track, identify and group datasets. For reference,
-`Universally Unique Identifiers
-<http://en.wikipedia.org/wiki/Universally_Unique_Identifier>`_ (UUIDs) are
-opaque identifiers using random 128-bit numbers, with an extremely low chance
-of collision. (See :ref:`SimulationNamesAndIdentifiers` for a longer
-description of these parameters.)
-
-``MetaDataIdentifier`` (external)
-    This is a character string without spaces (specifically, something
-    that can be picked by "%s"), that can be defined in a parameter
-    file, and will be written out in every following output, if it is
-    found.
-``MetaDataSimulationUUID`` (internal)
-    A UUID that will be written out in all of the following outputs.
-    Like ``MetaDataIdentifier``, an existing UUID will be kept, but if one
-    is not found, and new one will be generated.
-``MetaDataDatasetUUID`` (internal)
-    A UUID created for each specific output.
-``MetaDataRestartDatasetUUID`` (internal)
-    If a ``MetaDataDatasetUUID`` UUID is found when the parameter file is
-    read in, it will written to the following datasets. This is used to
-    track simulations across restarts and parameter adjustments.
-``MetaDataInitialConditionsUUID`` (internal)
-    This is similar to ``MetaDataRestartDatasetUUID``, except it's used to
-    track which initial conditions were used.
-

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

 .. toctree::
    :maxdepth: 2
 
-   analysis.rst 
-   bhform.rst   
-   conduction.rst
-   cooling.rst  
-   cosmology.rst
-   gravity.rst  
-   hierarchy.rst
-   hydro.rst    
-   identifier.rst
    initialization.rst
    io.rst       
-   mhd.rst      
+   hierarchy.rst
+   gravity.rst  
+   hydro.rst    
+   cooling.rst  
+   particles.rst
+   starform.rst 
+   radiation.rst
+   cosmology.rst
+   bhform.rst   
+   shocks.rst   
+   conduction.rst
+   analysis.rst 
    other.rst    
-   particles.rst
    problemtypes.rst
-   radiation.rst
-   shocks.rst   
-   starform.rst 
-   stopping.rst 
-   streaming.rst

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

 Initialization Parameters
--------------------------
+~~~~~~~~~~~~~~~~~~~~~~~~~
 
 ``TopGridRank`` (external)
     This specifies the dimensionality of the root grid and by extension
     For shearing boundaries, the boundary pair in another direction
     must be periodic. Note that self gravity will not be consistent
     with shearing boundary conditions. Default: 0 0 0
-``ShearingVelocityDirection`` (external)
-    Select direction of shearing boundary. Default is x direction. Changing this is probably not a good idea.
-``AngularVelocity`` (external)
-    The value of the angular velocity in the shearing boundary.
-    Default: 0.001
-``VelocityGradient`` (external)
-    The value of the per code length gradient in the angular velocity
-    in the shearing boundary. Default: 1.0
 ``BoundaryConditionName`` (external)
     While the above parameters provide an easy way to set an entire
     side of grid to a given boundary value, the possibility exists to
 ``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
-
+``ShearingVelocityDirection`` (external)
+    Select direction of shearing boundary. Default is x direction. Changing this is probably not a good idea.
+``AngularVelocity`` (external)
+    The value of the angular velocity in the shearing boundary.
+    Default: 0.001
+``VelocityGradient`` (external)
+    The value of the per code length gradient in the angular velocity
+    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)

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

 I/O Parameters
 --------------
 
+General 
+^^^^^^^
+
 There are three ways to specify the frequency of outputs:
 time-based, cycle-based (a cycle is a top-grid timestep), and, for
 cosmology simulations, redshift-based. There is also a shortened
 ``dtDataDump`` (external)
     The time interval, in code units, between time-based outputs. A
     value of 0 turns off the time-based outputs. Default: 0
+``dtInterpolatedDataDump`` (external)
+    The time interval, in code units, between time-based interpolated outputs. A
+    value of 0 turns off the time-based outputs. Default: 0
 ``CycleSkipDataDump`` (external)
     The number of cycles (top grid timesteps) between cycle-based
     outputs. Zero turns off the cycle-based outputs. Default: 0
+``SubcycleSkipDataDump`` (external)
+    The number of subcycles between subcycle-based
+    outputs. Zero turns off the subcycle-based outputs. Default: 0
+``dtTracerParticleDump`` (external)
+    The time interval, in code units, between time-based tracer particle outputs (defined in ComputeRandomForcingNormalization.C). A
+    value of 0 turns off this output. Default: 0
 ``DataDumpName`` (external)
     The base file name used for both time and cycle based outputs.
     Default: data
     will not be appended but the four R's will be converted to a
     redshift with an implied decimal point in the middle (i.e. z=1.24
     becomes 0124). Default: RedshiftOutput
+``TracerParticleDumpName`` (external)
+    The base file name used for tracer particle outputs.
+    Default: 
+``TracerParticleDumpDir`` (external)
+    The dir name used for tracer particle outputs.
+    Default: 
+``dtRestartDump``
+    Reserved for future use.
+``dtHistoryDump``
+    Reserved for future use.
+``CycleSkipRestartDump``
+    Reserved for future use.
+``CycleSkipHistoryDump``
+    Reserved for future use.
+``RestartDumpName``
+    Reserved for future use.
+``HistoryDumpName``
+    Reserved for future use.
 ``CosmologyOutputRedshift[NNNN]`` (external)
     The time and cycle-based outputs occur regularly at constant
     intervals, but the redshift outputs are specified individually.
     This parameter overrides the parameter ``RedshiftOutputName`` for this
     (only only this) redshift output. Can be used repeatedly in the
     same manner as the previous parameter. Default: none
+``FileDirectedOutput``
+    If this parameter is set to 1, whenever the finest level has finished
+    evolving Enzo will check for new signal files to output.  (See
+    :ref:`force_output_now`.)  Default 1.
+``TracerParticleOn``
+    This parameter is used to set the velocities of the tracer particles equal to the gas velocities in the current cells.   Tracer particles are massless and can be used to output values of the gas as they advect with the fluid.  Default: 0
 ``OutputFirstTimeAtLevel`` (external)
     This forces Enzo to output when a given level is reached, and at
     every level thereafter. Default is 0 (off). User can usefully
     specify anything up to the maximum number of levels in a given
     simulation.
-``FileDirectedOutput``
-    If this parameter is set to 1, whenever the finest level has finished
-    evolving Enzo will check for new signal files to output.  (See
-    :ref:`force_output_now`.)  Default 1.
 ``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
 ``ExtractFieldsOnly`` (external)
     Used for extractions (enzo -x ...) when only field data are needed
     instead of field + particle data. Default is 1 (TRUE).
-``dtRestartDump``
-    Reserved for future use.
-``dtHistoryDump``
-    Reserved for future use.
-``CycleSkipRestartDump``
-    Reserved for future use.
-``CycleSkipHistoryDump``
-    Reserved for future use.
-``RestartDumpName``
-    Reserved for future use.
-``HistoryDumpName``
-    Reserved for future use.
 ``ParallelRootGridIO`` (external)
     Normally for the mpi version, the root grid is read into the root
     processor and then partitioned to separate processors using communication.
     smoothed by an SPH kernel. Set to 2 to also output smoothed dark
     matter velocities and velocity dispersion. Set to 0 to turn off.
     Default: 0.
+``SmoothedDarkMatterNeighbors`` (external)
+    Number of nearest neighbors to smooth dark matter quantities over.
+    Default: 32.
 ``OutputGriddedStarParticle`` (external)
     Set to 1 or 2 to write out star particle data gridded onto mesh.
     This will be useful e.g. if you have lots of star particles in a
 ``BAnyl`` (external)
     Set to 1 if you want to output the divergence and vorticity of
     ``Bfield``. Works in 2D and 3D.
-``SmoothedDarkMatterNeighbors`` (external)
-    Number of nearest neighbors to smooth dark matter quantities over.
-    Default: 32.
+
+Stopping Parameters
+^^^^^^^^^^^^^^^^^^^
+
+``StopTime`` (external)
+    This parameter specifies the time (in code units) when the
+    calculation will halt. For cosmology simulations, this variable is
+    automatically set by ``CosmologyFinalRedshift``. *No default.*
+``StopCycle`` (external)
+    The cycle (top grid timestep) at which the calculation stops. A
+    value of zero indicates that this criterion is not be used.
+    *Default: 100,000*
+``StopFirstTimeAtLevel`` (external)
+    Causes the simulation to immediately stop when a specified level is
+    reached. Default value 0 (off), possible values are levels 1
+    through maximum number of levels in a given simulation.
+``NumberOfOutputsBeforeExit`` (external)
+    After this many datadumps have been written, the code will exit.  If 
+    set to 0 (default), this option will not be used.  Default: 0.
+``StopCPUTime`` (external)
+    Causes the simulation to stop if the wall time exceeds ``StopCPUTime``.
+    The simulation will output if the wall time after the next
+    top-level timestep will exceed ``StopCPUTime``, assuming that the wall
+    time elapsed during a top-level timestep the same as the previous
+    timestep. In units of seconds. Default: 2.592e6 (30 days)
+``ResubmitOn`` (external)
+    If set to 1, the simulation will stop if the wall time will exceed
+    ``StopCPUTime`` within the next top-level timestep and run a shell
+    script defined in ``ResubmitCommand`` that should resubmit the job
+    for the user. Default: 0.
+``ResubmitCommand`` (external)
+    Filename of a shell script that creates a queuing (e.g. PBS)
+    script from two arguments, the number of processors and parameter
+    file.  This script is run by the root processor when stopping with
+    ``ResubmitOn``. An example script can be found in
+    input/resubmit.sh. Default: (null)
+
+.. _streaming_param:
+
+Streaming Data Format
+^^^^^^^^^^^^^^^^^^^^^
+
+``NewMovieLeftEdge``, ``NewMovieRightEdge`` (external)
+    These two parameters control the region for which the streaming
+    data are written. Default: ``DomainLeftEdge`` and ``DomainRightEdge``.
+``MovieSkipTimestep`` (external)
+    Controls how many timesteps on a level are skipped between outputs
+    in the streaming data. Streaming format is off if this equals
+    ``INT_UNDEFINED``. Default: ``INT_UNDEFINED``
+``Movie3DVolume`` (external)
+    Set to 1 to write streaming data as 3-D arrays. This should always
+    be set to 1 if using the streaming format. A previous version had
+    2D maximum intensity projections, which now defunct. Default: 0.
+``MovieVertexCentered`` (external)
+    Set to 1 to write the streaming data interpolated to vertices. Set
+    to 0 for cell-centered data. Default: 0.
+``NewMovieDumpNumber`` (internal)
+    Counter for streaming data files. This should equal the cycle
+    number.
+``MovieTimestepCounter`` (internal)
+    Timestep counter for the streaming data files.
+``MovieDataField`` (external)
+    A maximum of 6 data fields can be written in the streaming format.
+    The data fields are specified by the array element of
+    BaryonField, i.e. 0 = Density, 7 = HII
+    Density. For writing temperature, a special value of 1000 is used.
+    This should be improved to be more transparent in which fields will
+    be written. Any element that equals ``INT_UNDEFINED`` indicates no
+    field will be written. Default: ``INT_UNDEFINED`` x 6
+``NewMovieParticleOn`` (external)
+    Set to 1 to write all particles in the grids. Set to 2 to write
+    ONLY particles that aren't dark matter, e.g. stars. Set to 3/4 to
+    write ONLY particles that aren't dark matter into a file separate
+    from the grid info. (For example, ``MoviePackParticle_P000.hdf5``,
+    etc. will be the file name; this will be very helpful in speeding
+    up the access to the star particle data, especially for the
+    visualization or for the star particle. See ``AMRH5writer.C``) Set to 0
+    for no particle output. Default: 0.
+
+Simulation Identifiers and UUIDs
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+These parameters help to track, identify and group datasets. For reference,
+`Universally Unique Identifiers
+<http://en.wikipedia.org/wiki/Universally_Unique_Identifier>`_ (UUIDs) are
+opaque identifiers using random 128-bit numbers, with an extremely low chance
+of collision. (See :ref:`SimulationNamesAndIdentifiers` for a longer
+description of these parameters.)
+
+``MetaDataIdentifier`` (external)
+    This is a character string without spaces (specifically, something
+    that can be picked by "%s"), that can be defined in a parameter
+    file, and will be written out in every following output, if it is
+    found.
+``MetaDataSimulationUUID`` (internal)
+    A UUID that will be written out in all of the following outputs.
+    Like ``MetaDataIdentifier``, an existing UUID will be kept, but if one
+    is not found, and new one will be generated.
+``MetaDataDatasetUUID`` (internal)
+    A UUID created for each specific output.
+``MetaDataRestartDatasetUUID`` (internal)
+    If a ``MetaDataDatasetUUID`` UUID is found when the parameter file is
+    read in, it will written to the following datasets. This is used to
+    track simulations across restarts and parameter adjustments.
+``MetaDataInitialConditionsUUID`` (internal)
+    This is similar to ``MetaDataRestartDatasetUUID``, except it's used to
+    track which initial conditions were used.
+

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

-Magnetohydrodynamic Parameters
-------------------------------
-
-``UseDivergenceCleaning`` (external)
-    Method 1 and 2 are a failed experiment to do divergence cleaning
-    using successive over relaxation. Method 3 uses conjugate gradient
-    with a 2 cell stencil and Method 4 uses a 4 cell stencil. 4 is more
-    accurate but can lead to aliasing effects. Default: 0
-``DivergenceCleaningBoundaryBuffer`` (external)
-    Choose to *not* correct in the active zone of a grid by a
-    boundary of cells this thick. Default: 0
-``DivergenceCleaningThreshold`` (external)
-    Calls divergence cleaning on a grid when magnetic field divergence
-    is above this threshold. Default: 0.001
-``PoissonApproximateThreshold`` (external)
-    Controls the accuracy of the resulting solution for divergence
-    cleaning Poisson solver. Default: 0.001
-``ResetMagneticField`` (external)
-    Set to 1 to reset the magnetic field in the regions that are denser
-    than the critical matter density. Very handy when you want to
-    re-simulate or restart the dumps with MHD. Default: 0
-``ResetMagneticFieldAmplitude`` (external)
-    The magnetic field values (in Gauss) that will be used for the
-    above parameter. Default: 0.0 0.0 0.0
-

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

+Other Parameters
+~~~~~~~~~~~~~~~~
+
 Other External Parameters
--------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^^
 
 ``huge_number`` (external)
     The largest reasonable number. Rarely used. Default: 1e+20
     Reserved for future use.
 
 Other Internal Parameters
--------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^^
 
+``TimeLastDataDump`` (internal)
+    The code time at which the last time-based output occurred.
+``TimeLastInterpolatedDataDump`` (internal)
+    The code time at which the last interpolated data dump occurred.
+``CycleLastDataDump`` (internal)
+    The last cycle on which a cycle dump was made
+``SubcycleLastDataDump`` (internal)
+    The last cycle on which a subcycle dump was made
+``TimeLastMovieDump`` (internal)
+    The code time at which the last movie dump occurred.
+``TimeLastTracerParticleDump`` (internal)
+    The code time at which the last tracer particle dump occurred.
 ``TimeLastRestartDump``
     Reserved for future use.
-``TimeLastDataDump`` (internal)
-    The code time at which the last time-based output occurred.
 ``TimeLastHistoryDump``
     Reserved for future use.
-``TimeLastMovieDump`` (internal)
-    The code time at which the last movie dump occurred.
 ``CycleLastRestartDump``
     Reserved for future use.
-``CycleLastDataDump`` (internal)
-    The last cycle on which a cycle dump was made
 ``CycleLastHistoryDump``
     Reserved for future use.
 ``InitialCPUTime``
     Reserved for future use.
 ``InitialCycleNumber`` (internal)
     The current cycle
-``RestartDumpNumber``
-    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[#]``
+``DataUnits[#]`` 
     Reserved for future use.
+``SubcycleNumber`` (internal)
+    The current subcycle
 ``DataDumpNumber`` (internal)
     The identification number of the next output file (the 0000 part of
     the output name). This is used and incremented by both the cycle
     based and time based outputs. Default: 0
+``MovieDumpNumber`` (internal)
+    The identification number of the next movie output file. Default: 0
+``TracerParticleDumpNumber`` (internal)
+    The identification number of the next tracer particle output file. Default: 0    
+``RestartDumpNumber``
+    Reserved for future use.
 ``HistoryDumpNumber``
     Reserved for future use.
-``MovieDumpNumber`` (internal)
-    The identification number of the next movie output file. Default: 0
 ``VersionNumber`` (internal)
     Sets the version number of the code which is written out to restart
     dumps.

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

 Particle Parameters
--------------------
+~~~~~~~~~~~~~~~~~~~
 
 ``ParticleBoundaryType`` (external)
     The boundary condition imposed on particles. At the moment, this

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

 30 	     :ref:`cosmologysimulation_param`
 31 	     :ref:`galaxysimulation_param`
 35 	     :ref:`shearingbox_param`
+36	     Shearing Box 2D Simulation
+37	     Stratifeid Shearing Box Simulation
 40 	     :ref:`supernovarestart_param`
 50 	     :ref:`photontest_param`
+51	     Photon Test Restart
 60 	     :ref:`turbulence_param` 
 61 	     :ref:`protostellar_param` 
 62 	     :ref:`coolingtest_param`
+63           One Zone Free Fall Test
+70	     Conduction Test with Hydro Off
+71	     Conduction Test with Hydro On
+72	     Conduction Bubble Test
+73	     Conduction Cloud Test
+80           Explosion in a Stratified Medium Test
 101          :ref:`3dcollapse_param`
 102          :ref:`1dcollapse_param`
 106          :ref:`mhdhydro_param`
 107          :ref:`putsink_param`
+108          Cluster Cooling Flow 
 200          :ref:`mhd1d_param`
 201          :ref:`mhd2d_param`
 202          :ref:`mhd3d_param`
 203          :ref:`mhdtcollapse_param`
+204          3D MHD Test
 207          :ref:`galaxydisk_param`
 208          :ref:`agndisk_param`
+209	     MHD 1D Waves
+210	     MHD Decaying Random Magnetic Fields
 300          :ref:`poissonsolver_param`
 400          :ref:`rdhtest1_param`
 401          :ref:`rdhtest2_param`
 ``GreyMarshDir`` (external)
    Propagation coordinate for Marshak problem. {0,1,2}. Default: 0
 
-
 .. _rdhtest5_param:
 
 Radiation-Hydrodynamics Test 5 - Radiating Shock (404/405)

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

+Radiation Parameters
+~~~~~~~~~~~~~~~~~~~~
+
 .. _radiation_backgrounds:
 
 Background Radiation Parameters
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 ``RadiationFieldType`` (external)
     This integer parameter specifies the type of radiation field that
     Add description. Default: 1.5.
 
 Radiative Transfer (Ray Tracing) Parameters
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 ``RadiativeTransfer`` (external)
     Set to 1 to turn on the adaptive ray tracing following Abel, Wise &
 ``RadiativeTransferPeriodicBoundary`` (external)
     Set to 1 to turn on periodic boundary conditions for photon
     packages. Default: 0.
-``RadiativeTransferTraceSpectrum`` (external)
-    reserved for experimentation. Default: 0.
-``RadiativeTransferTraceSpectrumTable`` (external)
-    reserved for experimentation. Default: ``spectrum_table.dat``
+``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
+``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
     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.
+``RadiativeTransferTraceSpectrum`` (external)
+    reserved for experimentation. Default: 0.
+``RadiativeTransferTraceSpectrumTable`` (external)
+    reserved for experimentation. Default: ``spectrum_table.dat``
 
 Radiative Transfer (FLD) Parameters
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 ``RadiativeTransferFLD`` (external)
     Set to 2 to turn on the fld-based radiation solvers following Reynolds,
     dissociating field from the ray-tracing solver. Default: 1.
 
 Radiative Transfer (FLD) Implicit Solver Parameters
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
     These parameters should be placed within the file named in
     ``RadHydroParamfile`` in the main parameter file. All are described in
     ``RadHydroModel`` 10. Default: [1 1 0 1 0].
 
 Radiative Transfer (FLD) Split Solver Parameters
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
     These parameters should be placed within the file named in
     ``RadHydroParamfile`` in the main parameter file. All are described in

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

 Shock Finding Parameters
 ~~~~~~~~~~~~~~~~~~~~~~~~
+
 For details on shock finding in Enzo see :ref:`shock_finding`.
 
 ``ShockMethod`` (external)

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

 
 For details on each of the different star formation methods available in Enzo see :ref:`star_particles`.
 
+General
+^^^^^^^
 
 ``StarParticleCreation`` (external)
     This parameter is bitwise so that multiple types of star formation
 
         #order: MBH mass (in Ms), MBH location[3], MBH creation time
         100000.0      0.48530579      0.51455688      0.51467896      0.0
+
+Sink Formation and Feedback
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The parameters below are considered in sink creation routines: sink_maker, star_maker8, star_maker9.
+
+``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/parameters/stopping.rst

-Stopping Parameters
--------------------
-
-``StopTime`` (external)
-    This parameter specifies the time (in code units) when the
-    calculation will halt. For cosmology simulations, this variable is
-    automatically set by ``CosmologyFinalRedshift``. *No default.*
-``StopCycle`` (external)
-    The cycle (top grid timestep) at which the calculation stops. A
-    value of zero indicates that this criterion is not be used.
-    *Default: 100,000*
-``StopFirstTimeAtLevel`` (external)
-    Causes the simulation to immediately stop when a specified level is
-    reached. Default value 0 (off), possible values are levels 1
-    through maximum number of levels in a given simulation.
-``NumberOfOutputsBeforeExit`` (external)
-    After this many datadumps have been written, the code will exit.  If 
-    set to 0 (default), this option will not be used.  Default: 0.
-``StopCPUTime`` (external)
-    Causes the simulation to stop if the wall time exceeds ``StopCPUTime``.
-    The simulation will output if the wall time after the next
-    top-level timestep will exceed ``StopCPUTime``, assuming that the wall
-    time elapsed during a top-level timestep the same as the previous
-    timestep. In units of seconds. Default: 2.592e6 (30 days)
-``ResubmitOn`` (external)
-    If set to 1, the simulation will stop if the wall time will exceed
-    ``StopCPUTime`` within the next top-level timestep and run a shell
-    script defined in ``ResubmitCommand`` that should resubmit the job
-    for the user. Default: 0.
-``ResubmitCommand`` (external)
-    Filename of a shell script that creates a queuing (e.g. PBS)
-    script from two arguments, the number of processors and parameter
-    file.  This script is run by the root processor when stopping with
-    ``ResubmitOn``. An example script can be found in
-    input/resubmit.sh. Default: (null)

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

-.. _streaming_param:
-
-Streaming Data Format
-~~~~~~~~~~~~~~~~~~~~~
-
-``NewMovieLeftEdge``, ``NewMovieRightEdge`` (external)
-    These two parameters control the region for which the streaming
-    data are written. Default: ``DomainLeftEdge`` and ``DomainRightEdge``.
-``MovieSkipTimestep`` (external)
-    Controls how many timesteps on a level are skipped between outputs
-    in the streaming data. Streaming format is off if this equals
-    ``INT_UNDEFINED``. Default: ``INT_UNDEFINED``
-``Movie3DVolume`` (external)
-    Set to 1 to write streaming data as 3-D arrays. This should always
-    be set to 1 if using the streaming format. A previous version had
-    2D maximum intensity projections, which now defunct. Default: 0.
-``MovieVertexCentered`` (external)
-    Set to 1 to write the streaming data interpolated to vertices. Set
-    to 0 for cell-centered data. Default: 0.
-``NewMovieDumpNumber`` (internal)
-    Counter for streaming data files. This should equal the cycle
-    number.
-``MovieTimestepCounter`` (internal)
-    Timestep counter for the streaming data files.
-``MovieDataField`` (external)
-    A maximum of 6 data fields can be written in the streaming format.
-    The data fields are specified by the array element of
-    BaryonField, i.e. 0 = Density, 7 = HII
-    Density. For writing temperature, a special value of 1000 is used.
-    This should be improved to be more transparent in which fields will
-    be written. Any element that equals ``INT_UNDEFINED`` indicates no
-    field will be written. Default: ``INT_UNDEFINED`` x 6
-``NewMovieParticleOn`` (external)
-    Set to 1 to write all particles in the grids. Set to 2 to write
-    ONLY particles that aren't dark matter, e.g. stars. Set to 3/4 to
-    write ONLY particles that aren't dark matter into a file separate
-    from the grid info. (For example, ``MoviePackParticle_P000.hdf5``,
-    etc. will be the file name; this will be very helpful in speeding
-    up the access to the star particle data, especially for the
-    visualization or for the star particle. See ``AMRH5writer.C``) Set to 0
-    for no particle output. Default: 0.

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

+Enzo Test Problem Parameters 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
 =================================== =================================== ======= 
 Directory                           Parameter File                      Source  
 =================================== =================================== ======= 

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

    EmbeddedPython.rst
    HierarchyFile.rst
    FlowChart.rst
+   TestProblems.rst

File src/enzo/star_maker8.C

 	      delz = zpos - zpold[n];
 	      dist2 = delx*delx + dely*dely + delz*delz;
 
-		/* If sink is within 5 cells and closest one, then add to it */
+		/* If sink is within 5 cells of the closest one, then add to it */
 	      if (dist2 < POW(BigStarSeparation,2) && dist2 < nearestdx2) {
 		nearestdx2 = dist2;
 		closest = n;		  

File src/enzo/star_maker9.C

 		delz = zpos - zpold[n];
 		dist2 = delx*delx + dely*dely + delz*delz;
 
-		/* If sink is within 5 cells and closest one, then add to it */
+		/* If sink is within 5 cells of the closest one, then add to it */
 		if (dist2 < POW(BigStarSeparation,2) && dist2 < nearestdx2) {
 		  nearestdx2 = dist2;
 		  closest = n;