1. Matthew Turk
  2. enzo-dev-answer-testing

Commits

Ji-hoon Kim  committed 6c927bd

reorganizing the parameter indexing a bit

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

View file
+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

View file
 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

View file
 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

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

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

View file
 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/hydro.rst

View file
-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 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
+``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/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

View file
 .. 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

View file
 Initialization Parameters
--------------------------
+~~~~~~~~~~~~~~~~~~~~~~~~~
 
 ``TopGridRank`` (external)
     This specifies the dimensionality of the root grid and by extension
 ``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.
+``GridVelocity`` (external)
+    The whole computational domain will have this velocity.  Experimental.  Default: 0 0 0

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

View file
 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
     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

View file
+Other Parameters
+~~~~~~~~~~~~~~~~
+
 Other External Parameters
--------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^^
 
 ``huge_number`` (external)
     The largest reasonable number. Rarely used. Default: 1e+20
     Reserved for future use.
 
 Other Internal Parameters
--------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^^
 
 ``TimeLastRestartDump``
     Reserved for future use.

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

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

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

View file
    Ambient radiation energy. Default 1.0e-10
 ``RadPulseDim`` (external)
    Number of dimensions for test {0,1,2}. Default: 0
-`
+
 .. _rdhtest4_param:
 
 Radiation-Hydrodynamics Test 4 - Grey Marshak Test (403)
 ``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

View file
+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 &
     particles emit X-rays. Default: 0.
 
 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

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

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

View file
 
 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
+
+Massive Black Hole Particle Formation
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The parameters below are considered in sink creation routines: sink_maker, star_maker8, star_maker9 .
+
+``MBHInsertLocationFilename`` (external)

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

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

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

View file
    EmbeddedPython.rst
    HierarchyFile.rst
    FlowChart.rst
+   TestProblems.rst