Commits

Ji-hoon Kim committed 960116f

intermediate commit - addition of various parameter descriptions

  • Participants
  • Parent commits 6c927bd

Comments (0)

Files changed (6)

doc/manual/source/parameters/hydro.rst

 Magnetohydrodynamics (CT) Parameters
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Coming soon...
+Coming very soon...!
 
 Magnetohydrodynamics (Dedner) Parameters
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 ``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
 ``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
 

doc/manual/source/parameters/initialization.rst

     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.
-``GridVelocity`` (external)
-    The whole computational domain will have this velocity.  Experimental.  Default: 0 0 0
+``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)

doc/manual/source/parameters/io.rst

 ``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.

doc/manual/source/parameters/other.rst

 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.

doc/manual/source/parameters/radiation.rst

 ``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
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

doc/manual/source/parameters/starform.rst

         #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
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Sink Formation and Feedback
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The parameters below are considered in sink creation routines: sink_maker, star_maker8, star_maker9 .
+The parameters below are considered in sink creation routines: sink_maker, star_maker8, star_maker9.
 
-``MBHInsertLocationFilename`` (external)
+``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]