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dannoryan  committed d639cd2 Merge

merged to week-of-code; required conversion of new file star_feedback_pn_snia.F in addition to smaller changes.

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Files changed (1258)

 DEPEND.bak
 auto_show_*.C
 enzo.exe
+inits.exe
+ring.exe
+anyl.exe
+enzohop.exe
 out.compile
 out.make.DEPEND
 svn_version.def
 Make.config.override
 *.mod
 
-src/inits/inits.exe
 src/mpgrafic/degraf/Makefile
 src/mpgrafic/degraf/config.h
 src/mpgrafic/degraf/config.log
 src/P-GroupFinder/P-GroupFinder
 
 doc/manual/build
+
+run/results.js

File doc/implicit_fld/gfldproblem_UG.tex

 \begin{equation}
 \label{eq:radiation_PDE}
   \partial_{t} E + \frac1a \nabla\cdot\(E\vb\) =
-    \nabla\cdot\(D\,\nabla E\) - \frac{\dot{a}}{a} E - c\kappa E + 4\pi\eta,
+    \nabla\cdot\(D\,\nabla E\) - \frac{\dot{a}}{a} E - c\kappa E + \eta,
 \end{equation}
 where here the comoving radiation energy density $E$, emissivity
 $\eta$ and opacity $\kappa$ are functions of space and time.  In this
 and $\Lambda$ corresponds to the local cooling rate,
 \begin{align}
 \label{eq:Lambda_LTE}
-  \Lambda = \frac{4\pi}{\rhob} \eta.
+  \Lambda = \frac{\eta}{\rhob}.
 \end{align}
 The user-defined energy mean opacity $\kappa$ is
 spatially-homogeneous, and is given by the formula
 a black-body emissivity given by 
 \begin{align}
 \label{eq:etaBB}
-  \eta = \frac{\kappa_P\,\sigma_{SB}\,T^4}{\pi},
+  \eta = 4\kappa_P\,\sigma_{SB}\,T^4,
 \end{align}
 where the user-defined Planck-mean opacity $\kappa_P$ is defined
 similarly to the energy-mean opacity \eqref{eq:opacityE},
 \begin{align}
   \label{eq:radiation_PDE_theta}
   E^n - E^{n-1} &- \theta\dt\left(\nabla\cdot\(D\,\nabla E^n\) - \frac{\dot{a}}{a} E^n -
-    c\kappa^n E^n + 4\pi\eta^n\right) \\ 
+    c\kappa^n E^n + \eta^n\right) \\ 
   \notag
   & - (1-\theta)\dt\left(\nabla\cdot\(D\,\nabla E^{n-1}\) - \frac{\dot{a}}{a} E^{n-1} -
-    c\kappa^{n-1} E^{n-1} + 4\pi\eta^{n-1}\right) = 0, \\ 
+    c\kappa^{n-1} E^{n-1} + \eta^{n-1}\right) = 0, \\ 
   \label{eq:energy_correction_theta}
   e_c^n - e_c^{n-1} &- \theta\dt\left(-\frac{2\dot{a}}{a}e_c^{n} + G^{n} -
     \Lambda^{n}\right) - (1-\theta)\dt\left(-\frac{2\dot{a}}{a}e_c^{n-1} + G^{n-1} -
 \begin{align}
   \label{eq:radiation_PDE_iqss}
   E^n - E^{n-1} &- \theta\dt\left(\nabla\cdot\(D\,\nabla E^n\) - \frac{\dot{a}}{a} E^n -
-    c\kappa^n E^n + 4\pi\eta^n\right) \\ 
+    c\kappa^n E^n + \eta^n\right) \\ 
   \notag
   & - (1-\theta)\dt\left(\nabla\cdot\(D\,\nabla E^{n-1}\) - \frac{\dot{a}}{a} E^{n-1} -
-    c\kappa^{n-1} E^{n-1} + 4\pi\eta^{n-1}\right) = 0, \\ 
+    c\kappa^{n-1} E^{n-1} + \eta^{n-1}\right) = 0, \\ 
   \label{eq:energy_correction_iqss}
   e_c^n &- \text{sol}_e\left(\frac{E^{n-1}+E^n}{2},\frac{\mn_{HI}^{n-1}+\mn_{HI}^n}{2},e_c^{n-1},t\right) = 0, \\
   \label{eq:hydrogen_iqss}

File doc/manual/source/EnzoParameters.rst

+.. _parameters:
+
 Enzo Parameter List
 ===================
 
     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
     must be periodic. Note that self gravity will not be consistent
     with shearing boundary conditions. Default: 0 0 0
 ``ShearingVelocityDirection`` (external)
-    When a shearing boundary is used and the other two boundary pairs
-    are both periodic, selected the direction of the shearing velocity.
+    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
        4 - refine by particle mass	       12 - refine by defined region "MustRefineRegion"
        5 - refine by baryon overdensity	       13 - refine by metallicity
        	  (currently disabled)
+       101 - avoid refinement in regions
+             defined in "AvoidRefineRegion"
 
 ``RefineRegionLeftEdge``, ``RefineRegionRightEdge`` (external)
     These two parameters control the region in which refinement is
 ``StaticRefineRegionLeftEdge[#]``, ``StaticRefineRegionRightEdge[#]`` (external)
     These two parameters specify the two corners of a statically
     refined region (see the previous parameter). Default: none
+``AvoidRefineRegionLevel[#]`` (external)
+    This parameter is used to limit the refinement to this level in a
+    rectangular region.  Up to MAX_STATIC_REGIONS regions can be used.
+``AvoidRefineRegionLeftEdge[#]``, ``AvoidRefineRegionRightEdge[#]`` (external) 
+    These two parameters specify the two corners of a region that
+    limits refinement to a certain level (see the previous
+    parameter). Default: none
 ``RefineByResistiveLength`` (external)
     Resistive length is defined as the curl of the magnetic field over
     the magnitude of the magnetic field. We make sure this length is
     methods). If using multiple species (i.e. ``MultiSpecies`` > 0), then
     this value is ignored in favor of a direct calculation (except for
     PPM LR) Default: 5/3.
+``Mu`` (external)
+    The molecular weight. Default: 0.6.
 ``ConservativeReconstruction`` (external)
     Experimental.  This option turns on the reconstruction of the
     left/right interfaces in the Riemann problem in the conserved
     completely baryon dominated. It is used to remove the discreteness
     effects of the few remaining dark matter particles. Not used if set
     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.
+
 ``PointSourceGravity`` (external)
-    This flag (1 - on, 0 - off) indicates if there is to be a
-    (constant) point source gravitational field. Default: 0
+    This parameter indicates that there is to be a
+    (constant) gravitational field with a point source profile (``PointSourceGravity`` =
+    1) or NFW profile (``PointSourceGravity`` = 2). Default: 0
 ``PointSourceGravityConstant`` (external)
-    The magnitude of the point source acceleration at a distance of 1
-    length unit. Default: 1
+    If ``PointSourceGravity`` = 1, this is the magnitude of the point
+    source acceleration at a distance of 1
+    length unit (i.e. GM in code units). If ``PointSourceGravity`` =
+    2, then it takes the mass of the dark matter halo in CGS
+    units. ``ProblemType`` = 31 (galaxy disk simulation) automatically calculates
+    values for ``PointSourceGravityConstant`` and
+    ``PointSourceGravityCoreRadius``. Default: 1
+``PointSourceGravityCoreRadius`` (external)
+    For ``PointSourceGravity`` = 1, this is the radius inside which
+    the acceleration field is smoothed in code units. With ``PointSourceGravity`` =
+    2, it is the scale radius, rs, in CGS units (see Navarro, Frank & White,
+    1997). Default: 0
 ``PointSourceGravityPosition`` (external)
     If the ``PointSourceGravity`` flag is turned on, this parameter
-    specifies the center of the point-source gravitational field.
-    Default: 0 0 0
+    specifies the center of the point-source gravitational field in
+    code units. Default: 0 0 0
+``ExternalGravity`` (external)
+   This fulfills the same purpose as ``PointSourceGravity`` but is
+   more aptly named. ``ExternalGravity = 1`` turns on an alternative
+   implementation of the NFW profile with properties
+   defined via the parameters ``HaloCentralDensity``, ``HaloConcentration`` and ``HaloVirialRadius``. Boxsize is assumed to be 1.0 in this case. ``ExternalGravity = 10`` gives a gravitational field defined by the logarithmic potential in Binney & Tremaine, corresponding to a disk with constant circular velocity.  Default: 0 
+``ExternalGravityConstant`` (external)
+    If ``ExternalGravity = 10``, this is the circular velocity of the disk in code units. Default: 0.0
+``ExternalGravityDensity`` 
+   Reserved for future use.
+``ExternalGravityPosition`` (external)
+    If ``ExternalGravity = 10``, this parameter specifies the center of the gravitational field in code units. Default: 0 0 0
+``ExternalGravityOrientation`` (external)
+    For ``ExternalGravity = 10``, this is the unit vector of the disk's angular momentum (e.g. a disk whose face-on view is oriented in the x-y plane would have ``ExternalGravityOrientation = 0 0 1``). Default: 0 0 0 
+``ExternalGravityRadius`` (external)
+   If ``ExternalGravity = 10``, this marks the inner radius of the disk in code units within which the velocity drops to zero. Default: 0.0
 ``UniformGravity`` (external)
     This flag (1 - on, 0 - off) indicates if there is to be a uniform
     gravitational field. Default: 0
 ``RadiativeCooling`` (external)
     This flag (1 - on, 0 - off) controls whether or not a radiative
     cooling module is called for each grid. There are currently several
-    possibilities, controlled by the value of another flag. Default: 0
+    possibilities, controlled by the value of another flag. See :ref:`cooling` 
+    for more information on the various cooling methods.  Default: 0
     
     -  If the ``MultiSpecies`` flag is off, then equilibrium cooling is
        assumed and one of the following two will happen. If the parameter
     is valid for temperatures greater than 10,000 K. This requires the
     file ``TREECOOL`` to execute. Default: 0
 ``MetalCooling`` (external)
-    This flag (0 - off, 1 - metal cooling from Glover & Jappsen 2007, 2
-    - Cen, 3 - Cloudy cooling from Smith, Sigurdsson, & Abel 2008)
-    turns on metal cooling for runs that track metallicity. Option 1 is
-    valid for temperatures between 100 K and 10\ :sup:`8`\  K because
-    it considers fine-structure line emission from carbon, oxygen, and
-    silicon and includes the additional metal cooling rates from
-    Sutherland & Dopita (1993). Option 2 is only valid for temperatures
-    above 10\ :sup:`4`\  K. Option 3 uses multi-dimensional tables of
-    heating/cooling values created with Cloudy and optionally coupled
-    to the ``MultiSpecies`` chemistry/cooling solver. This method is valid
-    from 10 K to 10\ :sup:`8`\  K. See the Cloudy Cooling parameters below.
-    Default: 0.
+    This flag (0 - off, 1 - metal cooling from Glover & Jappsen 2007,
+    2 - Cen et al (1995), 3 - Cloudy cooling from Smith, Sigurdsson, &
+    Abel 2008) turns on metal cooling for runs that track
+    metallicity. Option 1 is valid for temperatures between 100 K and
+    10\ :sup:`8`\ K because it considers fine-structure line emission
+    from carbon, oxygen, and silicon and includes the additional metal
+    cooling rates from Sutherland & Dopita (1993). Option 2 is only
+    valid for temperatures above 10\ :sup:`4`\ K. Option 3 uses
+    multi-dimensional tables of heating/cooling values created with
+    Cloudy and optionally coupled to the ``MultiSpecies``
+    chemistry/cooling solver. This method is valid from 10 K to 10\
+    :sup:`8`\ K. See the Cloudy Cooling parameters below.  Default: 0.
 ``MetalCoolingTable`` (internal)
     This field contains the metal cooling table required for
     ``MetalCooling`` option 1. In the top level directory input/, there are
     ``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, Gamma_pe = 5.1e-26 erg/s will be added uniformly
+    to the gas without any shielding (Tasker & Bryan 2008). At the
+    moment this is still experimental. Default: 0
 ``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).
 
+.. _cloudy_cooling:
+