update docs

toy_atm/README.md

@@ -0,0 +1,129 @@
+# `toy_atm`
+
+Create a 1-d hydrostatic, atmosphere with an isothermal region
+(`T_star`) representing the NS, a hyperbolic tangent rise to a
+peak temperature (`T_base`) representing the base of an accreted
+layer, an isoentropic profile down to a lower temperature (`T_lo`),
+and then isothermal. This can serve as an initial model for a
+nova or XRB.
+
+The temperature profile is:
+
+```
+        ^
+        |
+ T_base +        /\
+        |       /  \
+        |      /  . \
+ T_star +-----+      \
+        |     .   .   \
+        |              \
+        |     .   .     \
+ T_lo   +                +-----------
+        |     .   .
+        +-----+---+---------------> r
+        |      \  /
+        |      delta
+        |< H_star>|
+```
+
+We take `dens_base`, the density at the base of the isentropic layer
+as input.  The composition is "ash" in the lower isothermal region
+and "fuel" in the isentropic and upper isothermal regions.  In the
+linear transition region, we linearly interpolate the composition.
+
+The fuel and ash compositions are specified by the `fuel?_name`,
+`fuel?_frac` and `ash?_name`, `ash?_frac` parameters (name of the species
+and mass fraction).
+
+The model is placed into HSE by the following differencing:
+
+   (1/dr) [ <P>_i - <P>_{i-1} ] = (1/2) [ <rho>_i + <rho>_{i-1} ] g
+
+This will be iterated over in tandem with the EOS call,
+
+```
+   P(i-1) = P_eos(rho(i-1), T(i-1), X(i-1)
+```
+
+## Parameters
+
+The following parameters can be set in the inputs file (prefixed with
+`problem.`).
+
+### Thermodynamics
+
+* `dens_base` : density at the base of the fuel layer
+
+* `T_star` : temperature in the isothermal region beneath the fuel layer
+
+* `T_base` : temperature at the base of the fuel layer
+
+* `T_lo` : lowest temperature in the fuel layer.  Below this we switch from
+  being isentropic to isothermal
+
+* `H_star` : Height to base of the fuel layer
+
+* `delta` : with the transition region between `T_star` and `T_base`
+
+* `low_density_cutoff` : the density below which we don't worry about HSE.
+
+### Composition:
+
+The composition of the fuel is set by a pair of parameters, one giving
+the name of the species and the other giving the mass fraction.  These
+all have the form:
+
+* `fuel?_name`, `fuel?_frac`, where `?` can be 1, 2, ... 7.  At least the
+  first needs to be set.
+
+The ash composition is similarly set via:
+
+* `ash?_name`, `ash?_frac`, where `?` can be 1, 2, ... 7.  At least the
+  first needs to be set.
+
+Finally:
+
+* `smallx` : the smallest allowed mass fraction
+
+### Domain
+
+The domain size and resolution are set via:
+
+* `xmin` : coordinate of bottom of the model
+
+* `xmax` : coordinate of the top of the model
+
+* `nx` : number of points.
+
+These should be chosen to ensure that the grid spacing, dx = (xmax - xmin) / nx
+corresponds to the finest resolution in the simulation you will be running.
+
+### Gravity
+
+There are 2 options for gravity: constant and a `1/r**2` profile:
+
+* `g_const` : the constant gravitational acceleration
+
+* `M_enclosed` : for `1/r**2` gravity, the mass enclosed beneath the
+  model.  This will be used together with `xmin` to compute the
+  gravitational acceleration at the base of the model.
+
+* `do_invsq_grav` : do we use constant? or `1/r**2` gravity?
+
+
+## Science problems where this is used
+
+This setup is used for ``toy_convect`` and for the many of the XRB problems.
+The init code takes an input file:
+
+* `inputs.xrb_mixed.hi_dens.tall.CNO`
+
+   This is the `_params` file that is used for the `xrb_mixed` file
+
+* `inputs.xrb_mixed.hi_dens.tall2.CNO`
+
+   This version differs from the above one with more buffer beneath
+   the convective layer
+
+

toy_atm/init_1d.H

@@ -1,45 +1,3 @@
-//  Create a 1-d hydrostatic, atmosphere with an isothermal region
-//  (T_star) representing the NS, a hyperbolic tangent rise to a
-//  peak temperature (T_base) representing the base of an accreted
-//  layer, an isoentropic profile down to a lower temperature (T_lo),
-//  and then isothermal. This can serve as an initial model for a
-//  nova or XRB.
-//
-//  The temperature profile is:
-//
-//         ^
-//         |
-//  T_base +        /\
-//         |       /  \
-//         |      /  . \
-//  T_star +-----+      \
-//         |     .   .   \
-//         |              \
-//         |     .   .     \
-//  T_lo   +                +-----------
-//         |     .   .
-//         +-----+---+---------------> r
-//         |      \  /
-//         |      delta
-//         |< H_star>|
-//
-//  We take dens_base, the density at the base of the isentropic layer
-//  as input.  The composition is "ash" in the lower isothermal region
-//  and "fuel" in the isentropic and upper isothermal regions.  In the
-//  linear transition region, we linearly interpolate the composition.
-//
-//  The fuel and ash compositions are specified by the fuel?_name,
-//  fuel?_frac and ash?_name, ash?_frac parameters (name of the species
-//  and mass fraction).  Where ? = 1,2,3.
-//
-//  The model is placed into HSE by the following differencing:
-//
-//   (1/dr) [ <P>_i - <P>_{i-1} ] = (1/2) [ <rho>_i + <rho>_{i-1} ] g
-//
-//  This will be iterated over in tandem with the EOS call,
-//  P(i-1) = P_eos(rho(i-1), T(i-1), X(i-1)
-//
-
 #include <AMReX_Array.H>
 
 #include <sstream>