more updates

Docs/source/one_zone_tests.rst

@@ -29,15 +29,22 @@ with density held constant and the temperature found via the equation of state,
 $T = T(\rho, X_k, e)$.
 
 
+.. note::
+
+   Since the energy evolves due to the heat release (or loss)
+   from reactions, the temperature will change during the burn.
+
+
 Getting Started
 ---------------
 
-The ``burn_cell`` code are located in
+The ``burn_cell`` code is located in
 ``Microphysics/unit_test/burn_cell``.  An inputs file which sets the
 default parameters for your choice of network is needed to run the
-test.  There are a number of inputs file in the unit test directory
-already with a name list ``inputs_burn_network``, where network
-is the network you wish to use for your testing.
+test.  There are a number of inputs files in the unit test directory
+already with a name list ``inputs_network``, where ``network``
+is the network you wish to use for your testing.  These can be
+used as a starting point for any explorations.
 
 
 Setting the thermodynamics
@@ -53,7 +60,8 @@ The parameters that affect the thermodynamics are:
 
 * ``unit_test.small_dens`` : the low density cutoff used in the equation of state
 
-The composition can be set either by setting each mass fraction explicitly,
+The composition can be set either by setting each mass fraction explicitly via the
+parameters, ``unit_test.X1``, ``unit_test.X2``, ...,
 e.g.:
 
 ::
@@ -126,47 +134,48 @@ Microphysics build system parameters, e.g.,
 
    make NETWORK_DIR=aprox19 INTEGRATOR_DIR=rkc
 
+The build process will automatically create links in the build
+directory to the EOS table and any reaction rate tables needed by your
+choice of network.
+
+
+.. important::
+
+   You need to do a ``make clean`` before rebuilding with a different
+   network or integrator.
+
 
 To run the code, enter the burn_cell directory and run::
 
    ./main3d.gnu.ex inputs
 
 where ``inputs`` is the name of your inputs file.
 
-For each of the ``numsteps`` steps defined in the inputs
-file, the code will output a files into a new directory titled
-``run_prefix_output`` where ``run_prefix`` is the run prefix defined in the
-inputs file.  Each output file will be named using the run prefix
-defined in the inputs file and the corresponding timestep.
-
-Next, run ``burn_cell.py`` using python 3.x, giving the defined run prefix as an argument.
-For example::
+Working with Output
+-------------------
 
-    python3 burn_cell.py react_aprox13
+.. note::
 
-The ``burn_cell.py`` code will gather information from all of the
-output files and compile them into three graphs explained below.
+   For this part, we'll assume that the default ``aprox13`` and
+   ``VODE`` options were used for the network and integrator, and the
+   test was run with ``inputs.aprox13``.
 
-Graphs Output by ``burn_cell.py``
----------------------------------
+As the code runs, it will output to ``stdout`` details of the initial
+and final state and the number of integration steps taken (along with whether
+the burn was successful).  The full history of the thermodynamic state will also be output to a file,
+``state_over_time.txt``, with each line corresponding to one of the
+``nsteps`` requested in the time integration.
 
-The file ``run-prefix_logX.png`` and ``run-prefix_logX.eps`` will display a
-graph of the chemical abundances as a function of the time, both on
-logarithmic scales, for all species involved in the simulation.  An
-example of this graph is shown below.
+The script ``plot_burn_cell.py`` can be used to visualize the evolution:
 
-.. figure:: react_aprox13_logX.png
-   :alt: An example of a plot output by the burn_cell unit test. This is the logX output corresponding to the network aprox13.
-   :width: 4.5in
-
-   An example of a plot output by the burn_cell unit test. This is the
-   logX output corresponding to the network aprox13.
+.. prompt:: bash
 
+   python plot_burn_cell.py state_over_time.txt
 
+This will generate the following figure:
 
-The file ``run-prefix_ydot.png`` and ``run-prefix_ydot.eps`` will display the
-molar fraction (mass fraction / atomic weight) as a function of time,
-both on logarithmic scales, for all species involved in the code.
+.. figure:: state.png
+   :alt: An example of a plot output by the burn_cell unit test.
 
-The file ``run-prefix_T-edot.png`` and ``run-prefix_T-edot.eps`` will display
-the temperature and the energy generation rate as a function of time.
+Only the most abundant species are plotted.  The number of species to plot and the
+limits of $X$ can be set via runtime parameters (see ``python plot_burn_cell.py -h``).

Docs/source/runtime_parameters.rst

@@ -767,6 +767,30 @@ namespace: ``network``
 
 
 
+**NETWORK_DIR=he-burn.bak/he-burn-18a:**
+
++---------------------------------------+---------------------------------------------------------+------------------------------+
+| parameter                             | description                                             | default value                |
++=======================================+=========================================================+==============================+
+| ``disable_p_C12_to_N13``              |                                                         | 0                            |
++---------------------------------------+---------------------------------------------------------+------------------------------+
+| ``disable_He4_N13_to_p_O16``          |                                                         | 0                            |
++---------------------------------------+---------------------------------------------------------+------------------------------+
+
+
+
+**NETWORK_DIR=he-burn.bak/he-burn-22a:**
+
++---------------------------------------+---------------------------------------------------------+------------------------------+
+| parameter                             | description                                             | default value                |
++=======================================+=========================================================+==============================+
+| ``disable_p_C12_to_N13``              |                                                         | 0                            |
++---------------------------------------+---------------------------------------------------------+------------------------------+
+| ``disable_He4_N13_to_p_O16``          |                                                         | 0                            |
++---------------------------------------+---------------------------------------------------------+------------------------------+
+
+
+
 **NETWORK_DIR=metal_chem:**
 
 +---------------------------------------+---------------------------------------------------------+------------------------------+
@@ -1089,8 +1113,6 @@ namespace: ``unit_test``
 +---------------------------------------+---------------------------------------------------------+------------------------------+
 | parameter                             | description                                             | default value                |
 +=======================================+=========================================================+==============================+
-| ``run_prefix``                        |                                                         | ""                           |
-+---------------------------------------+---------------------------------------------------------+------------------------------+
 | ``small_temp``                        |                                                         | 1.e5                         |
 +---------------------------------------+---------------------------------------------------------+------------------------------+
 | ``small_dens``                        |                                                         | 1.e5                         |

unit_test/burn_cell/_parameters

@@ -1,7 +1,5 @@
 @namespace: unit_test
 
-run_prefix    string  ""
-
 small_temp    real       1.e5
 small_dens    real       1.e5
 

unit_test/burn_cell/inputs_aprox13

@@ -1,5 +1,3 @@
-unit_test.run_prefix = "react_aprox13_"
-
 unit_test.small_temp = 1.e5
 unit_test.small_dens = 1.e5
 

unit_test/burn_cell/inputs_aprox13_mott

@@ -1,5 +1,3 @@
-unit_test.run_prefix = "react_aprox13_mott_"
-
 unit_test.small_temp = 1e5
 unit_test.small_dens = 1e5
 

unit_test/burn_cell/inputs_aprox19

@@ -1,5 +1,3 @@
-unit_test.run_prefix = "react_aprox19_"
-
 unit_test.small_temp = 1.e5
 unit_test.small_dens = 1.e5
 

unit_test/burn_cell/inputs_aprox19.nse

@@ -1,5 +1,3 @@
-unit_test.run_prefix = "react_aprox19_nse_"
-
 unit_test.small_temp = 1.e5
 unit_test.small_dens = 1.e5
 

unit_test/burn_cell/inputs_aprox21

@@ -1,5 +1,3 @@
-unit_test.run_prefix = "react_aprox21_"
-
 unit_test.small_temp = 1e5
 unit_test.small_dens = 1e5
 

unit_test/burn_cell/inputs_aprox21_rot1

@@ -1,5 +1,3 @@
-unit_test.run_prefix = "react_aprox21_rot1_"
-
 unit_test.small_temp = 1e5
 unit_test.small_dens = 1e5
 

unit_test/burn_cell/inputs_aprox21_rot2

@@ -1,5 +1,3 @@
-unit_test.run_prefix = "react_aprox21_rot2_"
-
 unit_test.small_temp = 1e5
 unit_test.small_dens = 1e5
 

unit_test/burn_cell/inputs_ecsn

@@ -1,5 +1,3 @@
-unit_test.run_prefix = "react_ecsn_"
-
 unit_test.small_temp = 1.e5
 unit_test.small_dens = 1.e5
 

unit_test/burn_cell/inputs_ignition

@@ -1,5 +1,3 @@
-unit_test.run_prefix = "react_ignition_"
-
 unit_test.small_temp = 1e5
 unit_test.small_dens = 1e5
 

unit_test/burn_cell/inputs_ignition_chamulak

@@ -1,5 +1,3 @@
-unit_test.run_prefix = "react_ignition_chamulak_"
-
 unit_test.small_temp = 1e5
 unit_test.small_dens = 1e5
 

unit_test/burn_cell/inputs_iso7

@@ -1,5 +1,3 @@
-unit_test.run_prefix = "react_iso7_"
-
 unit_test.small_temp = 1e5
 unit_test.small_dens = 1e5
 

unit_test/burn_cell/inputs_rprox

@@ -1,5 +1,3 @@
-unit_test.run_prefix = "react_rprox_"
-
 unit_test.small_temp = 1e5
 unit_test.small_dens = 1e5
 

unit_test/burn_cell/inputs_subch_simple

@@ -1,5 +1,3 @@
-unit_test.run_prefix = "react_subch_simple_"
-
 unit_test.small_temp = 1.e5
 unit_test.small_dens = 1.e5
 

unit_test/burn_cell/inputs_triple

@@ -1,5 +1,3 @@
-unit_test.run_prefix = "react_triple_"
-
 unit_test.small_temp = 1e5
 unit_test.small_dens = 1e5
 

unit_test/burn_cell/inputs_vode_example

@@ -1,5 +1,3 @@
-unit_test.run_prefix = "react_vode_example_"
-
 unit_test.small_temp = 1.e5
 unit_test.small_dens = 1e5
 

unit_test/burn_cell/plot_burn_cell.py

@@ -0,0 +1,65 @@
+import argparse
+
+import matplotlib.pyplot as plt
+from matplotlib import ticker
+import numpy as np
+
+
+def doit(state_file, xmin, n_plot, outfile):
+
+    data = np.genfromtxt(state_file, names=True)
+
+    # find the keys of the most abundant species
+    maxX = {}
+    for k in data.dtype.names:
+        if k in ["Time", "Temperature"]:
+            continue
+        maxX[k] = data[k].max()
+
+    abundant = [k for k, v in sorted(maxX.items(), key=lambda item: item[1])][::-1]
+
+    fig , (ax1, ax2) = plt.subplots(2, 1, sharex=True)
+
+    ax1.plot(data["Time"], data["Temperature"])
+    ax1.set_xscale("log")
+    ax1.grid(ls=":")
+
+    ax1.set_ylabel("temperature [K]")
+    ax1.yaxis.set_major_formatter(ticker.ScalarFormatter(useMathText=True))
+
+    # now the species
+    for n in range(n_plot):
+        ax2.plot(data["Time"], data[abundant[n]], label=abundant[n])
+
+    ax2.set_xscale("log")
+    ax2.set_yscale("log")
+    ax2.set_ylim(xmin, 1.5)
+    ax2.grid(ls=":")
+
+    ax2.set_xlabel("time (s)")
+    ax2.set_ylabel("mass fraction")
+
+    ax2.legend(fontsize="small")
+
+    fig.tight_layout()
+
+    fig.set_size_inches(6, 7)
+
+    fig.savefig(outfile)
+
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--xmin", type=float, default=1.e-10,
+                        help="cutoff value for mass fractions")
+    parser.add_argument("-n", type=int, default=5,
+                        help="number of species to plot (most abundant shown)")
+    parser.add_argument("-o", type=str, default="state.png",
+                        help="name of plot output file")
+    parser.add_argument("state_file", type=str, nargs=1,
+                        help="burn cell state history file")
+
+    args = parser.parse_args()
+
+    doit(args.state_file[0], args.xmin, args.n, args.o)