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_sources/examples.rst.txt

@@ -12,46 +12,46 @@ directory of the :code:`VPLanet` repository.
 
 
 
-   examples/MagmOc_Earth
-   examples/HabEvapCore
-   examples/HabitableZone
+   examples/IceBelts
+   examples/CassiniStates
+   examples/ChaoticResonances
+   examples/MiniNeptuneEvap
+   examples/GalaxyEffects
+   examples/EarthInterior
+   examples/AtmEscKepler-36
    examples/CassiniMulti
-   examples/ParameterSweep
-   examples/NBodyAtmEsc
-   examples/StellarEvol
+   examples/MagneticBraking
+   examples/LuminosityCycle
+   examples/CircumbinaryOrbit
    examples/HLossTides
-   examples/TidalEarth
+   examples/VenusApproxInterior
+   examples/StellarEvol
+   examples/DiffLimWaterEscape
    examples/VenusWaterLoss
    examples/BinaryTides
-   examples/FfdProxCen
-   examples/STEEP
-   examples/AtmEscKepler-36
-   examples/SS_NBody
-   examples/ApseLock
-   examples/VenusApproxInterior
-   examples/CassiniStates
-   examples/SSDistOrbDistRot
+   examples/WaterLossTides
+   examples/TideLock
+   examples/MagmOc_GJ1132b
+   examples/ParameterSweep
    examples/MagmOc_Trappist1g
+   examples/HabitableZone
    examples/AtmEscRegimes
-   examples/IoHeat
-   examples/GalaxyEffects
-   examples/RadHeat
-   examples/CircumbinaryOrbit
-   examples/TideLock
-   examples/WaterLossTides
-   examples/AbioticO2
-   examples/IceBelts
-   examples/MagneticBraking
+   examples/FfdProxCen
+   examples/ApseLock
+   examples/NBodyAtmEsc
+   examples/TidalEarth
+   examples/AtmEscFlareProxCen
    examples/DampedCBP
+   examples/SS_NBody
+   examples/RadHeat
    examples/MDwarfLuminosity
+   examples/IoHeat
+   examples/MagmOc_Earth
+   examples/SSDistOrbDistRot
+   examples/HabEvapCore
    examples/EarthClimate
-   examples/EarthInterior
-   examples/DiffLimWaterEscape
-   examples/ChaoticResonances
-   examples/LuminosityCycle
-   examples/MiniNeptuneEvap
-   examples/AtmEscFlareProxCen
-   examples/MagmOc_GJ1132b
+   examples/AbioticO2
+   examples/STEEP
 
 
 Broken

_sources/primaryvariable.rst.txt

@@ -167,6 +167,10 @@ block of code that initializes the other pieces of the UPDATE struct.
            malloc(update[iBody].iNumPrimaryVariable * sizeof(int));
         control->Evolve.tmpUpdate[iBody].iaBody[iVar] =
            malloc(update[iBody].iNumPrimaryVariable * sizeof(int *));
+        for (iSubStep=0; iSubStep < 4; iSubStep++) {
+          control->Evolve.daDerivProc[iSubStep][iBody][iVar] =
+              malloc(update[iBody].iNumEqns[iVar] * sizeof(double));
+        }
       }
 
       // Now allocate memory for the number of processes that affect this variable
@@ -192,6 +196,28 @@ variable.
   assign a new value to this variable, you will overwrite the primary variable's
   derivative (which would be bad!).
 
+We then need to add some lines to ```module.c```. In InitializeModule, add
+
+.. code-block:: bash  
+
+module->fnFinalizeUpdatePhysics =
+        malloc(iNumBodies * sizeof(fnFinalizeUpdateCarbManModule));
+
+and in FinalizeModule, add
+
+.. code-block:: bash
+
+  module->fnFinalizeUpdatePhysics[iBody] =
+        malloc(iNumModules * sizeof(fnFinalizeUpdateCarbManModule));
+
+and
+
+.. code-block:: bash
+
+ module->fnFinalizeUpdatePhysics[iBody][iModule]   = &FinalizeUpdateNULL; 
+
+Please add them next to the other similar statements
+
 Next we need to add code to the module file, physics.c in this example, for
 which this primary variable will be added. First add a new function that
 continues the initialization process:

_sources/src.rst.txt

@@ -12,28 +12,28 @@ Detailed documentation of C source code.
    :maxdepth: 1
 
 
-   src/output
-   src/system
-   src/module
-   src/distrot
-   src/magmoc
-   src/atmesc
+   src/update
+   src/galhabit
    src/options
-   src/distorb
-   src/stellar
-   src/control
+   src/halt
+   src/vplanet
+   src/atmesc
+   src/binary
+   src/thermint
    src/radheat
-   src/galhabit
-   src/evolve
-   src/poise
-   src/eqtide
    src/flare
+   src/output
    src/body
-   src/update
-   src/thermint
    src/spinbody
-   src/binary
-   src/halt
-   src/vplanet
+   src/stellar
+   src/control
+   src/evolve
+   src/system
    src/verify
+   src/magmoc
+   src/eqtide
+   src/poise
+   src/distorb
+   src/module
+   src/distrot
 

_sources/tests.rst.txt

@@ -16,15 +16,23 @@ further enabling confidence in the code's accuracy.
 Test scripts live in the :code:`tests/` directory and are executed automatically 
 on every pull request with GitHub Actions. To perform the tests, we use :code:`pytest`, which will
 find all Python files with the word :code:`test` somewhere in their name (side note:
-if it's not meant to be a test, don't put :code:`test` in the file name!).
+if it's not meant to be a test, don't put :code:`test` in the file name!). Under the :code:`tests`
+directory are subdirectories whose names consists of VPLanet modules, e.g. BINARY and AtmescEqtideStellar.
+These subdirectories contain the tests available for the module combinations of the subdirectory name.
+
 
 The VPLanet team has made it easy to add or revise tests. Inside the :code:`tests/` directory
 is a file called :code:`maketest.py`, which will generate a unit test from a set of valid infiles.
 So a typical procedure to create a new test is to:
 
 - Create a simulation that executes previously untested functionality
 - Verify the results are accurate! (Obvious, we know, but please don't forget!)
-- Copy the .in files t
+- Create a subdirectory with a unique name for your test. 
+- Copy the .in files for your test into your new subdirectory
+- cd to the :code:`tests` directory and run ```python maketest.py <modules/subdir>```, which the 
+  argument is the relative to path to your new test
+- Commit your .in files and the new :code:`test_<subdir>.py" file to the repository
+- Issue a PR!
 
 These unit tests not only ensure new modification don't break parts of the code
 that already work. In addition, they are used to compute the fraction of the code