Merge pull request #179 from VirtualPlanetaryLaboratory/dev

Dev
VirtualPlanetaryLaboratory · Jun 7, 2021 · 4bca3b4 · 4bca3b4
2 parents f85c800 + 22f5928
commit 4bca3b4
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Showing 9 changed files with 17 additions and 13 deletions.
diff --git a/docs/VPLanetFlowChart.png b/docs/VPLanetFlowChart.png
diff --git a/docs/architecture.rst b/docs/architecture.rst
@@ -33,7 +33,7 @@ unphysical, e.g. eccentricities less than 0. Each of these checks must only
 apply to an individual option. More complicated checks are handled
 in Verify.
 
-:note::
+.. note::
 
   Some arrays and matrices are allocated prior to the ReadOptions call.
 
@@ -78,7 +78,7 @@ options can be input in a wide range of units, recording the state in system
 units allows users to determine if they have input something incorrectly, and
 also helps developers identify bugs.
 
-:note::
+.. note::
 
   If a user requests an output with a negative sign, which forces a specific
   unit, then the value in the log file will not be SI, but the custom units
@@ -106,7 +106,7 @@ system of equations that are required based on the options. The integration is
 broken down into five steps: Auxiliary Properties (sometimes shortened to
 AuxProps), One Step, Output, Force Behavior, and Halt.
 
-:note::
+.. note::
 
   If the user does not select a forward or backward integration, but does elect
   to write a log file, then the code will calculate all the initial conditions

diff --git a/docs/index.rst b/docs/index.rst
@@ -18,6 +18,7 @@ are available in separate repositories.
    vplot
    parametersweep
    tutorials
+   Workshop Lectures <http://faculty.washington.edu/rkb9/vplanet/Workshop21/>
    developers
    authors
    repos

diff --git a/docs/option.rst b/docs/option.rst
@@ -66,6 +66,7 @@ should be set to 0 as shown. Otherwise, set the value to equal the sum of module
 bits, such as is done for the inclination:
 
 .. code-block:: bash
+
     options[OPT_INC].iModuleBit = DISTORB + SPINBODY;
 
 In other words, each module is assigned a unique integer that is a power of 2 so
@@ -80,13 +81,15 @@ parameter that is used with the -H command line option, e.g. the verbosity
 benefits from a bit more explanation:
 
 .. code-block:: bash
-sprintf(options[OPT_VERBOSE].cLongDescr,
+
+  sprintf(options[OPT_VERBOSE].cLongDescr,
   "Set how much text is written to the screen. 0 = no output, 1 = only\n"
   "errors, 2 = progress updates, 3 = statements about input choices,  4 =\n"
   "information about unit choices, 5 = all possible output. Note that levels\n"
   "0 and 5 can be set at execution with the -q and -v options, respectively."
 
-:note::
+.. note::
+
   Any field that is omitted will be set to the default values that are defined
   in output.c:InitializeOutput.
 

diff --git a/docs/output.rst b/docs/output.rst
@@ -85,7 +85,7 @@ angle" requires a bit more explanation for a typical user:
     "the vernal equinox. This angle is a \"dog-leg\" angle as shown in Fig. 30\n"
     "of Barnes et al. (2020)."
 
-:note::
+.. note::
   Any field that is omitted will be set to the default values that are defined
   in output.c:InitializeOutput.
 

diff --git a/docs/quickstart.rst b/docs/quickstart.rst
@@ -82,7 +82,7 @@ vpl.in
     bVarDt        1                  # Use variable timestepping?
     dEta          0.01               # Coefficient for variable timestepping
     dStopTime     4.6e9              # Stop time for evolution
-    dOutputTime   1e6                # Output timesteps (assuming in body files)
+    dOutputTime   1e6                # Output interval for forward files
 
 .. note::
 

diff --git a/docs/tutorials.rst b/docs/tutorials.rst
@@ -1,5 +1,5 @@
-VPLanet Tutorials
-=================
+Tutorials
+=========
 
 Please view the following pages for written descriptions of how to:
 

diff --git a/examples/MagmOc_Earth/Earth.in b/examples/MagmOc_Earth/Earth.in
@@ -1,7 +1,7 @@
 # Planet a parameters
 sName         Earth                     # Body's name
 saModules     magmoc, atmesc                      # Modules to apply, exact spelling required
-cColor        13aed5
+sColor        13aed5
 
 # Physical Properties
 dMass         -1                       # Mass, negative -> Earth masses
@@ -39,4 +39,4 @@ dEcc          0.017                         # Eccentricity
 
 # Output
 saOutputOrder Time -PotTemp -SurfTemp -SolidRadius -WaterMassMOAtm -WaterMassSol -OxygenMassMOAtm -OxygenMassSol -PressWaterAtm -PressOxygenAtm -HydrogenMassSpace -OxygenMassSpace FracFe2O3Man NetFluxAtmo MeltFraction $
-WaterFracMelt 
+WaterFracMelt
diff --git a/src/options.h b/src/options.h
@@ -9,8 +9,8 @@
   1) Add integer definition here
   2) Add new option properties in InitializeOptions
   3) Write new fnReadOptions function
-  3) If necessary, modify the ReadOptions subroutine
-  4) If necessary, modify the WriteLog subroutine
+  4) If necessary, modify the ReadOptions subroutine
+  5) If necessary, modify the Verify process
 
 */