Merge branch 'main' into OptionsUpgrade

README.md

@@ -3,7 +3,7 @@
   <img width = "250" src="docs/VPLanetLogo.png?raw=true"/>
 </p>
 
-<h1 align="center">VSPACE: Explore Parameter Spaces with VPLanet</h1>
+<h1 align="center">vspace: Generate Parameter Spaces for VPLanet</h1>
 
 <p align="center">
   <a href="https://VirtualPlanetaryLaboratory.github.io/vspace/"><img src="https://img.shields.io/badge/read-the_docs-blue.svg?style=flat"></a>
@@ -15,7 +15,7 @@
 </p>
 
 
-``VSPACE`` is a tool to build input files for parameter sweeps with [``VPLanet``](https://github.com/VirtualPlanetaryLaboratory/vplanet).
-With ``VSPACE`` you can quickly and easily build input files with specific
+``vspace`` is a tool to build input files for parameter sweeps with [``VPLanet``](https://github.com/VirtualPlanetaryLaboratory/vplanet).
+With ``vspace`` you can quickly and easily build input files with specific
 parameters with different distributions, such as grids, normal distribution, even sines and cosines. After generating the trials, use the [``multi-planet`` package](https://github.com/VirtualPlanetaryLaboratory/multi-planet) to run the simulations
 on multi-core platforms, and use [``bigplanet``](https://github.com/VirtualPlanetaryLaboratory/bigplanet) to store and quickly analyze the results.

docs/conf.py

@@ -20,8 +20,8 @@
 # -- Project information -----------------------------------------------------
 
 project = 'vspace'
-copyright = '2021, Caitlyn Wilhelm'
-author = 'Caitlyn Wilhelm'
+copyright = '2021, The VPLanet Team'
+author = 'Russell Deitrick, Caitlyn Wilhelm, Rory Barnes'
 
 # The full version, including alpha/beta/rc tags
 release = '1.0'

docs/help.rst

@@ -1,5 +1,18 @@
-Input Files
-===========
+Running vspace
+==============
+
+Run vspace with the command
+
+.. code-block:: bash
+
+    vspace <file>
+
+where *file* is an ASCII text file that contains instructions on how to build the parameter space.
+This file is typically called ``vspace.in``.
+
+.. note::
+
+    The `multi-planet script <https://github.com/VirtualPlanetaryLaboratory/multi-planet>`_ also uses ``vspace``'s input file.
 
 vspace.in
 ---------
@@ -24,9 +37,9 @@ lines are described below and is based off the
     dEcc  [0.001,0.005,n5] ecc
     dObliquity [0,10,n5] obl
 
-The first line provides ``VSPACE`` with the location of a directory that contains the template
+The first line provides ``vspace`` with the location of a directory that contains the template
 ``VPLanet`` input files, such as vpl.in, star.in, etc. (see below). The format of these files
-is slightly different when used with ``VSPACE`` then when used with a single ``VPlanet`` run.
+is slightly different when used with ``vspace`` then when used with a single ``VPlanet`` run.
 
 
 Line 2 presents the name of the subdirectory that will contain all the initial conditions for 
@@ -51,11 +64,11 @@ while ``sPrimaryFile`` is the file that has simulation options (the default is v
 input option (exact match required), <sampling rule> sets how the values of the option 
 are to be sampled (see the `Sampling
 Rules <sampling>`_ section), and <identifier> is a string that is appended to the trialname
-prefix in the destfolder subdirectories. ``VSPACE`` will vary all parameters listed
+prefix in the destfolder subdirectories. ``vspace`` will vary all parameters listed
 after a "file" command until it reaches the next "file" command or the end of the
 file. In this example we are not varying any options for vpl.in or jupiter.in, so they have no options
-listed. However they must still be included to inform ``VSPACE`` that they should be copied into the 
-trial directories. In this case, "n5" tells ``VSPACE`` to create 5 evenly spaced values of dEcc between 0.001
+listed. However they must still be included to inform ``vspace`` that they should be copied into the 
+trial directories. In this case, "n5" tells ``vspace`` to create 5 evenly spaced values of dEcc between 0.001
 and 0.005.
 
 .. note::
@@ -83,11 +96,11 @@ Template Files
 The template files are nearly identical to standard ``VPLanet`` input files except
 that they should not include the parameters to be varied. 
 
-You can additionally instruct ``VSPACE`` to remove options from a template file with by including a line in
+You can additionally instruct ``vspace`` to remove options from a template file with by including a line in
 vspace.in like: 
 
 .. code-block:: bash
 
     rm <option name>
 
-``VSPACE`` will merely comments out the matching line.
+``vspace`` will merely comments out the matching line.

docs/index.rst

@@ -1,9 +1,9 @@
-VSPACE Documentation
+vspace Documentation
 ====================
-``VSPACE`` is a tool to build input files for a parameter sweep with ``VPLanet``, creating
+``vspace`` is a tool to build input files for a parameter sweep with ``VPLanet``, creating
 a set of individual directories that contain ``VPLanet`` input files that are ready to be simulated.
 
-With ``VSPACE`` you can quickly and easily build input files with specific
+With ``vspace`` you can quickly and easily build input files with specific
 parameters with a specific type of distribution. In **Grid Mode** you can build
 input files in which the initial conditions have regular spacings within specified
 limits and with either linear or logarithmic spacings. In **Random Mode** the
@@ -24,6 +24,6 @@ script to run.
 .. note::
 
     To maximize ``vspace``'s power, run ``mulit-planet`` with the ``-bp`` flag to automatically
-    build a bigplanet archive immediately after the simualtions finish.  Then create 
+    build a bigplanet archive immediately after the simulations finish.  Then create 
     bigplanet files from the archive as needed, and use ``bigplanet``'s `scripting functions <https://virtualplanetarylaboratory.github.io/bigplanet/Script.html>`_ to 
     extract vectors and matrices for plotting, statistical analyses, etc.

docs/install.rst

@@ -1,11 +1,11 @@
 Installation Guide
 ==================
 
-There are two ways to install ``VSPACE``: 1) in conjunction with 
+There are two ways to install ``vspace``: 1) in conjunction with 
 `VPLanet <https://github.com/VirtualPlanetaryLaboratory/vplanet>`_ and 
 its other support scripts, or 2) from source.
 
-To install ``VSPACE`` and the other ``VPLanet`` packages, use the command:
+To install ``vspace`` and the other ``VPLanet`` packages, use the command:
 
 .. code-block:: bash
 

docs/sampling.rst

@@ -1,8 +1,8 @@
 Sampling Rules
 ==============
 
-``VSPACE`` has two sampling modes: **grid** and **random**, which are specified with the word
-"sSampleMode" in the input file (vspace.in). For example:
+``vspace`` has two sampling modes: **grid** and **random**, which are specified with the word
+"samplemode" in the input file (vspace.in). For example:
 
 .. code-block:: bash
 
@@ -14,7 +14,7 @@ is not set, the default is grid mode.
 Grid Mode
 ---------
 
-``VSPACE`` allows for 3 submodes to generate trials that explore a gridded parameter
+``vspace`` allows for 3 submodes to generate trials that explore a gridded parameter
 space, i.e even spacing. These submodes are **explicit**, **linear**, and
 **logarithmic**. Each adheres the following syntax:
 
@@ -30,7 +30,7 @@ Explicit Grids
 ^^^^^^^^^^^^^^
 
 In this grid submode, the "spacing" value is just a number that represents the
-interval in between trials. ``VSPACE`` will create as many trials as necessary
+interval in between trials. ``vspace`` will create as many trials as necessary
 to follow the sampling rules, and will not necessarily include a trial at the
 end value. For example, to generate trials that vary ``dSemi`` from 1 to 2
 with a spacing of 0.1, the syntax is:
@@ -71,7 +71,7 @@ rather than ``dRadius [-1, -2, 0.1]  R``.
 
 .. warning::
 
-    ``VSPACE`` will NOT check whether a minus option causes
+    ``vspace`` will NOT check whether a minus option causes
     ``VPLanet`` to change the units.
     If you use negative values for a parameter that has alternate units for a
     negative option, the outcome will most likely be wrong! You can check the `VPLanet documentation <https://virtualplanetarylaboratory.github.io/vplanet/help.html#input-options>`_
@@ -183,6 +183,6 @@ not the sine or cosine of the angle.
 Histograms
 ----------
 
-If running in random mode, ``VSPACE`` will automatically generate histograms of the varied parameters.
+If running in random mode, ``vspace`` will automatically generate histograms of the varied parameters.
 In the *destfolder* will be PNG files with plots of each parameter's distribution. These plots are not
 publication ready, but can be used to verify that the distributions created match your expectations.