Merge pull request #420 from kyleabeauchamp/docfix

Fixing some sphinx doc typos

docs/usersguide/application.rst

@@ -95,7 +95,7 @@ in the new window.
 
 If you plan to use the CUDA platform, OpenMM also needs to locate the CUDA
 kernel compiler (nvcc).  By default it looks for it in the location
-/usr/local/cuda/bin/nvcc.  If you have installed the CUDA toolkit in a different
+:file:`/usr/local/cuda/bin/nvcc`.  If you have installed the CUDA toolkit in a different
 location, you can set OPENMM_CUDA_COMPILER to tell OpenMM where to find it.  For
 example,
 ::
@@ -174,7 +174,7 @@ the new window.
 
 If you plan to use the CUDA platform, OpenMM also needs to locate the CUDA
 kernel compiler (nvcc).  By default it looks for it in the location
-/usr/local/cuda/bin/nvcc.  If you have installed the CUDA toolkit in a different
+:file:`/usr/local/cuda/bin/nvcc`.  If you have installed the CUDA toolkit in a different
 location, you can set OPENMM_CUDA_COMPILER to tell OpenMM where to find it.  For
 example,
 ::
@@ -197,8 +197,8 @@ Installing on Windows
 *********************
 
 1. Download the pre-compiled binary of OpenMM for Windows, then double click the
-.zip file to expand it.  Move the files to C:\\Program Files\\OpenMM.  (On 64 bit
-Windows, use C:\\Program Files (x86)\\OpenMM).
+.zip file to expand it.  Move the files to :file:`C:\\Program Files\\OpenMM`.  (On 64 bit
+Windows, use :file:`C:\\Program Files (x86)\\OpenMM`).
 
 2. Make sure you have the 32-bit version of Python 3.3 (other versions will not
 work) installed on your computer.  To do this, launch the Python program (either
@@ -248,7 +248,7 @@ your PATH.
 
         dir C:\py*
 
-    The files are typically located in a directory like C:\\Python33.  Remember this
+    The files are typically located in a directory like :file:`C:\\Python33`.  Remember this
     location.  You will need to enter it, along with the location of the OpenMM
     libraries, later in this process.
 
@@ -257,7 +257,7 @@ your PATH.
   * Click on the “Advanced” tab or the “Advanced system settings” link
   * Click “Environment Variables”
   * Under “System variables,” select the line for “Path” and click “Edit…”
-  * Add C:\\Program Files\\OpenMM\\lib and C:\\Program Files\\OpenMM\\lib\\plugins
+  * Add :file:`C:\\Program Files\\OpenMM\\lib` and :file:`C:\\Program Files\\OpenMM\\lib\\plugins`
     to the “Variable value”.  If you also need to add Python or FFTW to your
     PATH, enter their directory locations here.  Directory locations need to be
     separated by semi-colons (;).
@@ -265,8 +265,8 @@ your PATH.
 
     If you installed OpenMM somewhere other than the default location, you must also
     set OPENMM_PLUGIN_DIR to point to the plugins directory.  If this variable is
-    not set, it will assume plugins are in the default location (C:\\Program
-    Files\\OpenMM\\lib\\plugins or C:\\Program Files (x86)\\OpenMM\\lib\\plugins).
+    not set, it will assume plugins are in the default location (:file:`C:\\Program
+    Files\\OpenMM\\lib\\plugins` or :file:`C:\\Program Files (x86)\\OpenMM\\lib\\plugins`).
 
 7. Verify your installation by running the “testInstallation.py” script found in
 the “examples” folder of your OpenMM installation.  To run it, open a command
@@ -328,8 +328,8 @@ on setting up the window to use OpenMM).  Navigate to the “examples” folder
 
     cd <examples_directory>
 
-where the typical directory is :code:`/usr/local/openmm/examples` on Linux
-and Mac machines and  “\ :code:`C:\\Program Files\\OpenMM\\examples”` on Windows
+where the typical directory is :file:`/usr/local/openmm/examples` on Linux
+and Mac machines and  :file:`C:\\Program Files\\OpenMM\\examples` on Windows
 machines.
 
 Then type
@@ -566,8 +566,8 @@ which stores all the force field parameters directly in a prmtop file, Gromacs j
 references to force field definition files that are installed with the Gromacs
 application.  OpenMM needs to know where to find these files, so the
 :code:`includeDir` parameter specifies the directory containing them.  If you
-omit this parameter, OpenMM will assume the default location
-/usr/local/gromacs/share/gromacs/top, which is often where they are installed on
+omit this parameter, OpenMM will assume the default location :file:`/usr/local/gromacs/share/gromacs/top`, 
+which is often where they are installed on
 Unix-like operating systems.  So in :numref:`Example,Gromacs example` we actually could have omitted
 this parameter, but if the Gromacs files were installed in any other location,
 we would need to include it.
@@ -620,7 +620,7 @@ The following lines specify to use the CUDA Platform:
     platform = Platform.getPlatformByName('CUDA')
     simulation = Simulation(prmtop.topology, system, integrator, platform)
 
-The Platform name should be :code:`OpenCL`\ , :code:`CUDA`\ , or
+The Platform name should be :code:`OpenCL`\ , :code:`CUDA`\ , :code:`CPU`\, or
 :code:`Reference`\ .
 
 You also can specify Platform-specific properties that customize how

docs/usersguide/introduction.rst

@@ -11,7 +11,7 @@ OpenMM consists of two parts:
    to run simulations
 
 
-This guide is devided into three sections:
+This guide is divided into three sections:
 
 * Part I (Chapters :ref:`the-openmm-application-layer-introduction`\ -\ :ref:`creating-force-fields`\ )
   describes the application layer.  It is relevant to all users, but especially relevant to people

docs/usersguide/library.rst

@@ -2733,7 +2733,7 @@ Multiplication or division of two Units results in a composite Unit.
 
     mps = meter / second
 
-Unlike amount (moles), angle (radians) is arguably dimensionless.  Butsimtk.unit
+Unlike amount (moles), angle (radians) is arguably dimensionless.  But simtk.unit
 treats angle as another dimension.   Use the trigonometric functions from the
 simtk.unit module (not those from the Python math module!) when dealing with
 Units and Quantities.