Vlasov1D documentation update (#64)

README.md

@@ -1,4 +1,7 @@
 # ADEPT
+
+![ADEPT](./docs/source/adept-logo.png)
+
 ADEPT is an **A**utomatic **D**ifferentation **E**nabled **P**lasma **T**ransport code.
 
 ## Installation

adept/vlasov1d/solvers/vector_field.py

@@ -12,6 +12,9 @@ class TimeIntegrator:
     This is the base class for all time integrators. This makes it so that we dont have to
     load the electric field solver and the Vlasov pushers in every time integrator
 
+    The available solvers for E df/dv are "exponential" and "cubic-spline"
+    The only solver for v df/dx is "exponential"
+
     :param cfg: Dict
 
     """

docs/source/solvers/datamodels/vlasov1d.rst

@@ -0,0 +1,5 @@
+
+Each of these items is actually a dictionary.  These dictionaries, once initialized, need to be compiled into a megadictionary that is passed to the solver. This is basically the contents of the ``yaml`` files that are in the repo.
+
+.. automodule:: adept.vlasov1d.datamodel
+    :members:

docs/source/solvers/vlasov1d1v.rst

@@ -20,8 +20,48 @@ The electric field can be "driven" using :math:`E_D` which is a user defined fun
 
 Solver Options
 ================
-This is where we should have a list of the different solvers that can be chosen including the collision operator. #TODO
 
-Configuration parameters
-========================
-This is where there should be a line by line explanation of everything in a config file... #TODO
+Velocity space advection
+=========================
+1. ``exponential`` - This solver (incorrectly) assumes periodic boundaries in the velocity direction and uses a direct exponential solve such that 
+
+.. math::
+    f^{n+1} = f^n \times \exp(A*dt) 
+
+where :math:`A` is the advection operator. This is a much faster solver than the cubic-spline solver, but is less accurate. Use this if you are confident that the distribution function will be well behaved in the tails
+
+2. ``cubic-spline`` - This is a semi-Lagrangian solver that uses a cubic-spline interpolator to advect the distribution function in velocity space. Use this if you have trouble with the exponential solver.
+
+
+Spatial advection
+=================
+1. ``exponential`` - This is the only solver that is available. We only have periodic boundaries implemented in space (for the plasma) so this is perfectly fine. It is also very fast.
+
+
+Field solver
+============
+
+1. ``poisson`` - This is the only field solver that is available. It uses a spectral solver to solve the Poisson equation. This is the fastest and most accurate solver available.
+2. ``hampere`` - This solver uses a Hamiltonian formulation of the Vlasov-Ampere system that conserves energy exactly. This is the 2nd most reliable solver.
+3. ``ampere`` - This solver uses the Ampere's law to solve for the electric field.
+
+Collisions
+==========
+1. ``none`` - No collisions are included in the simulation
+2. ``lenard-bernstein`` - This solver uses the Lenard-Bernstein collision operator to include collisions in the simulation. 
+3. ``daugherty`` - This solver uses the Daugherty collision operator to include collisions in the simulation.
+
+
+Configuration Options
+======================
+``ADEPT`` needs a ``yaml`` file with the following datamodel to run the simulation. The datamodel is defined in the following class.
+
+.. autoclass:: adept.vlasov1d.datamodel.ConfigModel
+    :members: __init__
+
+Each of the objects used to initialize this datamodel are defined in the following classes.    
+
+.. toctree::
+   datamodels/vlasov1d
+   :maxdepth: 1
+   :caption: Configuration Options: