Docs: roadmap, internals, docstrings

snek5000 · Aug 3, 2020 · 2fae4b3 · 2fae4b3
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diff --git a/README.md b/README.md
@@ -105,13 +105,6 @@ sim.make.exec(["run"])  # actual simulation
   not so hard, btw)
 
 ## Roadmap
-
-### Short term
-- Implement post processing API: with matplotlib and Paraview
-
-### Long term
-- Interface Nek5000 states and time-integration event loop
-
 ## Contributing
 
 Contributions are welcome! You can help by testing out the code, filing issues

diff --git a/docs/index.rst b/docs/index.rst
@@ -44,7 +44,7 @@ Welcome to *snek5000*'s documentation!
    :caption: Help & Reference
 
    roadmap
-   boundary_cond
+   internals
    filtering
    CONTRIBUTING
    CHANGELOG

diff --git a/docs/boundary_cond.rst → docs/internals.rst b/docs/boundary_cond.rst → docs/internals.rst
@@ -1,3 +1,6 @@
+Notes on Nek5000 internals
+##########################
+
 Boundary condition
 ==================
 
@@ -52,13 +55,13 @@ Also if ``igeom=2``:
       -  bdry?
       -  ``opmask``: set 0 to dirichlet BC, masked from the update
 
-Boundary conditions
--------------------
+Boundary condition subroutines
+------------------------------
 
 Periodicity: node numbering
 
-``bcdirvc``
-~~~~~~~~~~~
+``bcdirvc``: Dirichlet
+~~~~~~~~~~~~~~~~~~~~~~
 
 -  ``CB = V (Constant Dirichlet in rea file)``
 -  ``CB = v (user provided Dirichlet in userbc)``:
@@ -102,19 +105,15 @@ No mask
 
 Velocity should be ``v=0``
 
-Caution: Pressure preconditioner BC are related
-
-To Do
-~~~~~
+Caution: Pressure preconditioner and BC are related
 
-Set velocity v=0, normal component of velocity is zero, opposite of
-``on`` boundary condition.
+.. todo::
 
-FAQ
-===
+   Set velocity v=0, normal component of velocity is zero, opposite of ``on``
+   boundary condition.
 
 Time-stepping algebra
----------------------
+=====================
 
 Mass matrix requires time levels (n, n-1, n-2): extrapolated Conv /
 Stiffness requires time levels (n-1, n-2): explicit
@@ -133,4 +132,4 @@ correction in each sub-step.
 CFL number
 ~~~~~~~~~~
 
-BDF3/EXT3: CFL=0.6. Characteristic emthod
+BDF3/EXT3: CFL=0.6. Characteristic method
diff --git a/docs/roadmap.rst b/docs/roadmap.rst
@@ -1,5 +1,26 @@
 Roadmap
 =======
 
+Short term
+----------
+
+- Implement post processing API: with matplotlib and Paraview. Status:
+  * Paraview_ reader is implemented. Requires clean up.
+  * Pymech_ reader which extends xarray is implemented.
+
+.. _paraview: https://github.com/exabl/sandbox/blob/master/paraview/nekio.py
+.. _pymech: https://pymech.readthedocs.io/en/latest/dataset.html
+
+Long term
+---------
+
+- Interface Nek5000 states and time-integration event loop. Status:
+  * Experiments are underway to interface using cffi_.
+
+.. _cffi: https://github.com/exabl/sandbox/tree/master/interface/test_case
+
+Miscellaneous
+-------------
+
 .. todolist::
 
diff --git a/src/snek5000/__init__.py b/src/snek5000/__init__.py
@@ -6,22 +6,22 @@
 .. autosummary::
    :toctree:
 
+   assets
    output
    solvers
+   util
 
 **Modules**
 
 .. autosummary::
    :toctree:
 
-   assets
    info
    log
    magic
    make
    operators
    params
-   util
 
 """
 import importlib.resources

diff --git a/src/snek5000/assets/__init__.py b/src/snek5000/assets/__init__.py
@@ -0,0 +1,6 @@
+"""Assets for building
+======================
+
+Contains common snakemake rules and jinja templates.
+
+"""
diff --git a/src/snek5000/operators.py b/src/snek5000/operators.py
@@ -3,9 +3,6 @@
 
 Information regarding mesh, mathematical operators, and domain decomposition.
 
-.. todo:: Move length to abl.par file and extrude it to allow double precision
-          values.
-
 .. note:: We deliberately try not to use the variable names used in Nek5000, as
           those are ambiguously named.