Cleanup and comment

.gitignore

@@ -59,4 +59,4 @@ docs/_build/
 target/
 
 # PyCharm
-.idea
+.idea/

README.md

@@ -19,7 +19,7 @@ Bloch boundary conditions are not included but wouldn't be very hard to add.
 The default solver (opencl_fdfd.cg_solver(...)) located in main.py implements
 the E-field wave operator directly (ie, as a list of OpenCL instructions
 rather than a matrix). Additionally, there is a slower (and slightly more
-versatile) sovler in csr.py which attempts to solve an arbitrary sparse
+versatile) solver in csr.py which attempts to solve an arbitrary sparse
 matrix in compressed sparse row (CSR) format using the same conjugate gradient
 method as the default solver. The CSR solver is significantly slower, but can
 be very useful for testing alternative formulations of the FDFD wave equation.
@@ -29,9 +29,29 @@ generalization to multiple GPUs should be pretty straightforward
 (ie, just copy over edge values during the matrix multiplication step).
 
 
+## Installation
+
 **Dependencies:**
 * python 3 (written and tested with 3.5) 
 * numpy
 * pyopencl
 * jinja2
-* [fdfd_tools](https://mpxd.net/gogs/jan/fdfd_tools)
+* [fdfd_tools](https://mpxd.net/gogs/jan/fdfd_tools)
+
+
+Install with pip, via git:
+```bash
+pip install git+https://mpxd.net/gogs/jan/opencl_fdfd.git@release
+```
+
+
+## Use
+
+See the documentation for opencl_fdfd.cg_solver(...)
+(located in main.py) for details about how to call the solver.
+ 
+An alternate (slower) FDFD solver and a general gpu-based sparse matrix
+solver is available in csr.py . These aren't particularly well-optimized,
+and something like [MAGMA](http://icl.cs.utk.edu/magma/index.html) would
+probably be a better choice if you absolutely need to solve arbitrary
+sparse matrices and can tolerate writing and compiling C/C++ code.

opencl_fdfd/__init__.py

@@ -19,7 +19,7 @@
   The default solver (opencl_fdfd.cg_solver(...)) located in main.py implements
    the E-field wave operator directly (ie, as a list of OpenCL instructions
    rather than a matrix). Additionally, there is a slower (and slightly more
-   versatile) sovler in csr.py which attempts to solve an arbitrary sparse
+   versatile) solver in csr.py which attempts to solve an arbitrary sparse
    matrix in compressed sparse row (CSR) format using the same conjugate gradient
    method as the default solver. The CSR solver is significantly slower, but can
    be very useful for testing alternative formulations of the FDFD wave equation.

opencl_fdfd/csr.py

@@ -1,3 +1,19 @@
+"""
+Sparse matrix solvers
+
+This file holds the sparse matrix solvers, as well as the
+CSRMatrix sparse matrix representation.
+
+The FDFD solver (fdfd_cg_solver()) solves an FDFD problem by
+creating a sparse matrix representing the problem (using
+fdfd_tools) and then passing it to cg(), which performs a
+conjugate gradient solve.
+
+cg() is capable of solving arbitrary sparse matrices which
+satisfy the constraints for the 'conjugate gradient' algorithm
+(positive definite, symmetric) and some that don't.
+"""
+
 from typing import List, Dict, Any
 import time
 
@@ -133,16 +149,16 @@ def cg(a: 'scipy.sparse.csr_matrix',
     return x
 
 
-def cg_solver(omega: complex,
+def fdfd_cg_solver(omega: complex,
-              dxes: List[List[numpy.ndarray]],
+                   dxes: List[List[numpy.ndarray]],
-              J: numpy.ndarray,
+                   J: numpy.ndarray,
-              epsilon: numpy.ndarray,
+                   epsilon: numpy.ndarray,
-              mu: numpy.ndarray = None,
+                   mu: numpy.ndarray = None,
-              pec: numpy.ndarray = None,
+                   pec: numpy.ndarray = None,
-              pmc: numpy.ndarray = None,
+                   pmc: numpy.ndarray = None,
-              adjoint: bool = False,
+                   adjoint: bool = False,
-              solver_opts: Dict[str, Any] = None,
+                   solver_opts: Dict[str, Any] = None,
-              ) -> numpy.ndarray:
+                   ) -> numpy.ndarray:
     """
     Conjugate gradient FDFD solver using CSR sparse matrices, mainly for
      testing and development since it's much slower than the solver in main.py.

opencl_fdfd/main.py

@@ -1,3 +1,11 @@
+"""
+Default FDFD solver
+
+This file holds the default FDFD solver, which uses an E-field wave
+operator implemented directly as OpenCL arithmetic (rather than as
+a matrix).
+"""
+
 from typing import List
 import time
 

opencl_fdfd/ops.py

@@ -1,3 +1,12 @@
+"""
+Basic PyOpenCL operations
+
+The functions are mostly concerned with creating and compiling OpenCL
+kernels for use by the other solvers.
+
+See kernels/ for any of the .cl files loaded in this file.
+"""
+
 from typing import List, Callable
 
 import numpy
@@ -8,6 +17,7 @@ import pyopencl.array
 from pyopencl.elementwise import ElementwiseKernel
 from pyopencl.reduction import ReductionKernel
 
+
 # Create jinja2 env on module load
 jinja_env = jinja2.Environment(loader=jinja2.PackageLoader(__name__, 'kernels'))
 

setup.py

@@ -3,7 +3,7 @@
 from setuptools import setup, find_packages
 
 setup(name='opencl_fdfd',
-      version='0.1',
+      version='0.2',
       description='Opencl FDFD solver',
       author='Jan Petykiewicz',
       author_email='anewusername@gmail.com',