README update, include to Doxyfile.

Former-commit-id: cab9d665ae32308d1669dad426a7a84accc4ac6f

Doxyfile

@@ -753,7 +753,7 @@ WARN_LOGFILE           =
 # spaces.
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-INPUT                  = qpms
+INPUT                  = qpms finite_systems.md README.md README.Triton.md finite_systems.md lattices.md
 
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 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -889,7 +889,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE =
+USE_MDFILE_AS_MAINPAGE = README.md
 
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README.md

@@ -0,0 +1,84 @@
+QPMS README
+===========
+
+QPMS is a toolkit for frequency-domain simulations of photonic systems
+consisting of compact objects (particles) inside a homogeneous medium. Scattering
+properties of the individual particles are described by their T-matrices
+(which can be obtained e.g. with the `scuff-tmatrix` tool from 
+the [SCUFF-EM] suite).
+
+QPMS handles the multiple scattering of electromagnetic radiation between 
+the particles. The system can consist either of a finite number of particles
+or an infinite number of periodically arranged lattices (with finite number
+of particles in a single unit cell).
+
+Features
+========
+
+Finite systems
+--------------
+ * Computing multipole excitations *and fields (TODO)* scattered from nanoparticle
+   clusters illuminated by plane, spherical or *cylindrical (TODO)* waves.
+ * Finding eigenmodes.
+ * *Calculating cross sections (TODO).*
+ * Reducing numerical complexity of the computations by exploiting
+   symmetries of the cluster (decomposition to irreducible representations).
+
+Infinite systems (lattices)
+---------------------------
+ * 2D-periodic systems supported. (TODO 1D and 3D.)
+ * *Calculation of transmission and reflection properties (TODO).*
+ * Finding eigenmodes and calculating dispersion relations.
+ * *Calculation of far-field radiation patterns of an excited array (TODO).*
+ * Reducing numerical complexity of the computations by exploiting
+   symmetries of the lattice (decomposition to irreducible representations).
+
+
+Installation
+============
+The package depends on several python modules and GSL (>= 2.0).
+The python module dependencies should be installed automatically when running
+the installation script. If you have a recent enough OS,
+you can get GSL easily from the repositories; on Debian and derivatives,
+just run `apt-get install libgsl-dev` under root. Alternatively,
+you can [get the source and compile it yourself][GSL].
+
+You also need a fresh enough version of [cmake][].
+
+After GSL is installed, you can install qpms to your local python library using::
+
+```
+  cmake .
+  make amos
+  python3 setup.py install --user
+```
+
+If GSL is not installed the standard library path on your system, you might 
+need to pass it to the installation script using the
+`LIBRARY_PATH` and `LD_LIBRARY_PATH` environment
+variables.
+
+Special care has often be taken when installing QPMS in cluster environments.
+Specific installation instructions for Aalto University's Triton cluster
+can be found in a [separate document][TRITON-README].
+
+Documentation
+=============
+
+Documentation of QPMS is a work in progress. Most of the newer code
+is documented using doxygen comments. To build the documentation, just run
+`doxygen`
+in the root directory; the documentation will then be found in 
+`docs/html/index.html`.
+
+Of course, the prerequisite of this is having doxygen installed.
+If you don't, you will probably find it easily in your OS's
+repositories. On Debian and derivatives, simply run `apt-get install doxygen`
+under root.
+
+
+[SCUFF-EM]: https://homerreid.github.io/scuff-em-documentation/
+[GSL]: https://www.gnu.org/software/gsl/
+[cmake]: https://cmake.org
+[TRITON-README]: README.Triton.md
+

README.rst

@@ -1,40 +0,0 @@
-Quantum photonic multiple scattering
-====================================
-
-TODO description
-
-Installation
-============
-The package depends on several python modules and GSL (>= 2.0).
-The python module dependencies should be installed automatically when running
-the installation script. If you have a recent enough OS,
-you can get GSL easily from the repositories; on Debian and derivatives,
-just run ``apt-get install libgsl-dev`` under root. Alternatively,
-you can `get the source 
-<https://www.gnu.org/software/gsl/>`_ get the source and compile it yourself.
-
-You also need a fresh enough version of ``cmake``.
-
-After GSL is installed, you can install qpms to your local python library using::
-
-  cmake .
-  make amos
-  python3 setup.py install --user
-
-If GSL is not installed the standard library path on your system, you might 
-need to pass it to the installation script using the LD_LIBRARY_PATH environment
-variable.
-
-Documentation
-=============
-
-Documentation of QPMS is a work in progress. Most of the newer code
-is documented using doxygen comments. To build the documentation, just run
-``doxygen``
-in the root directory; the documentation will then be found in 
-``docs/html/index.html``.
-
-Of course, the prerequisite of this is having doxygen installed.
-If you don't, you will probably find it easily in your OS's
-repositories. On Debian and derivatives, simply run ``apt-get install doxygen``
-under root.