Update INSTALL.md with FFTW and HYPRE information

INSTALL.md

@@ -1,6 +1,22 @@
 Installing DALES
 ================
 
+These are installation instruuctions for DALES. See also the [installation notes](https://github.com/dalesteam/dales/wiki/Installation-notes) in the DALES wiki for further notes on specific systems.
+
+DEPENDENCIES
+------------
+
+Dependencies of DALES are
+1) MPI 
+2) NetCDF (optional)
+3) CMake
+4) FFTW version 3.x (optional) 
+5) HYPRE (optional) for the iterative Poisson solver.
+6) Doxygen, DOT and LaTeX for building the documentation
+
+Compiling
+---------
+
 Packages are available at <https://github.com/dalesteam/dales>
 If git is installed, the best way to obtain DALES is with:
 
@@ -13,6 +29,7 @@ git pull origin master
 Then follow the following instructions:
 ```
 cd dales 
+# git checkout <branch>  optionally switch to another branch
 mkdir build 
 cd build 
 cmake ..
@@ -21,6 +38,31 @@ make
 ```
 This should provide the dales4 binary in the build/src directory. New builds can be made by `make` in the build directory. The documentation is built by typing `make docs` in the build directory.
 
+Compiling with HYPRE or FFTW
+----------------------------
+
+To compile DALES with support for HYPRE and/or FFTW, add the following flags on the cmake command line.
+For HYPRE:
+```
+cmake .. -DUSE_HYPRE=True -DHYPRE_LIB=path-to-libHYPRE.so
+```
+where -DHYPRE_LIB is needed if the library is not automatically found.
+For FFTW:
+```
+cmake .. -DUSE_FFTW=True -DFFTW_LIB=path-to-libfftw3.so
+```
+where the path again is needed only if the library is not automatically found.
+
+Even when compiled with these libraries, DALES will use the traditional FFT-based Poisson solver unless
+one of the alternatives are specified in the namelist, e.g. to use FFTW:
+
+```
+&SOLVER
+solver_id = 100
+/
+```
+See the [Wiki](https://github.com/dalesteam/dales/wiki/Alternative-Poisson-solvers) for the options for the iterative solver.
+
 Optimization and tuning
 -----------------------
 
@@ -30,28 +72,21 @@ export SYST=gnu-fast
 ```
 which triggers compilation with more aggressive optimization options, in particular `-Ofast` and `-march=native`. Other pre-defined sets of compilation options are included in the file `CMakeLists.txt`.
 
-ALTERNATIVE BUILDS
-==================
+Choosing debug or release builds
+--------------------------------
 
 One can change between release and debug options by invoking commandline options of cmake:
 ```
 cmake -DCMAKE_BUILD_TYPE="DEBUG" ..
 ```
-or `"RELEASE"`, if that is the build-type desired.
+or `"RELEASE"`, if that is the build-type desired.  `"RELEASE"` is the default.
 Various case specific routines can be found in de dales/case/<casename> and are built by invoking
 ```
 cmake -DCASE="<casename>"
 ```
 where `<casename>` could be something like "rico". Regardless of the case built, the standard DALES runs are always possible (and default).
 
 
-DEPENDENCIES
-============
 
-Dependencies of DALES are
-1) MPI (the only obligatory one)
-2) NetCDF (optional)
-3) CMake (alternatively, the old makefile icw makedepf90 still works)
-4) Doxygen, DOT and LaTeX for building the documentation
 
-See also the [installation notes](https://github.com/dalesteam/dales/wiki/Installation-notes) in the DALES wiki for further notes on specific systems.
+

README.md

@@ -15,3 +15,4 @@ DALES is made available under the terms of the GNU GPL version 3, see the file C
 ## References
 Formulation of the Dutch Atmospheric Large-Eddy Simulation (DALES) and overview of its applications, T. Heus et al, [Geosci. Model Dev., 3, 415-444, 2010](https://doi.org/10.5194/gmd-3-415-2010)
 
+Ouwersloot, H.G., Moene, A.F., Attema, J.J. et al. Large-Eddy Simulation Comparison of Neutral Flow Over a Canopy: Sensitivities to Physical and Numerical Conditions, and Similarity to Other Representations. [Boundary-Layer Meteorol 162, 71–89 (2017)](https://doi.org/10.1007/s10546-016-0182-5)