Overview

Building and Running RMHD2D:

1. Edit one of the machine-dependent Makefiles,
   e.g. Make.reynolds-linux, to set up the various compilers, compiler
   flags, libraries, and Fortran-to-C translation directives.

2. Link this machine-dependent Makefile to Make.machine: e.g.
   ln -s Make.reynolds-linux Make.machine

3. To set the problem size and parallelism topology, do either of the
   following two steps:

   3a. Edit the file include/make_uparms_static.h to set the problem
       size (nx, ny and nz give the total problem dimensions) along
       with the parallelism topology information (xprocs, yprocs and
       zprocs give the number of processors in each cartesian
       dimension). 

   3b. Edit Make.config to ensure that -DDYNAMIC is set.  Then copy 
       the input parameter file ./inputs/mesh.inp to the
       runtime-directory.  Edit this file with the same information as
       in 4a.  
       NOTE: this option allows runs of differing dimension without
       re-compiling the executable.

4. Edit one of the problem configuration makefiles,
   e.g. Make.config-KH, to set up the appropriate dimensionality (2D
   vs 2.5D), boundary conditions, flux discretization choices,
   parallelism, and preconditioning for the type of problem that you
   wish to run.

5. Link this problem-dependent Makefile to Make.config: e.g.
   ln -s Make.config-KH Make.config

6. Type 'make <target>', where <target> specifies the type of executable
   (problem type and time integration algorithm) that you wish to
   build.  Typing 'make' alone will bring up a list of possible
   targets.

7. Copy problem-specific input files to the run-time directory from
   the ./inputs directory.  You will need the files mhd.inp and
   prop.inp for all problems (remove the problem specifier suffix from
   the file name).  For some problems, you will also need the
   problem-specific input parameter files provided in this directory,
   e.g. the Kelvin-Helmholtz problem requires kh_init.inp.  If the
   time-integration algorithm is KINSOL, you will also need
   kincontrol.inp; if it is CVODE, you will need cvcontrol.inp.

8. Edit the input files to your tastes and run your executable.