*Moved DateTime code to "LTR-para/common/src".  Modified LFM-para Makefiles to properly link to libcommon.a.
*Initial writeup of documentation on compiling the code.


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Compilation environment variable is now $(MACHINE) rather than $(machine).


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Makfile updates for MIX

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moved MHDInnerBoundaryInterface to libcommon

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Revision 244 fixed build environment so LFM-MIX compiles on Twister.  This revision (245) fixes the build environment so LFM-MIX compiles on bluevista.


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Adding doxyfile for common code.

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1. Small change in MIX/src/ionosphere.C - now parameter flushFrequency
is used in the DX_OUT mode to dump every flushFrequency cycles.

2. Added TinyXML package to the common/src directory. Based on this
small XML parser is the function parse_xjd (see
common/src/parse_xjd.C) which grabs the local component name and the
number of processors from the XJD file.

3. Added jpara_wrapper.C to the MIX/src directory and put the
necessary files in MIX/test.



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Minor code changes to compile with Portland Group Compilers.
Simplified code in second.c Adding Makefiles for compiling with
Portland Group compilers on tor.hao.ucar.edu (a 32-bit linux machine).



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Adding master make target to generate doxygen documentation

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Adding 
 * Unit Testing framework for testing C++ code (CxxTest, [http://cxxtest.sourceforge.net/]).
 * unit tests for the DateTime class
 * bug fixes for the DateTime class (note:  bugs identified because of the unit testing!)


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REFACTORING:
 * Using more sane variable names for compiler information in the Makefiles (i.e. "MPICC" rather than "Ccompiler", "MPICXX" vs "CXX", etc.) 


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Adding "distclean" make target to remove ALL of the files generated by the LTR-para codebase.

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Adding software to check LFM-para data files for correctness:  Compare two datafiles and compute the RMS error, and checks data files for infs and NaNs.

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Common does not need to build the "RMSerror" executable to build MSPHERE, which is good since RMSerror gives build errors on AIX systems.  Removing RMSerror from common makefile.

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BUGFIX:  Fixed problem with iostream include and the std namespace.  Now RMSerror compiles on twister.

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Automating the local mklfmscripts.pl dependency installation.

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BUGFIX:  tar on twister cant handle gzip files with the "-z" flag.  Need to first use gunzip, then tar to extract these packages.

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Fixing lib install for AIX systems.

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Adding documentation for perl dependencies.

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Some 64 bit machines (i.e. the NOAA 64-bit linux machine wJet) install the libraries to "lib64" rather than "lib".  Modified the scripts to take care of this.

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