Index: ThirdParty/mpqc_open/doc/Makefile
===================================================================
--- ThirdParty/mpqc_open/doc/Makefile	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
+++ ThirdParty/mpqc_open/doc/Makefile	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
@@ -0,0 +1,90 @@
+TOPDIR=..
+ifndef SRCDIR
+  SRCDIR=$(shell pwd)
+endif
+
+include $(SRCDIR)/$(TOPDIR)/lib/GlobalMakefile
+
+DOXYGEN=doxygen
+
+# Get rid of end-of-comments.  This is done so all pages can be combined
+# into a single man page.
+MAN_SED_PAGE = (sed s.*/..)
+
+# This makes pages into sections and sections into subsections.  That way
+# all the documentation is stuck into a single man page.  The opening
+# comment is also removed, because all the pages have to be combined into a
+# single comment to suit doxygen.
+MAN_SED_SEC = (sed 's.^*/.\<br\>.' | sed 's+\\subsection+\\subsubsection+'| sed 's+\\section+\\subsection+' | sed 's+/\**.*\\page+\\section+')
+
+# This makes the bullets into an 'o', which looks better in the text man pages.
+NROFF_SED = sed 's/\\(bu/o/'
+
+.PHONY: all
+all:: html
+ifeq ($(DOXYGEN_MAN),YES)
+all:: man1 man3
+endif
+
+.PHONY: man1
+man1: mpqc.man.dox
+	$(DOXYGEN) doxygen.man1.cfg
+	$(NROFF_SED) < man/man1/mpqc.1 > man/man1/mpqc.1.tmp
+	/bin/mv man/man1/mpqc.1.tmp man/man1/mpqc.1
+
+.PHONY: man3
+man3:
+	$(DOXYGEN) doxygen.man3.cfg
+
+.PHONY: mpqc.man.dox
+mpqc.man.dox:
+	/bin/rm -f $@
+	$(MAN_SED_PAGE) < $(SRCDIR)/$(TOPDIR)/src/bin/mpqc/mpqc.dox > $@
+	$(MAN_SED_SEC) < $(SRCDIR)/$(TOPDIR)/src/bin/mpqc/mpqcover.dox >> $@
+	$(MAN_SED_SEC) < $(SRCDIR)/$(TOPDIR)/src/bin/mpqc/mpqcrunning.dox >> $@
+	$(MAN_SED_SEC) < $(SRCDIR)/$(TOPDIR)/src/bin/mpqc/mpqcinp.dox >> $@
+	$(MAN_SED_SEC) < $(SRCDIR)/$(TOPDIR)/src/bin/mpqc/mpqcsimp.dox >> $@
+	$(MAN_SED_SEC) < $(SRCDIR)/$(TOPDIR)/src/bin/mpqc/mpqcoo.dox >> $@
+	$(MAN_SED_SEC) < $(SRCDIR)/$(TOPDIR)/src/bin/mpqc/mpqcval.dox >> $@
+	$(MAN_SED_SEC) < $(SRCDIR)/$(TOPDIR)/src/lib/chemistry/qc/psi/mpqcpsi.dox >> $@
+	$(MAN_SED_SEC) < $(SRCDIR)/$(TOPDIR)/src/lib/chemistry/cca/mpqccomponents.dox >> $@
+	$(MAN_SED_SEC) < $(SRCDIR)/$(TOPDIR)/src/bin/mpqc/mpqclic.dox >> $@
+	$(MAN_SED_SEC) < $(SRCDIR)/$(TOPDIR)/src/bin/mpqc/mpqcwar.dox >> $@
+	echo "*/" >> $@
+
+.PHONY: html
+html:
+	$(DOXYGEN) doxygen.cfg
+
+.PHONY: veryclean
+veryclean:
+	/bin/rm -rf html latex man
+	/bin/rm -rf *~
+
+.PHONY: clean
+clean:
+	/bin/rm -rf *~
+
+install:
+	$(INSTALL) $(INSTALLDIROPT) $(installroot)$(prefix)
+	/bin/cp -r html $(installroot)$(prefix)
+
+install_devel: install_man install_samples
+
+.PHONY: install_man
+install_man:
+	$(INSTALL) $(INSTALLDIROPT) $(installroot)$(prefix)
+	/bin/cp -r man $(installroot)$(prefix)
+
+.PHONY: install_samples
+install_samples:
+	$(INSTALL) $(INSTALLDIROPT) $(installroot)$(prefix)
+	$(INSTALL) $(INSTALLDIROPT) $(installroot)$(prefix)/examples
+	$(INSTALL) $(INSTALLDIROPT) $(installroot)$(prefix)/examples/mp2
+	$(INSTALL) $(INSTALLLIBOPT) $(SRCDIR)/devsamp/mp2.cc \
+		$(installroot)$(prefix)/examples/mp2
+	$(INSTALL) $(INSTALLLIBOPT) $(SRCDIR)/devsamp/mp2.in \
+		$(installroot)$(prefix)/examples/mp2
+	sed "s+/usr/local/mpqc/current+$(prefix)+" < \
+		$(SRCDIR)/devsamp/Makefile \
+		> $(installroot)$(prefix)/examples/mp2/Makefile
Index: ThirdParty/mpqc_open/doc/compile.dox
===================================================================
--- ThirdParty/mpqc_open/doc/compile.dox	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
+++ ThirdParty/mpqc_open/doc/compile.dox	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
@@ -0,0 +1,297 @@
+
+/** \page compile Compiling
+
+<ul>
+  <li> \ref compilepre   
+  <li> \ref compilepreopt
+  <li> \ref compileconf  
+  <ul>
+    <li> \ref compilecca
+  </ul>
+  <li> \ref compilecomp
+  <li> \ref compilecheck
+</ul>
+
+\section compilepre Prerequisites
+
+Make sure that you have the following programs available. Most can be found
+at any GNU software FTP repository.
+
+<ul>
+
+    <li> Compilers for the C, C++, and FORTRAN languages are needed.  The
+         FORTRAN compiler is used to determine the linkage conventions for
+         the BLAS libraries, however, you can turn off the use of a FORTRAN
+         compiler by giving <tt>--without-f77</tt> as an option to the
+         configure script, however, this will not work unless you
+         only want the utility libraries.  The compilers listed below are
+         known to work.  Other ISO C++ compilers should work as well.
+
+       <ul>
+
+           <li> GCC 2.96 and later, available from <a
+                href="http://gcc.gnu.org">http://gcc.gnu.org</a>.  However,
+                the 3.0 and 3.0.1 releases of GCC are not recommended.
+
+           <li> IBM xlC 5.0.2 and later work with both 32 and 64 bit modes
+                Use the versions of the compilers with the "_r" appended to
+                the name, since SC uses multi-threading.  You must also
+                specify that RTTI is used: <tt>--with-cxx='xlC_r
+                -qrtti'</tt>.
+
+           <li> Compaq/Alpha/Linux with Compaq C++ 6.3.6.8 and later work.
+                Special configure options are needed: <tt>--with-cxx='cxx
+                -D__USE_STD_IOSTREAM'</tt>
+
+           <li> The Intel 5.0.1 Linux compilers for IA-32 work.  Version
+                5.0.1 for IA-64 will not work.
+
+           <li> The KAI version 4.0e1 compiler works.  Special configure
+                options are needed: <tt>--with-cxx='KCC
+                --one_instantiation_per_object' --with-ar=KCC
+                --with-ar-flags=-o</tt>
+
+       </ul>
+
+    <li> The Basic Linear Algebra Subprograms (BLAS) are required.  A
+         prepackaged version of BLAS is available for most machines.
+         Consult you operating system documentation for more information.
+         If precompiled BLAS routines are not available for your machine,
+         the source can be obtained from <a
+         href="http://www.netlib.org/blas">http://www.netlib.org/blas</a>.
+         The file blas.tgz contains the source for all of the BLAS
+         routines.  If the BLAS library is not named libblas.a or is not
+         installed in the default library search path, then configure must
+         be given --with-libs, --with-libdirs, or both.
+
+    <li> The Linear Algebra Package (LAPACK) 3.0 is required.  A
+         prepackaged version of LAPACK is available for most machines.
+         Consult you operating system documentation for more information.
+         If a precompiled LAPACK is not available for your machine, the
+         source can be obtained from <a
+         href="http://www.netlib.org/lapack">http://www.netlib.org/lapack</a>.
+         The file lapack.tgz contains the source for all of the LAPACK
+         routines.  If the LAPACK library is not named liblapack.a or is
+         not installed in the default library search path, then configure
+         must be given --with-libs, --with-libdirs, or both.
+
+    <li> If you modify the scanner source file, then a
+         lexical analyzer generator is required to generate code to read
+	 input files.  The flex program is used for this purpose.
+	 However, the most common version of flex, 2.5.4a, does
+	 not generate legal C++.  It may be necessary to download,
+	 compile, and install a more recent version of flex from <a
+	 href="http://lex.sourceforge.net">http://lex.sourceforge.net</a>.
+
+         Make sure that <tt>FlexLexer.h</tt> from flex is in your include
+         path. You may need to give the path to <tt>FlexLexer.h</tt> to
+         configure with an argument that looks something like:
+         <tt>--with-include=-I/usr/local/include</tt>
+
+    <li> If you modify a parser source file, then GNU bison (version 1.24
+         or greater) is needed.  This is a parser generator used to
+         generate code to read input files.
+
+    <li> GNU gmake (version 3.70 or greater): GNU specific extensions to make
+         are used extensively.
+
+    <li> perl: This is used to convert template classes to macros, generate
+         and check the validation suite etc.  To compile SC, either perl 4
+         or perl 5 will work.  To generate the validation inputs and
+         automatically check the outputs, perl 5.003 or later is needed.
+
+  </ul>
+
+\section compilepreopt Optional Packages
+
+The following packages are not necessary to compile MPQC, but may provide additional
+features.
+
+<ul>
+
+    <li> A Message Passing Interface (MPI) is required to use MPQC in
+         parallel on distributed memory machines.
+
+    <li> The parallel MP2 and MP2-R12 methods require direct access to
+         remote memory.  This requires one of two features: A thread-safe
+         MPI (<a href="http://www.mpi-softtech.com">MPI Software
+         Technology, Inc.</a> has developed a thread-safe MPI) or the <a
+         href="http://www.emsl.pnl.gov/docs/parsoft/armci/">Aggregate
+         Remote Memory Copy Interface (ARMCI)</a>.  These respectively
+         permit remote memory access through the ARMCIMemoryGrp and the
+         MTMPIMemoryGrp classes, respectively.
+
+    <li> Libint (version 1.1.0 or higher): This is a machine-generated
+         library that can be used for evaluation of certain molecular
+         integrals. IntegralCints and MBPT2_R12 classes depend on this
+         library. The library is freely available under GNU Public License
+         (GPL) from <a
+         href="http://www.ccmst.gatech.edu/evaleev/libint/">www.ccmst.gatech.edu/evaleev/libint/</a>.
+
+    <li> Cca-chem-generic (version 0.2.0 or higher, and associated CCA tools):
+         This package allows both stand-alone and embedded component applications  
+         to be formed using MPQC-based components.  Visit the
+         <a href="http://cca-forum.org/~cca-chem">CCA Chemistry Component Toolkit Homepage</a>
+         for information on the freely available source code.
+
+</ul>
+
+\section compileconf Configuration
+
+ You can build MPQC in the source code directory or you can make a
+companion directory which will be used to hold all of the files generated
+by the compilation.  You may name this directory anything you want.
+Typically, this directory is named to indicate the architecture
+(e.g. <tt>mpqc.i686-linux</tt>) and will be referred to as the target
+directory below.
+
+ In the target directory execute the <tt>configure</tt> command which is
+located in the SC source directory.  Use the absolute pathname to the
+configure script.  This command should build a hierarchy of target
+directories and the necessary makefiles. Do a <tt>configure --help</tt> to
+see a list of options.  Options are specified with an equals sign, as in
+<tt>configure --prefix=/usr/local</tt>.  Some options, such as all the
+<tt>enable</tt> and <tt>disable</tt> options, do not require an argument.
+Useful options to configure include:
+
+<dl>
+
+<dt><tt>--prefix</tt><dd>Specifies the installation directory.  The default
+  is <tt>/usr/local/mpqc/</tt><i>version-number</i>
+
+<dt><tt>--enable-debug</tt><dd>Options for debugging will be given to the
+  compiler.  Use <tt>--enable-debug=opt</tt> to use both debugging and
+  optimization options.
+
+<dt><tt>--with-default-parallel</tt><dd>Gives the default parallism
+  specializations.  Can be <tt>none</tt> for no default or <tt>mtmpi</tt>
+  for MTMPIMemoryGrp (MPI must be fully thread-safe) and MPIMessageGrp
+  specializations.  The parallelism model can be overridden with command
+  line arguments or environmental variables.
+
+<dt><tt>--enable-always-use-mpi</tt>This can be given if MPIMessageGrp
+  is to be the only MessageGrp that will be used.  This option should
+  be given if the real argc and argv must be given to MPI_Init.
+
+<dt><tt>--disable-parallel</tt><dd>Do not try to find communications
+  libraries.
+
+<dt><tt>--disable-threads</tt><dd>Do not try to find the multi-thread
+  libraries.
+
+<dt><tt>--enable-shared</tt><dd>Use shared libraries.  This will
+  reduce the size of executables, if shared libraries are supported
+  on your system.
+
+<dt><tt>--disable-static</tt><dd>Do not build libraries for static linking.
+
+<dt><tt>--enable-ref-debug</tt><dd>Check for overwrites and overflows of
+  reference counts.  Implied by ``--enable-debug''.
+
+<dt><tt>--disable-ref-macros</tt><dd>Use template classes for reference
+  counting.  The default is to use a CPP macro to generate a class
+  definition.
+
+<dt><tt>--enable-cross-compile</tt><dd>If this option is set then the
+  configure script will take care to not execute any compiled test
+  programs.
+
+<dt><tt>--enable-shared-libs</tt><dd>This will generate shared objects and
+  link with them instead of standard ``.a'' libraries.  This works on a
+  Linux-ELF system.
+
+<dt><tt>--enable-components</tt><dd>This will generate CCA components and
+  enable embedded CCA frameworks within MPQC.
+
+<dt><tt>--with-build-id</tt><dd>This is used to generate unique shared
+  library names and a unique default prefix for an MPQC installation.
+  Unique shared library names must be used used by package distributors if
+  a non-official ABI is used.  The official ABI is GCC-3.2.  Earlier
+  versions of GCC are not compatible.  Installations with multiple C++
+  compilers that use shared libraries should use --with-build-id to avoid
+  accidentally dynamically linking with the wrong libraries.
+
+<dt><tt>--with-default-memory</tt><dd>This specifies the default
+memory allocation, which is used in absense of the memory> keyword in user's input.
+The default is 32 million bytes (roughly, 32 MB).
+
+<dt><tt>--with-cc</tt><dd>Gives the name of the C compiler.
+
+<dt><tt>--with-cc-optflags</tt><dd>By default configure will attempt to
+  guess a reasonable set of optimization flags.  These flags will be
+  overridden by the argument given to this keyword.
+
+<dt><tt>--with-cxx</tt><dd>Gives the name of the C++ compiler.
+
+<dt><tt>--with-cxx-optflags</tt><dd>By default configure will attempt to
+  guess a reasonable set of optimization flags.  These flags will be
+  overridden by the argument given to this keyword.
+
+<dt><tt>--with-f77</tt><dd>Gives the name of the FORTRAN compiler.
+
+<dt><tt>--without-f77</tt><dd>configure will not try to find a FORTRAN
+  compiler.  This can only be used if nothing more than the utility
+  libraries are needed.
+
+<dt><tt>--with-ranlib</tt><dd>Gives the name of the archive indexing
+  utility.
+
+<dt><tt>--with-ar</tt><dd>Gives the name of the program that makes
+  libraries.
+
+<dt><tt>--with-ld</tt><dd>Gives the name of the object linker.
+
+<dt><tt>--with-include</tt><dd>Gives directories in which include files
+  should be sought.  For example, <tt>--with-include="-I/u/local/inc
+  -I/u/cljanss/include"</tt>
+
+<dt><tt>--with-libs</tt><dd>Specifies libraries that executables should be
+  linked with.  For example, <tt>--with-libs=-llapack_IRIX.a</tt>.
+
+<dt><tt>--with-libdirs</tt><dd>Gives the directories in which libraries
+  should be sought.  For example,
+  <tt>--with-libdirs=-L/usr/local/lib64</tt>.
+
+<dt><tt>--with-cca-chem-config</tt><dd>Specifies the config script for the
+  cca-chem-generic package (prerequisite for CCA components).
+
+</dl>
+
+  If you would like to further customize your target directory,
+you can edit <tt>src/lib/scconfig.h</tt> and <tt>lib/LocalMakefile</tt> to
+suit your needs.  The next time you run configure, these files and
+all the makefiles will be overwritten.
+
+\subsection compilecca Notes on CCA Configuration
+
+<ul>
+  <li> Use the <tt>--enable-components</tt> flag to generate CCA components and enable 
+       embedded frameworks within MPQC.  
+  <li> The <tt>cca-chem-config</tt> script must be found in the user's path or 
+       specified using the <tt>--with-cca-chem-config</tt>.
+  <li> To fully support runtime configuration of component applications, 
+       compile using <tt>--enable-shared</tt>.
+  <li> Run <tt>make install_devel</tt> after compiling to install the <tt>sc-config</tt>
+       script (required by <tt>cca-chem-apps</tt>).
+</ul>
+
+\section compilecomp Compilation
+
+ Now you are ready to build the libraries and executables.  Do this by
+typing <tt>make</tt> in your target directory.  If you are running on a
+symmetric multi-processor, you can use GNU make to parallelize the
+compilation.  To compile four files at a time, type <tt>make -j4</tt>.
+This feature works correctly with GNU make version 3.78.1 or later; for
+older versions of GNU make use <tt>make JOBS=-j4</tt>.
+
+ You can install the executables and data files with <tt>make install</tt>.
+
+ You can install the libraries and header files with <tt>make
+install_devel</tt>, however, <tt>make install</tt> must be also be run to
+install the files needed for run-time support.
+
+\section compilecheck Checking the Compilation
+
+See \ref mpqcval for instructions for checking your compilation.
+
+*/
Index: ThirdParty/mpqc_open/doc/develop.dox
===================================================================
--- ThirdParty/mpqc_open/doc/develop.dox	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
+++ ThirdParty/mpqc_open/doc/develop.dox	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
@@ -0,0 +1,398 @@
+
+/** \page develop Developing Code Using SC
+
+In addition to the executables, the Scientific Computing toolkit libraries
+and include files can be installed on your machine.  This is described in
+the \ref compile section of this manual.
+
+The <tt>sc-config</tt> program can be use to obtain the compilers, compiler
+options, and libraries needed to use the SC toolkit from your program.
+This utility is discussed below, along with how the SC toolkit must be
+initialized in your <tt>main</tt> subroutine.
+
+<ul>
+  <li> \ref scconfig
+  <li> \ref scinit
+  <li> \ref devsamp
+  <li> \ref scexcept
+  <li> \ref devcheck
+</ul>
+
+\section scconfig The sc-config Program
+
+The sc-config program returns information about how SC was compiled
+and installed.  See \ref sc-config for more information.                        
+
+\section scinit Initializing SC
+
+First the execution environment must be initialized using
+the ExEnv init member.
+
+<pre>
+  ExEnv::init(argc, argv);
+</pre>
+
+By default, all output will go to the console stream, cout.  To change
+this, use the following code:
+
+<pre>
+  ostream *outstream = new ofstream(outputfilename);
+  ExEnv::set_out(outstream);
+</pre>
+
+MPI is allowed wait until MPI_Init is called to fill in argc and argv, so
+you may have to call MPI_Init before you even know that we ready to
+construct MPIMessageGrp.  So if an MPIMessageGrp is needed, it is up to the
+developer to call MPI_Init to get the argument list for certain MPI
+implementations.
+
+<pre>
+  MPI_Init(&argc, &argv);
+</pre>
+
+When files are read and written, an extension is added to a
+basename to construct the file name.  The default is "SC".
+To use another basename, make the following call, where
+<tt>basename</tt> is a <tt>const char *</tt>:
+
+<pre>
+  SCFormIO::set_default_basename(basename);
+</pre>
+
+If your job might run in parallel, then make the following
+call or the nodes will print redundant information.  The
+<tt>myproc</tt> argument is the rank of the called node.
+
+<pre>
+  SCFormIO::init_mp(myproc);
+</pre>
+
+This segment of code sets up an object to provide multi-threading:
+
+<pre>
+  RefThreadGrp thread = ThreadGrp::initial_threadgrp(argc, argv);
+  ThreadGrp::set_default_threadgrp(thread);
+  if (thread.nonnull())
+    ThreadGrp::set_default_threadgrp(thread);
+  else
+    thread = ThreadGrp::get_default_threadgrp();
+</pre>
+
+This segment of code sets up the message passing object:
+
+<pre>
+  RefMessageGrp grp = MessageGrp::initial_messagegrp(argc, argv);
+  if (grp.nonnull())
+    MessageGrp::set_default_messagegrp(grp);
+  else
+    grp = MessageGrp::get_default_messagegrp();
+</pre>
+
+\section devsamp MP2 Implementation Example
+
+This section illustrates how to add a new method a new method to MPQC.
+
+\subsection devsampsrc MP2 Implementation Example: Source
+
+This example code illustrates a complete MP2 energy
+implementation using the SC Toolkit.  First an MP2 class is
+declared and the necesary base class member functions are
+provided.  Next a ClassDesc is defined.  Finally, the member
+functions are defined.
+
+Note that no main routine is provided.  This is because this file
+is designed to be used to extend the functionality of the mpqc
+executable.  To generate a new mpqc executable with the new class
+available for use, see the \ref devsampmak section.
+
+\include mp2.cc
+
+\subsection devsampmak MP2 Implementation Example: Makefile
+
+This example Makefile demonstrates how to link in a new class to
+form a new mpqc executable, here named mp2.  The code is given in
+the \ref devsampsrc section.  The \ref scconfig "sc-config command"
+is used to obtain information about how the SC toolkit
+was compiled and installed.  The library specified with -lmpqc
+provides the main routine from mpqc.
+
+\include Makefile
+
+\subsection devsampinp MP2 Implementation Example: Input
+
+This input file can be used with the program illustrated in
+the \ref devsampsrc section.  It will compute the MP2 energy
+using the new MP2 class.  Note that only the
+\ref mpqcoo "object-oriented input format" can be used with
+user provided classes.
+
+\include mp2.in
+
+\section scexcept Exception Handling in SC
+
+The development of SC began before exception handling was available in C++.
+A retrofit of the code to use exceptions is in progress.  It is difficult
+to retrofit a code, especially a parallel code, to do exception handling.
+There will be some limitations: exception handling will not work well for
+parallel jobs, objects whose members throw might be left in a questionable
+state, etc.  However, it is intended that SC objects will be usable in an
+interactive environment.  It is also planned that exceptions be used
+internally to facilitate recover from certain problems.
+
+All new code should use exceptions instead of exit or abort and allocate
+resources in such a way that, if an exception occurs, all resources such as
+memory or locks are released.  A hierarchy of exception classes has been
+created that maps better to scientific computing than the standard
+exceptions.  More information is below, as well as in the documentation for
+the SCException class and its derivatives.
+
+<ul>
+  <li> \ref scexceptmem
+  <li> \ref scexceptlocks
+  <li> \ref scexcepttimer
+  <li> \ref scexceptexample
+  <li> \ref scexceptdebug
+</ul>
+
+\subsection scexceptmem Exceptions and Memory Allocation
+
+Consider the following code fragment:
+
+<pre>
+Object *obj = new Object;
+double *array = new double[n];
+
+f(obj, array, mol);
+
+delete obj;
+delete[] array;
+</pre>
+
+If an exception is thrown in the function f(), then storage for array and
+obj will not be released.  The standard C++ library provides a class,
+auto_ptr, to deal with obj, and the SC toolkit provides a class, auto_vec,
+to deal with array.
+
+The include files for these two classes are:
+
+<pre>
+#include \<memory\>
+#include \<util/misc/autovec.h\>
+</pre>
+
+the code would be modified as follows:
+
+<pre>
+std::auto_ptr<Object> obj(new Object);
+sc::auto_vec<double> array(new double[n]);
+
+f(obj.get(), array.get());
+
+obj.release();  // or just let the destructor release it
+array.release();  // or just let the destructor release it
+</pre>
+
+Note that when sc::Ref is used to store pointers, the storage will
+automatically be released when necessary.  No special treatment is needed
+to deal with exceptions.
+
+\subsection scexceptlocks Exceptions and Locks
+
+Consider the following code fragment:
+
+<pre>
+g(const sc::Ref<sc::ThreadLock> &lock)
+{
+  lock->lock();
+  f();
+  lock->unlock();
+}
+</pre>
+
+If f() throws, then the lock is never released.  The ThreadLock
+lock() and unlock() members should not be used anymore.  Now
+do the following:
+
+<pre>
+g(const sc::Ref<sc::ThreadLock> &lock)
+{
+  sc::ThreadLockHolder lockholder(lock);
+  f();
+  lockholder->unlock(); // or let the destructor unlock it
+}
+</pre>
+
+\subsection scexcepttimer Exceptions and Region Timers
+
+Consider the following code fragment:
+
+<pre>
+g(const sc::Ref<sc::RegionTimer> &regtim)
+{
+  regtim->enter("f()");
+  f();
+  regtim->exit();
+}
+</pre>
+
+If f() throws, then the "f()" timing region is never exited.
+Instead use the following:
+
+<pre>
+g(const sc::Ref<sc::RegionTimer> &regtim)
+{
+  sc::Timer timer(regtim, "f()");
+  f();
+  timer.reset(); // or let the destructor exit the region
+}
+</pre>
+
+\subsection scexceptexample Using the SC Exception Classes
+
+The SC exceptions provide information that can be used into two
+ways. First, text information is provided so that if the exception is not
+caught at a lower level, then the mpqc executable will catch it and write
+information about the problem to the terminal or an output file.  Second,
+information about the nature of the problem is provided, to permit
+developers to catch the exception and deal with it in some way.  The
+documentation for sc::SCException and all of its derivatives gives more
+information about the exceptions that are available.  As an example,
+consider the following loop, where a maximum number of iterations is
+permitted:
+
+<pre>
+XYZ::update()
+{
+  for (int i=0; i<maxiter; i++) {
+    // ... compute xyz update ...
+    if (residual < threshold) return;
+  }
+  throw MaxIterExceeded("too many iterations xyz computation",
+                        __FILE__, __LINE__, maxiter, class_desc());
+}
+</pre>
+
+The first argument to the exception class is a brief description of the
+error.  Additional information can be provided,
+see SCException::elaborate() description below.
+The next two arguments are
+the filename and line number.  The C preprocessor provides these for you
+with the __FILE__ and __LINE__ macros.  The next argument is specific to
+the MaxIterExceeded exception; it is the maximum number of iterations.
+Finally, a ClassDesc* can be given, which will be used to print out the
+class name of the object that failed.  All of these arguments are optional;
+however, the first three should always be given.
+
+It is possible to provide additional information using the
+SCException::elaborate() member.  This will return a ostream, and the
+additional information can be written to this stream.  However, if for some
+reason it is not possible to write to this stream (say, there wasn't enough
+memory to allocate it), then an exception will be thrown.  For this reason,
+the string description given as the first argument should be informative
+since the additional information might not be available, and attempts to
+use elaborate() should be in a try block.  So, for example, the elaborate()
+member could be used in the above example as follows:
+
+<pre>
+XYZ::update()
+{
+  for (int i=0; i<maxiter; i++) {
+    // ... compute xyz update ...
+    if (residual < threshold) return;
+  }
+  MaxIterExceeded ex("too many iterations in xyz computation",
+                     __FILE__, __LINE__, maxiter, class_desc());
+  try {
+    ex.elaborate() << "this can happen when the stepsize is too small"
+                   << std::endl
+                   << "the stepsize is " << stepsize
+                   << std::endl;
+  }
+  catch (...) {}
+  throw ex;
+}
+</pre>
+
+Note that writing to stream returned by elaborate() won't necessarily cause
+anything to get written to the terminal or an output file.  The information
+will be available when the what() member is called, if writing to the
+stream succeeds.  If the exception is caught by the mpqc main routine, then
+it will be printed for the user to see.  If the program catches the
+exception and determines that it is possible to proceed in a different way,
+then the user will never see the text.
+
+\subsection scexceptdebug Debugging Code with Exceptions
+
+Usually, exceptions are not the desired behaviour in a program, and it is
+necessary to debug a program that throws an exception.  This was easy when
+abort was called, because abort would raise a signal that was caught by the
+debugger and the code is stopped at the appropriate place.  With exceptions
+the matter is more complex, because the stack is unwound when an exception
+is thrown and most debugging information is lost.  To work around this
+problem, a breakpoint can be set in code that will be reached only in an
+exception, and will be run before the stack unwind begins.  A useful place
+to do this when GCC is used as the compiler is in the routine
+__cxa_allocate_exception().  So, in gdb, the following could be done:
+
+<pre>
+$ gdb ./scextest
+(gdb) b main
+(gdb) run
+Breakpoint 1, main () at /home/cljanss/src/SC/src/lib/util/misc/scextest.cc:172
+172           f();
+(gdb) b __cxa_allocate_exception
+(gdb) cont
+Breakpoint 2, 0x40582d46 in __cxa_allocate_exception ()
+   from /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.5/libstdc++.so.5
+(gdb) where
+#0  0x40582d46 in __cxa_allocate_exception ()
+   from /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.5/libstdc++.so.5
+#1  0x0804b3f7 in f () at /home/cljanss/src/SC/src/lib/util/misc/scextest.cc:60
+#2  0x0804b9e9 in main ()
+    at /home/cljanss/src/SC/src/lib/util/misc/scextest.cc:172
+</pre>
+
+Giving gdb "b main" followed by "run" was required before gdb could find the
+__cxa_allocate_exception symbol.
+
+\section devcheck Adding Test Cases to the Verification Suite
+
+There are two ways to test an MPQC build.  The <tt>testbuild</tt> and
+<tt>testrun</tt> make targets can be used to run test programs in
+various library directories, and the <tt>check</tt> and related make
+targets can be used to run MPQC on sets of input files.  See
+\ref mpqcval for more information about how to run the tests.
+
+Test programs can be added to the library directories by providing a source
+file with a main routine.  The set of test programs that is to be built and
+run by <tt>testbuild</tt> and <tt>testrun</tt>, respectively, is given by
+the <tt>TESTPROGS</tt> variable in the library's <tt>Makefile</tt>.  It may
+be necessary for an explicit rule to be given for building the test program
+to ensure that necessary libraries are linked in.  If a file named after
+the test program with a <tt>.out</tt> suffix is found in the source
+directory, then <tt>testrun</tt> fail if the command's output differs from
+that file.  Care must be taken to ensure that the output is architecture
+independent in this case.  Otherwise, <tt>testrun</tt> will fail only if
+running the command results in a nonzero return code.
+
+Additional MPQC test inputs can be added in the
+<tt>src/bin/mpqc/validate</tt> directory.  These inputs can be provided in
+one of two ways.  An input which is used to automatically generate multiple
+test cases can be written (with a <tt>.qci</tt> suffix), or a subdirectory
+with each input can be made.  See <tt>Makefile</tt>, <tt>basis1.qci</tt>,
+and <tt>input</tt> in the <tt>src/bin/mpqc/validate</tt> directory for
+examples.
+
+After you have added new inputs and modified the Makefile, change into the
+<tt>src/bin/mpqc/validate</tt> subdirectory of your object directory (where
+you compiled MPQC) and type <tt>make inputs</tt>.  This will create a
+<tt>input</tt> subdirectory containing MPQC input files with a
+<tt>.in</tt> suffix.  Files ending with a <tt>.qci</tt> suffix will also be
+placed in the <tt>input</tt> directory.  These contain a description of the
+calculation that is used by the utility program that checks the results of
+the validation suite.  Both the <tt>.in</tt> and <tt>.qci</tt> files for the
+new test cases must be copied into the <tt>ref</tt> directory in the source
+tree.  Note that inputs that are not useful in your build environment are
+not created by <tt>make inputs</tt>.
+
+*/
Index: ThirdParty/mpqc_open/doc/devsamp/Makefile
===================================================================
--- ThirdParty/mpqc_open/doc/devsamp/Makefile	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
+++ ThirdParty/mpqc_open/doc/devsamp/Makefile	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
@@ -0,0 +1,12 @@
+# Change this to the path to your installed sc-config script.
+SCCONFIG = /usr/local/mpqc/current/bin/sc-config
+CXX := $(shell $(SCCONFIG) --cxx)
+CXXFLAGS := $(shell $(SCCONFIG) --cxxflags)
+CPPFLAGS := $(shell $(SCCONFIG) --cppflags)
+LIBS := $(shell $(SCCONFIG) --libs)
+LIBDIR  := $(shell $(SCCONFIG) --libdir)
+LTLINK := $(shell $(SCCONFIG) --ltlink)
+LTLINKBINOPTS := $(shell $(SCCONFIG) --ltlinkbinopts)
+
+mp2: mp2.o
+	$(LTLINK) $(CXX) $(CXXFLAGS) -o $@ $^ -L$(LIBDIR) -lmpqc $(LIBS) $(LTLINKBINOPTS)
Index: ThirdParty/mpqc_open/doc/devsamp/mp2.cc
===================================================================
--- ThirdParty/mpqc_open/doc/devsamp/mp2.cc	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
+++ ThirdParty/mpqc_open/doc/devsamp/mp2.cc	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
@@ -0,0 +1,231 @@
+
+#include <stddef.h>
+#include <util/misc/autovec.h>
+#include <util/misc/scexception.h>
+#include <chemistry/qc/wfn/obwfn.h>
+#include <chemistry/qc/scf/clhf.h>
+
+using namespace std;
+using namespace sc;
+
+class MP2: public Wavefunction {
+    Ref<OneBodyWavefunction> ref_mp2_wfn_;
+    double compute_mp2_energy();
+
+  public: 
+    MP2(const Ref<KeyVal> &);
+    MP2(StateIn &);
+    void save_data_state(StateOut &);
+    void compute(void);
+    void obsolete(void);
+    int nelectron(void);
+    RefSymmSCMatrix density(void);
+    int spin_polarized(void);
+    int value_implemented(void) const;
+};
+
+static ClassDesc MP2_cd(typeid(MP2), "MP2", 1, "public Wavefunction",
+                        0, create<MP2>, create<MP2>);
+
+MP2::MP2(const Ref<KeyVal> &keyval):Wavefunction(keyval) {
+  ref_mp2_wfn_ << keyval->describedclassvalue("reference");
+  if(ref_mp2_wfn_.null()) {
+      throw InputError("require a OneBodyWavefunction object",
+                       __FILE__, __LINE__, "reference", 0,
+                       class_desc());
+  }
+}
+
+MP2::MP2(StateIn &statein):Wavefunction(statein)
+{
+  ref_mp2_wfn_ << SavableState::restore_state(statein);
+}
+
+void
+MP2::save_data_state(StateOut &stateout) {
+  Wavefunction::save_data_state(stateout);
+
+  SavableState::save_state(ref_mp2_wfn_.pointer(),stateout);
+}
+
+void
+MP2::compute(void)
+{
+  if(gradient_needed()) {
+      throw FeatureNotImplemented("no gradients yet",
+                                  __FILE__, __LINE__, class_desc());
+  }
+
+  double extra_hf_acc = 10.;
+  ref_mp2_wfn_->set_desired_value_accuracy(desired_value_accuracy()
+                                           / extra_hf_acc);
+  double refenergy = ref_mp2_wfn_->energy();
+  double mp2energy = compute_mp2_energy();
+
+  ExEnv::out0() << indent << "MP2 Energy = " << mp2energy << endl;
+
+  set_value(refenergy + mp2energy);
+  set_actual_value_accuracy(ref_mp2_wfn_->actual_value_accuracy()
+                            * extra_hf_acc);
+}
+
+void
+MP2::obsolete(void) {
+  Wavefunction::obsolete();
+  ref_mp2_wfn_->obsolete();
+}
+
+int
+MP2::nelectron(void) {
+  return ref_mp2_wfn_->nelectron();
+}
+
+RefSymmSCMatrix
+MP2::density(void) {
+  throw FeatureNotImplemented("no density yet",
+                              __FILE__, __LINE__, class_desc());
+  return 0;
+}
+
+int
+MP2::spin_polarized(void) {
+  return 0;
+}
+
+int
+MP2::value_implemented(void) const {
+  return 1;
+}
+
+double
+MP2::compute_mp2_energy()
+{
+  if(molecule()->point_group()->char_table().order() != 1) {
+      throw FeatureNotImplemented("C1 symmetry only",
+                                  __FILE__, __LINE__, class_desc());
+  }
+
+  RefSCMatrix vec = ref_mp2_wfn_->eigenvectors();
+
+  int nao = vec.nrow();
+  int nmo = vec.ncol();
+  int nocc = ref_mp2_wfn_->nelectron()/2;
+  int nvir = nmo - nocc;
+
+  auto_vec<double> cvec_av(new double [vec.nrow() * vec.ncol()]);
+  double *cvec = cvec_av.get();
+  vec->convert(cvec);
+
+  auto_vec<double> pqrs_av(new double [nao * nao * nao * nao]);
+  double *pqrs = pqrs_av.get();
+  for(int n = 0; n < nao*nao*nao*nao; n++) pqrs[n] = 0.0;
+
+  Ref<TwoBodyInt> twoint = integral()->electron_repulsion();
+  const double *buffer = twoint->buffer();
+
+  Ref<GaussianBasisSet> basis = this->basis();
+
+  int nshell = basis->nshell();
+  for(int P = 0; P < nshell; P++) {
+    int nump = basis->shell(P).nfunction();
+
+    for(int Q = 0; Q < nshell; Q++) {
+      int numq = basis->shell(Q).nfunction();
+
+      for(int R = 0; R < nshell; R++) {
+	int numr = basis->shell(R).nfunction();
+
+	for(int S = 0; S < nshell; S++) {
+	  int nums = basis->shell(S).nfunction();
+
+	  twoint->compute_shell(P,Q,R,S);
+
+	  int index = 0;
+	  for(int p=0; p < nump; p++) {
+	    int op = basis->shell_to_function(P)+p;
+
+	    for(int q = 0; q < numq; q++) {
+	      int oq = basis->shell_to_function(Q)+q;
+
+	      for(int r = 0; r < numr; r++) {
+		int oor = basis->shell_to_function(R)+r;
+
+		for(int s = 0; s < nums; s++,index++) {
+		  int os = basis->shell_to_function(S)+s;
+
+		  int ipqrs = (((op*nao+oq)*nao+oor)*nao+os);
+
+		  pqrs[ipqrs] = buffer[index];
+
+		}
+	      }
+	    }
+	  }
+
+	}
+      }
+    }
+  }
+
+  twoint = 0;
+
+  auto_vec<double> ijkl_av(new double [nmo * nmo * nmo * nmo]);
+  double *ijkl = ijkl_av.get();
+
+  int idx = 0;
+  for(int i = 0; i < nmo; i++) {
+    for(int j = 0; j < nmo; j++) {
+      for(int k = 0; k < nmo; k++) {
+	for(int l = 0; l < nmo; l++, idx++) {
+
+	  ijkl[idx] = 0.0;
+
+	  int index = 0;
+	  for(int p = 0; p < nao; p++) {
+	    for(int q = 0; q < nao; q++) {
+	      for(int r = 0; r < nao; r++) {
+		for(int s = 0; s < nao; s++,index++) {
+
+		  ijkl[idx] += cvec[p*nmo + i] * cvec[q*nmo +j]
+		    * cvec[r*nmo + k] * cvec[s*nmo + l]
+		    * pqrs[index];
+
+		}
+	      }
+	    }
+	  }
+
+	}
+      }
+    }
+  }
+
+  pqrs_av.release(); pqrs = 0;
+  cvec_av.release(); cvec = 0;
+
+  auto_vec<double> evals_av(new double [nmo]);
+  double *evals = evals_av.get();
+  ref_mp2_wfn_->eigenvalues()->convert(evals);
+
+  double energy = 0.0;
+  for(int i=0; i < nocc; i++) {
+    for(int j=0; j < nocc; j++) {
+      for(int a=nocc; a < nmo; a++) {
+	for(int b=nocc; b < nmo; b++) {
+
+	  int iajb = (((i*nmo+a)*nmo+j)*nmo+b);
+	  int ibja = (((i*nmo+b)*nmo+j)*nmo+a);
+
+	  energy += (2 * ijkl[iajb] - ijkl[ibja]) * ijkl[iajb]/
+	    (evals[i] + evals[j] - evals[a] - evals[b]);
+
+	}
+      }
+    }
+  }
+
+  ijkl_av.release(); ijkl = 0;
+  evals_av.release(); evals = 0;
+
+  return energy;
+}
Index: ThirdParty/mpqc_open/doc/devsamp/mp2.in
===================================================================
--- ThirdParty/mpqc_open/doc/devsamp/mp2.in	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
+++ ThirdParty/mpqc_open/doc/devsamp/mp2.in	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
@@ -0,0 +1,30 @@
+% emacs should use -*- KeyVal -*- mode
+molecule<Molecule>: (
+  symmetry = C1
+  unit = angstrom
+  { atoms geometry } = {
+    O     [     0.00000000     0.00000000     0.37000000 ]
+    H     [     0.78000000     0.00000000    -0.18000000 ]
+    H     [    -0.78000000     0.00000000    -0.18000000 ]
+  }
+)
+basis<GaussianBasisSet>: (
+  name = "STO-3G"
+  molecule = $:molecule
+)
+mpqc: (
+  checkpoint = no
+  savestate = no
+  % MP2 is the new class.  Change MP2 to MBPT2 to test
+  % against the standard MP2 code
+  mole<MP2>: (
+    molecule = $:molecule
+    basis = $:basis
+    reference<CLHF>: (
+      molecule = $:molecule
+      basis = $:basis
+      memory = 16000000
+    )
+  )
+)
+
Index: ThirdParty/mpqc_open/doc/download.dox
===================================================================
--- ThirdParty/mpqc_open/doc/download.dox	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
+++ ThirdParty/mpqc_open/doc/download.dox	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
@@ -0,0 +1,11 @@
+/** \page download Download
+
+   The Scientific Computing toolkit (SC) and the Massively Parallel Quantum
+   Chemistry program (MPQC) are distributed together.  The library code is
+   distributed under the Library GNU Public License and the accompanying
+   programs are distributed under the GNU Public License.
+
+   The latest version of the source code is available from
+   <a href="http://www.mpqc.org">http://www.mpqc.org</a>.
+
+*/
Index: ThirdParty/mpqc_open/doc/doxygen.cfg.in
===================================================================
--- ThirdParty/mpqc_open/doc/doxygen.cfg.in	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
+++ ThirdParty/mpqc_open/doc/doxygen.cfg.in	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
@@ -0,0 +1,1104 @@
+# Doxyfile 1.3.5
+
+# This file describes the settings to be used by the documentation system
+# doxygen (www.doxygen.org) for a project
+#
+# All text after a hash (#) is considered a comment and will be ignored
+# The format is:
+#       TAG = value [value, ...]
+# For lists items can also be appended using:
+#       TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (" ")
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded 
+# by quotes) that should identify the project.
+
+PROJECT_NAME           = MPQC
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number. 
+# This could be handy for archiving the generated documentation or 
+# if some version control system is used.
+
+PROJECT_NUMBER         = @SC_VERSION@
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) 
+# base path where the generated documentation will be put. 
+# If a relative path is entered, it will be relative to the location 
+# where doxygen was started. If left blank the current directory will be used.
+
+OUTPUT_DIRECTORY       = ./
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all 
+# documentation generated by doxygen is written. Doxygen will use this 
+# information to generate all constant output in the proper language. 
+# The default language is English, other supported languages are: 
+# Brazilian, Catalan, Chinese, Chinese-Traditional, Croatian, Czech, Danish, Dutch, 
+# Finnish, French, German, Greek, Hungarian, Italian, Japanese, Japanese-en 
+# (Japanese with English messages), Korean, Norwegian, Polish, Portuguese, 
+# Romanian, Russian, Serbian, Slovak, Slovene, Spanish, Swedish, and Ukrainian.
+
+OUTPUT_LANGUAGE        = English
+
+# This tag can be used to specify the encoding used in the generated output. 
+# The encoding is not always determined by the language that is chosen, 
+# but also whether or not the output is meant for Windows or non-Windows users. 
+# In case there is a difference, setting the USE_WINDOWS_ENCODING tag to YES 
+# forces the Windows encoding (this is the default for the Windows binary), 
+# whereas setting the tag to NO uses a Unix-style encoding (the default for 
+# all platforms other than Windows).
+
+USE_WINDOWS_ENCODING   = NO
+
+# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will 
+# include brief member descriptions after the members that are listed in 
+# the file and class documentation (similar to JavaDoc). 
+# Set to NO to disable this.
+
+BRIEF_MEMBER_DESC      = YES
+
+# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend 
+# the brief description of a member or function before the detailed description. 
+# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the 
+# brief descriptions will be completely suppressed.
+
+REPEAT_BRIEF           = YES
+
+# This tag implements a quasi-intelligent brief description abbreviator 
+# that is used to form the text in various listings. Each string 
+# in this list, if found as the leading text of the brief description, will be 
+# stripped from the text and the result after processing the whole list, is used 
+# as the annotated text. Otherwise, the brief description is used as-is. If left 
+# blank, the following values are used ("$name" is automatically replaced with the 
+# name of the entity): "The $name class" "The $name widget" "The $name file" 
+# "is" "provides" "specifies" "contains" "represents" "a" "an" "the"
+
+ABBREVIATE_BRIEF       = 
+
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then 
+# Doxygen will generate a detailed section even if there is only a brief 
+# description.
+
+ALWAYS_DETAILED_SEC    = NO
+
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all inherited 
+# members of a class in the documentation of that class as if those members were 
+# ordinary class members. Constructors, destructors and assignment operators of 
+# the base classes will not be shown.
+
+INLINE_INHERITED_MEMB  = NO
+
+# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full 
+# path before files name in the file list and in the header files. If set 
+# to NO the shortest path that makes the file name unique will be used.
+
+FULL_PATH_NAMES        = NO
+
+# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag 
+# can be used to strip a user-defined part of the path. Stripping is 
+# only done if one of the specified strings matches the left-hand part of 
+# the path. It is allowed to use relative paths in the argument list.
+
+STRIP_FROM_PATH        = @top_srcdir@
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter 
+# (but less readable) file names. This can be useful is your file systems 
+# doesn't support long names like on DOS, Mac, or CD-ROM.
+
+SHORT_NAMES            = NO
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen 
+# will interpret the first line (until the first dot) of a JavaDoc-style 
+# comment as the brief description. If set to NO, the JavaDoc 
+# comments will behave just like the Qt-style comments (thus requiring an 
+# explicit @brief command for a brief description.
+
+JAVADOC_AUTOBRIEF      = YES
+
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen 
+# treat a multi-line C++ special comment block (i.e. a block of //! or /// 
+# comments) as a brief description. This used to be the default behaviour. 
+# The new default is to treat a multi-line C++ comment block as a detailed 
+# description. Set this tag to YES if you prefer the old behaviour instead.
+
+MULTILINE_CPP_IS_BRIEF = NO
+
+# If the DETAILS_AT_TOP tag is set to YES then Doxygen 
+# will output the detailed description near the top, like JavaDoc.
+# If set to NO, the detailed description appears after the member 
+# documentation.
+
+DETAILS_AT_TOP         = NO
+
+# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented 
+# member inherits the documentation from any documented member that it 
+# re-implements.
+
+INHERIT_DOCS           = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC 
+# tag is set to YES, then doxygen will reuse the documentation of the first 
+# member in the group (if any) for the other members of the group. By default 
+# all members of a group must be documented explicitly.
+
+DISTRIBUTE_GROUP_DOC   = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab. 
+# Doxygen uses this value to replace tabs by spaces in code fragments.
+
+TAB_SIZE               = 8
+
+# This tag can be used to specify a number of aliases that acts 
+# as commands in the documentation. An alias has the form "name=value". 
+# For example adding "sideeffect=\par Side Effects:\n" will allow you to 
+# put the command \sideeffect (or @sideeffect) in the documentation, which 
+# will result in a user-defined paragraph with heading "Side Effects:". 
+# You can put \n's in the value part of an alias to insert newlines.
+
+ALIASES                = 
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources 
+# only. Doxygen will then generate output that is more tailored for C. 
+# For instance, some of the names that are used will be different. The list 
+# of all members will be omitted, etc.
+
+OPTIMIZE_OUTPUT_FOR_C  = NO
+
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java sources 
+# only. Doxygen will then generate output that is more tailored for Java. 
+# For instance, namespaces will be presented as packages, qualified scopes 
+# will look different, etc.
+
+OPTIMIZE_OUTPUT_JAVA   = NO
+
+# Set the SUBGROUPING tag to YES (the default) to allow class member groups of 
+# the same type (for instance a group of public functions) to be put as a 
+# subgroup of that type (e.g. under the Public Functions section). Set it to 
+# NO to prevent subgrouping. Alternatively, this can be done per class using 
+# the \nosubgrouping command.
+
+SUBGROUPING            = YES
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in 
+# documentation are documented, even if no documentation was available. 
+# Private class members and static file members will be hidden unless 
+# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+
+EXTRACT_ALL            = NO
+
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class 
+# will be included in the documentation.
+
+EXTRACT_PRIVATE        = NO
+
+# If the EXTRACT_STATIC tag is set to YES all static members of a file 
+# will be included in the documentation.
+
+EXTRACT_STATIC         = NO
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) 
+# defined locally in source files will be included in the documentation. 
+# If set to NO only classes defined in header files are included.
+
+EXTRACT_LOCAL_CLASSES  = YES
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all 
+# undocumented members of documented classes, files or namespaces. 
+# If set to NO (the default) these members will be included in the 
+# various overviews, but no documentation section is generated. 
+# This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_MEMBERS     = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all 
+# undocumented classes that are normally visible in the class hierarchy. 
+# If set to NO (the default) these classes will be included in the various 
+# overviews. This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_CLASSES     = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all 
+# friend (class|struct|union) declarations. 
+# If set to NO (the default) these declarations will be included in the 
+# documentation.
+
+HIDE_FRIEND_COMPOUNDS  = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any 
+# documentation blocks found inside the body of a function. 
+# If set to NO (the default) these blocks will be appended to the 
+# function's detailed documentation block.
+
+HIDE_IN_BODY_DOCS      = NO
+
+# The INTERNAL_DOCS tag determines if documentation 
+# that is typed after a \internal command is included. If the tag is set 
+# to NO (the default) then the documentation will be excluded. 
+# Set it to YES to include the internal documentation.
+
+INTERNAL_DOCS          = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate 
+# file names in lower-case letters. If set to YES upper-case letters are also 
+# allowed. This is useful if you have classes or files whose names only differ 
+# in case and if your file system supports case sensitive file names. Windows 
+# users are advised to set this option to NO.
+
+CASE_SENSE_NAMES       = YES
+
+# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen 
+# will show members with their full class and namespace scopes in the 
+# documentation. If set to YES the scope will be hidden.
+
+HIDE_SCOPE_NAMES       = NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen 
+# will put a list of the files that are included by a file in the documentation 
+# of that file.
+
+SHOW_INCLUDE_FILES     = YES
+
+# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] 
+# is inserted in the documentation for inline members.
+
+INLINE_INFO            = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen 
+# will sort the (detailed) documentation of file and class members 
+# alphabetically by member name. If set to NO the members will appear in 
+# declaration order.
+
+SORT_MEMBER_DOCS       = YES
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or 
+# disable (NO) the todo list. This list is created by putting \todo 
+# commands in the documentation.
+
+GENERATE_TODOLIST      = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or 
+# disable (NO) the test list. This list is created by putting \test 
+# commands in the documentation.
+
+GENERATE_TESTLIST      = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or 
+# disable (NO) the bug list. This list is created by putting \bug 
+# commands in the documentation.
+
+GENERATE_BUGLIST       = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or 
+# disable (NO) the deprecated list. This list is created by putting 
+# \deprecated commands in the documentation.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional 
+# documentation sections, marked by \if sectionname ... \endif.
+
+ENABLED_SECTIONS       = html
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines 
+# the initial value of a variable or define consists of for it to appear in 
+# the documentation. If the initializer consists of more lines than specified 
+# here it will be hidden. Use a value of 0 to hide initializers completely. 
+# The appearance of the initializer of individual variables and defines in the 
+# documentation can be controlled using \showinitializer or \hideinitializer 
+# command in the documentation regardless of this setting.
+
+MAX_INITIALIZER_LINES  = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated 
+# at the bottom of the documentation of classes and structs. If set to YES the 
+# list will mention the files that were used to generate the documentation.
+
+SHOW_USED_FILES        = YES
+
+#---------------------------------------------------------------------------
+# configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated 
+# by doxygen. Possible values are YES and NO. If left blank NO is used.
+
+QUIET                  = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are 
+# generated by doxygen. Possible values are YES and NO. If left blank 
+# NO is used.
+
+WARNINGS               = YES
+
+# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings 
+# for undocumented members. If EXTRACT_ALL is set to YES then this flag will 
+# automatically be disabled.
+
+WARN_IF_UNDOCUMENTED   = NO
+
+# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for 
+# potential errors in the documentation, such as not documenting some 
+# parameters in a documented function, or documenting parameters that 
+# don't exist or using markup commands wrongly.
+
+WARN_IF_DOC_ERROR      = YES
+
+# The WARN_FORMAT tag determines the format of the warning messages that 
+# doxygen can produce. The string should contain the $file, $line, and $text 
+# tags, which will be replaced by the file and line number from which the 
+# warning originated and the warning text.
+
+WARN_FORMAT            = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning 
+# and error messages should be written. If left blank the output is written 
+# to stderr.
+
+WARN_LOGFILE           = 
+
+#---------------------------------------------------------------------------
+# configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag can be used to specify the files and/or directories that contain 
+# documented source files. You may enter file names like "myfile.cpp" or 
+# directories like "/usr/src/myproject". Separate the files or directories 
+# with spaces.
+
+INPUT                  = @top_srcdir@/src \
+                         @top_srcdir@/bin \
+                         @top_srcdir@/doc
+
+# If the value of the INPUT tag contains directories, you can use the 
+# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
+# and *.h) to filter out the source-files in the directories. If left 
+# blank the following patterns are tested: 
+# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx *.hpp 
+# *.h++ *.idl *.odl *.cs *.php *.php3 *.inc
+
+FILE_PATTERNS          = *.h *.hh \
+                         *.dox
+
+# The RECURSIVE tag can be used to turn specify whether or not subdirectories 
+# should be searched for input files as well. Possible values are YES and NO. 
+# If left blank NO is used.
+
+RECURSIVE              = YES
+
+# The EXCLUDE tag can be used to specify files and/or directories that should 
+# excluded from the INPUT source files. This way you can easily exclude a 
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+
+EXCLUDE                = @top_srcdir@/src/lib/chemistry/qc/cints/eri_quartet_data.h \
+                         @top_srcdir@/src/lib/chemistry/qc/cints/grt_quartet_data.h \
+                         @top_srcdir@/src/lib/chemistry/qc/mbptr12/eri_quartet_data.h \
+                         @top_srcdir@/src/lib/chemistry/qc/mbptr12/grt_quartet_data.h
+
+# The EXCLUDE_SYMLINKS tag can be used select whether or not files or directories 
+# that are symbolic links (a Unix filesystem feature) are excluded from the input.
+
+EXCLUDE_SYMLINKS       = NO
+
+# If the value of the INPUT tag contains directories, you can use the 
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude 
+# certain files from those directories.
+
+EXCLUDE_PATTERNS       = 
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or 
+# directories that contain example code fragments that are included (see 
+# the \include command).
+
+EXAMPLE_PATH           = @top_srcdir@/doc/devsamp
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the 
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
+# and *.h) to filter out the source-files in the directories. If left 
+# blank all files are included.
+
+EXAMPLE_PATTERNS       = 
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be 
+# searched for input files to be used with the \include or \dontinclude 
+# commands irrespective of the value of the RECURSIVE tag. 
+# Possible values are YES and NO. If left blank NO is used.
+
+EXAMPLE_RECURSIVE      = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or 
+# directories that contain image that are included in the documentation (see 
+# the \image command).
+
+IMAGE_PATH             = 
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should 
+# invoke to filter for each input file. Doxygen will invoke the filter program 
+# by executing (via popen()) the command <filter> <input-file>, where <filter> 
+# is the value of the INPUT_FILTER tag, and <input-file> is the name of an 
+# input file. Doxygen will then use the output that the filter program writes 
+# to standard output.
+
+INPUT_FILTER           = 
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using 
+# INPUT_FILTER) will be used to filter the input files when producing source 
+# files to browse (i.e. when SOURCE_BROWSER is set to YES).
+
+FILTER_SOURCE_FILES    = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will 
+# be generated. Documented entities will be cross-referenced with these sources. 
+# Note: To get rid of all source code in the generated output, make sure also 
+# VERBATIM_HEADERS is set to NO.
+
+SOURCE_BROWSER         = NO
+
+# Setting the INLINE_SOURCES tag to YES will include the body 
+# of functions and classes directly in the documentation.
+
+INLINE_SOURCES         = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct 
+# doxygen to hide any special comment blocks from generated source code 
+# fragments. Normal C and C++ comments will always remain visible.
+
+STRIP_CODE_COMMENTS    = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES (the default) 
+# then for each documented function all documented 
+# functions referencing it will be listed.
+
+REFERENCED_BY_RELATION = YES
+
+# If the REFERENCES_RELATION tag is set to YES (the default) 
+# then for each documented function all documented entities 
+# called/used by that function will be listed.
+
+REFERENCES_RELATION    = YES
+
+# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen 
+# will generate a verbatim copy of the header file for each class for 
+# which an include is specified. Set to NO to disable this.
+
+VERBATIM_HEADERS       = YES
+
+#---------------------------------------------------------------------------
+# configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index 
+# of all compounds will be generated. Enable this if the project 
+# contains a lot of classes, structs, unions or interfaces.
+
+ALPHABETICAL_INDEX     = NO
+
+# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then 
+# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns 
+# in which this list will be split (can be a number in the range [1..20])
+
+COLS_IN_ALPHA_INDEX    = 5
+
+# In case all classes in a project start with a common prefix, all 
+# classes will be put under the same header in the alphabetical index. 
+# The IGNORE_PREFIX tag can be used to specify one or more prefixes that 
+# should be ignored while generating the index headers.
+
+IGNORE_PREFIX          = 
+
+#---------------------------------------------------------------------------
+# configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES (the default) Doxygen will 
+# generate HTML output.
+
+GENERATE_HTML          = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `html' will be used as the default path.
+
+HTML_OUTPUT            = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for 
+# each generated HTML page (for example: .htm,.php,.asp). If it is left blank 
+# doxygen will generate files with .html extension.
+
+HTML_FILE_EXTENSION    = .html
+
+# The HTML_HEADER tag can be used to specify a personal HTML header for 
+# each generated HTML page. If it is left blank doxygen will generate a 
+# standard header.
+
+HTML_HEADER            = 
+
+# The HTML_FOOTER tag can be used to specify a personal HTML footer for 
+# each generated HTML page. If it is left blank doxygen will generate a 
+# standard footer.
+
+HTML_FOOTER            = @top_srcdir@/doc/@FOOTER_HTML@
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading 
+# style sheet that is used by each HTML page. It can be used to 
+# fine-tune the look of the HTML output. If the tag is left blank doxygen 
+# will generate a default style sheet. Note that doxygen will try to copy 
+# the style sheet file to the HTML output directory, so don't put your own 
+# stylesheet in the HTML output directory as well, or it will be erased!
+
+HTML_STYLESHEET        = 
+
+# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, 
+# files or namespaces will be aligned in HTML using tables. If set to 
+# NO a bullet list will be used.
+
+HTML_ALIGN_MEMBERS     = YES
+
+# If the GENERATE_HTMLHELP tag is set to YES, additional index files 
+# will be generated that can be used as input for tools like the 
+# Microsoft HTML help workshop to generate a compressed HTML help file (.chm) 
+# of the generated HTML documentation.
+
+GENERATE_HTMLHELP      = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can 
+# be used to specify the file name of the resulting .chm file. You 
+# can add a path in front of the file if the result should not be 
+# written to the html output directory.
+
+CHM_FILE               = 
+
+# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can 
+# be used to specify the location (absolute path including file name) of 
+# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run 
+# the HTML help compiler on the generated index.hhp.
+
+HHC_LOCATION           = 
+
+# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag 
+# controls if a separate .chi index file is generated (YES) or that 
+# it should be included in the master .chm file (NO).
+
+GENERATE_CHI           = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag 
+# controls whether a binary table of contents is generated (YES) or a 
+# normal table of contents (NO) in the .chm file.
+
+BINARY_TOC             = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members 
+# to the contents of the HTML help documentation and to the tree view.
+
+TOC_EXPAND             = NO
+
+# The DISABLE_INDEX tag can be used to turn on/off the condensed index at 
+# top of each HTML page. The value NO (the default) enables the index and 
+# the value YES disables it.
+
+DISABLE_INDEX          = NO
+
+# This tag can be used to set the number of enum values (range [1..20]) 
+# that doxygen will group on one line in the generated HTML documentation.
+
+ENUM_VALUES_PER_LINE   = 4
+
+# If the GENERATE_TREEVIEW tag is set to YES, a side panel will be
+# generated containing a tree-like index structure (just like the one that 
+# is generated for HTML Help). For this to work a browser that supports 
+# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+, 
+# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are 
+# probably better off using the HTML help feature.
+
+GENERATE_TREEVIEW      = NO
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be 
+# used to set the initial width (in pixels) of the frame in which the tree 
+# is shown.
+
+TREEVIEW_WIDTH         = 250
+
+#---------------------------------------------------------------------------
+# configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will 
+# generate Latex output.
+
+GENERATE_LATEX         = NO
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `latex' will be used as the default path.
+
+LATEX_OUTPUT           = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be 
+# invoked. If left blank `latex' will be used as the default command name.
+
+LATEX_CMD_NAME         = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to 
+# generate index for LaTeX. If left blank `makeindex' will be used as the 
+# default command name.
+
+MAKEINDEX_CMD_NAME     = makeindex
+
+# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact 
+# LaTeX documents. This may be useful for small projects and may help to 
+# save some trees in general.
+
+COMPACT_LATEX          = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used 
+# by the printer. Possible values are: a4, a4wide, letter, legal and 
+# executive. If left blank a4wide will be used.
+
+PAPER_TYPE             = a4wide
+
+# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX 
+# packages that should be included in the LaTeX output.
+
+EXTRA_PACKAGES         = 
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for 
+# the generated latex document. The header should contain everything until 
+# the first chapter. If it is left blank doxygen will generate a 
+# standard header. Notice: only use this tag if you know what you are doing!
+
+LATEX_HEADER           = 
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated 
+# is prepared for conversion to pdf (using ps2pdf). The pdf file will 
+# contain links (just like the HTML output) instead of page references 
+# This makes the output suitable for online browsing using a pdf viewer.
+
+PDF_HYPERLINKS         = NO
+
+# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of 
+# plain latex in the generated Makefile. Set this option to YES to get a 
+# higher quality PDF documentation.
+
+USE_PDFLATEX           = NO
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. 
+# command to the generated LaTeX files. This will instruct LaTeX to keep 
+# running if errors occur, instead of asking the user for help. 
+# This option is also used when generating formulas in HTML.
+
+LATEX_BATCHMODE        = NO
+
+# If LATEX_HIDE_INDICES is set to YES then doxygen will not 
+# include the index chapters (such as File Index, Compound Index, etc.) 
+# in the output.
+
+LATEX_HIDE_INDICES     = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output 
+# The RTF output is optimized for Word 97 and may not look very pretty with 
+# other RTF readers or editors.
+
+GENERATE_RTF           = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `rtf' will be used as the default path.
+
+RTF_OUTPUT             = rtf
+
+# If the COMPACT_RTF tag is set to YES Doxygen generates more compact 
+# RTF documents. This may be useful for small projects and may help to 
+# save some trees in general.
+
+COMPACT_RTF            = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated 
+# will contain hyperlink fields. The RTF file will 
+# contain links (just like the HTML output) instead of page references. 
+# This makes the output suitable for online browsing using WORD or other 
+# programs which support those fields. 
+# Note: wordpad (write) and others do not support links.
+
+RTF_HYPERLINKS         = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's 
+# config file, i.e. a series of assignments. You only have to provide 
+# replacements, missing definitions are set to their default value.
+
+RTF_STYLESHEET_FILE    = 
+
+# Set optional variables used in the generation of an rtf document. 
+# Syntax is similar to doxygen's config file.
+
+RTF_EXTENSIONS_FILE    = 
+
+#---------------------------------------------------------------------------
+# configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES (the default) Doxygen will 
+# generate man pages
+
+GENERATE_MAN           = NO
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `man' will be used as the default path.
+
+MAN_OUTPUT             = man
+
+# The MAN_EXTENSION tag determines the extension that is added to 
+# the generated man pages (default is the subroutine's section .3)
+
+MAN_EXTENSION          = .3
+
+# If the MAN_LINKS tag is set to YES and Doxygen generates man output, 
+# then it will generate one additional man file for each entity 
+# documented in the real man page(s). These additional files 
+# only source the real man page, but without them the man command 
+# would be unable to find the correct page. The default is NO.
+
+MAN_LINKS              = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES Doxygen will 
+# generate an XML file that captures the structure of 
+# the code including all documentation.
+
+GENERATE_XML           = NO
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `xml' will be used as the default path.
+
+XML_OUTPUT             = xml
+
+# The XML_SCHEMA tag can be used to specify an XML schema, 
+# which can be used by a validating XML parser to check the 
+# syntax of the XML files.
+
+XML_SCHEMA             = 
+
+# The XML_DTD tag can be used to specify an XML DTD, 
+# which can be used by a validating XML parser to check the 
+# syntax of the XML files.
+
+XML_DTD                = 
+
+# If the XML_PROGRAMLISTING tag is set to YES Doxygen will 
+# dump the program listings (including syntax highlighting 
+# and cross-referencing information) to the XML output. Note that 
+# enabling this will significantly increase the size of the XML output.
+
+XML_PROGRAMLISTING     = YES
+
+#---------------------------------------------------------------------------
+# configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will 
+# generate an AutoGen Definitions (see autogen.sf.net) file 
+# that captures the structure of the code including all 
+# documentation. Note that this feature is still experimental 
+# and incomplete at the moment.
+
+GENERATE_AUTOGEN_DEF   = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES Doxygen will 
+# generate a Perl module file that captures the structure of 
+# the code including all documentation. Note that this 
+# feature is still experimental and incomplete at the 
+# moment.
+
+GENERATE_PERLMOD       = NO
+
+# If the PERLMOD_LATEX tag is set to YES Doxygen will generate 
+# the necessary Makefile rules, Perl scripts and LaTeX code to be able 
+# to generate PDF and DVI output from the Perl module output.
+
+PERLMOD_LATEX          = NO
+
+# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be 
+# nicely formatted so it can be parsed by a human reader.  This is useful 
+# if you want to understand what is going on.  On the other hand, if this 
+# tag is set to NO the size of the Perl module output will be much smaller 
+# and Perl will parse it just the same.
+
+PERLMOD_PRETTY         = YES
+
+# The names of the make variables in the generated doxyrules.make file 
+# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. 
+# This is useful so different doxyrules.make files included by the same 
+# Makefile don't overwrite each other's variables.
+
+PERLMOD_MAKEVAR_PREFIX = 
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor   
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will 
+# evaluate all C-preprocessor directives found in the sources and include 
+# files.
+
+ENABLE_PREPROCESSING   = NO
+
+# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro 
+# names in the source code. If set to NO (the default) only conditional 
+# compilation will be performed. Macro expansion can be done in a controlled 
+# way by setting EXPAND_ONLY_PREDEF to YES.
+
+MACRO_EXPANSION        = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES 
+# then the macro expansion is limited to the macros specified with the 
+# PREDEFINED and EXPAND_AS_PREDEFINED tags.
+
+EXPAND_ONLY_PREDEF     = NO
+
+# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files 
+# in the INCLUDE_PATH (see below) will be search if a #include is found.
+
+SEARCH_INCLUDES        = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that 
+# contain include files that are not input files but should be processed by 
+# the preprocessor.
+
+INCLUDE_PATH           = 
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard 
+# patterns (like *.h and *.hpp) to filter out the header-files in the 
+# directories. If left blank, the patterns specified with FILE_PATTERNS will 
+# be used.
+
+INCLUDE_FILE_PATTERNS  = 
+
+# The PREDEFINED tag can be used to specify one or more macro names that 
+# are defined before the preprocessor is started (similar to the -D option of 
+# gcc). The argument of the tag is a list of macros of the form: name 
+# or name=definition (no spaces). If the definition and the = are 
+# omitted =1 is assumed.
+
+PREDEFINED             = 
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then 
+# this tag can be used to specify a list of macro names that should be expanded. 
+# The macro definition that is found in the sources will be used. 
+# Use the PREDEFINED tag if you want to use a different macro definition.
+
+EXPAND_AS_DEFINED      = 
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then 
+# doxygen's preprocessor will remove all function-like macros that are alone 
+# on a line, have an all uppercase name, and do not end with a semicolon. Such 
+# function macros are typically used for boiler-plate code, and will confuse the 
+# parser if not removed.
+
+SKIP_FUNCTION_MACROS   = YES
+
+#---------------------------------------------------------------------------
+# Configuration::addtions related to external references   
+#---------------------------------------------------------------------------
+
+# The TAGFILES option can be used to specify one or more tagfiles. 
+# Optionally an initial location of the external documentation 
+# can be added for each tagfile. The format of a tag file without 
+# this location is as follows: 
+#   TAGFILES = file1 file2 ... 
+# Adding location for the tag files is done as follows: 
+#   TAGFILES = file1=loc1 "file2 = loc2" ... 
+# where "loc1" and "loc2" can be relative or absolute paths or 
+# URLs. If a location is present for each tag, the installdox tool 
+# does not have to be run to correct the links.
+# Note that each tag file must have a unique name
+# (where the name does NOT include the path)
+# If a tag file is not located in the directory in which doxygen 
+# is run, you must also specify the path to the tagfile here.
+
+TAGFILES               = 
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create 
+# a tag file that is based on the input files it reads.
+
+GENERATE_TAGFILE       = 
+
+# If the ALLEXTERNALS tag is set to YES all external classes will be listed 
+# in the class index. If set to NO only the inherited external classes 
+# will be listed.
+
+ALLEXTERNALS           = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed 
+# in the modules index. If set to NO, only the current project's groups will 
+# be listed.
+
+EXTERNAL_GROUPS        = YES
+
+# The PERL_PATH should be the absolute path and name of the perl script 
+# interpreter (i.e. the result of `which perl').
+
+PERL_PATH              = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool   
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will 
+# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base or 
+# super classes. Setting the tag to NO turns the diagrams off. Note that this 
+# option is superseded by the HAVE_DOT option below. This is only a fallback. It is 
+# recommended to install and use dot, since it yields more powerful graphs.
+
+CLASS_DIAGRAMS         = YES
+
+# If set to YES, the inheritance and collaboration graphs will hide 
+# inheritance and usage relations if the target is undocumented 
+# or is not a class.
+
+HIDE_UNDOC_RELATIONS   = YES
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is 
+# available from the path. This tool is part of Graphviz, a graph visualization 
+# toolkit from AT&T and Lucent Bell Labs. The other options in this section 
+# have no effect if this option is set to NO (the default)
+
+HAVE_DOT               = @HAVE_DOT@
+
+# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen 
+# will generate a graph for each documented class showing the direct and 
+# indirect inheritance relations. Setting this tag to YES will force the 
+# the CLASS_DIAGRAMS tag to NO.
+
+CLASS_GRAPH            = YES
+
+# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen 
+# will generate a graph for each documented class showing the direct and 
+# indirect implementation dependencies (inheritance, containment, and 
+# class references variables) of the class with other documented classes.
+
+COLLABORATION_GRAPH    = YES
+
+# If the UML_LOOK tag is set to YES doxygen will generate inheritance and 
+# collaboration diagrams in a style similar to the OMG's Unified Modeling 
+# Language.
+
+UML_LOOK               = NO
+
+# If set to YES, the inheritance and collaboration graphs will show the 
+# relations between templates and their instances.
+
+TEMPLATE_RELATIONS     = NO
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT 
+# tags are set to YES then doxygen will generate a graph for each documented 
+# file showing the direct and indirect include dependencies of the file with 
+# other documented files.
+
+INCLUDE_GRAPH          = YES
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and 
+# HAVE_DOT tags are set to YES then doxygen will generate a graph for each 
+# documented header file showing the documented files that directly or 
+# indirectly include this file.
+
+INCLUDED_BY_GRAPH      = YES
+
+# If the CALL_GRAPH and HAVE_DOT tags are set to YES then doxygen will 
+# generate a call dependency graph for every global function or class method. 
+# Note that enabling this option will significantly increase the time of a run. 
+# So in most cases it will be better to enable call graphs for selected 
+# functions only using the \callgraph command.
+
+CALL_GRAPH             = NO
+
+# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen 
+# will graphical hierarchy of all classes instead of a textual one.
+
+GRAPHICAL_HIERARCHY    = YES
+
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images 
+# generated by dot. Possible values are png, jpg, or gif
+# If left blank png will be used.
+
+DOT_IMAGE_FORMAT       = png
+
+# The tag DOT_PATH can be used to specify the path where the dot tool can be 
+# found. If left blank, it is assumed the dot tool can be found on the path.
+
+DOT_PATH               = @DOT_PATH@
+
+# The DOTFILE_DIRS tag can be used to specify one or more directories that 
+# contain dot files that are included in the documentation (see the 
+# \dotfile command).
+
+DOTFILE_DIRS           = 
+
+# The MAX_DOT_GRAPH_WIDTH tag can be used to set the maximum allowed width 
+# (in pixels) of the graphs generated by dot. If a graph becomes larger than 
+# this value, doxygen will try to truncate the graph, so that it fits within 
+# the specified constraint. Beware that most browsers cannot cope with very 
+# large images.
+
+MAX_DOT_GRAPH_WIDTH    = 1024
+
+# The MAX_DOT_GRAPH_HEIGHT tag can be used to set the maximum allows height 
+# (in pixels) of the graphs generated by dot. If a graph becomes larger than 
+# this value, doxygen will try to truncate the graph, so that it fits within 
+# the specified constraint. Beware that most browsers cannot cope with very 
+# large images.
+
+MAX_DOT_GRAPH_HEIGHT   = 1024
+
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the 
+# graphs generated by dot. A depth value of 3 means that only nodes reachable 
+# from the root by following a path via at most 3 edges will be shown. Nodes that 
+# lay further from the root node will be omitted. Note that setting this option to 
+# 1 or 2 may greatly reduce the computation time needed for large code bases. Also 
+# note that a graph may be further truncated if the graph's image dimensions are 
+# not sufficient to fit the graph (see MAX_DOT_GRAPH_WIDTH and MAX_DOT_GRAPH_HEIGHT). 
+# If 0 is used for the depth value (the default), the graph is not depth-constrained.
+
+MAX_DOT_GRAPH_DEPTH    = 0
+
+# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will 
+# generate a legend page explaining the meaning of the various boxes and 
+# arrows in the dot generated graphs.
+
+GENERATE_LEGEND        = YES
+
+# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will 
+# remove the intermediate dot files that are used to generate 
+# the various graphs.
+
+DOT_CLEANUP            = YES
+
+#---------------------------------------------------------------------------
+# Configuration::addtions related to the search engine   
+#---------------------------------------------------------------------------
+
+# The SEARCHENGINE tag specifies whether or not a search engine should be 
+# used. If set to NO the values of all tags below this one will be ignored.
+
+SEARCHENGINE           = NO
Index: ThirdParty/mpqc_open/doc/doxygen.man1.cfg.in
===================================================================
--- ThirdParty/mpqc_open/doc/doxygen.man1.cfg.in	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
+++ ThirdParty/mpqc_open/doc/doxygen.man1.cfg.in	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
@@ -0,0 +1,1098 @@
+# Doxyfile 1.3.5
+
+# This file describes the settings to be used by the documentation system
+# doxygen (www.doxygen.org) for a project
+#
+# All text after a hash (#) is considered a comment and will be ignored
+# The format is:
+#       TAG = value [value, ...]
+# For lists items can also be appended using:
+#       TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (" ")
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded 
+# by quotes) that should identify the project.
+
+PROJECT_NAME           = MPQC
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number. 
+# This could be handy for archiving the generated documentation or 
+# if some version control system is used.
+
+PROJECT_NUMBER         = @SC_VERSION@
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) 
+# base path where the generated documentation will be put. 
+# If a relative path is entered, it will be relative to the location 
+# where doxygen was started. If left blank the current directory will be used.
+
+OUTPUT_DIRECTORY       = ./
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all 
+# documentation generated by doxygen is written. Doxygen will use this 
+# information to generate all constant output in the proper language. 
+# The default language is English, other supported languages are: 
+# Brazilian, Catalan, Chinese, Chinese-Traditional, Croatian, Czech, Danish, Dutch, 
+# Finnish, French, German, Greek, Hungarian, Italian, Japanese, Japanese-en 
+# (Japanese with English messages), Korean, Norwegian, Polish, Portuguese, 
+# Romanian, Russian, Serbian, Slovak, Slovene, Spanish, Swedish, and Ukrainian.
+
+OUTPUT_LANGUAGE        = English
+
+# This tag can be used to specify the encoding used in the generated output. 
+# The encoding is not always determined by the language that is chosen, 
+# but also whether or not the output is meant for Windows or non-Windows users. 
+# In case there is a difference, setting the USE_WINDOWS_ENCODING tag to YES 
+# forces the Windows encoding (this is the default for the Windows binary), 
+# whereas setting the tag to NO uses a Unix-style encoding (the default for 
+# all platforms other than Windows).
+
+USE_WINDOWS_ENCODING   = NO
+
+# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will 
+# include brief member descriptions after the members that are listed in 
+# the file and class documentation (similar to JavaDoc). 
+# Set to NO to disable this.
+
+BRIEF_MEMBER_DESC      = YES
+
+# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend 
+# the brief description of a member or function before the detailed description. 
+# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the 
+# brief descriptions will be completely suppressed.
+
+REPEAT_BRIEF           = YES
+
+# This tag implements a quasi-intelligent brief description abbreviator 
+# that is used to form the text in various listings. Each string 
+# in this list, if found as the leading text of the brief description, will be 
+# stripped from the text and the result after processing the whole list, is used 
+# as the annotated text. Otherwise, the brief description is used as-is. If left 
+# blank, the following values are used ("$name" is automatically replaced with the 
+# name of the entity): "The $name class" "The $name widget" "The $name file" 
+# "is" "provides" "specifies" "contains" "represents" "a" "an" "the"
+
+ABBREVIATE_BRIEF       = 
+
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then 
+# Doxygen will generate a detailed section even if there is only a brief 
+# description.
+
+ALWAYS_DETAILED_SEC    = NO
+
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all inherited 
+# members of a class in the documentation of that class as if those members were 
+# ordinary class members. Constructors, destructors and assignment operators of 
+# the base classes will not be shown.
+
+INLINE_INHERITED_MEMB  = NO
+
+# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full 
+# path before files name in the file list and in the header files. If set 
+# to NO the shortest path that makes the file name unique will be used.
+
+FULL_PATH_NAMES        = NO
+
+# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag 
+# can be used to strip a user-defined part of the path. Stripping is 
+# only done if one of the specified strings matches the left-hand part of 
+# the path. It is allowed to use relative paths in the argument list.
+
+STRIP_FROM_PATH        = @top_srcdir@
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter 
+# (but less readable) file names. This can be useful is your file systems 
+# doesn't support long names like on DOS, Mac, or CD-ROM.
+
+SHORT_NAMES            = NO
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen 
+# will interpret the first line (until the first dot) of a JavaDoc-style 
+# comment as the brief description. If set to NO, the JavaDoc 
+# comments will behave just like the Qt-style comments (thus requiring an 
+# explicit @brief command for a brief description.
+
+JAVADOC_AUTOBRIEF      = YES
+
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen 
+# treat a multi-line C++ special comment block (i.e. a block of //! or /// 
+# comments) as a brief description. This used to be the default behaviour. 
+# The new default is to treat a multi-line C++ comment block as a detailed 
+# description. Set this tag to YES if you prefer the old behaviour instead.
+
+MULTILINE_CPP_IS_BRIEF = NO
+
+# If the DETAILS_AT_TOP tag is set to YES then Doxygen 
+# will output the detailed description near the top, like JavaDoc.
+# If set to NO, the detailed description appears after the member 
+# documentation.
+
+DETAILS_AT_TOP         = NO
+
+# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented 
+# member inherits the documentation from any documented member that it 
+# re-implements.
+
+INHERIT_DOCS           = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC 
+# tag is set to YES, then doxygen will reuse the documentation of the first 
+# member in the group (if any) for the other members of the group. By default 
+# all members of a group must be documented explicitly.
+
+DISTRIBUTE_GROUP_DOC   = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab. 
+# Doxygen uses this value to replace tabs by spaces in code fragments.
+
+TAB_SIZE               = 8
+
+# This tag can be used to specify a number of aliases that acts 
+# as commands in the documentation. An alias has the form "name=value". 
+# For example adding "sideeffect=\par Side Effects:\n" will allow you to 
+# put the command \sideeffect (or @sideeffect) in the documentation, which 
+# will result in a user-defined paragraph with heading "Side Effects:". 
+# You can put \n's in the value part of an alias to insert newlines.
+
+ALIASES                = 
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources 
+# only. Doxygen will then generate output that is more tailored for C. 
+# For instance, some of the names that are used will be different. The list 
+# of all members will be omitted, etc.
+
+OPTIMIZE_OUTPUT_FOR_C  = NO
+
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java sources 
+# only. Doxygen will then generate output that is more tailored for Java. 
+# For instance, namespaces will be presented as packages, qualified scopes 
+# will look different, etc.
+
+OPTIMIZE_OUTPUT_JAVA   = NO
+
+# Set the SUBGROUPING tag to YES (the default) to allow class member groups of 
+# the same type (for instance a group of public functions) to be put as a 
+# subgroup of that type (e.g. under the Public Functions section). Set it to 
+# NO to prevent subgrouping. Alternatively, this can be done per class using 
+# the \nosubgrouping command.
+
+SUBGROUPING            = YES
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in 
+# documentation are documented, even if no documentation was available. 
+# Private class members and static file members will be hidden unless 
+# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+
+EXTRACT_ALL            = NO
+
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class 
+# will be included in the documentation.
+
+EXTRACT_PRIVATE        = NO
+
+# If the EXTRACT_STATIC tag is set to YES all static members of a file 
+# will be included in the documentation.
+
+EXTRACT_STATIC         = NO
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) 
+# defined locally in source files will be included in the documentation. 
+# If set to NO only classes defined in header files are included.
+
+EXTRACT_LOCAL_CLASSES  = YES
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all 
+# undocumented members of documented classes, files or namespaces. 
+# If set to NO (the default) these members will be included in the 
+# various overviews, but no documentation section is generated. 
+# This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_MEMBERS     = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all 
+# undocumented classes that are normally visible in the class hierarchy. 
+# If set to NO (the default) these classes will be included in the various 
+# overviews. This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_CLASSES     = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all 
+# friend (class|struct|union) declarations. 
+# If set to NO (the default) these declarations will be included in the 
+# documentation.
+
+HIDE_FRIEND_COMPOUNDS  = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any 
+# documentation blocks found inside the body of a function. 
+# If set to NO (the default) these blocks will be appended to the 
+# function's detailed documentation block.
+
+HIDE_IN_BODY_DOCS      = NO
+
+# The INTERNAL_DOCS tag determines if documentation 
+# that is typed after a \internal command is included. If the tag is set 
+# to NO (the default) then the documentation will be excluded. 
+# Set it to YES to include the internal documentation.
+
+INTERNAL_DOCS          = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate 
+# file names in lower-case letters. If set to YES upper-case letters are also 
+# allowed. This is useful if you have classes or files whose names only differ 
+# in case and if your file system supports case sensitive file names. Windows 
+# users are advised to set this option to NO.
+
+CASE_SENSE_NAMES       = YES
+
+# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen 
+# will show members with their full class and namespace scopes in the 
+# documentation. If set to YES the scope will be hidden.
+
+HIDE_SCOPE_NAMES       = NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen 
+# will put a list of the files that are included by a file in the documentation 
+# of that file.
+
+SHOW_INCLUDE_FILES     = YES
+
+# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] 
+# is inserted in the documentation for inline members.
+
+INLINE_INFO            = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen 
+# will sort the (detailed) documentation of file and class members 
+# alphabetically by member name. If set to NO the members will appear in 
+# declaration order.
+
+SORT_MEMBER_DOCS       = YES
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or 
+# disable (NO) the todo list. This list is created by putting \todo 
+# commands in the documentation.
+
+GENERATE_TODOLIST      = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or 
+# disable (NO) the test list. This list is created by putting \test 
+# commands in the documentation.
+
+GENERATE_TESTLIST      = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or 
+# disable (NO) the bug list. This list is created by putting \bug 
+# commands in the documentation.
+
+GENERATE_BUGLIST       = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or 
+# disable (NO) the deprecated list. This list is created by putting 
+# \deprecated commands in the documentation.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional 
+# documentation sections, marked by \if sectionname ... \endif.
+
+ENABLED_SECTIONS       = man
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines 
+# the initial value of a variable or define consists of for it to appear in 
+# the documentation. If the initializer consists of more lines than specified 
+# here it will be hidden. Use a value of 0 to hide initializers completely. 
+# The appearance of the initializer of individual variables and defines in the 
+# documentation can be controlled using \showinitializer or \hideinitializer 
+# command in the documentation regardless of this setting.
+
+MAX_INITIALIZER_LINES  = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated 
+# at the bottom of the documentation of classes and structs. If set to YES the 
+# list will mention the files that were used to generate the documentation.
+
+SHOW_USED_FILES        = YES
+
+#---------------------------------------------------------------------------
+# configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated 
+# by doxygen. Possible values are YES and NO. If left blank NO is used.
+
+QUIET                  = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are 
+# generated by doxygen. Possible values are YES and NO. If left blank 
+# NO is used.
+
+WARNINGS               = YES
+
+# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings 
+# for undocumented members. If EXTRACT_ALL is set to YES then this flag will 
+# automatically be disabled.
+
+WARN_IF_UNDOCUMENTED   = NO
+
+# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for 
+# potential errors in the documentation, such as not documenting some 
+# parameters in a documented function, or documenting parameters that 
+# don't exist or using markup commands wrongly.
+
+WARN_IF_DOC_ERROR      = YES
+
+# The WARN_FORMAT tag determines the format of the warning messages that 
+# doxygen can produce. The string should contain the $file, $line, and $text 
+# tags, which will be replaced by the file and line number from which the 
+# warning originated and the warning text.
+
+WARN_FORMAT            = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning 
+# and error messages should be written. If left blank the output is written 
+# to stderr.
+
+WARN_LOGFILE           = 
+
+#---------------------------------------------------------------------------
+# configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag can be used to specify the files and/or directories that contain 
+# documented source files. You may enter file names like "myfile.cpp" or 
+# directories like "/usr/src/myproject". Separate the files or directories 
+# with spaces.
+
+INPUT                  = mpqc.man.dox @top_srcdir@/src/bin/mpqc/mpqcrun.dox @top_srcdir@/src/bin/scls/scls.dox @top_srcdir@/src/bin/scpr/scpr.dox @top_srcdir@/src/bin/molrender/molrender.dox @top_srcdir@/bin
+
+# If the value of the INPUT tag contains directories, you can use the 
+# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
+# and *.h) to filter out the source-files in the directories. If left 
+# blank the following patterns are tested: 
+# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx *.hpp 
+# *.h++ *.idl *.odl *.cs *.php *.php3 *.inc
+
+FILE_PATTERNS          = *.dox
+
+# The RECURSIVE tag can be used to turn specify whether or not subdirectories 
+# should be searched for input files as well. Possible values are YES and NO. 
+# If left blank NO is used.
+
+RECURSIVE              = YES
+
+# The EXCLUDE tag can be used to specify files and/or directories that should 
+# excluded from the INPUT source files. This way you can easily exclude a 
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+
+EXCLUDE                = 
+
+# The EXCLUDE_SYMLINKS tag can be used select whether or not files or directories 
+# that are symbolic links (a Unix filesystem feature) are excluded from the input.
+
+EXCLUDE_SYMLINKS       = NO
+
+# If the value of the INPUT tag contains directories, you can use the 
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude 
+# certain files from those directories.
+
+EXCLUDE_PATTERNS       = 
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or 
+# directories that contain example code fragments that are included (see 
+# the \include command).
+
+EXAMPLE_PATH           = @top_srcdir@/doc/devsamp
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the 
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
+# and *.h) to filter out the source-files in the directories. If left 
+# blank all files are included.
+
+EXAMPLE_PATTERNS       = 
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be 
+# searched for input files to be used with the \include or \dontinclude 
+# commands irrespective of the value of the RECURSIVE tag. 
+# Possible values are YES and NO. If left blank NO is used.
+
+EXAMPLE_RECURSIVE      = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or 
+# directories that contain image that are included in the documentation (see 
+# the \image command).
+
+IMAGE_PATH             = 
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should 
+# invoke to filter for each input file. Doxygen will invoke the filter program 
+# by executing (via popen()) the command <filter> <input-file>, where <filter> 
+# is the value of the INPUT_FILTER tag, and <input-file> is the name of an 
+# input file. Doxygen will then use the output that the filter program writes 
+# to standard output.
+
+INPUT_FILTER           = 
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using 
+# INPUT_FILTER) will be used to filter the input files when producing source 
+# files to browse (i.e. when SOURCE_BROWSER is set to YES).
+
+FILTER_SOURCE_FILES    = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will 
+# be generated. Documented entities will be cross-referenced with these sources. 
+# Note: To get rid of all source code in the generated output, make sure also 
+# VERBATIM_HEADERS is set to NO.
+
+SOURCE_BROWSER         = NO
+
+# Setting the INLINE_SOURCES tag to YES will include the body 
+# of functions and classes directly in the documentation.
+
+INLINE_SOURCES         = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct 
+# doxygen to hide any special comment blocks from generated source code 
+# fragments. Normal C and C++ comments will always remain visible.
+
+STRIP_CODE_COMMENTS    = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES (the default) 
+# then for each documented function all documented 
+# functions referencing it will be listed.
+
+REFERENCED_BY_RELATION = YES
+
+# If the REFERENCES_RELATION tag is set to YES (the default) 
+# then for each documented function all documented entities 
+# called/used by that function will be listed.
+
+REFERENCES_RELATION    = YES
+
+# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen 
+# will generate a verbatim copy of the header file for each class for 
+# which an include is specified. Set to NO to disable this.
+
+VERBATIM_HEADERS       = YES
+
+#---------------------------------------------------------------------------
+# configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index 
+# of all compounds will be generated. Enable this if the project 
+# contains a lot of classes, structs, unions or interfaces.
+
+ALPHABETICAL_INDEX     = NO
+
+# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then 
+# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns 
+# in which this list will be split (can be a number in the range [1..20])
+
+COLS_IN_ALPHA_INDEX    = 5
+
+# In case all classes in a project start with a common prefix, all 
+# classes will be put under the same header in the alphabetical index. 
+# The IGNORE_PREFIX tag can be used to specify one or more prefixes that 
+# should be ignored while generating the index headers.
+
+IGNORE_PREFIX          = 
+
+#---------------------------------------------------------------------------
+# configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES (the default) Doxygen will 
+# generate HTML output.
+
+GENERATE_HTML          = NO
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `html' will be used as the default path.
+
+HTML_OUTPUT            = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for 
+# each generated HTML page (for example: .htm,.php,.asp). If it is left blank 
+# doxygen will generate files with .html extension.
+
+HTML_FILE_EXTENSION    = .html
+
+# The HTML_HEADER tag can be used to specify a personal HTML header for 
+# each generated HTML page. If it is left blank doxygen will generate a 
+# standard header.
+
+HTML_HEADER            = 
+
+# The HTML_FOOTER tag can be used to specify a personal HTML footer for 
+# each generated HTML page. If it is left blank doxygen will generate a 
+# standard footer.
+
+HTML_FOOTER            = @top_srcdir@/doc/@FOOTER_HTML@
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading 
+# style sheet that is used by each HTML page. It can be used to 
+# fine-tune the look of the HTML output. If the tag is left blank doxygen 
+# will generate a default style sheet. Note that doxygen will try to copy 
+# the style sheet file to the HTML output directory, so don't put your own 
+# stylesheet in the HTML output directory as well, or it will be erased!
+
+HTML_STYLESHEET        = 
+
+# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, 
+# files or namespaces will be aligned in HTML using tables. If set to 
+# NO a bullet list will be used.
+
+HTML_ALIGN_MEMBERS     = YES
+
+# If the GENERATE_HTMLHELP tag is set to YES, additional index files 
+# will be generated that can be used as input for tools like the 
+# Microsoft HTML help workshop to generate a compressed HTML help file (.chm) 
+# of the generated HTML documentation.
+
+GENERATE_HTMLHELP      = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can 
+# be used to specify the file name of the resulting .chm file. You 
+# can add a path in front of the file if the result should not be 
+# written to the html output directory.
+
+CHM_FILE               = 
+
+# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can 
+# be used to specify the location (absolute path including file name) of 
+# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run 
+# the HTML help compiler on the generated index.hhp.
+
+HHC_LOCATION           = 
+
+# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag 
+# controls if a separate .chi index file is generated (YES) or that 
+# it should be included in the master .chm file (NO).
+
+GENERATE_CHI           = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag 
+# controls whether a binary table of contents is generated (YES) or a 
+# normal table of contents (NO) in the .chm file.
+
+BINARY_TOC             = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members 
+# to the contents of the HTML help documentation and to the tree view.
+
+TOC_EXPAND             = NO
+
+# The DISABLE_INDEX tag can be used to turn on/off the condensed index at 
+# top of each HTML page. The value NO (the default) enables the index and 
+# the value YES disables it.
+
+DISABLE_INDEX          = NO
+
+# This tag can be used to set the number of enum values (range [1..20]) 
+# that doxygen will group on one line in the generated HTML documentation.
+
+ENUM_VALUES_PER_LINE   = 4
+
+# If the GENERATE_TREEVIEW tag is set to YES, a side panel will be
+# generated containing a tree-like index structure (just like the one that 
+# is generated for HTML Help). For this to work a browser that supports 
+# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+, 
+# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are 
+# probably better off using the HTML help feature.
+
+GENERATE_TREEVIEW      = NO
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be 
+# used to set the initial width (in pixels) of the frame in which the tree 
+# is shown.
+
+TREEVIEW_WIDTH         = 250
+
+#---------------------------------------------------------------------------
+# configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will 
+# generate Latex output.
+
+GENERATE_LATEX         = NO
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `latex' will be used as the default path.
+
+LATEX_OUTPUT           = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be 
+# invoked. If left blank `latex' will be used as the default command name.
+
+LATEX_CMD_NAME         = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to 
+# generate index for LaTeX. If left blank `makeindex' will be used as the 
+# default command name.
+
+MAKEINDEX_CMD_NAME     = makeindex
+
+# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact 
+# LaTeX documents. This may be useful for small projects and may help to 
+# save some trees in general.
+
+COMPACT_LATEX          = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used 
+# by the printer. Possible values are: a4, a4wide, letter, legal and 
+# executive. If left blank a4wide will be used.
+
+PAPER_TYPE             = a4wide
+
+# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX 
+# packages that should be included in the LaTeX output.
+
+EXTRA_PACKAGES         = 
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for 
+# the generated latex document. The header should contain everything until 
+# the first chapter. If it is left blank doxygen will generate a 
+# standard header. Notice: only use this tag if you know what you are doing!
+
+LATEX_HEADER           = 
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated 
+# is prepared for conversion to pdf (using ps2pdf). The pdf file will 
+# contain links (just like the HTML output) instead of page references 
+# This makes the output suitable for online browsing using a pdf viewer.
+
+PDF_HYPERLINKS         = NO
+
+# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of 
+# plain latex in the generated Makefile. Set this option to YES to get a 
+# higher quality PDF documentation.
+
+USE_PDFLATEX           = NO
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. 
+# command to the generated LaTeX files. This will instruct LaTeX to keep 
+# running if errors occur, instead of asking the user for help. 
+# This option is also used when generating formulas in HTML.
+
+LATEX_BATCHMODE        = NO
+
+# If LATEX_HIDE_INDICES is set to YES then doxygen will not 
+# include the index chapters (such as File Index, Compound Index, etc.) 
+# in the output.
+
+LATEX_HIDE_INDICES     = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output 
+# The RTF output is optimized for Word 97 and may not look very pretty with 
+# other RTF readers or editors.
+
+GENERATE_RTF           = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `rtf' will be used as the default path.
+
+RTF_OUTPUT             = rtf
+
+# If the COMPACT_RTF tag is set to YES Doxygen generates more compact 
+# RTF documents. This may be useful for small projects and may help to 
+# save some trees in general.
+
+COMPACT_RTF            = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated 
+# will contain hyperlink fields. The RTF file will 
+# contain links (just like the HTML output) instead of page references. 
+# This makes the output suitable for online browsing using WORD or other 
+# programs which support those fields. 
+# Note: wordpad (write) and others do not support links.
+
+RTF_HYPERLINKS         = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's 
+# config file, i.e. a series of assignments. You only have to provide 
+# replacements, missing definitions are set to their default value.
+
+RTF_STYLESHEET_FILE    = 
+
+# Set optional variables used in the generation of an rtf document. 
+# Syntax is similar to doxygen's config file.
+
+RTF_EXTENSIONS_FILE    = 
+
+#---------------------------------------------------------------------------
+# configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES (the default) Doxygen will 
+# generate man pages
+
+GENERATE_MAN           = YES
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `man' will be used as the default path.
+
+MAN_OUTPUT             = man
+
+# The MAN_EXTENSION tag determines the extension that is added to 
+# the generated man pages (default is the subroutine's section .3)
+
+MAN_EXTENSION          = .1
+
+# If the MAN_LINKS tag is set to YES and Doxygen generates man output, 
+# then it will generate one additional man file for each entity 
+# documented in the real man page(s). These additional files 
+# only source the real man page, but without them the man command 
+# would be unable to find the correct page. The default is NO.
+
+MAN_LINKS              = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES Doxygen will 
+# generate an XML file that captures the structure of 
+# the code including all documentation.
+
+GENERATE_XML           = NO
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `xml' will be used as the default path.
+
+XML_OUTPUT             = xml
+
+# The XML_SCHEMA tag can be used to specify an XML schema, 
+# which can be used by a validating XML parser to check the 
+# syntax of the XML files.
+
+XML_SCHEMA             = 
+
+# The XML_DTD tag can be used to specify an XML DTD, 
+# which can be used by a validating XML parser to check the 
+# syntax of the XML files.
+
+XML_DTD                = 
+
+# If the XML_PROGRAMLISTING tag is set to YES Doxygen will 
+# dump the program listings (including syntax highlighting 
+# and cross-referencing information) to the XML output. Note that 
+# enabling this will significantly increase the size of the XML output.
+
+XML_PROGRAMLISTING     = YES
+
+#---------------------------------------------------------------------------
+# configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will 
+# generate an AutoGen Definitions (see autogen.sf.net) file 
+# that captures the structure of the code including all 
+# documentation. Note that this feature is still experimental 
+# and incomplete at the moment.
+
+GENERATE_AUTOGEN_DEF   = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES Doxygen will 
+# generate a Perl module file that captures the structure of 
+# the code including all documentation. Note that this 
+# feature is still experimental and incomplete at the 
+# moment.
+
+GENERATE_PERLMOD       = NO
+
+# If the PERLMOD_LATEX tag is set to YES Doxygen will generate 
+# the necessary Makefile rules, Perl scripts and LaTeX code to be able 
+# to generate PDF and DVI output from the Perl module output.
+
+PERLMOD_LATEX          = NO
+
+# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be 
+# nicely formatted so it can be parsed by a human reader.  This is useful 
+# if you want to understand what is going on.  On the other hand, if this 
+# tag is set to NO the size of the Perl module output will be much smaller 
+# and Perl will parse it just the same.
+
+PERLMOD_PRETTY         = YES
+
+# The names of the make variables in the generated doxyrules.make file 
+# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. 
+# This is useful so different doxyrules.make files included by the same 
+# Makefile don't overwrite each other's variables.
+
+PERLMOD_MAKEVAR_PREFIX = 
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor   
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will 
+# evaluate all C-preprocessor directives found in the sources and include 
+# files.
+
+ENABLE_PREPROCESSING   = NO
+
+# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro 
+# names in the source code. If set to NO (the default) only conditional 
+# compilation will be performed. Macro expansion can be done in a controlled 
+# way by setting EXPAND_ONLY_PREDEF to YES.
+
+MACRO_EXPANSION        = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES 
+# then the macro expansion is limited to the macros specified with the 
+# PREDEFINED and EXPAND_AS_PREDEFINED tags.
+
+EXPAND_ONLY_PREDEF     = NO
+
+# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files 
+# in the INCLUDE_PATH (see below) will be search if a #include is found.
+
+SEARCH_INCLUDES        = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that 
+# contain include files that are not input files but should be processed by 
+# the preprocessor.
+
+INCLUDE_PATH           = 
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard 
+# patterns (like *.h and *.hpp) to filter out the header-files in the 
+# directories. If left blank, the patterns specified with FILE_PATTERNS will 
+# be used.
+
+INCLUDE_FILE_PATTERNS  = 
+
+# The PREDEFINED tag can be used to specify one or more macro names that 
+# are defined before the preprocessor is started (similar to the -D option of 
+# gcc). The argument of the tag is a list of macros of the form: name 
+# or name=definition (no spaces). If the definition and the = are 
+# omitted =1 is assumed.
+
+PREDEFINED             = 
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then 
+# this tag can be used to specify a list of macro names that should be expanded. 
+# The macro definition that is found in the sources will be used. 
+# Use the PREDEFINED tag if you want to use a different macro definition.
+
+EXPAND_AS_DEFINED      = 
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then 
+# doxygen's preprocessor will remove all function-like macros that are alone 
+# on a line, have an all uppercase name, and do not end with a semicolon. Such 
+# function macros are typically used for boiler-plate code, and will confuse the 
+# parser if not removed.
+
+SKIP_FUNCTION_MACROS   = YES
+
+#---------------------------------------------------------------------------
+# Configuration::addtions related to external references   
+#---------------------------------------------------------------------------
+
+# The TAGFILES option can be used to specify one or more tagfiles. 
+# Optionally an initial location of the external documentation 
+# can be added for each tagfile. The format of a tag file without 
+# this location is as follows: 
+#   TAGFILES = file1 file2 ... 
+# Adding location for the tag files is done as follows: 
+#   TAGFILES = file1=loc1 "file2 = loc2" ... 
+# where "loc1" and "loc2" can be relative or absolute paths or 
+# URLs. If a location is present for each tag, the installdox tool 
+# does not have to be run to correct the links.
+# Note that each tag file must have a unique name
+# (where the name does NOT include the path)
+# If a tag file is not located in the directory in which doxygen 
+# is run, you must also specify the path to the tagfile here.
+
+TAGFILES               = 
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create 
+# a tag file that is based on the input files it reads.
+
+GENERATE_TAGFILE       = 
+
+# If the ALLEXTERNALS tag is set to YES all external classes will be listed 
+# in the class index. If set to NO only the inherited external classes 
+# will be listed.
+
+ALLEXTERNALS           = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed 
+# in the modules index. If set to NO, only the current project's groups will 
+# be listed.
+
+EXTERNAL_GROUPS        = YES
+
+# The PERL_PATH should be the absolute path and name of the perl script 
+# interpreter (i.e. the result of `which perl').
+
+PERL_PATH              = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool   
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will 
+# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base or 
+# super classes. Setting the tag to NO turns the diagrams off. Note that this 
+# option is superseded by the HAVE_DOT option below. This is only a fallback. It is 
+# recommended to install and use dot, since it yields more powerful graphs.
+
+CLASS_DIAGRAMS         = YES
+
+# If set to YES, the inheritance and collaboration graphs will hide 
+# inheritance and usage relations if the target is undocumented 
+# or is not a class.
+
+HIDE_UNDOC_RELATIONS   = YES
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is 
+# available from the path. This tool is part of Graphviz, a graph visualization 
+# toolkit from AT&T and Lucent Bell Labs. The other options in this section 
+# have no effect if this option is set to NO (the default)
+
+HAVE_DOT               = @HAVE_DOT@
+
+# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen 
+# will generate a graph for each documented class showing the direct and 
+# indirect inheritance relations. Setting this tag to YES will force the 
+# the CLASS_DIAGRAMS tag to NO.
+
+CLASS_GRAPH            = YES
+
+# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen 
+# will generate a graph for each documented class showing the direct and 
+# indirect implementation dependencies (inheritance, containment, and 
+# class references variables) of the class with other documented classes.
+
+COLLABORATION_GRAPH    = YES
+
+# If the UML_LOOK tag is set to YES doxygen will generate inheritance and 
+# collaboration diagrams in a style similar to the OMG's Unified Modeling 
+# Language.
+
+UML_LOOK               = NO
+
+# If set to YES, the inheritance and collaboration graphs will show the 
+# relations between templates and their instances.
+
+TEMPLATE_RELATIONS     = NO
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT 
+# tags are set to YES then doxygen will generate a graph for each documented 
+# file showing the direct and indirect include dependencies of the file with 
+# other documented files.
+
+INCLUDE_GRAPH          = YES
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and 
+# HAVE_DOT tags are set to YES then doxygen will generate a graph for each 
+# documented header file showing the documented files that directly or 
+# indirectly include this file.
+
+INCLUDED_BY_GRAPH      = YES
+
+# If the CALL_GRAPH and HAVE_DOT tags are set to YES then doxygen will 
+# generate a call dependency graph for every global function or class method. 
+# Note that enabling this option will significantly increase the time of a run. 
+# So in most cases it will be better to enable call graphs for selected 
+# functions only using the \callgraph command.
+
+CALL_GRAPH             = NO
+
+# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen 
+# will graphical hierarchy of all classes instead of a textual one.
+
+GRAPHICAL_HIERARCHY    = YES
+
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images 
+# generated by dot. Possible values are png, jpg, or gif
+# If left blank png will be used.
+
+DOT_IMAGE_FORMAT       = png
+
+# The tag DOT_PATH can be used to specify the path where the dot tool can be 
+# found. If left blank, it is assumed the dot tool can be found on the path.
+
+DOT_PATH               = @DOT_PATH@
+
+# The DOTFILE_DIRS tag can be used to specify one or more directories that 
+# contain dot files that are included in the documentation (see the 
+# \dotfile command).
+
+DOTFILE_DIRS           = 
+
+# The MAX_DOT_GRAPH_WIDTH tag can be used to set the maximum allowed width 
+# (in pixels) of the graphs generated by dot. If a graph becomes larger than 
+# this value, doxygen will try to truncate the graph, so that it fits within 
+# the specified constraint. Beware that most browsers cannot cope with very 
+# large images.
+
+MAX_DOT_GRAPH_WIDTH    = 1024
+
+# The MAX_DOT_GRAPH_HEIGHT tag can be used to set the maximum allows height 
+# (in pixels) of the graphs generated by dot. If a graph becomes larger than 
+# this value, doxygen will try to truncate the graph, so that it fits within 
+# the specified constraint. Beware that most browsers cannot cope with very 
+# large images.
+
+MAX_DOT_GRAPH_HEIGHT   = 1024
+
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the 
+# graphs generated by dot. A depth value of 3 means that only nodes reachable 
+# from the root by following a path via at most 3 edges will be shown. Nodes that 
+# lay further from the root node will be omitted. Note that setting this option to 
+# 1 or 2 may greatly reduce the computation time needed for large code bases. Also 
+# note that a graph may be further truncated if the graph's image dimensions are 
+# not sufficient to fit the graph (see MAX_DOT_GRAPH_WIDTH and MAX_DOT_GRAPH_HEIGHT). 
+# If 0 is used for the depth value (the default), the graph is not depth-constrained.
+
+MAX_DOT_GRAPH_DEPTH    = 0
+
+# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will 
+# generate a legend page explaining the meaning of the various boxes and 
+# arrows in the dot generated graphs.
+
+GENERATE_LEGEND        = YES
+
+# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will 
+# remove the intermediate dot files that are used to generate 
+# the various graphs.
+
+DOT_CLEANUP            = YES
+
+#---------------------------------------------------------------------------
+# Configuration::addtions related to the search engine   
+#---------------------------------------------------------------------------
+
+# The SEARCHENGINE tag specifies whether or not a search engine should be 
+# used. If set to NO the values of all tags below this one will be ignored.
+
+SEARCHENGINE           = NO
Index: ThirdParty/mpqc_open/doc/doxygen.man3.cfg.in
===================================================================
--- ThirdParty/mpqc_open/doc/doxygen.man3.cfg.in	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
+++ ThirdParty/mpqc_open/doc/doxygen.man3.cfg.in	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
@@ -0,0 +1,1098 @@
+# Doxyfile 1.3.5
+
+# This file describes the settings to be used by the documentation system
+# doxygen (www.doxygen.org) for a project
+#
+# All text after a hash (#) is considered a comment and will be ignored
+# The format is:
+#       TAG = value [value, ...]
+# For lists items can also be appended using:
+#       TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (" ")
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded 
+# by quotes) that should identify the project.
+
+PROJECT_NAME           = MPQC
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number. 
+# This could be handy for archiving the generated documentation or 
+# if some version control system is used.
+
+PROJECT_NUMBER         = @SC_VERSION@
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) 
+# base path where the generated documentation will be put. 
+# If a relative path is entered, it will be relative to the location 
+# where doxygen was started. If left blank the current directory will be used.
+
+OUTPUT_DIRECTORY       = ./
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all 
+# documentation generated by doxygen is written. Doxygen will use this 
+# information to generate all constant output in the proper language. 
+# The default language is English, other supported languages are: 
+# Brazilian, Catalan, Chinese, Chinese-Traditional, Croatian, Czech, Danish, Dutch, 
+# Finnish, French, German, Greek, Hungarian, Italian, Japanese, Japanese-en 
+# (Japanese with English messages), Korean, Norwegian, Polish, Portuguese, 
+# Romanian, Russian, Serbian, Slovak, Slovene, Spanish, Swedish, and Ukrainian.
+
+OUTPUT_LANGUAGE        = English
+
+# This tag can be used to specify the encoding used in the generated output. 
+# The encoding is not always determined by the language that is chosen, 
+# but also whether or not the output is meant for Windows or non-Windows users. 
+# In case there is a difference, setting the USE_WINDOWS_ENCODING tag to YES 
+# forces the Windows encoding (this is the default for the Windows binary), 
+# whereas setting the tag to NO uses a Unix-style encoding (the default for 
+# all platforms other than Windows).
+
+USE_WINDOWS_ENCODING   = NO
+
+# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will 
+# include brief member descriptions after the members that are listed in 
+# the file and class documentation (similar to JavaDoc). 
+# Set to NO to disable this.
+
+BRIEF_MEMBER_DESC      = YES
+
+# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend 
+# the brief description of a member or function before the detailed description. 
+# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the 
+# brief descriptions will be completely suppressed.
+
+REPEAT_BRIEF           = YES
+
+# This tag implements a quasi-intelligent brief description abbreviator 
+# that is used to form the text in various listings. Each string 
+# in this list, if found as the leading text of the brief description, will be 
+# stripped from the text and the result after processing the whole list, is used 
+# as the annotated text. Otherwise, the brief description is used as-is. If left 
+# blank, the following values are used ("$name" is automatically replaced with the 
+# name of the entity): "The $name class" "The $name widget" "The $name file" 
+# "is" "provides" "specifies" "contains" "represents" "a" "an" "the"
+
+ABBREVIATE_BRIEF       = 
+
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then 
+# Doxygen will generate a detailed section even if there is only a brief 
+# description.
+
+ALWAYS_DETAILED_SEC    = NO
+
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all inherited 
+# members of a class in the documentation of that class as if those members were 
+# ordinary class members. Constructors, destructors and assignment operators of 
+# the base classes will not be shown.
+
+INLINE_INHERITED_MEMB  = NO
+
+# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full 
+# path before files name in the file list and in the header files. If set 
+# to NO the shortest path that makes the file name unique will be used.
+
+FULL_PATH_NAMES        = NO
+
+# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag 
+# can be used to strip a user-defined part of the path. Stripping is 
+# only done if one of the specified strings matches the left-hand part of 
+# the path. It is allowed to use relative paths in the argument list.
+
+STRIP_FROM_PATH        = @top_srcdir@
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter 
+# (but less readable) file names. This can be useful is your file systems 
+# doesn't support long names like on DOS, Mac, or CD-ROM.
+
+SHORT_NAMES            = NO
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen 
+# will interpret the first line (until the first dot) of a JavaDoc-style 
+# comment as the brief description. If set to NO, the JavaDoc 
+# comments will behave just like the Qt-style comments (thus requiring an 
+# explicit @brief command for a brief description.
+
+JAVADOC_AUTOBRIEF      = YES
+
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen 
+# treat a multi-line C++ special comment block (i.e. a block of //! or /// 
+# comments) as a brief description. This used to be the default behaviour. 
+# The new default is to treat a multi-line C++ comment block as a detailed 
+# description. Set this tag to YES if you prefer the old behaviour instead.
+
+MULTILINE_CPP_IS_BRIEF = NO
+
+# If the DETAILS_AT_TOP tag is set to YES then Doxygen 
+# will output the detailed description near the top, like JavaDoc.
+# If set to NO, the detailed description appears after the member 
+# documentation.
+
+DETAILS_AT_TOP         = NO
+
+# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented 
+# member inherits the documentation from any documented member that it 
+# re-implements.
+
+INHERIT_DOCS           = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC 
+# tag is set to YES, then doxygen will reuse the documentation of the first 
+# member in the group (if any) for the other members of the group. By default 
+# all members of a group must be documented explicitly.
+
+DISTRIBUTE_GROUP_DOC   = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab. 
+# Doxygen uses this value to replace tabs by spaces in code fragments.
+
+TAB_SIZE               = 8
+
+# This tag can be used to specify a number of aliases that acts 
+# as commands in the documentation. An alias has the form "name=value". 
+# For example adding "sideeffect=\par Side Effects:\n" will allow you to 
+# put the command \sideeffect (or @sideeffect) in the documentation, which 
+# will result in a user-defined paragraph with heading "Side Effects:". 
+# You can put \n's in the value part of an alias to insert newlines.
+
+ALIASES                = 
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources 
+# only. Doxygen will then generate output that is more tailored for C. 
+# For instance, some of the names that are used will be different. The list 
+# of all members will be omitted, etc.
+
+OPTIMIZE_OUTPUT_FOR_C  = NO
+
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java sources 
+# only. Doxygen will then generate output that is more tailored for Java. 
+# For instance, namespaces will be presented as packages, qualified scopes 
+# will look different, etc.
+
+OPTIMIZE_OUTPUT_JAVA   = NO
+
+# Set the SUBGROUPING tag to YES (the default) to allow class member groups of 
+# the same type (for instance a group of public functions) to be put as a 
+# subgroup of that type (e.g. under the Public Functions section). Set it to 
+# NO to prevent subgrouping. Alternatively, this can be done per class using 
+# the \nosubgrouping command.
+
+SUBGROUPING            = YES
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in 
+# documentation are documented, even if no documentation was available. 
+# Private class members and static file members will be hidden unless 
+# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+
+EXTRACT_ALL            = NO
+
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class 
+# will be included in the documentation.
+
+EXTRACT_PRIVATE        = NO
+
+# If the EXTRACT_STATIC tag is set to YES all static members of a file 
+# will be included in the documentation.
+
+EXTRACT_STATIC         = NO
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) 
+# defined locally in source files will be included in the documentation. 
+# If set to NO only classes defined in header files are included.
+
+EXTRACT_LOCAL_CLASSES  = YES
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all 
+# undocumented members of documented classes, files or namespaces. 
+# If set to NO (the default) these members will be included in the 
+# various overviews, but no documentation section is generated. 
+# This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_MEMBERS     = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all 
+# undocumented classes that are normally visible in the class hierarchy. 
+# If set to NO (the default) these classes will be included in the various 
+# overviews. This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_CLASSES     = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all 
+# friend (class|struct|union) declarations. 
+# If set to NO (the default) these declarations will be included in the 
+# documentation.
+
+HIDE_FRIEND_COMPOUNDS  = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any 
+# documentation blocks found inside the body of a function. 
+# If set to NO (the default) these blocks will be appended to the 
+# function's detailed documentation block.
+
+HIDE_IN_BODY_DOCS      = NO
+
+# The INTERNAL_DOCS tag determines if documentation 
+# that is typed after a \internal command is included. If the tag is set 
+# to NO (the default) then the documentation will be excluded. 
+# Set it to YES to include the internal documentation.
+
+INTERNAL_DOCS          = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate 
+# file names in lower-case letters. If set to YES upper-case letters are also 
+# allowed. This is useful if you have classes or files whose names only differ 
+# in case and if your file system supports case sensitive file names. Windows 
+# users are advised to set this option to NO.
+
+CASE_SENSE_NAMES       = YES
+
+# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen 
+# will show members with their full class and namespace scopes in the 
+# documentation. If set to YES the scope will be hidden.
+
+HIDE_SCOPE_NAMES       = NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen 
+# will put a list of the files that are included by a file in the documentation 
+# of that file.
+
+SHOW_INCLUDE_FILES     = YES
+
+# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] 
+# is inserted in the documentation for inline members.
+
+INLINE_INFO            = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen 
+# will sort the (detailed) documentation of file and class members 
+# alphabetically by member name. If set to NO the members will appear in 
+# declaration order.
+
+SORT_MEMBER_DOCS       = YES
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or 
+# disable (NO) the todo list. This list is created by putting \todo 
+# commands in the documentation.
+
+GENERATE_TODOLIST      = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or 
+# disable (NO) the test list. This list is created by putting \test 
+# commands in the documentation.
+
+GENERATE_TESTLIST      = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or 
+# disable (NO) the bug list. This list is created by putting \bug 
+# commands in the documentation.
+
+GENERATE_BUGLIST       = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or 
+# disable (NO) the deprecated list. This list is created by putting 
+# \deprecated commands in the documentation.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional 
+# documentation sections, marked by \if sectionname ... \endif.
+
+ENABLED_SECTIONS       = html
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines 
+# the initial value of a variable or define consists of for it to appear in 
+# the documentation. If the initializer consists of more lines than specified 
+# here it will be hidden. Use a value of 0 to hide initializers completely. 
+# The appearance of the initializer of individual variables and defines in the 
+# documentation can be controlled using \showinitializer or \hideinitializer 
+# command in the documentation regardless of this setting.
+
+MAX_INITIALIZER_LINES  = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated 
+# at the bottom of the documentation of classes and structs. If set to YES the 
+# list will mention the files that were used to generate the documentation.
+
+SHOW_USED_FILES        = YES
+
+#---------------------------------------------------------------------------
+# configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated 
+# by doxygen. Possible values are YES and NO. If left blank NO is used.
+
+QUIET                  = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are 
+# generated by doxygen. Possible values are YES and NO. If left blank 
+# NO is used.
+
+WARNINGS               = YES
+
+# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings 
+# for undocumented members. If EXTRACT_ALL is set to YES then this flag will 
+# automatically be disabled.
+
+WARN_IF_UNDOCUMENTED   = NO
+
+# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for 
+# potential errors in the documentation, such as not documenting some 
+# parameters in a documented function, or documenting parameters that 
+# don't exist or using markup commands wrongly.
+
+WARN_IF_DOC_ERROR      = YES
+
+# The WARN_FORMAT tag determines the format of the warning messages that 
+# doxygen can produce. The string should contain the $file, $line, and $text 
+# tags, which will be replaced by the file and line number from which the 
+# warning originated and the warning text.
+
+WARN_FORMAT            = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning 
+# and error messages should be written. If left blank the output is written 
+# to stderr.
+
+WARN_LOGFILE           = 
+
+#---------------------------------------------------------------------------
+# configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag can be used to specify the files and/or directories that contain 
+# documented source files. You may enter file names like "myfile.cpp" or 
+# directories like "/usr/src/myproject". Separate the files or directories 
+# with spaces.
+
+INPUT                  = @top_srcdir@/src/lib
+
+# If the value of the INPUT tag contains directories, you can use the 
+# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
+# and *.h) to filter out the source-files in the directories. If left 
+# blank the following patterns are tested: 
+# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx *.hpp 
+# *.h++ *.idl *.odl *.cs *.php *.php3 *.inc
+
+FILE_PATTERNS          = *.h
+
+# The RECURSIVE tag can be used to turn specify whether or not subdirectories 
+# should be searched for input files as well. Possible values are YES and NO. 
+# If left blank NO is used.
+
+RECURSIVE              = YES
+
+# The EXCLUDE tag can be used to specify files and/or directories that should 
+# excluded from the INPUT source files. This way you can easily exclude a 
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+
+EXCLUDE                = 
+
+# The EXCLUDE_SYMLINKS tag can be used select whether or not files or directories 
+# that are symbolic links (a Unix filesystem feature) are excluded from the input.
+
+EXCLUDE_SYMLINKS       = NO
+
+# If the value of the INPUT tag contains directories, you can use the 
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude 
+# certain files from those directories.
+
+EXCLUDE_PATTERNS       = 
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or 
+# directories that contain example code fragments that are included (see 
+# the \include command).
+
+EXAMPLE_PATH           = @top_srcdir@/doc/devsamp
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the 
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
+# and *.h) to filter out the source-files in the directories. If left 
+# blank all files are included.
+
+EXAMPLE_PATTERNS       = 
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be 
+# searched for input files to be used with the \include or \dontinclude 
+# commands irrespective of the value of the RECURSIVE tag. 
+# Possible values are YES and NO. If left blank NO is used.
+
+EXAMPLE_RECURSIVE      = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or 
+# directories that contain image that are included in the documentation (see 
+# the \image command).
+
+IMAGE_PATH             = 
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should 
+# invoke to filter for each input file. Doxygen will invoke the filter program 
+# by executing (via popen()) the command <filter> <input-file>, where <filter> 
+# is the value of the INPUT_FILTER tag, and <input-file> is the name of an 
+# input file. Doxygen will then use the output that the filter program writes 
+# to standard output.
+
+INPUT_FILTER           = 
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using 
+# INPUT_FILTER) will be used to filter the input files when producing source 
+# files to browse (i.e. when SOURCE_BROWSER is set to YES).
+
+FILTER_SOURCE_FILES    = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will 
+# be generated. Documented entities will be cross-referenced with these sources. 
+# Note: To get rid of all source code in the generated output, make sure also 
+# VERBATIM_HEADERS is set to NO.
+
+SOURCE_BROWSER         = NO
+
+# Setting the INLINE_SOURCES tag to YES will include the body 
+# of functions and classes directly in the documentation.
+
+INLINE_SOURCES         = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct 
+# doxygen to hide any special comment blocks from generated source code 
+# fragments. Normal C and C++ comments will always remain visible.
+
+STRIP_CODE_COMMENTS    = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES (the default) 
+# then for each documented function all documented 
+# functions referencing it will be listed.
+
+REFERENCED_BY_RELATION = YES
+
+# If the REFERENCES_RELATION tag is set to YES (the default) 
+# then for each documented function all documented entities 
+# called/used by that function will be listed.
+
+REFERENCES_RELATION    = YES
+
+# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen 
+# will generate a verbatim copy of the header file for each class for 
+# which an include is specified. Set to NO to disable this.
+
+VERBATIM_HEADERS       = YES
+
+#---------------------------------------------------------------------------
+# configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index 
+# of all compounds will be generated. Enable this if the project 
+# contains a lot of classes, structs, unions or interfaces.
+
+ALPHABETICAL_INDEX     = NO
+
+# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then 
+# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns 
+# in which this list will be split (can be a number in the range [1..20])
+
+COLS_IN_ALPHA_INDEX    = 5
+
+# In case all classes in a project start with a common prefix, all 
+# classes will be put under the same header in the alphabetical index. 
+# The IGNORE_PREFIX tag can be used to specify one or more prefixes that 
+# should be ignored while generating the index headers.
+
+IGNORE_PREFIX          = 
+
+#---------------------------------------------------------------------------
+# configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES (the default) Doxygen will 
+# generate HTML output.
+
+GENERATE_HTML          = NO
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `html' will be used as the default path.
+
+HTML_OUTPUT            = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for 
+# each generated HTML page (for example: .htm,.php,.asp). If it is left blank 
+# doxygen will generate files with .html extension.
+
+HTML_FILE_EXTENSION    = .html
+
+# The HTML_HEADER tag can be used to specify a personal HTML header for 
+# each generated HTML page. If it is left blank doxygen will generate a 
+# standard header.
+
+HTML_HEADER            = 
+
+# The HTML_FOOTER tag can be used to specify a personal HTML footer for 
+# each generated HTML page. If it is left blank doxygen will generate a 
+# standard footer.
+
+HTML_FOOTER            = @top_srcdir@/doc/@FOOTER_HTML@
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading 
+# style sheet that is used by each HTML page. It can be used to 
+# fine-tune the look of the HTML output. If the tag is left blank doxygen 
+# will generate a default style sheet. Note that doxygen will try to copy 
+# the style sheet file to the HTML output directory, so don't put your own 
+# stylesheet in the HTML output directory as well, or it will be erased!
+
+HTML_STYLESHEET        = 
+
+# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, 
+# files or namespaces will be aligned in HTML using tables. If set to 
+# NO a bullet list will be used.
+
+HTML_ALIGN_MEMBERS     = YES
+
+# If the GENERATE_HTMLHELP tag is set to YES, additional index files 
+# will be generated that can be used as input for tools like the 
+# Microsoft HTML help workshop to generate a compressed HTML help file (.chm) 
+# of the generated HTML documentation.
+
+GENERATE_HTMLHELP      = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can 
+# be used to specify the file name of the resulting .chm file. You 
+# can add a path in front of the file if the result should not be 
+# written to the html output directory.
+
+CHM_FILE               = 
+
+# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can 
+# be used to specify the location (absolute path including file name) of 
+# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run 
+# the HTML help compiler on the generated index.hhp.
+
+HHC_LOCATION           = 
+
+# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag 
+# controls if a separate .chi index file is generated (YES) or that 
+# it should be included in the master .chm file (NO).
+
+GENERATE_CHI           = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag 
+# controls whether a binary table of contents is generated (YES) or a 
+# normal table of contents (NO) in the .chm file.
+
+BINARY_TOC             = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members 
+# to the contents of the HTML help documentation and to the tree view.
+
+TOC_EXPAND             = NO
+
+# The DISABLE_INDEX tag can be used to turn on/off the condensed index at 
+# top of each HTML page. The value NO (the default) enables the index and 
+# the value YES disables it.
+
+DISABLE_INDEX          = NO
+
+# This tag can be used to set the number of enum values (range [1..20]) 
+# that doxygen will group on one line in the generated HTML documentation.
+
+ENUM_VALUES_PER_LINE   = 4
+
+# If the GENERATE_TREEVIEW tag is set to YES, a side panel will be
+# generated containing a tree-like index structure (just like the one that 
+# is generated for HTML Help). For this to work a browser that supports 
+# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+, 
+# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are 
+# probably better off using the HTML help feature.
+
+GENERATE_TREEVIEW      = NO
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be 
+# used to set the initial width (in pixels) of the frame in which the tree 
+# is shown.
+
+TREEVIEW_WIDTH         = 250
+
+#---------------------------------------------------------------------------
+# configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will 
+# generate Latex output.
+
+GENERATE_LATEX         = NO
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `latex' will be used as the default path.
+
+LATEX_OUTPUT           = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be 
+# invoked. If left blank `latex' will be used as the default command name.
+
+LATEX_CMD_NAME         = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to 
+# generate index for LaTeX. If left blank `makeindex' will be used as the 
+# default command name.
+
+MAKEINDEX_CMD_NAME     = makeindex
+
+# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact 
+# LaTeX documents. This may be useful for small projects and may help to 
+# save some trees in general.
+
+COMPACT_LATEX          = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used 
+# by the printer. Possible values are: a4, a4wide, letter, legal and 
+# executive. If left blank a4wide will be used.
+
+PAPER_TYPE             = a4wide
+
+# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX 
+# packages that should be included in the LaTeX output.
+
+EXTRA_PACKAGES         = 
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for 
+# the generated latex document. The header should contain everything until 
+# the first chapter. If it is left blank doxygen will generate a 
+# standard header. Notice: only use this tag if you know what you are doing!
+
+LATEX_HEADER           = 
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated 
+# is prepared for conversion to pdf (using ps2pdf). The pdf file will 
+# contain links (just like the HTML output) instead of page references 
+# This makes the output suitable for online browsing using a pdf viewer.
+
+PDF_HYPERLINKS         = NO
+
+# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of 
+# plain latex in the generated Makefile. Set this option to YES to get a 
+# higher quality PDF documentation.
+
+USE_PDFLATEX           = NO
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. 
+# command to the generated LaTeX files. This will instruct LaTeX to keep 
+# running if errors occur, instead of asking the user for help. 
+# This option is also used when generating formulas in HTML.
+
+LATEX_BATCHMODE        = NO
+
+# If LATEX_HIDE_INDICES is set to YES then doxygen will not 
+# include the index chapters (such as File Index, Compound Index, etc.) 
+# in the output.
+
+LATEX_HIDE_INDICES     = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output 
+# The RTF output is optimized for Word 97 and may not look very pretty with 
+# other RTF readers or editors.
+
+GENERATE_RTF           = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `rtf' will be used as the default path.
+
+RTF_OUTPUT             = rtf
+
+# If the COMPACT_RTF tag is set to YES Doxygen generates more compact 
+# RTF documents. This may be useful for small projects and may help to 
+# save some trees in general.
+
+COMPACT_RTF            = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated 
+# will contain hyperlink fields. The RTF file will 
+# contain links (just like the HTML output) instead of page references. 
+# This makes the output suitable for online browsing using WORD or other 
+# programs which support those fields. 
+# Note: wordpad (write) and others do not support links.
+
+RTF_HYPERLINKS         = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's 
+# config file, i.e. a series of assignments. You only have to provide 
+# replacements, missing definitions are set to their default value.
+
+RTF_STYLESHEET_FILE    = 
+
+# Set optional variables used in the generation of an rtf document. 
+# Syntax is similar to doxygen's config file.
+
+RTF_EXTENSIONS_FILE    = 
+
+#---------------------------------------------------------------------------
+# configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES (the default) Doxygen will 
+# generate man pages
+
+GENERATE_MAN           = YES
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `man' will be used as the default path.
+
+MAN_OUTPUT             = man
+
+# The MAN_EXTENSION tag determines the extension that is added to 
+# the generated man pages (default is the subroutine's section .3)
+
+MAN_EXTENSION          = .3
+
+# If the MAN_LINKS tag is set to YES and Doxygen generates man output, 
+# then it will generate one additional man file for each entity 
+# documented in the real man page(s). These additional files 
+# only source the real man page, but without them the man command 
+# would be unable to find the correct page. The default is NO.
+
+MAN_LINKS              = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES Doxygen will 
+# generate an XML file that captures the structure of 
+# the code including all documentation.
+
+GENERATE_XML           = NO
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `xml' will be used as the default path.
+
+XML_OUTPUT             = xml
+
+# The XML_SCHEMA tag can be used to specify an XML schema, 
+# which can be used by a validating XML parser to check the 
+# syntax of the XML files.
+
+XML_SCHEMA             = 
+
+# The XML_DTD tag can be used to specify an XML DTD, 
+# which can be used by a validating XML parser to check the 
+# syntax of the XML files.
+
+XML_DTD                = 
+
+# If the XML_PROGRAMLISTING tag is set to YES Doxygen will 
+# dump the program listings (including syntax highlighting 
+# and cross-referencing information) to the XML output. Note that 
+# enabling this will significantly increase the size of the XML output.
+
+XML_PROGRAMLISTING     = YES
+
+#---------------------------------------------------------------------------
+# configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will 
+# generate an AutoGen Definitions (see autogen.sf.net) file 
+# that captures the structure of the code including all 
+# documentation. Note that this feature is still experimental 
+# and incomplete at the moment.
+
+GENERATE_AUTOGEN_DEF   = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES Doxygen will 
+# generate a Perl module file that captures the structure of 
+# the code including all documentation. Note that this 
+# feature is still experimental and incomplete at the 
+# moment.
+
+GENERATE_PERLMOD       = NO
+
+# If the PERLMOD_LATEX tag is set to YES Doxygen will generate 
+# the necessary Makefile rules, Perl scripts and LaTeX code to be able 
+# to generate PDF and DVI output from the Perl module output.
+
+PERLMOD_LATEX          = NO
+
+# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be 
+# nicely formatted so it can be parsed by a human reader.  This is useful 
+# if you want to understand what is going on.  On the other hand, if this 
+# tag is set to NO the size of the Perl module output will be much smaller 
+# and Perl will parse it just the same.
+
+PERLMOD_PRETTY         = YES
+
+# The names of the make variables in the generated doxyrules.make file 
+# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. 
+# This is useful so different doxyrules.make files included by the same 
+# Makefile don't overwrite each other's variables.
+
+PERLMOD_MAKEVAR_PREFIX = 
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor   
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will 
+# evaluate all C-preprocessor directives found in the sources and include 
+# files.
+
+ENABLE_PREPROCESSING   = NO
+
+# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro 
+# names in the source code. If set to NO (the default) only conditional 
+# compilation will be performed. Macro expansion can be done in a controlled 
+# way by setting EXPAND_ONLY_PREDEF to YES.
+
+MACRO_EXPANSION        = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES 
+# then the macro expansion is limited to the macros specified with the 
+# PREDEFINED and EXPAND_AS_PREDEFINED tags.
+
+EXPAND_ONLY_PREDEF     = NO
+
+# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files 
+# in the INCLUDE_PATH (see below) will be search if a #include is found.
+
+SEARCH_INCLUDES        = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that 
+# contain include files that are not input files but should be processed by 
+# the preprocessor.
+
+INCLUDE_PATH           = 
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard 
+# patterns (like *.h and *.hpp) to filter out the header-files in the 
+# directories. If left blank, the patterns specified with FILE_PATTERNS will 
+# be used.
+
+INCLUDE_FILE_PATTERNS  = 
+
+# The PREDEFINED tag can be used to specify one or more macro names that 
+# are defined before the preprocessor is started (similar to the -D option of 
+# gcc). The argument of the tag is a list of macros of the form: name 
+# or name=definition (no spaces). If the definition and the = are 
+# omitted =1 is assumed.
+
+PREDEFINED             = 
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then 
+# this tag can be used to specify a list of macro names that should be expanded. 
+# The macro definition that is found in the sources will be used. 
+# Use the PREDEFINED tag if you want to use a different macro definition.
+
+EXPAND_AS_DEFINED      = 
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then 
+# doxygen's preprocessor will remove all function-like macros that are alone 
+# on a line, have an all uppercase name, and do not end with a semicolon. Such 
+# function macros are typically used for boiler-plate code, and will confuse the 
+# parser if not removed.
+
+SKIP_FUNCTION_MACROS   = YES
+
+#---------------------------------------------------------------------------
+# Configuration::addtions related to external references   
+#---------------------------------------------------------------------------
+
+# The TAGFILES option can be used to specify one or more tagfiles. 
+# Optionally an initial location of the external documentation 
+# can be added for each tagfile. The format of a tag file without 
+# this location is as follows: 
+#   TAGFILES = file1 file2 ... 
+# Adding location for the tag files is done as follows: 
+#   TAGFILES = file1=loc1 "file2 = loc2" ... 
+# where "loc1" and "loc2" can be relative or absolute paths or 
+# URLs. If a location is present for each tag, the installdox tool 
+# does not have to be run to correct the links.
+# Note that each tag file must have a unique name
+# (where the name does NOT include the path)
+# If a tag file is not located in the directory in which doxygen 
+# is run, you must also specify the path to the tagfile here.
+
+TAGFILES               = 
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create 
+# a tag file that is based on the input files it reads.
+
+GENERATE_TAGFILE       = 
+
+# If the ALLEXTERNALS tag is set to YES all external classes will be listed 
+# in the class index. If set to NO only the inherited external classes 
+# will be listed.
+
+ALLEXTERNALS           = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed 
+# in the modules index. If set to NO, only the current project's groups will 
+# be listed.
+
+EXTERNAL_GROUPS        = YES
+
+# The PERL_PATH should be the absolute path and name of the perl script 
+# interpreter (i.e. the result of `which perl').
+
+PERL_PATH              = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool   
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will 
+# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base or 
+# super classes. Setting the tag to NO turns the diagrams off. Note that this 
+# option is superseded by the HAVE_DOT option below. This is only a fallback. It is 
+# recommended to install and use dot, since it yields more powerful graphs.
+
+CLASS_DIAGRAMS         = YES
+
+# If set to YES, the inheritance and collaboration graphs will hide 
+# inheritance and usage relations if the target is undocumented 
+# or is not a class.
+
+HIDE_UNDOC_RELATIONS   = YES
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is 
+# available from the path. This tool is part of Graphviz, a graph visualization 
+# toolkit from AT&T and Lucent Bell Labs. The other options in this section 
+# have no effect if this option is set to NO (the default)
+
+HAVE_DOT               = @HAVE_DOT@
+
+# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen 
+# will generate a graph for each documented class showing the direct and 
+# indirect inheritance relations. Setting this tag to YES will force the 
+# the CLASS_DIAGRAMS tag to NO.
+
+CLASS_GRAPH            = YES
+
+# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen 
+# will generate a graph for each documented class showing the direct and 
+# indirect implementation dependencies (inheritance, containment, and 
+# class references variables) of the class with other documented classes.
+
+COLLABORATION_GRAPH    = YES
+
+# If the UML_LOOK tag is set to YES doxygen will generate inheritance and 
+# collaboration diagrams in a style similar to the OMG's Unified Modeling 
+# Language.
+
+UML_LOOK               = NO
+
+# If set to YES, the inheritance and collaboration graphs will show the 
+# relations between templates and their instances.
+
+TEMPLATE_RELATIONS     = NO
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT 
+# tags are set to YES then doxygen will generate a graph for each documented 
+# file showing the direct and indirect include dependencies of the file with 
+# other documented files.
+
+INCLUDE_GRAPH          = YES
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and 
+# HAVE_DOT tags are set to YES then doxygen will generate a graph for each 
+# documented header file showing the documented files that directly or 
+# indirectly include this file.
+
+INCLUDED_BY_GRAPH      = YES
+
+# If the CALL_GRAPH and HAVE_DOT tags are set to YES then doxygen will 
+# generate a call dependency graph for every global function or class method. 
+# Note that enabling this option will significantly increase the time of a run. 
+# So in most cases it will be better to enable call graphs for selected 
+# functions only using the \callgraph command.
+
+CALL_GRAPH             = NO
+
+# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen 
+# will graphical hierarchy of all classes instead of a textual one.
+
+GRAPHICAL_HIERARCHY    = YES
+
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images 
+# generated by dot. Possible values are png, jpg, or gif
+# If left blank png will be used.
+
+DOT_IMAGE_FORMAT       = png
+
+# The tag DOT_PATH can be used to specify the path where the dot tool can be 
+# found. If left blank, it is assumed the dot tool can be found on the path.
+
+DOT_PATH               = @DOT_PATH@
+
+# The DOTFILE_DIRS tag can be used to specify one or more directories that 
+# contain dot files that are included in the documentation (see the 
+# \dotfile command).
+
+DOTFILE_DIRS           = 
+
+# The MAX_DOT_GRAPH_WIDTH tag can be used to set the maximum allowed width 
+# (in pixels) of the graphs generated by dot. If a graph becomes larger than 
+# this value, doxygen will try to truncate the graph, so that it fits within 
+# the specified constraint. Beware that most browsers cannot cope with very 
+# large images.
+
+MAX_DOT_GRAPH_WIDTH    = 1024
+
+# The MAX_DOT_GRAPH_HEIGHT tag can be used to set the maximum allows height 
+# (in pixels) of the graphs generated by dot. If a graph becomes larger than 
+# this value, doxygen will try to truncate the graph, so that it fits within 
+# the specified constraint. Beware that most browsers cannot cope with very 
+# large images.
+
+MAX_DOT_GRAPH_HEIGHT   = 1024
+
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the 
+# graphs generated by dot. A depth value of 3 means that only nodes reachable 
+# from the root by following a path via at most 3 edges will be shown. Nodes that 
+# lay further from the root node will be omitted. Note that setting this option to 
+# 1 or 2 may greatly reduce the computation time needed for large code bases. Also 
+# note that a graph may be further truncated if the graph's image dimensions are 
+# not sufficient to fit the graph (see MAX_DOT_GRAPH_WIDTH and MAX_DOT_GRAPH_HEIGHT). 
+# If 0 is used for the depth value (the default), the graph is not depth-constrained.
+
+MAX_DOT_GRAPH_DEPTH    = 0
+
+# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will 
+# generate a legend page explaining the meaning of the various boxes and 
+# arrows in the dot generated graphs.
+
+GENERATE_LEGEND        = YES
+
+# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will 
+# remove the intermediate dot files that are used to generate 
+# the various graphs.
+
+DOT_CLEANUP            = YES
+
+#---------------------------------------------------------------------------
+# Configuration::addtions related to the search engine   
+#---------------------------------------------------------------------------
+
+# The SEARCHENGINE tag specifies whether or not a search engine should be 
+# used. If set to NO the values of all tags below this one will be ignored.
+
+SEARCHENGINE           = NO
Index: ThirdParty/mpqc_open/doc/footer.html
===================================================================
--- ThirdParty/mpqc_open/doc/footer.html	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
+++ ThirdParty/mpqc_open/doc/footer.html	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
@@ -0,0 +1,14 @@
+<hr>
+<address>
+<small>
+
+Generated at $datetime for <a
+href="http://www.mpqc.org">$projectname</a>
+$projectnumber using the documentation package <a
+href="http://www.doxygen.org">Doxygen</a>
+$doxygenversion.
+
+</small>
+</address>
+</body>
+</html>
Index: ThirdParty/mpqc_open/doc/overview.dox
===================================================================
--- ThirdParty/mpqc_open/doc/overview.dox	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
+++ ThirdParty/mpqc_open/doc/overview.dox	(revision 860145ede0311b3539e419277d8ca4a3091f40b2)
@@ -0,0 +1,32 @@
+
+/** \page overview Overview
+
+The Scientific Computing toolkit (SC) provides C++ class libraries for
+scientific computation.  Included are classes for managing memory, saving
+and restoring the state of objects, reading objects from an input file,
+parallel communication, matrix algebra, among others.
+
+Class libraries supporting quantum chemistry applications are provided with
+the full distribution of SC.  Also included is the Massively Parallel
+Quantum Chemistry program (MPQC) which is built upon these libraries.
+
+MPQC and SC are works-in-progress.  They are experimental codes that are
+used to apply new computational approaches to problems in scientific
+programming in general and, in particular, to quantum chemistry.  Thus,
+this manual is incomplete.  Furthermore, some of the classes in the
+distribution may be on the verge of obsolescence and others may be
+unfinished work that are intended to provide new functionality in later
+releases.
+
+The development of SC has been driven by the development of the Massively
+Parallel Quantum Chemistry (MPQC) program.  While, currently, MPQC and SC
+are distributed together, the SC code is problem-domain independent.  For
+example, the utility classes provided in src/lib/util do not require the
+code in src/lib/math or src/lib/chemistry and the src/lib/math classes do
+not require src/lib/chemistry.
+
+MPQC and SC run on Unix compatible workstations (Intel/Linux, SGI/IRIX IBM
+RS/6000), symmetric multi-processors (Intel/Linux, SGI/IRIX), and massively
+parallel computers (IBM SP, Intel Paragon).
+
+*/
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+<hr>
+<address>
+<small>
+
+Generated at $datetime for <a
+href="http://www.mpqc.org">$projectname</a>
+$projectnumber using the documentation package <a
+href="http://www.doxygen.org">Doxygen</a>
+$doxygenversion.
+<br>
+These pages are hosted on
+<a href="http://sourceforge.net"><img style="vertical-align: middle;" src="http://sflogo.sourceforge.net/sflogo.php?group_id=6610&amp;type=1" width="88" height="31" border="0" alt="SourceForge.net" /></a>
+
+</small>
+</address>
+</body>
+</html>
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+/** \page srctree The Source Tree
+
+<dl>
+
+<dt><tt>bin</tt><dd>This directory mainly contains commands that
+  are used to help with the compilation of SC.
+
+<dt><tt>lib/basis</tt><dd>The Gaussian basis set data files are in this
+  directory.
+
+<dt><tt>lib/elisp</tt><dd>If you are an emacs user, some useful
+  modes and C++ programming style specifications can be found
+  here.
+
+<dt><tt>lib/perl</tt><dd>Perl modules that are used by the MPQC
+  validation suite are found here.
+
+<dt><tt>src/lib/util/options</tt>
+  <dd>This contains the GetLongOpt command line argument parsing facility
+  written by S. Manoharan, with some modifications.
+
+<dt><tt>src/lib/util/ref</tt>
+  <dd>This library provides memory management for objects.
+  See \ref ref for more information.
+
+<dt><tt>src/lib/util/container</tt><dd>This library provides container
+  classes.  Some of these classes are not very efficient and it is likely
+  that they will be replaced by the C++ Standard Template Library (STL)
+  when it is supported fully by more compilers.  If your C++ implementation
+  supports the STL you can configure with the <tt>--enable-stl</tt> option
+  to use STL containers in place of the containers provided by this
+  library.
+
+<dt><tt>src/lib/util/misc</tt><dd>This contains a variety of independent
+  classes that don't belong anywhere else.  Here one can find classes to
+  assist with debugging, provide information about the execution
+  environment, help make the output prettier, maintain detailed timing
+  information, etc.
+
+<dt><tt>src/lib/util/class</tt><dd>This library provides base classes for
+  classes that require meta-information about the class.  This
+  meta-information includes the class name, meta-information about the
+  parent class and derived classes, pointers to functions that can create
+  instances of the class, and so on.  See \ref class
+  for more information.
+
+<dt><tt>src/lib/util/keyval</tt><dd>This library provides classes that read
+  keyword/value pairs from an input file.  See \ref keyval
+  for more information.
+
+<dt><tt>src/lib/util/state</tt><dd>The state library provides a base class
+  for persistent objects and classes to read and write these objects to a
+  stream.  See \ref state for more information.
+
+<dt><tt>src/lib/util/group</tt><dd>This group library provides classes to
+  utilize multiple processors of a parallel machine.  Message passing,
+  distributed shared memory, and multi-threaded models are supported.
+  See \ref group for more information.
+
+<dt><tt>src/lib/util/render</tt><dd>This library provides a standard
+  interface to rendering packages.
+
+<dt><tt>src/lib/math/linpackd</tt><dd>This library contains double precision
+  C versions of some of the linpack routines.
+
+<dt><tt>src/lib/math/scmat</tt><dd>This library defines an abstract matrix
+  class and supplies concrete implementations of parallel replicated and
+  distributed matrices.  See \ref scmat for more information.
+
+<dt><tt>src/lib/math/optimize</tt><dd>The optimize library provides classes
+  to perform optimizations and base classes for objects that compute a
+  scalar quantity as a function of several coordinates.
+
+<dt><tt>src/lib/math/isosurf</tt><dd>This library can be used to compute a
+  triangulated approximation to an isosurface.
+
+<dt><tt>src/lib/math/symmetry</tt><dd>The symmetry library contains classes
+  useful for describing point group symmetry.  See \ref symmetry
+  for more information.
+
+<dt><tt>src/lib/chemistry/molecule</tt><dd>This library has classes to
+  describe molecules and internal molecular coordinates. A base class for
+  classes that map the molecular coordinates to an energy is provided to
+  permit the optimization of the molecular coordinates.
+
+<dt><tt>src/lib/chemistry/solvent</tt><dd> This code can be used to
+  describe solvated molecules.
+
+<dt><tt>src/lib/chemistry/qc/basis</tt><dd>The basis library has classes
+  that describe Gaussian basis sets and base classes for libraries that
+  compute integrals involving these functions.
+
+<dt><tt>src/lib/chemistry/qc/oint3</tt><dd>This library is comprised of
+  machine generated code that is only used by the intv3 library.
+
+<dt><tt>src/lib/chemistry/qc/intv3</tt><dd>The intv3 library computes
+  integrals involving Gaussian basis functions.
+
+<dt><tt>src/lib/chemistry/qc/wfn</tt><dd>The wfn library contains base
+  classes for classes that, given a molecule and a basis set, compute the
+  energy and other properties of the molecule.
+
+<dt><tt>src/lib/chemistry/qc/scf</tt><dd>The scf library is used to compute
+  self-consistent-field energies and gradients.  Specializations for
+  Hartree-Fock theory are provided.
+
+<dt><tt>src/lib/chemistry/qc/dft</tt><dd>The dft library provides
+  implementations of density functional theory energies and gradients.
+
+<dt><tt>src/lib/chemistry/qc/mbpt</tt><dd>This library computes second-order
+  perturbation theory energies and gradients.
+
+<dt><tt>src/lib/chemistry/qc/psi</tt><dd>This provides an example of
+  interfacing MPQC to an external quantum chemistry package.
+
+<dt><tt>src/bin/mpqc</tt><dd>The Massively Parallel Quantum Chemistry program
+  is in this directory.  See \ref mpqc for more information.
+
+<dt><tt>src/bin/scls</tt><dd>This program lists the contents of files created
+  by \ref state.  See \ref scls for more
+  information.
+
+<dt><tt>src/bin/scpr</tt><dd>This program prints objects contained in files
+  created by \ref state.  See \ref scpr for more
+  information.
+
+</dl>
+
+*/
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+
+/** \mainpage The Massively Parallel Quantum Chemistry Program (MPQC) and the Scientific Computing Toolkit (SC)
+
+The Massively Parallel Quantum Chemistry program (MPQC) computes
+the properties of molecules, <i>ab initio</i>, on a wide variety
+of computer architectures.
+
+The Scientific Computing toolkit (SC) provides C++ class libraries for
+scientific computation.  Included are classes for managing memory, saving
+and restoring the state of objects, reading objects from an input file,
+parallel communication, matrix algebra, among others.
+
+<ul>
+  <li> \ref overview
+  <li> \ref download
+  <li> \ref compile
+</ul>
+
+\section userref Command Reference
+<ul>
+  <li> \ref mpqc
+  <li> \ref mpqcrun
+  <li> \ref scpr
+  <li> \ref scls
+  <li> \ref molrender
+  <li> \ref sc-config
+  <li> \ref sc-libtool
+  <li> \ref sc-mkf77sym
+</ul>
+
+\section develref Developer's Reference
+<ul>
+  <li> \ref develop
+  <li> \ref srctree
+  <li> \ref ref
+  <li> \ref class
+  <li> \ref state
+  <li> \ref keyval
+  <li> \ref group
+  <li> \ref scmat
+  <li> \ref symmetry
+</ul>
+
+*/
