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Peter Lichtner committed 7ee62f7

Minor changes to QG.

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File docs/user_manual/governing_eqns.tex

 Output is given in terms of $\alpha$ and $C$ from which the mean age $A$ can be obtained as $A\eq\alpha/C$. 
 
 \subsection{Thermodynamic Database}
+\label{thermo:database}
 
 PFLOTRAN reads thermodynamic data from a database that may be customized by the user. Reactions included in the database consist of aqueous complexation, mineral precipitation and dissolution, gaseous reactions, and surface complexation. Ion exchange reactions and their selectivity coefficients are entered directly from the input file. 
 A standard database supplied with the code is referred to as {\tt hanford.dat} and is found in the {\tt ./database} directory in the PFLOTRAN mercurial repository. This database is an ascii text file that can be edited by any editor and is equivalent to the EQ3/6 database:

File docs/user_manual/keywords.tex

 
 \noindent{\bf Explanation:}
 
+\scriptsize
+\begin{Verbatim}
+typedef enum {/* converged */
+    SNES_CONVERGED_FNORM_ABS         =  2, /* ||F|| < atol */
+    SNES_CONVERGED_FNORM_RELATIVE    =  3, /* ||F|| < rtol*||F_initial|| */
+    SNES_CONVERGED_SNORM_RELATIVE    =  4, /* Newton computed step size small; 
+                                              || delta x || < stol || x ||*/
+    SNES_CONVERGED_ITS               =  5, /* maximum iterations reached */
+    SNES_CONVERGED_TR_DELTA          =  7,
+    
+              /* diverged */
+    SNES_DIVERGED_FUNCTION_DOMAIN     = -1, /* the new x location passed the function is 
+                                               not in the domain of F */
+    SNES_DIVERGED_FUNCTION_COUNT      = -2,
+    SNES_DIVERGED_LINEAR_SOLVE        = -3, /* the linear solve failed */
+    SNES_DIVERGED_FNORM_NAN           = -4,
+    SNES_DIVERGED_MAX_IT              = -5,
+    SNES_DIVERGED_LINE_SEARCH         = -6, /* the line search failed */
+    SNES_DIVERGED_INNER               = -7, /* inner solve failed */
+    SNES_DIVERGED_LOCAL_MIN           = -8, /* || J^T b || is small, implies converged to 
+                                               local minimum of F() */
+    SNES_CONVERGED_ITERATING          =  0} SNESConvergedReason;
+\end{Verbatim}
+\normalsize
+
 \noindent{\bf Example:}
 
 \hyperlink{target_key}{\return}

File docs/user_manual/quick_start.tex

 \end{itemize}
 \item \href{https://bitbucket.org/pflotran/pflotran-dev}{PFLOTRAN}
 \end{itemize}
+\end{description}
 
+\subsection{Installing PFLOTRAN}
+
+\begin{description}
 \item[Step 1: Installing PETSc] The first step is to download the developer version of PETSc, \href{http://www.mcs.anl.gov/petsc/developers/index.html}{petsc-dev}. To do this follow the directions at the PETSc Developer web site. The recommended approach is to use \href{http://mercurial.selenic.com/}{Mercurial}---also needed to obtain the PFLOTRAN source code. Mercurial(hg) is the version control system used by both PETSc and PFLOTRAN. Often one can find executables for particular platforms and there is no need to compile the application from scratch. On a UNIX system you can check to see if Mercurial is already installed by issuing the command: {\footnotesize\tt which hg}.
 
 To compile PETSc it is first necessary to configure the makefile. To this end define the environmental variables {\footnotesize\tt PETSC\_DIR} and {\footnotesize\tt PETSC\_ARCH} pointing to the directory where petsc-dev is installed and an identifying name for the installation, respectively. E.g. if using the t-shell on MacOSX 10.8.2 and gcc-4.8 enter into the .tcshrc file:
 \vspace{3mm}
 \begin{tabular}{lcc}
 \toprule
-MODE & \multicolumn{1}{c}{Description} & Requirements\\
+MODE & \multicolumn{1}{c}{Description} & Required Databases$^\dag$\\
 \midrule
-RICHARDS & Solves Richards equation & \\
-MPHASE & Supercritcal CO$_2$ & co2data0.dat database\\
-TH & Thermal-Hydrology mode & \\
-CHEMISTRY & Reactive Transport & thermodynamic database\\
+RICHARDS & Solves Richards equation & ---\\
+MPHASE & Supercritcal CO$_2$ & {\tt co2data0.dat} \\
+TH & Thermal-Hydrology mode & ---\\
+CHEMISTRY & Reactive Transport & {\tt hanford.dat}$^\ddag$ \\
 \bottomrule
 \end{tabular}
+
+\vspace{3mm}
+
+\parbox{4.5in}{
+\indent $^\dag$ Provided with the PFLOTRAN distribution in directory {\tt ./pflotran/database}.
+
+\medskip
+
+\indent $^\ddag$ An equivalent user supplied thermodynamic database for chemical reactions may also be used (see \S\ref{thermo:database} for a description of the database format). 
+}
 \end{table}
 
 An example input file is listed in \S\ref{exinput} for a coupled problem using Richards and Chemistry modes.