Added all chapters and sections

and addressed Goran's comment to clarify
how the phase shift was handled at the
reaction threshold

docs/tex/appendices.tex

+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+%                                                                 %
+%                           Appendices                            %
+%                                                                 %
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+
+\chapter{Appendices}\label{ch:appendices}
\ No newline at end of file

docs/tex/auxiliary-programs.tex

+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+%                                                                 %
+%                         Auxiliary Programs                      %
+%                                                                 %
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+
+\chapter{Auxiliary Programs}\label{ch:auxiliary-programs}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{angodf: Convert From Energy/Angle To Angle/Energy} \label{sec:angodf}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{convrt: Convert From Refit Input to Sammy or Vice Versa} \label{sec:convrt}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{samamr: Add, Mix, or Recover Variables} \label{sec:samamr}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{samamx: Modify a Single Value} \label{sec:samamx}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{samcpr: Compare Results} \label{sec:samcpr}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{samdis: Statistical Distributions} \label{sec:samdis}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{samftz: Fix TZERO ($t_0$)} \label{sec:samftz}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{samort: Plot The Oak Ridge Resolution Function} \label{sec:samort}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{samplt: Alternative Form For Plot Files} \label{sec:samplt}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{samqua: Resonance Quantum Numbers} \label{sec:samqua}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{samrpt: Plot RPI Resolution Function} \label{sec:samrpt}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{samrst: Plot Resolution Function} \label{sec:samrst}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{samsmc: Monte Carlo Multiple Scattering} \label{sec:samsmc_monte_carlo}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{samsta: Staircase Plots} \label{sec:samsta}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{samthn: Thinning Data} \label{sec:samthn}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{suggel: Estimating L and J} \label{sec:suggel}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{samrml: Calculate Cross Sections From Endf File 2} \label{sec:samrml}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{samgy2: Smooth The Tabulated Y2 Function} \label{sec:samgy2}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+

docs/tex/computer-code.tex

+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+%                                                                 %
+%                          Computer Code                          %
+%                                                                 %
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+
+\chapter{Computer Code}\label{ch:computer-code}
+
+\textcolor{red}{Use of the more modern CMake system should remove most of computer dependence now.}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Dynamic Allocation Of Array Storage} \label{sec:dynamic-arrays}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Use Of Temporary Data Files To Store Intermediate Results} \label{sec:temporary-files}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Division Of The Program Into Autonomous Segments} \label{sec:modularity}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Computer-specific Features} \label{sec:computer-specific-feat}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{ORELA Data Format} \label{sec:odf}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Configuration And Distribution System} \label{sec:config-and-dist}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\ No newline at end of file

docs/tex/evaluation-connection.tex

+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+%                                                                 %
+%                       Evaluation Connection                     %
+%                                                                 %
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+
+\chapter{Evaluation Connection}\label{ch:eval-connection}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{CSEWG Constants} \label{sec:csewg-constants}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\ No newline at end of file

docs/tex/examples.tex

+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+%                                                                 %
+%                              Examples                           %
+%                                                                 %
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+
+\chapter{Examples}\label{ch:examples}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Tutorial} \label{sec:tutorial}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Test Cases} \label{sec:test-cases}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Monte Carlo Simulations of Multiple-scattering Corrections} \label{sec:mc-test-cases}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\ No newline at end of file

docs/tex/fitting-procedure.tex

+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+%                                                                 %
+%                          Fitting Procedure                      %
+%                                                                 %
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+
+\chapter{Fitting Procedure}\label{ch:fitting-procedure}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Derivation Of Bayes' Equations} \label{sec:derivation-bayes-eqs}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Implementation Of Bayes' Equations} \label{sec:implementation-bayes-eqs}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Constructing The Parameter Set} \label{sec:construct-par-set}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Treatment Of Data Covariance Matrices} \label{sec:data-cov-matrices}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Miscellaneous Topics Related To Covariances} \label{sec:miscellaneous-cov}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

docs/tex/helpful-hints.tex

+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+%                                                                 %
+%                           Helpful Hints                         %
+%                                                                 %
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+
+\chapter{Helpful Hints}\label{ch:helpful-hints}
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Strategy For Data Evaluation With Sammy} \label{sec:eval-strategy}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Procedures To Follow When You Have Problems} \label{sec:problem-procedure}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Miscellaneous Comments And Suggestions} \label{sec:miscel-suggestions}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\ No newline at end of file

docs/tex/input.tex

+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+%                                                                 %
+%                              Input                              %
+%                                                                 %
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+
+\chapter{Input}\label{ch:input}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{The INPut File} \label{sec:input-file}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{The PARameter File} \label{sec:par-file}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{The DATa and Data CoVariance Files} \label{sec:dat-dcv-files}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Integral Data File} \label{sec:int-data-file}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Interactive Input To Sammy} \label{sec:interactive-inp}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Other Input Files For Sammy} \label{sec:other-inp-files}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+

docs/tex/introduction.tex

@@ -8,31 +8,31 @@
 
 This document serves as a users' guide to the multilevel multichannel R-matrix code SAMMY. Beginning with Revision 6, the organization of this manual has been redesigned in an effort to make it more legible, logical, and useful. A summary of the structure of this document is given here.
 
-Introductions for the original version of this manual through the previous revision are available in Appendix A. An introduction specifically for the current revision, describing recent modifications and additions to the code and the manual, is found immediately following this general introduction. All SAMMY users are encouraged to read Section I.A for an overview of recent developments.
+Introductions for the original version of this manual through the previous revision are available in Appendix A. An introduction specifically for the current revision, describing recent modifications and additions to the code and the manual, is found immediately following this general introduction. All SAMMY users are encouraged to read \S I.A for an overview of recent developments.
 
-Analysis of neutron cross-section data in the resolved resonance region (RRR) has three distinct aspects, each of which must be included in any analysis code: First, an appropriate formalism is needed for generating theoretical cross sections. Second, a plausible mathematical description must be provided for every experimental condition that affects the values of the quantities being measured. Third, a fitting procedure must be available to determine the parameter values which provide the ``best'' fit of theoretical to experimental numbers. These three aspects of the SAMMY code are described in Sections II\ref{ch:scattering_theory}, III\ref{}, and IV\ref{} of this manual, respectively.
+Analysis of neutron cross-section data in the resolved resonance region (RRR) has three distinct aspects, each of which must be included in any analysis code: First, an appropriate formalism is needed for generating theoretical cross sections. Second, a plausible mathematical description must be provided for every experimental condition that affects the values of the quantities being measured. Third, a fitting procedure must be available to determine the parameter values which provide the ``best'' fit of theoretical to experimental numbers. These three aspects of the SAMMY code are described in \S II (\ref{ch:scattering_theory}), III (\ref{ch:exp-conditions}), and IV (\ref{ch:fitting-procedure}) of this manual, respectively.
 
-Calculation of the cross sections in the RRR is described in Section II\ref{}, with emphasis on the Reich-Moore approximation to R-matrix theory. Explicit equations are given for the various types of energy-differential cross sections (total, elastic, capture, fission, other reaction) and for the angle and energy-differential cross sections (elastic, reaction). Both Coulomb and non-Coulomb (neutron) formulae are shown.
+Calculation of the cross sections in the RRR is described in \S II (\ref{ch:scattering_theory}), with emphasis on the Reich-Moore approximation to R-matrix theory. Explicit equations are given for the various types of energy-differential cross sections (total, elastic, capture, fission, other reaction) and for the angle and energy-differential cross sections (elastic, reaction). Both Coulomb and non-Coulomb (neutron) formulae are shown.
 
-Experimental modifications to the theoretical cross sections in the RRR are described in Section III\ref{}. Included here are such effects as Doppler and resolution broadening, normalization and backgrounds, finite-size corrections, and treatment of more than one nuclide in the target sample. SAMMY's fitting procedure is described in Section IV\ref{}. Bayes' equations are derived from Bayes' theorem plus assumptions about normality and linearity. The relationship between Bayes' equations and the more familiar least-squares equations is described. Emphasis is placed on methodologies for properly including all measurement uncertainty in the analysis process, including the many SAMMY options for inclusion of data covariance information.
+Experimental modifications to the theoretical cross sections in the RRR are described in \S III(\ref{ch:exp-conditions}). Included here are such effects as Doppler and resolution broadening, normalization and backgrounds, finite-size corrections, and treatment of more than one nuclide in the target sample. SAMMY's fitting procedure is described in \S IV(\ref{ch:fitting-procedure}). Bayes' equations are derived from Bayes' theorem plus assumptions about normality and linearity. The relationship between Bayes' equations and the more familiar least-squares equations is described. Emphasis is placed on methodologies for properly including all measurement uncertainty in the analysis process, including the many SAMMY options for inclusion of data covariance information.
 
-Section V\ref{} describes such topics as post-processor options (calculating multigroup cross sections or other averages) and other miscellaneous features.
+\S V(\ref{ch:miscellaneous}) describes such topics as post-processor options (calculating multigroup cross sections or other averages) and other miscellaneous features.
 
-The input to SAMMY is detailed in Section VI\ref{}. Output is described in Section VII\ref{}.
+The input to SAMMY is detailed in \S VI(\ref{ch:input}). Output is described in \S VII(\ref{ch:output}).
 
-SAMMY's treatment of the unresolved resonance region (URR) is discussed in Section VIII\ref{}.
+SAMMY's treatment of the unresolved resonance region (URR) is discussed in \S VIII(\ref{ch:urr}).
 
 The theoretical treatment was borrowed directly from Fritz Fr\"{o}hner's FITACS program; subsequently, input/output and certain details of the calculation have been augmented to increase the functionality of this code.
 
-Section IX\ref{} describes the relationship of SAMMY to the Evaluated Nuclear Data Files (ENDF). Certain types of ENDF files can be used to provide resonance parameters, parameter covariance matrices, or experimental data as input to SAMMY. Likewise, SAMMY can produce ENDF files containing resonance parameters, point-wise cross sections, or uncertainty information.
+\S IX(\ref{ch:eval-connection}) describes the relationship of SAMMY to the Evaluated Nuclear Data Files (ENDF). Certain types of ENDF files can be used to provide resonance parameters, parameter covariance matrices, or experimental data as input to SAMMY. Likewise, SAMMY can produce ENDF files containing resonance parameters, point-wise cross sections, or uncertainty information.
 
-A number of auxiliary programs are available for use with SAMMY input or output. Section X\ref{} contains a brief description of those for which the SAMMY author has maintenance responsibility.
+A number of auxiliary programs are available for use with SAMMY input or output. \S X(\ref{ch:auxiliary-programs}) contains a brief description of those for which the SAMMY author has maintenance responsibility.
 
-Advice for running SAMMY is presented in Section XI\ref{}. Even experienced SAMMY users are encouraged to read this section, as it contains information about recent developments that may be unfamiliar (but potentially useful) to long-time users. Novices are likely to find valuable suggestions in this section. Anyone requesting the author's help is expected to have read and followed the procedures outlined in Section XI.B\ref{}.
+Advice for running SAMMY is presented in \S XI(\ref{ch:helpful-hints}). Even experienced SAMMY users are encouraged to read this section, as it contains information about recent developments that may be unfamiliar (but potentially useful) to long-time users. Novices are likely to find valuable suggestions in this section. Anyone requesting the author's help is expected to have read and followed the procedures outlined in \S XI.B(\ref{sec:problem-procedure}).
 
-Sample runs are described in Section XII\ref{}. These include (1) tutorial exercises (designed to familiarize a novice user with running the code), (2) test cases (designed for quality control, to ensure that the code gives consistent answers from one platform to another and from one version to another, but also useful as examples of input for specific features of the code), and (3) simulations (Monte Carlo simulations of multiple-scattering corrections, designed to test the accuracy of the SAMMY treatment for those corrections).
+Sample runs are described in \S XII(\ref{ch:examples}). These include (1) tutorial exercises (designed to familiarize a novice user with running the code), (2) test cases (designed for quality control, to ensure that the code gives consistent answers from one platform to another and from one version to another, but also useful as examples of input for specific features of the code), and (3) simulations (Monte Carlo simulations of multiple-scattering corrections, designed to test the accuracy of the SAMMY treatment for those corrections).
 
-Section XIII\ref{} provides an introduction to the computer code itself, for the benefit of the code managers at various sites. The casual user will probably not need the information from this section.
+\S XIII(\ref{ch:computer-code}) provides an introduction to the computer code itself, for the benefit of the code managers at various sites. The casual user will probably not need the information from this section.
 
 
 

docs/tex/miscellaneous.tex

+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+%                                                                 %
+%                            Miscellaneous                        %
+%                                                                 %
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+
+\chapter{Miscellaneous}\label{ch:miscellaneous}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Reconstructing Point-wise Cross Sections} \label{sec:pointwise-xs}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Integral Quantities} \label{sec:integral-quantities}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Averaging The Cross Sections} \label{sec:average-xs-out}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Stellar-averaged Capture Cross Sections} \label{sec:stellar-avg-xs}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Pseudo Cross Sections For Testing} \label{sec:pseudo-xs-for-tests}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Summed Strength Function} \label{sec:sum-strength-function}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+

docs/tex/output.tex

+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+%                                                                 %
+%                              Output                              %
+%                                                                 %
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
+
+\chapter{Output}\label{ch:output}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Line-printer Output} \label{sec:lpt-out}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Output To Be Used As Input} \label{sec:out-as-inp}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Plot Output} \label{sec:plot-out}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Complete Set Of Partial Derivatives For Resonance Parameters} \label{sec:derivs-out}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Compact Format For Parameter Covariance Information} \label{sec:compact-cov-out}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Publication Aids} \label{sec:pub-out}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Other Output Files} \label{sec:other-out}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\ No newline at end of file

docs/tex/sammy_main.tex

@@ -87,10 +87,19 @@
 	\include{abstract} % abstract
 	\include{introduction}
 	\include{scattering-theory}
-	\include{multScat} % Section
+	\include{exp-conditions}
+	\include{fitting-procedure}
+	\include{miscellaneous}
+	\include{input}
+	\include{output}
 	\include{urr}
+	\include{evaluation-connection}
+	\include{auxiliary-programs}
+	\include{helpful-hints}
+	\include{examples}
+	\include{computer-code}
 	\include{sammybib} % bibliography
 	% \bibliography{sammy_refs}
 	% \renewcommand*\thetable{\Alph{chapter}.\arabic{table}} % to get the tables to use chapter letters
-	% \include{} % appendix
+	\include{appendices}
 \end{document}

docs/tex/urr.tex

@@ -4,7 +4,7 @@
 %                                                                 %
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 
-\chapter{Unresolved Resonance Region}\label{ch:unresolved-res-region}
+\chapter{Unresolved Resonance Region}\label{ch:urr}
 
 As a first step towards expansion into the unresolved resonance region, Fritz Fr\"{o}hner's code
 FITACS \cite{frohner1989evaluation} has been obtained and inserted into SAMMY. FITACS uses Hauser-Feshbach
@@ -682,7 +682,7 @@ As with the resolved resonance region, each SAMMY/URR run may produce several ou
 
 \begin{enumerate}
     \item The SAMMY.LPT file contains details of the calculations.
-    \item For runs which involve the solution of Bayes' equations and hence the generation of updated parameter values (a ``Bayes run'' as opposed to a ``no-Bayes run'' which simply calculates cross sections), an output file SAMMY.PAR is provided in the annotated form described in Table \ref{annotated-urr-par-input}. (This file, of course, is quite different from the file by the same name produced in a resolved resonance region run.)
+    \item For runs which involve the solution of Bayes' equations and hence the generation of updated parameter values (a ``Bayes run'' as opposed to a ``no-Bayes run'' which simply calculates cross sections), an output file SAMMY.PAR is provided in the annotated form described in Table \ref{table:annotated-urr-par-input}. (This file, of course, is quite different from the file by the same name produced in a resolved resonance region run.)
     \item For Bayes runs, a COVariance file SAMMY.COV is produced, which contains (among other things) the final parameter covariance matrix; see below for more detail.
     \item Files SAMMY.NDF and SAMMY.N32 contain the URR portion of ENDF File 2 and 32, respectively; these files are produced when the appropriate command is in the INPut file.
     \item Files SAMMY.NDX and SAMMY.N3X contain the same information as in SAMMY.NDF and SAMMY.N32 respectively, but also include comment lines defining the parameters whose values are given. Only the uncertainty values are given in SAMMY.N3X; correlations are printed only in SAMMY.N32.
@@ -695,7 +695,7 @@ similar fashion to sequential runs in the RRR. There are slight differences, how
 this COVariance file; no auxiliary program comparable to SAMAMR is required here, as there is
 only one type of data-reduction parameter (the normalizations). The user must simply rename and
 modify the SAMMY.PAR file to contain the appropriate normalization parameters for the data sets
-about to be analyzed. The output PARameter file will contain card set 10a of Table \ref{annotated-urr-par-input};
+about to be analyzed. The output PARameter file will contain card set 10a of Table \ref{table:annotated-urr-par-input};
 PARameter files to be used as input will use either card set 10 (for new data sets for which the
 normalizations have not yet been defined) or card set 10a (to re-use normalizations already defined
 for the current data sets). See test case tr145 for examples.