Added rough chapter outlines

diff --git a/tex/src/Makefile b/tex/src/Makefile
index 3fa6f120042b5ac6e15c6b5964f133c3a936d29c..dc4028bc004cce5e148864cd215a3e0dd061fd3f 100644 (file)
--- a/tex/src/Makefile
+++ b/tex/src/Makefile
@@ -1,4 +1,6 @@
-SUBDIRS = packages sawsim unfolding_distributions cantilever_calib
+SUBDIRS = packages apparatus cantilever cantilever-calib contour-space \
+       future introduction sawsim temperature temperature-theory \
+       tension unfolding unfolding-distributions viscocity
 
 all :
        @for i in $(SUBDIRS); do \

diff --git a/tex/src/apparatus/main.tex b/tex/src/apparatus/main.tex
new file mode 100644 (file)
index 0000000..9416383
--- /dev/null
+++ b/tex/src/apparatus/main.tex
@@ -0,0 +1 @@
+\chapter{Apparatus}

diff --git a/tex/src/cantilever_calib/Makefile b/tex/src/cantilever-calib/Makefile
similarity index 100%
rename from tex/src/cantilever_calib/Makefile
rename to tex/src/cantilever-calib/Makefile

diff --git a/tex/src/cantilever_calib/README b/tex/src/cantilever-calib/README
similarity index 100%
rename from tex/src/cantilever_calib/README
rename to tex/src/cantilever-calib/README

diff --git a/tex/src/cantilever_calib/contour.asy b/tex/src/cantilever-calib/contour.asy
similarity index 100%
rename from tex/src/cantilever_calib/contour.asy
rename to tex/src/cantilever-calib/contour.asy

diff --git a/tex/src/cantilever_calib/contour_integration.tex b/tex/src/cantilever-calib/contour_integration.tex
similarity index 96%
rename from tex/src/cantilever_calib/contour_integration.tex
rename to tex/src/cantilever-calib/contour_integration.tex
index 5a3d0872c91373ddf8b076e64faefd80449c8986..3f3df7bea57b537301654245c611a9da50179f50 100644 (file)
--- a/tex/src/cantilever_calib/contour_integration.tex
+++ b/tex/src/cantilever-calib/contour_integration.tex
@@ -2,7 +2,7 @@
 
 \begin{figure}
   \begin{centering}
-    \includegraphics[width=0.3\textwidth]{cantilever_calib/contour} \\
+    \includegraphics[width=0.3\textwidth]{cantilever-calib/contour} \\
     \caption{Integral contour \C\ enclosing the upper half plane.}
     \label{f.UHP_contour}
   \end{centering}

diff --git a/tex/src/cantilever_calib/dot/concept_map.dot b/tex/src/cantilever-calib/dot/concept_map.dot
similarity index 100%
rename from tex/src/cantilever_calib/dot/concept_map.dot
rename to tex/src/cantilever-calib/dot/concept_map.dot

diff --git a/tex/src/cantilever_calib/integrals.tex b/tex/src/cantilever-calib/integrals.tex
similarity index 100%
rename from tex/src/cantilever_calib/integrals.tex
rename to tex/src/cantilever-calib/integrals.tex

diff --git a/tex/src/cantilever_calib/cantilever_calib.bib b/tex/src/cantilever-calib/main.bib
similarity index 100%
rename from tex/src/cantilever_calib/cantilever_calib.bib
rename to tex/src/cantilever-calib/main.bib

diff --git a/tex/src/cantilever-calib/main.tex b/tex/src/cantilever-calib/main.tex
new file mode 100644 (file)
index 0000000..8a5555f
--- /dev/null
+++ b/tex/src/cantilever-calib/main.tex
@@ -0,0 +1,7 @@
+\chapter{Cantilever Calibration}
+\input{cantilever-calib/overview}
+\input{cantilever-calib/setup_general}
+\input{cantilever-calib/solve_highly_damped}
+\input{cantilever-calib/solve_general}
+\input{cantilever-calib/contour_integration}
+\input{cantilever-calib/integrals}

diff --git a/tex/src/cantilever_calib/overview.tex b/tex/src/cantilever-calib/overview.tex
similarity index 100%
rename from tex/src/cantilever_calib/overview.tex
rename to tex/src/cantilever-calib/overview.tex

diff --git a/tex/src/cantilever_calib/setup_general.tex b/tex/src/cantilever-calib/setup_general.tex
similarity index 100%
rename from tex/src/cantilever_calib/setup_general.tex
rename to tex/src/cantilever-calib/setup_general.tex

diff --git a/tex/src/cantilever_calib/solve_general.tex b/tex/src/cantilever-calib/solve_general.tex
similarity index 100%
rename from tex/src/cantilever_calib/solve_general.tex
rename to tex/src/cantilever-calib/solve_general.tex

diff --git a/tex/src/cantilever_calib/solve_highly_damped.tex b/tex/src/cantilever-calib/solve_highly_damped.tex
similarity index 100%
rename from tex/src/cantilever_calib/solve_highly_damped.tex
rename to tex/src/cantilever-calib/solve_highly_damped.tex

diff --git a/tex/src/cantilever_calib/test/Lorentz_root.py b/tex/src/cantilever-calib/test/Lorentz_root.py
similarity index 100%
rename from tex/src/cantilever_calib/test/Lorentz_root.py
rename to tex/src/cantilever-calib/test/Lorentz_root.py

diff --git a/tex/src/cantilever_calib/test/Makefile b/tex/src/cantilever-calib/test/Makefile
similarity index 100%
rename from tex/src/cantilever_calib/test/Makefile
rename to tex/src/cantilever-calib/test/Makefile

diff --git a/tex/src/cantilever_calib/test/locate_roots.py b/tex/src/cantilever-calib/test/locate_roots.py
similarity index 100%
rename from tex/src/cantilever_calib/test/locate_roots.py
rename to tex/src/cantilever-calib/test/locate_roots.py

diff --git a/tex/src/cantilever_calib/test/test_integral.py b/tex/src/cantilever-calib/test/test_integral.py
similarity index 100%
rename from tex/src/cantilever_calib/test/test_integral.py
rename to tex/src/cantilever-calib/test/test_integral.py

diff --git a/tex/src/cantilever_calib/test/test_roots.py b/tex/src/cantilever-calib/test/test_roots.py
similarity index 100%
rename from tex/src/cantilever_calib/test/test_roots.py
rename to tex/src/cantilever-calib/test/test_roots.py

diff --git a/tex/src/cantilever/main.tex b/tex/src/cantilever/main.tex
new file mode 100644 (file)
index 0000000..652b193
--- /dev/null
+++ b/tex/src/cantilever/main.tex
@@ -0,0 +1 @@
+\chapter{Cantilever dependent unfolding experiments}

diff --git a/tex/src/cantilever_calib/main.tex b/tex/src/cantilever_calib/main.tex
deleted file mode 100644 (file)
index 5d9dd02..0000000
--- a/tex/src/cantilever_calib/main.tex
+++ /dev/null
@@ -1,7 +0,0 @@
-\chapter{Cantilever Calibration}
-\input{cantilever_calib/overview}
-\input{cantilever_calib/setup_general}
-\input{cantilever_calib/solve_highly_damped}
-\input{cantilever_calib/solve_general}
-\input{cantilever_calib/contour_integration}
-\input{cantilever_calib/integrals}

diff --git a/tex/src/contour-space/main.tex b/tex/src/contour-space/main.tex
new file mode 100644 (file)
index 0000000..5a07ff2
--- /dev/null
+++ b/tex/src/contour-space/main.tex
@@ -0,0 +1 @@
+\chapter{Contour space}

diff --git a/tex/src/future/main.tex b/tex/src/future/main.tex
new file mode 100644 (file)
index 0000000..211dd41
--- /dev/null
+++ b/tex/src/future/main.tex
@@ -0,0 +1 @@
+\chapter{Conclusions}

diff --git a/tex/src/introduction/main.tex b/tex/src/introduction/main.tex
new file mode 100644 (file)
index 0000000..f4ec3a1
--- /dev/null
+++ b/tex/src/introduction/main.tex
@@ -0,0 +1 @@
+\chapter{Introduction}

diff --git a/tex/src/root.tex b/tex/src/root.tex
index 1b501ec4991e9f351526e4475627778bb015f0be..c74fd94592d802211dbee8c5eab1bb6eec99da45 100644 (file)
--- a/tex/src/root.tex
+++ b/tex/src/root.tex
@@ -41,19 +41,27 @@ R01-GM071793.
 
 \begin{thesis}
 \pdfbookmark[-1]{Mainmatter}{Mainmatter}
-\include{unfolding_distributions/main}
+\include{introduction/main}
+\include{unfolding/main}
+\include{tension/main}
+\include{unfolding-distributions/main}
 \include{sawsim/main}
-\include{hyeon_temp/main}
+\include{contour-space} % TODO: conventional name?
+\include{apparatus/main}
+\include{temperature-theory/main}
+\include{temperature/main}
+\include{cantilever/main}
+\include{future/main}
 \end{thesis}
 
 \bibliography{%
-%              unfolding_distributions/unfolding_distributions,
-%              sawsim/sawsim,% currently empty
-              cantilever_calib/cantilever_calib,%
+%              unfolding-distributions/main,
+%              sawsim/main,% currently empty
+              cantilever-calib/main,%
               wtk}
 
 \appendix
-\include{cantilever_calib/main}
+\include{cantilever-calib/main}
 \include{viscocity/main}
 
 \begin{vita}

diff --git a/tex/src/hyeon_temp/main.tex b/tex/src/temperature-theory/main.tex
similarity index 98%
rename from tex/src/hyeon_temp/main.tex
rename to tex/src/temperature-theory/main.tex
index 430b89a9cf66df40828bda936b182b729ffb5090..5901bee3e5045ca5c934ad6ac232924afcc44e41 100644 (file)
--- a/tex/src/hyeon_temp/main.tex
+++ b/tex/src/temperature-theory/main.tex
@@ -1,4 +1,4 @@
-\chapter{Temperature dependent unfolding}
+\chapter{Temperature dependent unfolding theory}
 
 \section{Energy landscape roughness}
 

diff --git a/tex/src/temperature/main.tex b/tex/src/temperature/main.tex
new file mode 100644 (file)
index 0000000..accb47f
--- /dev/null
+++ b/tex/src/temperature/main.tex
@@ -0,0 +1 @@
+\chapter{Temperature dependent unfolding experiments}

diff --git a/tex/src/tension/main.tex b/tex/src/tension/main.tex
new file mode 100644 (file)
index 0000000..3d626d4
--- /dev/null
+++ b/tex/src/tension/main.tex
@@ -0,0 +1 @@
+\chapter{Chain Tension}

diff --git a/tex/src/unfolding_distributions/Makefile b/tex/src/unfolding-distributions/Makefile
similarity index 100%
rename from tex/src/unfolding_distributions/Makefile
rename to tex/src/unfolding-distributions/Makefile

diff --git a/tex/src/unfolding_distributions/kramers.tex b/tex/src/unfolding-distributions/kramers.tex
similarity index 100%
rename from tex/src/unfolding_distributions/kramers.tex
rename to tex/src/unfolding-distributions/kramers.tex

diff --git a/tex/src/unfolding_distributions/main.tex b/tex/src/unfolding-distributions/main.tex
similarity index 100%
rename from tex/src/unfolding_distributions/main.tex
rename to tex/src/unfolding-distributions/main.tex

diff --git a/tex/src/unfolding_distributions/overview.tex b/tex/src/unfolding-distributions/overview.tex
similarity index 100%
rename from tex/src/unfolding_distributions/overview.tex
rename to tex/src/unfolding-distributions/overview.tex

diff --git a/tex/src/unfolding_distributions/review.tex b/tex/src/unfolding-distributions/review.tex
similarity index 100%
rename from tex/src/unfolding_distributions/review.tex
rename to tex/src/unfolding-distributions/review.tex

diff --git a/tex/src/unfolding_distributions/singledomain_constantloading.tex b/tex/src/unfolding-distributions/singledomain_constantloading.tex
similarity index 100%
rename from tex/src/unfolding_distributions/singledomain_constantloading.tex
rename to tex/src/unfolding-distributions/singledomain_constantloading.tex

diff --git a/tex/src/unfolding/main.tex b/tex/src/unfolding/main.tex
new file mode 100644 (file)
index 0000000..7b0e701
--- /dev/null
+++ b/tex/src/unfolding/main.tex
@@ -0,0 +1 @@
+\chapter{Unfolding Theory}