From: W. Trevor King <wking@drexel.edu>
Date: Thu, 18 Feb 2010 00:22:21 +0000 (-0500)
Subject: Broke the figures out into their own src subdirectory.
X-Git-Tag: v1.0~458
X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=ee5bcd36ffa6071a9b2f9ae6c69284e8d3679e9e;p=thesis.git

Broke the figures out into their own src subdirectory.

They used to live under the different chapters, but the new structure
will make it easier to share figure-generation code between chapters.
---

diff --git a/tex/src/Makefile b/tex/src/Makefile
index e99154c..b747772 100644
--- a/tex/src/Makefile
+++ b/tex/src/Makefile
@@ -1,5 +1,5 @@
 SUBDIRS = packages apparatus cantilever cantilever-calib contour-space \
-	future introduction sawsim temperature temperature-theory \
+	figures future introduction sawsim temperature temperature-theory \
 	tension unfolding unfolding-distributions viscocity
 
 all :
diff --git a/tex/src/apparatus/Makefile b/tex/src/apparatus/Makefile
new file mode 100644
index 0000000..a1f4f4c
--- /dev/null
+++ b/tex/src/apparatus/Makefile
@@ -0,0 +1,3 @@
+all :
+
+clean :
diff --git a/tex/src/cantilever-calib/Makefile b/tex/src/cantilever-calib/Makefile
index 0c98a97..a260214 100644
--- a/tex/src/cantilever-calib/Makefile
+++ b/tex/src/cantilever-calib/Makefile
@@ -1,16 +1,3 @@
-GEN_FILES = contour.pdf #dot/concept_map.png
-
-all : $(GEN_FILES)
+all : 
 
 clean :
-	rm -f $(GEN_FILES)
-	$(MAKE) -C test clean
-
-check :
-	$(MAKE) -C test all
-
-contour.pdf :
-	asy -f pdf contour.asy
-
-dot/concept_map.png :
-	dot -Tpng dot/concept_map.dot > $@
diff --git a/tex/src/cantilever-calib/contour_integration.tex b/tex/src/cantilever-calib/contour_integration.tex
index 3f3df7b..591b575 100644
--- 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]{figures/contour/contour} \\
     \caption{Integral contour \C\ enclosing the upper half plane.}
     \label{f.UHP_contour}
   \end{centering}
diff --git a/tex/src/cantilever/Makefile b/tex/src/cantilever/Makefile
new file mode 100644
index 0000000..a1f4f4c
--- /dev/null
+++ b/tex/src/cantilever/Makefile
@@ -0,0 +1,3 @@
+all :
+
+clean :
diff --git a/tex/src/contour-space/Makefile b/tex/src/contour-space/Makefile
new file mode 100644
index 0000000..a1f4f4c
--- /dev/null
+++ b/tex/src/contour-space/Makefile
@@ -0,0 +1,3 @@
+all :
+
+clean :
diff --git a/tex/src/sawsim/figures/Makefile b/tex/src/figures/Makefile
similarity index 66%
rename from tex/src/sawsim/figures/Makefile
rename to tex/src/figures/Makefile
index 0030b18..adafb9c 100644
--- a/tex/src/sawsim/figures/Makefile
+++ b/tex/src/figures/Makefile
@@ -1,5 +1,6 @@
-SUBDIRS = expt-sawtooth fit-space kappa-sawteeth order-dep \
-	schematic sim-hist sim-sawtooth v-dep
+SUBDIRS = expt-sawtooth fit-space contour kappa-sawteeth order-dep \
+	schematic sim-hist sim-sawtooth v-dep \
+	# calibration-concept-map
 
 all :
 	@for i in $(SUBDIRS); do \
diff --git a/tex/src/figures/calibration-concept-map/Makefile b/tex/src/figures/calibration-concept-map/Makefile
new file mode 100644
index 0000000..b9f8fec
--- /dev/null
+++ b/tex/src/figures/calibration-concept-map/Makefile
@@ -0,0 +1,7 @@
+all : concept_map.png
+
+clean :
+	rm -f concept_map.png
+
+concept_map.png :
+	dot -Tpng concept_map.dot > $@
diff --git a/tex/src/cantilever-calib/dot/concept_map.dot b/tex/src/figures/calibration-concept-map/concept_map.dot
similarity index 100%
rename from tex/src/cantilever-calib/dot/concept_map.dot
rename to tex/src/figures/calibration-concept-map/concept_map.dot
diff --git a/tex/src/figures/contour/Makefile b/tex/src/figures/contour/Makefile
new file mode 100644
index 0000000..8936b13
--- /dev/null
+++ b/tex/src/figures/contour/Makefile
@@ -0,0 +1,7 @@
+all : contour.pdf
+
+clean :
+	rm -f contour.pdf
+
+contour.pdf :
+	asy -f pdf contour.asy
diff --git a/tex/src/cantilever-calib/contour.asy b/tex/src/figures/contour/contour.asy
similarity index 100%
rename from tex/src/cantilever-calib/contour.asy
rename to tex/src/figures/contour/contour.asy
diff --git a/tex/src/sawsim/figures/sim-sawtooth/Makefile b/tex/src/figures/expt-sawtooth/Makefile
similarity index 100%
rename from tex/src/sawsim/figures/sim-sawtooth/Makefile
rename to tex/src/figures/expt-sawtooth/Makefile
diff --git a/tex/src/sawsim/figures/expt-sawtooth/NOTES b/tex/src/figures/expt-sawtooth/NOTES
similarity index 100%
rename from tex/src/sawsim/figures/expt-sawtooth/NOTES
rename to tex/src/figures/expt-sawtooth/NOTES
diff --git a/tex/src/sawsim/figures/expt-sawtooth/expt.d b/tex/src/figures/expt-sawtooth/expt.d
similarity index 100%
rename from tex/src/sawsim/figures/expt-sawtooth/expt.d
rename to tex/src/figures/expt-sawtooth/expt.d
diff --git a/tex/src/sawsim/figures/expt-sawtooth/plot.gp b/tex/src/figures/expt-sawtooth/plot.gp
similarity index 100%
rename from tex/src/sawsim/figures/expt-sawtooth/plot.gp
rename to tex/src/figures/expt-sawtooth/plot.gp
diff --git a/tex/src/sawsim/figures/expt-sawtooth/sawmodel.xml b/tex/src/figures/expt-sawtooth/sawmodel.xml
similarity index 100%
rename from tex/src/sawsim/figures/expt-sawtooth/sawmodel.xml
rename to tex/src/figures/expt-sawtooth/sawmodel.xml
diff --git a/tex/src/sawsim/figures/fit-space/Best_2002_detailed_unfolding_pathway/fig3.ppm b/tex/src/figures/fit-space/Best_2002_detailed_unfolding_pathway/fig3.ppm
similarity index 100%
rename from tex/src/sawsim/figures/fit-space/Best_2002_detailed_unfolding_pathway/fig3.ppm
rename to tex/src/figures/fit-space/Best_2002_detailed_unfolding_pathway/fig3.ppm
diff --git a/tex/src/sawsim/figures/fit-space/Best_2002_detailed_unfolding_pathway/fig3a.clicks b/tex/src/figures/fit-space/Best_2002_detailed_unfolding_pathway/fig3a.clicks
similarity index 100%
rename from tex/src/sawsim/figures/fit-space/Best_2002_detailed_unfolding_pathway/fig3a.clicks
rename to tex/src/figures/fit-space/Best_2002_detailed_unfolding_pathway/fig3a.clicks
diff --git a/tex/src/sawsim/figures/fit-space/Best_2002_detailed_unfolding_pathway/fig3a.data b/tex/src/figures/fit-space/Best_2002_detailed_unfolding_pathway/fig3a.data
similarity index 100%
rename from tex/src/sawsim/figures/fit-space/Best_2002_detailed_unfolding_pathway/fig3a.data
rename to tex/src/figures/fit-space/Best_2002_detailed_unfolding_pathway/fig3a.data
diff --git a/tex/src/sawsim/figures/fit-space/Best_2002_detailed_unfolding_pathway/fig3a.data.loglog b/tex/src/figures/fit-space/Best_2002_detailed_unfolding_pathway/fig3a.data.loglog
similarity index 100%
rename from tex/src/sawsim/figures/fit-space/Best_2002_detailed_unfolding_pathway/fig3a.data.loglog
rename to tex/src/figures/fit-space/Best_2002_detailed_unfolding_pathway/fig3a.data.loglog
diff --git a/tex/src/sawsim/figures/fit-space/Best_2002_detailed_unfolding_pathway/fig3a.summary b/tex/src/figures/fit-space/Best_2002_detailed_unfolding_pathway/fig3a.summary
similarity index 100%
rename from tex/src/sawsim/figures/fit-space/Best_2002_detailed_unfolding_pathway/fig3a.summary
rename to tex/src/figures/fit-space/Best_2002_detailed_unfolding_pathway/fig3a.summary
diff --git a/tex/src/sawsim/figures/fit-space/Best_2002_detailed_unfolding_pathway/fit.log b/tex/src/figures/fit-space/Best_2002_detailed_unfolding_pathway/fit.log
similarity index 100%
rename from tex/src/sawsim/figures/fit-space/Best_2002_detailed_unfolding_pathway/fit.log
rename to tex/src/figures/fit-space/Best_2002_detailed_unfolding_pathway/fit.log
diff --git a/tex/src/sawsim/figures/fit-space/Best_2002_detailed_unfolding_pathway/king_expt.data b/tex/src/figures/fit-space/Best_2002_detailed_unfolding_pathway/king_expt.data
similarity index 100%
rename from tex/src/sawsim/figures/fit-space/Best_2002_detailed_unfolding_pathway/king_expt.data
rename to tex/src/figures/fit-space/Best_2002_detailed_unfolding_pathway/king_expt.data
diff --git a/tex/src/sawsim/figures/fit-space/Best_2002_detailed_unfolding_pathway/king_extrap.data b/tex/src/figures/fit-space/Best_2002_detailed_unfolding_pathway/king_extrap.data
similarity index 100%
rename from tex/src/sawsim/figures/fit-space/Best_2002_detailed_unfolding_pathway/king_extrap.data
rename to tex/src/figures/fit-space/Best_2002_detailed_unfolding_pathway/king_extrap.data
diff --git a/tex/src/sawsim/figures/fit-space/Best_2002_detailed_unfolding_pathway/king_sim-566.data b/tex/src/figures/fit-space/Best_2002_detailed_unfolding_pathway/king_sim-566.data
similarity index 100%
rename from tex/src/sawsim/figures/fit-space/Best_2002_detailed_unfolding_pathway/king_sim-566.data
rename to tex/src/figures/fit-space/Best_2002_detailed_unfolding_pathway/king_sim-566.data
diff --git a/tex/src/sawsim/figures/fit-space/Best_2002_detailed_unfolding_pathway/loglog_to_normal.py b/tex/src/figures/fit-space/Best_2002_detailed_unfolding_pathway/loglog_to_normal.py
similarity index 100%
rename from tex/src/sawsim/figures/fit-space/Best_2002_detailed_unfolding_pathway/loglog_to_normal.py
rename to tex/src/figures/fit-space/Best_2002_detailed_unfolding_pathway/loglog_to_normal.py
diff --git a/tex/src/sawsim/figures/sim-hist/Makefile b/tex/src/figures/fit-space/Makefile
similarity index 100%
rename from tex/src/sawsim/figures/sim-hist/Makefile
rename to tex/src/figures/fit-space/Makefile
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similarity index 100%
rename from tex/src/sawsim/figures/fit-space/data
rename to tex/src/figures/fit-space/data
diff --git a/tex/src/sawsim/figures/fit-space/extract_fit_valley.py b/tex/src/figures/fit-space/extract_fit_valley.py
similarity index 100%
rename from tex/src/sawsim/figures/fit-space/extract_fit_valley.py
rename to tex/src/figures/fit-space/extract_fit_valley.py
diff --git a/tex/src/sawsim/figures/fit-space/fit.log b/tex/src/figures/fit-space/fit.log
similarity index 100%
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diff --git a/tex/src/sawsim/figures/fit-space/fit_valley.data b/tex/src/figures/fit-space/fit_valley.data
similarity index 100%
rename from tex/src/sawsim/figures/fit-space/fit_valley.data
rename to tex/src/figures/fit-space/fit_valley.data
diff --git a/tex/src/sawsim/figures/fit-space/king_vs_best.gp b/tex/src/figures/fit-space/king_vs_best.gp
similarity index 100%
rename from tex/src/sawsim/figures/fit-space/king_vs_best.gp
rename to tex/src/figures/fit-space/king_vs_best.gp
diff --git a/tex/src/sawsim/figures/fit-space/king_vs_best.png b/tex/src/figures/fit-space/king_vs_best.png
similarity index 100%
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diff --git a/tex/src/sawsim/figures/folded-model-hists/fig.pdf b/tex/src/figures/folded-model-hists/fig.pdf
similarity index 100%
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rename to tex/src/figures/folded-model-hists/fig.pdf
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
rename from tex/src/sawsim/figures/order-dep/Makefile
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diff --git a/tex/src/sawsim/figures/order-dep/data/hist3i.hist b/tex/src/figures/order-dep/data/hist3i.hist
similarity index 100%
rename from tex/src/sawsim/figures/order-dep/data/hist3i.hist
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similarity index 100%
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diff --git a/tex/src/sawsim/figures/order-dep/data/hist3ii.hist b/tex/src/figures/order-dep/data/hist3ii.hist
similarity index 100%
rename from tex/src/sawsim/figures/order-dep/data/hist3ii.hist
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similarity index 100%
rename from tex/src/sawsim/figures/order-dep/data/hist3ii.note
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similarity index 100%
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diff --git a/tex/src/future/Makefile b/tex/src/future/Makefile
new file mode 100644
index 0000000..a1f4f4c
--- /dev/null
+++ b/tex/src/future/Makefile
@@ -0,0 +1,3 @@
+all :
+
+clean :
diff --git a/tex/src/introduction/Makefile b/tex/src/introduction/Makefile
new file mode 100644
index 0000000..a1f4f4c
--- /dev/null
+++ b/tex/src/introduction/Makefile
@@ -0,0 +1,3 @@
+all :
+
+clean :
diff --git a/tex/src/introduction/main.tex b/tex/src/introduction/main.tex
index 927a76c..47ed3fa 100644
--- a/tex/src/introduction/main.tex
+++ b/tex/src/introduction/main.tex
@@ -112,9 +112,9 @@ single molecule mechanical unfolding experiments.
 
 \begin{figure}
 \begin{center}
-\subfloat[][]{\includegraphics{sawsim/schematic}\label{fig:schematic}}
+\subfloat[][]{\includegraphics{figures/schematic/unfolding}\label{fig:schematic}}
 %\hspace{.25in}%
-\subfloat[][]{\includegraphics{sawsim/expt-sawtooth}\label{fig:expt-sawtooth}}
+\subfloat[][]{\includegraphics{figures/expt-sawtooth/fig}\label{fig:expt-sawtooth}}
 \caption{(a) Schematic of the experimental setup for mechanical
   unfolding of proteins using an AFM (not to scale).  An experiment
   starts with the tip in contact with the substrate surface, which is
diff --git a/tex/src/sawsim/Makefile b/tex/src/sawsim/Makefile
index 91ae5b1..a1f4f4c 100644
--- a/tex/src/sawsim/Makefile
+++ b/tex/src/sawsim/Makefile
@@ -1,10 +1,3 @@
-all : figures
+all :
 
-clean : figures-clean
-
-.PHONY : figures
-figures :
-	$(MAKE) --directory figures all
-
-figures-clean :
-	$(MAKE) --directory figures clean
+clean :
diff --git a/tex/src/sawsim/discussion.tex b/tex/src/sawsim/discussion.tex
index 6e65fd6..151aa41 100644
--- a/tex/src/sawsim/discussion.tex
+++ b/tex/src/sawsim/discussion.tex
@@ -23,9 +23,9 @@ deviation of $25\U{pN}$.
 \begin{figure}
 \vspace{-1in}
 \begin{center}
-\subfloat[][]{\includegraphics{sawsim/sim-sawtooth}\label{fig:sawsim:sim-sawtooth}%
+\subfloat[][]{\includegraphics{figures/sim-sawtooth/fig}\label{fig:sawsim:sim-sawtooth}%
 }\\
-\subfloat[][]{\includegraphics{sawsim/sim-hist}\label{fig:sawsim:sim-hist}%
+\subfloat[][]{\includegraphics{figures/sim-hist/fig}\label{fig:sawsim:sim-hist}%
 }
 \caption{(a) Three simulated force curves from pulling a polymer of
   eight identical protein molecules.  The simulation was carried out
@@ -152,25 +152,26 @@ quite different for the same protein because of the differences in
 unfolding order and polymer length.
 
 \begin{figure}
-\begin{center}
-\includegraphics{sawsim/order-dep}
-\caption{The dependence of the unfolding force on the temporal
-  unfolding order for four polymers with $4$, $8$, $12$, and $16$
-  molecules of identical proteins.  Each point in the figure is the
-  average of $400$ data points.  The first point in each curve
-  represents the average of only the first peak in each of the $400$
-  simulated force curves, the second point represents the average of
-  only the second peak, and so on.  The solid lines are fits of
-  \cref{eq:sawsim:order-dep} to the simulated data, with best fit
-  $\kappa_\text{WLC}=203$, $207$, $161$, and $157\U{pN/nm}$,
-  respectively, for lengths $4$ through $16$.  The insets show the
-  force distributions of the first, fourth, and eighth peaks, left to
-  right, for the polymer with eight protein molecules.  The parameters
-  used for generating the data were the same as those used for
-  \cref{fig:sawsim:sim-sawtooth}, except the polymer length, and the
-  histograms in the insets were normalized in the same way as in
-  \cref{fig:sawsim:sim-hist}.\label{fig:sawsim:order-dep}}
-\end{center}
+  \begin{center}
+  \includegraphics{figures/order-dep/fig}
+  \caption{The dependence of the unfolding force on the temporal
+    unfolding order for four polymers with $4$, $8$, $12$, and $16$
+    molecules of identical proteins.  Each point in the figure is the
+    average of $400$ data points.  The first point in each curve
+    represents the average of only the first peak in each of the $400$
+    simulated force curves, the second point represents the average of
+    only the second peak, and so on.  The solid lines are fits of
+    \cref{eq:sawsim:order-dep} to the simulated data, with best fit
+    $\kappa_\text{WLC}=203$, $207$, $161$, and $157\U{pN/nm}$,
+    respectively, for lengths $4$ through $16$.  The insets show the
+    force distributions of the first, fourth, and eighth peaks, left
+    to right, for the polymer with eight protein molecules.  The
+    parameters used for generating the data were the same as those
+    used for \cref{fig:sawsim:sim-sawtooth}, except the polymer
+    length, and the histograms in the insets were normalized in the
+    same way as in
+    \cref{fig:sawsim:sim-hist}.\label{fig:sawsim:order-dep}}
+  \end{center}
 \end{figure}
 
 \subsection{The effect of polymer inhomogeneity}
@@ -236,7 +237,7 @@ to WLC or other polymer models (\cref{fig:expt-sawtooth}).
 
 \begin{figure}
 \begin{center}
-\includegraphics{sawsim/kappa-sawteeth}
+\includegraphics{figures/kappa-sawteeth/fig}
 \caption{Simulated force curves obtained from pulling a polymer with
   eight protein molecules using cantilevers with different force
   constants $\kappa_c$.  Parameters used in generating these curves
@@ -319,37 +320,39 @@ the unfolding force distribution, as well as any relevant information
 about the protein from other sources.
 
 \begin{figure}
-\begin{center}
-\subfloat[][]{\includegraphics{sawsim/v-dep}\label{fig:sawsim:v-dep}%
-} \\
-\subfloat[][]{\includegraphics{sawsim/v-dep-sd}\label{fig:sawsim:width-v-dep}%
-}
-\caption{(a) The dependence of the unfolding forces on the pulling
-  speed for three different model protein molecules characterized by
-  the parameters $k_{u0}$ and $\Delta x_u$.  The polymer length is
-  eight molecules, and each symbol is the average of $3200$ data
-  points.  (b) The dependence of standard deviation of the unfolding
-  force distribution on the pulling speed for the simulation data
-  shown in (a), using the same symbols.  The insets show the force
-  distribution histograms for the three proteins at the pulling speed
-  of $1\U{$\mu$m/s}$.  The left, middle and right histograms are for
-  the proteins represented by the top, middle, and bottom lines in (a),
-  respectively.\label{fig:sawsim:all-v-dep}}
-\end{center}
+  \begin{center}
+  \subfloat[][]{\includegraphics{figures/v-dep/fig}%
+    \label{fig:sawsim:v-dep}%
+  } \\
+  \subfloat[][]{\includegraphics{figures/v-dep/fig-sd}%
+    \label{fig:sawsim:width-v-dep}%
+  }
+  \caption{(a) The dependence of the unfolding forces on the pulling
+    speed for three different model protein molecules characterized by
+    the parameters $k_{u0}$ and $\Delta x_u$.  The polymer length is
+    eight molecules, and each symbol is the average of $3200$ data
+    points.  (b) The dependence of standard deviation of the unfolding
+    force distribution on the pulling speed for the simulation data
+    shown in (a), using the same symbols.  The insets show the force
+    distribution histograms for the three proteins at the pulling
+    speed of $1\U{$\mu$m/s}$.  The left, middle and right histograms
+    are for the proteins represented by the top, middle, and bottom
+    lines in (a), respectively.\label{fig:sawsim:all-v-dep}}
+  \end{center}
 \end{figure}
 
 \begin{figure}
-\begin{center}
-\includegraphics{sawsim/fit-space}
-\caption{Fit quality between an experimental data set and simulated
-  data sets obtained using various values of unfolding rate parameters
-  $k_{u0}$ and $\Delta x_u$.  The experimental data are from octameric
-  ubiquitin pulled at $1\U{$\mu$m/s}$\citep{chyan04}, and the other
-  model parameters are the same as those in \cref{fig:sawsim:sim-all}.  The
-  best fit parameters are $\Delta x_u=0.17\U{nm}$ and
-  $k_{u0}=1.2\E{-2}\U{s$^{-1}$}$.  The simulation histograms were
-  built from $400$ pulls at for each parameter pair.  The color scale
-  shown on the right is $log_{10}(D_\text{JS})$.
-\label{fig:sawsim:fit-space}}
-\end{center}
+  \begin{center}
+  \includegraphics{figures/fit-space/fig}
+  \caption{Fit quality between an experimental data set and simulated
+    data sets obtained using various values of unfolding rate
+    parameters $k_{u0}$ and $\Delta x_u$.  The experimental data are
+    from octameric ubiquitin pulled at $1\U{$\mu$m/s}$\citep{chyan04},
+    and the other model parameters are the same as those in
+    \cref{fig:sawsim:sim-all}.  The best fit parameters are $\Delta
+    x_u=0.17\U{nm}$ and $k_{u0}=1.2\E{-2}\U{s$^{-1}$}$.  The
+    simulation histograms were built from $400$ pulls at for each
+    parameter pair.  The color scale shown on the right is
+    $log_{10}(D_\text{JS})$.\label{fig:sawsim:fit-space}}
+  \end{center}
 \end{figure}
diff --git a/tex/src/sawsim/expt-sawtooth.pdf b/tex/src/sawsim/expt-sawtooth.pdf
deleted file mode 120000
index 8bceed8..0000000
--- a/tex/src/sawsim/expt-sawtooth.pdf
+++ /dev/null
@@ -1 +0,0 @@
-figures/expt-sawtooth/fig.pdf
\ No newline at end of file
diff --git a/tex/src/sawsim/figures/README b/tex/src/sawsim/figures/README
deleted file mode 100644
index a519c6f..0000000
--- a/tex/src/sawsim/figures/README
+++ /dev/null
@@ -1,23 +0,0 @@
-Tiffs (.tif) for raster
-EPS/PDF (.eps/.pdf) for vector
-
-Figure sizes:
-  1 column   :  90mm wide
-  1.5 columns: 140mm wide
-  2 columns  : 190mm wide
-
-Raster resolutions
-  Halftone/Gray/RGB:  300dpi
-  Line art         : 1000dpi
-  Combination art  :  500dpi
-
-EPS: include preview/thumbnail
-
-Artwork lettering: 7pt for normal text (rule of thumb).
-Embed fonts, use Arial, Courier, Times, Symbol.
-  (I can't figure out how to embed fonts in gnuplot's PDF terminal,
-  but times shouldn't change all that much, so don't worry about
-  it...)
-
-Naming:
-  fig1.tif, etc. ...
diff --git a/tex/src/sawsim/fit-space.pdf b/tex/src/sawsim/fit-space.pdf
deleted file mode 120000
index e90d165..0000000
--- a/tex/src/sawsim/fit-space.pdf
+++ /dev/null
@@ -1 +0,0 @@
-figures/fit-space/fig.pdf
\ No newline at end of file
diff --git a/tex/src/sawsim/kappa-sawteeth.pdf b/tex/src/sawsim/kappa-sawteeth.pdf
deleted file mode 120000
index d283893..0000000
--- a/tex/src/sawsim/kappa-sawteeth.pdf
+++ /dev/null
@@ -1 +0,0 @@
-figures/kappa-sawteeth/fig.pdf
\ No newline at end of file
diff --git a/tex/src/sawsim/order-dep.pdf b/tex/src/sawsim/order-dep.pdf
deleted file mode 120000
index 190675b..0000000
--- a/tex/src/sawsim/order-dep.pdf
+++ /dev/null
@@ -1 +0,0 @@
-figures/order-dep/fig.pdf
\ No newline at end of file
diff --git a/tex/src/sawsim/schematic.pdf b/tex/src/sawsim/schematic.pdf
deleted file mode 120000
index eb7a025..0000000
--- a/tex/src/sawsim/schematic.pdf
+++ /dev/null
@@ -1 +0,0 @@
-figures/schematic/unfolding.pdf
\ No newline at end of file
diff --git a/tex/src/sawsim/sim-hist.pdf b/tex/src/sawsim/sim-hist.pdf
deleted file mode 120000
index 0d3dfc3..0000000
--- a/tex/src/sawsim/sim-hist.pdf
+++ /dev/null
@@ -1 +0,0 @@
-figures/sim-hist/fig.pdf
\ No newline at end of file
diff --git a/tex/src/sawsim/sim-sawtooth.pdf b/tex/src/sawsim/sim-sawtooth.pdf
deleted file mode 120000
index ed1d2a8..0000000
--- a/tex/src/sawsim/sim-sawtooth.pdf
+++ /dev/null
@@ -1 +0,0 @@
-figures/sim-sawtooth/fig.pdf
\ No newline at end of file
diff --git a/tex/src/sawsim/v-dep-sd.pdf b/tex/src/sawsim/v-dep-sd.pdf
deleted file mode 120000
index ffb79d8..0000000
--- a/tex/src/sawsim/v-dep-sd.pdf
+++ /dev/null
@@ -1 +0,0 @@
-figures/v-dep/fig-sd.pdf
\ No newline at end of file
diff --git a/tex/src/sawsim/v-dep.pdf b/tex/src/sawsim/v-dep.pdf
deleted file mode 120000
index 0f2e340..0000000
--- a/tex/src/sawsim/v-dep.pdf
+++ /dev/null
@@ -1 +0,0 @@
-figures/v-dep/fig.pdf
\ No newline at end of file
diff --git a/tex/src/temperature-theory/Makefile b/tex/src/temperature-theory/Makefile
new file mode 100644
index 0000000..a1f4f4c
--- /dev/null
+++ b/tex/src/temperature-theory/Makefile
@@ -0,0 +1,3 @@
+all :
+
+clean :
diff --git a/tex/src/temperature/Makefile b/tex/src/temperature/Makefile
new file mode 100644
index 0000000..a1f4f4c
--- /dev/null
+++ b/tex/src/temperature/Makefile
@@ -0,0 +1,3 @@
+all :
+
+clean :
diff --git a/tex/src/tension/Makefile b/tex/src/tension/Makefile
new file mode 100644
index 0000000..a1f4f4c
--- /dev/null
+++ b/tex/src/tension/Makefile
@@ -0,0 +1,3 @@
+all :
+
+clean :
diff --git a/tex/src/unfolding/Makefile b/tex/src/unfolding/Makefile
new file mode 100644
index 0000000..a1f4f4c
--- /dev/null
+++ b/tex/src/unfolding/Makefile
@@ -0,0 +1,3 @@
+all :
+
+clean :