From df9f72d6086a4722c20ed2bf3b9b89b7cfa5304e Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Tue, 9 Feb 2010 17:25:13 -0500 Subject: [PATCH] Added rough chapter outlines --- tex/src/Makefile | 4 +++- tex/src/apparatus/main.tex | 1 + .../Makefile | 0 .../README | 0 .../contour.asy | 0 .../contour_integration.tex | 2 +- .../dot/concept_map.dot | 0 .../integrals.tex | 0 .../main.bib} | 0 tex/src/cantilever-calib/main.tex | 7 +++++++ .../overview.tex | 0 .../setup_general.tex | 0 .../solve_general.tex | 0 .../solve_highly_damped.tex | 0 .../test/Lorentz_root.py | 0 .../test/Makefile | 0 .../test/locate_roots.py | 0 .../test/test_integral.py | 0 .../test/test_roots.py | 0 tex/src/cantilever/main.tex | 1 + tex/src/cantilever_calib/main.tex | 7 ------- tex/src/contour-space/main.tex | 1 + tex/src/future/main.tex | 1 + tex/src/introduction/main.tex | 1 + tex/src/root.tex | 20 +++++++++++++------ .../main.tex | 2 +- tex/src/temperature/main.tex | 1 + tex/src/tension/main.tex | 1 + .../Makefile | 0 .../kramers.tex | 0 .../main.tex | 0 .../overview.tex | 0 .../review.tex | 0 .../singledomain_constantloading.tex | 0 tex/src/unfolding/main.tex | 1 + 35 files changed, 34 insertions(+), 16 deletions(-) create mode 100644 tex/src/apparatus/main.tex rename tex/src/{cantilever_calib => cantilever-calib}/Makefile (100%) rename tex/src/{cantilever_calib => cantilever-calib}/README (100%) rename tex/src/{cantilever_calib => cantilever-calib}/contour.asy (100%) rename tex/src/{cantilever_calib => cantilever-calib}/contour_integration.tex (96%) rename tex/src/{cantilever_calib => cantilever-calib}/dot/concept_map.dot (100%) rename tex/src/{cantilever_calib => cantilever-calib}/integrals.tex (100%) rename tex/src/{cantilever_calib/cantilever_calib.bib => cantilever-calib/main.bib} (100%) create mode 100644 tex/src/cantilever-calib/main.tex rename tex/src/{cantilever_calib => cantilever-calib}/overview.tex (100%) rename tex/src/{cantilever_calib => cantilever-calib}/setup_general.tex (100%) rename tex/src/{cantilever_calib => cantilever-calib}/solve_general.tex (100%) rename tex/src/{cantilever_calib => cantilever-calib}/solve_highly_damped.tex (100%) rename tex/src/{cantilever_calib => cantilever-calib}/test/Lorentz_root.py (100%) rename tex/src/{cantilever_calib => cantilever-calib}/test/Makefile (100%) rename tex/src/{cantilever_calib => cantilever-calib}/test/locate_roots.py (100%) rename tex/src/{cantilever_calib => cantilever-calib}/test/test_integral.py (100%) rename tex/src/{cantilever_calib => cantilever-calib}/test/test_roots.py (100%) create mode 100644 tex/src/cantilever/main.tex delete mode 100644 tex/src/cantilever_calib/main.tex create mode 100644 tex/src/contour-space/main.tex create mode 100644 tex/src/future/main.tex create mode 100644 tex/src/introduction/main.tex rename tex/src/{hyeon_temp => temperature-theory}/main.tex (98%) create mode 100644 tex/src/temperature/main.tex create mode 100644 tex/src/tension/main.tex rename tex/src/{unfolding_distributions => unfolding-distributions}/Makefile (100%) rename tex/src/{unfolding_distributions => unfolding-distributions}/kramers.tex (100%) rename tex/src/{unfolding_distributions => unfolding-distributions}/main.tex (100%) rename tex/src/{unfolding_distributions => unfolding-distributions}/overview.tex (100%) rename tex/src/{unfolding_distributions => unfolding-distributions}/review.tex (100%) rename tex/src/{unfolding_distributions => unfolding-distributions}/singledomain_constantloading.tex (100%) create mode 100644 tex/src/unfolding/main.tex diff --git a/tex/src/Makefile b/tex/src/Makefile index 3fa6f12..dc4028b 100644 --- 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 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 5a3d087..3f3df7b 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]{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 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 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 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 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 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 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 1b501ec..c74fd94 100644 --- 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 430b89a..5901bee 100644 --- 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 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 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 index 0000000..7b0e701 --- /dev/null +++ b/tex/src/unfolding/main.tex @@ -0,0 +1 @@ +\chapter{Unfolding Theory} -- 2.26.2