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W. Trevor King [Thu, 29 Apr 2010 06:33:13 +0000 (02:33 -0400)]
Add Alias('bibtex-files') dependency as SCons' LaTeX scanner doesn't seem to.
W. Trevor King [Thu, 29 Apr 2010 05:59:00 +0000 (01:59 -0400)]
Add king_vs_best dependency rules to SCons build tree
W. Trevor King [Thu, 29 Apr 2010 05:21:10 +0000 (01:21 -0400)]
Rework Alias('asymptote-figures'). Previous implementation didn't build the asyfig targets.
W. Trevor King [Thu, 29 Apr 2010 04:22:09 +0000 (00:22 -0400)]
Adjustments to graphMatrixFile for much smaller output.
New implementation converts input x/y/z arrays to x and y sets
specifying coordinates for a z matrix, which asymptote handles more
cleanly than nominally non-gridded data.
Also fixed palette positioning, which was broken in the previous
implementation.
W. Trevor King [Wed, 28 Apr 2010 22:51:24 +0000 (18:51 -0400)]
Fix exponent "^-1" -> "^{-1}" in fit-valley.asy
W. Trevor King [Wed, 28 Apr 2010 22:44:26 +0000 (18:44 -0400)]
Removed wtk_graph.asy symlink from fit-space
Local wtk_graph creation is handled by link_wtk_graph() in the
SConscript file.
W. Trevor King [Wed, 28 Apr 2010 22:24:18 +0000 (18:24 -0400)]
Converted figures/fit-space/fig.gp to fit-valley.asy.
But the current output PDF is big and slow :(.
W. Trevor King [Wed, 28 Apr 2010 21:56:01 +0000 (17:56 -0400)]
Add Alias('asymptote-figures') for explicit \asyfig dependencies.
Also:
* Use env.Alias and env.Depends vs. the bare SCons.Script forms.
* Add figures/cantilever-sim/loading-rate.asy back to build tree.
W. Trevor King [Wed, 28 Apr 2010 21:22:27 +0000 (17:22 -0400)]
Add dsfont files to src/packages/
W. Trevor King [Wed, 28 Apr 2010 21:18:24 +0000 (17:18 -0400)]
Add explicit dependency thesis -> Alias('extra-packages').
SCons' LaTeX scanner doesn't pick them up automatically as of SCons
v1.3.
W. Trevor King [Wed, 28 Apr 2010 21:13:28 +0000 (17:13 -0400)]
Really build thesis.pdf vs. old dummy Touch command.
W. Trevor King [Wed, 28 Apr 2010 21:11:57 +0000 (17:11 -0400)]
Only add DISPLAY to the SCons build environment if the user has set it
W. Trevor King [Wed, 28 Apr 2010 12:14:53 +0000 (08:14 -0400)]
Merge SCons transition with some Gnuplot->Asymptote work.
Conflicts:
tex/src/figures/cantilever-data/Makefile
tex/src/figures/fit-space/Makefile
tex/src/figures/fit-space/king_vs_best.gp
W. Trevor King [Wed, 28 Apr 2010 12:03:40 +0000 (08:03 -0400)]
Removed Gnuplot portions of cantilever-data/v-dep
W. Trevor King [Wed, 28 Apr 2010 12:02:18 +0000 (08:02 -0400)]
Added untested graphMatrixFile to wtk_graph.asy
W. Trevor King [Wed, 28 Apr 2010 12:01:11 +0000 (08:01 -0400)]
Tranitioned king_vs_best from Gnuplot to Asymptote
W. Trevor King [Wed, 28 Apr 2010 11:58:17 +0000 (07:58 -0400)]
sdfont -> dsfont typo correction
W. Trevor King [Fri, 16 Apr 2010 05:13:21 +0000 (01:13 -0400)]
Transitioned build system from Make to SCons
W. Trevor King [Thu, 8 Apr 2010 18:01:26 +0000 (14:01 -0400)]
Removed fit-space/fit.log
I don't know where it came from, but it's a Gnuplot-generated fit log
from something, so it shouldn't get versioned.
W. Trevor King [Thu, 8 Apr 2010 17:56:36 +0000 (13:56 -0400)]
Add improved extract_fit_valley.py to fit-space Makefile flow
W. Trevor King [Tue, 6 Apr 2010 14:53:41 +0000 (10:53 -0400)]
Use mathds over mathbb for double struck fonts
W. Trevor King [Sun, 4 Apr 2010 22:13:47 +0000 (18:13 -0400)]
Fix DOI for wking10 in root.bib
W. Trevor King [Thu, 1 Apr 2010 02:34:28 +0000 (22:34 -0400)]
Need to run latex between bibtex runs to resolve citation note references
W. Trevor King [Fri, 19 Mar 2010 10:26:35 +0000 (06:26 -0400)]
Merge branch 'master' of ssh://einstein/~/public_html/code/git/thesis
W. Trevor King [Thu, 18 Mar 2010 20:27:25 +0000 (16:27 -0400)]
Fix Kpathsea search path configuration in asyprocess.
From the Kpathsea manual:
http://www.chemie.fu-berlin.de/chemnet/use/info/kpathsea/kpathsea_4.html
"
A search path can come from many sources. In priority order (meaning
Kpathsea will use whichever it finds first):
1. A user-set environment variable, e.g., `TEXINPUTS'.
2. A program-specific configuration file, e.g., an `S /a:/b' line
in Dvips' `config.ps'.
3. A line in a Kpathsea configuration file `texmf.cnf', e.g.,
`TEXINPUTS=/c:/d'. See section below.
4. The compile-time default (specified in `kpathsea/paths.h').
...
If the highest-priority search path (in the list in the previous
section) contains an extra colon (i.e., leading, trailing, or
doubled), Kpathsea inserts the next-highest-priority search path that
is set at that point.
...
For example, given
setenv TEXINPUTS /home/karl:
and a `TEXINPUTS' value from `texmf.cnf' of
.:$TEXMF//tex
then the final value used for searching will be:
/home/karl:.:$TEXMF//tex
W. Trevor King [Mon, 15 Mar 2010 21:25:20 +0000 (17:25 -0400)]
Fix \notation -> \nomenclature in singledomain_constantloading.tex
W. Trevor King [Mon, 15 Mar 2010 20:18:03 +0000 (16:18 -0400)]
Fixed cantilever-data figure Makefile dependencies (again :p)
W. Trevor King [Mon, 15 Mar 2010 18:07:26 +0000 (14:07 -0400)]
Added \equiv to the notation list.
Fixed up cantilever-data/Makefile to trigger DATA_DIRS generation.
All cantilever-data/*.sh scrips now exit on errors.
W. Trevor King [Mon, 15 Mar 2010 17:25:11 +0000 (13:25 -0400)]
Completed cantilever data figure integration.
W. Trevor King [Mon, 15 Mar 2010 13:12:38 +0000 (09:12 -0400)]
Renamed "plot-splits" to the more obvious "v-dep"
W. Trevor King [Mon, 15 Mar 2010 13:07:15 +0000 (09:07 -0400)]
Working cantilever-data generation into the Makefile
W. Trevor King [Mon, 15 Mar 2010 11:18:13 +0000 (07:18 -0400)]
Brought in cantilever-data generation scripts.
W. Trevor King [Mon, 15 Mar 2010 00:39:02 +0000 (20:39 -0400)]
Added temporary caption to fig:cantilever:loading-rate (thanks Mom).
W. Trevor King [Mon, 15 Mar 2010 00:10:22 +0000 (20:10 -0400)]
Added monte-carlo.asy figure (and the epsdice package it depends on).
Added a second pass through BibTeX to pick up any references in
the "note" field. There don't seem to be any new inclusions after
that point.
Corrected press92 key (had been 02. Oops :p).
Relabeled eq:model-psd. We don't fit the post-equipartition theorem
version (eq:DHO-psd), because we're preparing to test the fit, and
we don't gain anything by plugging in a few more scaling factors.
W. Trevor King [Sun, 14 Mar 2010 12:40:23 +0000 (08:40 -0400)]
Cleaned up cantilever-calib equations.
Replaced all remaining \cite{} calls with natbib's \citep{} and
\citet{}.
Switched from semicolon to comma to separate multiple citations.
Switched from plainnat to unsrtnat so citations are numbered in
the order in which they appear.
Upgraded to drexel-thesis v0.7 (\iffinal).
W. Trevor King [Fri, 12 Mar 2010 05:24:34 +0000 (00:24 -0500)]
Use a bit less negative space for \logp{}
W. Trevor King [Fri, 12 Mar 2010 04:23:19 +0000 (23:23 -0500)]
Fixed the bulk of Mom's remaining typos and clarification requests
W. Trevor King [Thu, 11 Mar 2010 18:34:16 +0000 (13:34 -0500)]
Fixed typos Mom found in the appenidicies + switched cantilver-calib to cref
Use - instead of _ in labels (I think it looks nicer :).
Note that using multiple references in \cref in appendicies
\cref{eq:res-thm,eq:res-simple}
breaks with cleveref v0.14.2 (but works with v0.15.3). The errors were:
! Missing number, treated as zero.
<to be read again>
{
l.94 Applying \cref{eq:res_thm,eq:res_simple}
Caused by \@results like
{
2147483647}\@result
rather than the newer
2147483647,\@result
W. Trevor King [Thu, 11 Mar 2010 17:43:00 +0000 (12:43 -0500)]
Addressed Mom's concerns about WLC indexing and fixed some sawsim typos
W. Trevor King [Thu, 11 Mar 2010 15:07:55 +0000 (10:07 -0500)]
Add Index and Nomenclature sections
W. Trevor King [Thu, 25 Feb 2010 15:35:00 +0000 (10:35 -0500)]
Moved figures/contour/contour.asy to asyfig workflow
W. Trevor King [Thu, 25 Feb 2010 15:23:57 +0000 (10:23 -0500)]
Fix i_dep.d -> i-dep.d
W. Trevor King [Thu, 25 Feb 2010 15:10:10 +0000 (10:10 -0500)]
Add FIGS variable to asyprocess Makefiles to reduce duplication
Also moved the other two schematic ASY figures over from external
builds to asyfig.
W. Trevor King [Thu, 25 Feb 2010 15:09:23 +0000 (10:09 -0500)]
Added labels to cantilever simulation figures
W. Trevor King [Thu, 25 Feb 2010 15:01:00 +0000 (10:01 -0500)]
Pull out cantilever peak index simulation figure.
W. Trevor King [Thu, 25 Feb 2010 14:44:51 +0000 (09:44 -0500)]
Use packages.tex in asyprocess calls
W. Trevor King [Thu, 25 Feb 2010 12:34:31 +0000 (07:34 -0500)]
Working my 2009 Biophys Soc poster into cantilever/
Several large asymptote figures, so rather than using fully external
asy (non-matching fonts, etc) or \usepackage[inline]{asymptote}
(recompiles all asy graphics every time), I've switched to asyfig
http://www.ctan.org/tex-archive/macros/latex/contrib/asyfig/
The current CTAN version is v0.1b, but that wasn't quite flexible
enough, but Will Robertson versions in git, so I cloned his branch
http://github.com/wspr/asyfig
and added what I needed
http://www.physics.drexel.edu/~wking/code/git/asyfig.git/
I don't think it's all working yet, but there's a lot of work since my
last commit, so here's a checkpoint ;).
W. Trevor King [Tue, 23 Feb 2010 20:06:34 +0000 (15:06 -0500)]
Fix other errata listed on wiki.creativecommons.org/Legalcode_errata
W. Trevor King [Tue, 23 Feb 2010 19:27:18 +0000 (14:27 -0500)]
Added I27 introduction to sec:cantilever
W. Trevor King [Tue, 23 Feb 2010 16:19:24 +0000 (11:19 -0500)]
Added Introduction \section{Thesis Outline}.
Spellchecked introduction/main.tex.
Changed title (again :p) to:
"Temperature and cantilever dependent protein unfolding"
W. Trevor King [Tue, 23 Feb 2010 15:09:51 +0000 (10:09 -0500)]
Changed title to "Mechanical protein unfolding analysis"
W. Trevor King [Tue, 23 Feb 2010 15:07:08 +0000 (10:07 -0500)]
Oops. \copyrightCCBYSA -> \copyrighttextCCBYSA
W. Trevor King [Tue, 23 Feb 2010 14:46:10 +0000 (09:46 -0500)]
Move Sawsim into paragraph fully into sawsim/introduction.tex
W. Trevor King [Tue, 23 Feb 2010 14:45:27 +0000 (09:45 -0500)]
GNU FDL too restrictive, use CC-by-sa instead.
W. Trevor King [Tue, 23 Feb 2010 02:25:23 +0000 (21:25 -0500)]
Tied unfolding model paragraph into single molecule methods paragraph
W. Trevor King [Tue, 23 Feb 2010 01:30:00 +0000 (20:30 -0500)]
Fix drexe -> drexel typos in README URLs
W. Trevor King [Tue, 23 Feb 2010 01:23:50 +0000 (20:23 -0500)]
Use \chapter{}, \section{}, and \ref{} in fdl.txt.
Also revert bustamante08 -> betterment08 spellcheck error introduced
in
96237f4dfe4fe90895e36f36199235cfb8282560
W. Trevor King [Mon, 22 Feb 2010 23:29:18 +0000 (18:29 -0500)]
Added FDL appendix
W. Trevor King [Mon, 22 Feb 2010 23:19:35 +0000 (18:19 -0500)]
Added README and COPYING (GNU FDL)
W. Trevor King [Mon, 22 Feb 2010 23:01:12 +0000 (18:01 -0500)]
Added "Double T" folding pathway example
W. Trevor King [Mon, 22 Feb 2010 21:36:25 +0000 (16:36 -0500)]
Added pathway / landscape folding model paragraph
W. Trevor King [Mon, 22 Feb 2010 15:57:35 +0000 (10:57 -0500)]
Working through ligand/receptor figure
W. Trevor King [Mon, 22 Feb 2010 01:16:37 +0000 (20:16 -0500)]
Working through introductory citations, HGP and Levinthal.
W. Trevor King [Thu, 18 Feb 2010 21:53:01 +0000 (16:53 -0500)]
Fix figure 1.1 referencing/labeling
W. Trevor King [Thu, 18 Feb 2010 20:51:49 +0000 (15:51 -0500)]
Merge branch 'master' of yang:./rsrch/notes/thesis
W. Trevor King [Thu, 18 Feb 2010 20:50:53 +0000 (15:50 -0500)]
Some work cleaning up the introductory text
W. Trevor King [Thu, 18 Feb 2010 20:35:53 +0000 (15:35 -0500)]
Draw Laser and Photodiode in AFM schematic.
W. Trevor King [Thu, 18 Feb 2010 17:34:14 +0000 (12:34 -0500)]
Moved AFM-drawing functions from unfolding.asy to base_afm.asy & made substrate motion controllable
W. Trevor King [Thu, 18 Feb 2010 00:22:21 +0000 (19:22 -0500)]
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.
W. Trevor King [Wed, 17 Feb 2010 23:53:33 +0000 (18:53 -0500)]
Broke sawsim chapter into sections and added local_words
W. Trevor King [Wed, 17 Feb 2010 23:33:04 +0000 (18:33 -0500)]
Updated unfolding-distributions input paths in u..-d../main.tex
W. Trevor King [Tue, 9 Feb 2010 22:25:13 +0000 (17:25 -0500)]
Added rough chapter outlines
W. Trevor King [Tue, 9 Feb 2010 20:15:05 +0000 (15:15 -0500)]
Fix linenumbers handling and use 'subfig' drexel-thesis option
W. Trevor King [Tue, 9 Feb 2010 12:33:23 +0000 (07:33 -0500)]
Moved chapter files to */main.tex
W. Trevor King [Thu, 14 Jan 2010 19:13:51 +0000 (14:13 -0500)]
Merged viscocity notes
W. Trevor King [Thu, 14 Jan 2010 18:43:56 +0000 (13:43 -0500)]
Merged my hyeon03 equation derivation
W. Trevor King [Thu, 14 Jan 2010 17:19:01 +0000 (12:19 -0500)]
Brought in unfolding_distributions
W. Trevor King [Thu, 14 Jan 2010 02:20:44 +0000 (21:20 -0500)]
Merged sawsim paper.
W. Trevor King [Thu, 14 Jan 2010 00:28:48 +0000 (19:28 -0500)]
Converted to drexel-thesis class, compiles at home, multiple bibs.
W. Trevor King [Sat, 19 Dec 2009 00:00:07 +0000 (19:00 -0500)]
Transitioned contour figure from MetaPost to Asymptote
W. Trevor King [Wed, 2 Dec 2009 20:22:15 +0000 (15:22 -0500)]
Added latex framework and cantilever_calib appendix.
W. Trevor King [Wed, 2 Dec 2009 07:51:22 +0000 (02:51 -0500)]
Began versioning