2018-04-16 09:35

13 files changed, 85 insertions, 275 deletions

diff --git a/PEDOT_PSS/chapter.tex b/PEDOT_PSS/chapter.tex
index d932787..a0ef8e3 100644
--- a/PEDOT_PSS/chapter.tex
+++ b/PEDOT_PSS/chapter.tex
@@ -37,14 +37,14 @@ even more structural inhomogeneity.
 In summary, PEDOT:PSS has a complex, nested microstructure.  %
 From smallest to largest:
 \begin{ditemize}
-  \item PEDOT oligomers (6---18-mers) [CITE 14]
+  \item PEDOT oligomers (6---18-mers) % [CITE 14]
   \item these oligomers $\pi$-stack to form small nanocrystalites, 3 to 14 oligomers for pristine
-    films to as many as 13---14 oligomers for more conductive solvent treated films [CITE 15]
+    films to as many as 13---14 oligomers for more conductive solvent treated films % [CITE 15]
   \item nanocrystallites then arrange into globular conductive particles in a pancake-like shape
-    [CITE 16, 17]
+   %   [CITE 16, 17]
   \item these particles themselves are then linked via PSS-rich domains and assembled into
-    nanofibril geometry akin to a string of pearls [CITE 6, 21]
-  \item nanofibrils interweave to form thin films, with PSS capping layer at surface [CITE 19, 22]
+    nanofibril geometry akin to a string of pearls  %[CITE 6, 21]
+  \item nanofibrils interweave to form thin films, with PSS capping layer at surface %[CITE 19, 22]
 \end{ditemize}
 
 In order to be conductive, PEDOT:PSS needs to have good spatial and energetic overlap between
diff --git a/PbSe_global_analysis/.gitignore b/PbSe_global_analysis/.gitignore
deleted file mode 100644
index 0e5cf51..0000000
--- a/PbSe_global_analysis/.gitignore
+++ /dev/null
@@ -1,234 +0,0 @@
-*.png
-*.#*
-
-## Simulation files
-simulations/ellipticity/*
-simulations/NISE_output/Batch A/*
-simulations/NISE_output/Batch B/*
-
-*.h5
-
-## Core latex/pdflatex auxiliary files:
-*.aux
-*.lof
-*.log
-*.lot
-*.fls
-*.out
-*.toc
-*.fmt
-*.fot
-*.cb
-*.cb2
-
-## Intermediate documents:
-*.dvi
-*-converted-to.*
-*.pdf
-
-## Generated if empty string is given at "Please type another file name for output:"
-.pdf
-
-## Bibliography auxiliary files (bibtex/biblatex/biber):
-*.bbl
-*.bcf
-*.blg
-*-blx.aux
-*-blx.bib
-*.run.xml
-
-## Build tool auxiliary files:
-*.fdb_latexmk
-*.synctex
-*.synctex(busy)
-*.synctex.gz
-*.synctex.gz(busy)
-*.pdfsync
-
-## Auxiliary and intermediate files from other packages:
-# algorithms
-*.alg
-*.loa
-
-# achemso
-acs-*.bib
-
-# amsthm
-*.thm
-
-# beamer
-*.nav
-*.pre
-*.snm
-*.vrb
-
-# changes
-*.soc
-
-# cprotect
-*.cpt
-
-# elsarticle (documentclass of Elsevier journals)
-*.spl
-
-# endnotes
-*.ent
-
-# fixme
-*.lox
-
-# feynmf/feynmp
-*.mf
-*.mp
-*.t[1-9]
-*.t[1-9][0-9]
-*.tfm
-
-#(r)(e)ledmac/(r)(e)ledpar
-*.end
-*.?end
-*.[1-9]
-*.[1-9][0-9]
-*.[1-9][0-9][0-9]
-*.[1-9]R
-*.[1-9][0-9]R
-*.[1-9][0-9][0-9]R
-*.eledsec[1-9]
-*.eledsec[1-9]R
-*.eledsec[1-9][0-9]
-*.eledsec[1-9][0-9]R
-*.eledsec[1-9][0-9][0-9]
-*.eledsec[1-9][0-9][0-9]R
-
-# glossaries
-*.acn
-*.acr
-*.glg
-*.glo
-*.gls
-*.glsdefs
-
-# gnuplottex
-*-gnuplottex-*
-
-# gregoriotex
-*.gaux
-*.gtex
-
-# hyperref
-*.brf
-
-# knitr
-*-concordance.tex
-# TODO Comment the next line if you want to keep your tikz graphics files
-*.tikz
-*-tikzDictionary
-
-# listings
-*.lol
-
-# makeidx
-*.idx
-*.ilg
-*.ind
-*.ist
-
-# minitoc
-*.maf
-*.mlf
-*.mlt
-*.mtc[0-9]*
-*.slf[0-9]*
-*.slt[0-9]*
-*.stc[0-9]*
-
-# minted
-_minted*
-*.pyg
-
-# morewrites
-*.mw
-
-# nomencl
-*.nlo
-
-# pax
-*.pax
-
-# pdfpcnotes
-*.pdfpc
-
-# sagetex
-*.sagetex.sage
-*.sagetex.py
-*.sagetex.scmd
-
-# scrwfile
-*.wrt
-
-# sympy
-*.sout
-*.sympy
-sympy-plots-for-*.tex/
-
-# pdfcomment
-*.upa
-*.upb
-
-# pythontex
-*.pytxcode
-pythontex-files-*/
-
-# thmtools
-*.loe
-
-# TikZ & PGF
-*.dpth
-*.md5
-*.auxlock
-
-# todonotes
-*.tdo
-
-# easy-todo
-*.lod
-
-# xindy
-*.xdy
-
-# xypic precompiled matrices
-*.xyc
-
-# endfloat
-*.ttt
-*.fff
-
-# Latexian
-TSWLatexianTemp*
-
-## Editors:
-# WinEdt
-*.bak
-*.sav
-
-# Texpad
-.texpadtmp
-
-# Kile
-*.backup
-
-# KBibTeX
-*~[0-9]*
-
-# emacs
-/auto/*
-_*.tex
-
-# vim
-*.swp
-
-# expex forward references with \gathertags
-*-tags.tex
-
-# python
-*__pycache__*
diff --git a/PbSe_global_analysis/driven_complete.png b/PbSe_global_analysis/driven_complete.png
new file mode 100644
index 0000000..d5c90de
--- /dev/null
+++ b/PbSe_global_analysis/driven_complete.png
diff --git a/PbSe_global_analysis/kramers_kronig.png b/PbSe_global_analysis/kramers_kronig.png
new file mode 100644
index 0000000..067e470
--- /dev/null
+++ b/PbSe_global_analysis/kramers_kronig.png
diff --git a/PbSe_global_analysis/model_system.png b/PbSe_global_analysis/model_system.png
new file mode 100644
index 0000000..8bed2cc
--- /dev/null
+++ b/PbSe_global_analysis/model_system.png
diff --git a/PbSe_global_analysis/movies_combined.pdf b/PbSe_global_analysis/movies_combined.pdf
new file mode 100644
index 0000000..2b454bb
--- /dev/null
+++ b/PbSe_global_analysis/movies_combined.pdf
diff --git a/PbSe_global_analysis/movies_fitted.pdf b/PbSe_global_analysis/movies_fitted.pdf
new file mode 100644
index 0000000..e79d696
--- /dev/null
+++ b/PbSe_global_analysis/movies_fitted.pdf
diff --git a/PbSe_global_analysis/ta_vs_tg.png b/PbSe_global_analysis/ta_vs_tg.png
new file mode 100644
index 0000000..f83f052
--- /dev/null
+++ b/PbSe_global_analysis/ta_vs_tg.png
diff --git a/abstract.tex b/abstract.tex
index 8dd75a3..e0bfc4a 100644
--- a/abstract.tex
+++ b/abstract.tex
@@ -9,7 +9,7 @@ This approach has several unique capabilities:
 \begin{denumerate}
   \item resolving congested states \cite{ZhaoWei1999b, DonaldsonPaulMurray2008a}
   \item extracting spectra that would otherwise be selection-rule disallowed
-    \cite{BoyleErinSelene2013b, BoyleErinSelene2014b},
+    \cite{BoyleErinSelene2013b, BoyleErinSelene2014a},
   \item resolving fully coherent dynamics \cite{PakoulevAndreiV2009a}, 
   \item measuring coupling \cite{WrightJohnCurtis2011a}, and
   \item resolving ultrafast dynamics.  % TODO: cite
diff --git a/bibliography.bib b/bibliography.bib
index f933496..02f2d3c 100644
--- a/bibliography.bib
+++ b/bibliography.bib
@@ -133,6 +133,19 @@
   publisher =    {Springer Nature},

 }

 

+@article{BaxterSusanM2006a,

+  author =       {Susan M. Baxter and Steven W. Day and Jacquelyn S. Fetrow and Stephanie J.

+                  Reisinger},

+  title =        {Scientific Software Development Is Not an Oxymoron},

+  journal =      {{PLoS} Computational Biology},

+  volume =       2,

+  number =       9,

+  pages =        {e87},

+  year =         2006,

+  doi =          {10.1371/journal.pcbi.0020087},

+  publisher =    {Public Library of Science ({PLoS})},

+}

+

 @article{BesemannDanielM2004a,

   author =       {Besemann, Daniel M. and Meyer, Kent A. and Wright, John C.},

   title =        {{Spectroscopic Characteristics of Triply Vibrationally Enhanced Four-Wave Mixing

@@ -206,7 +219,7 @@
   month =        {nov},

 }

 

-@article{BoyleErinSelene2014b,

+@article{BoyleErinSelene2014a,

   author =       {Boyle, Erin S and Neff-Mallon, Nathan A. and Handali, Jonathan D and Wright, John

                   C},

   title =        {{Resonance IR: A Coherent Multidimensional Analogue of Resonance Raman}},

@@ -613,6 +626,21 @@
   pmid =         15012426,

 }

 

+@article{DeGeyterBram2012a,

+  author =       {{De Geyter}, Bram and Geiregat, Pieter and Gao, Yunan and {Ten Cate}, Sybren and

+                  Houtepen, Arjan J. and Schins, Juleon M. and {Van Thourhout}, Dries and

+                  Siebbeles, Laurens D A and Hens, Zeger},

+  title =        {{Broadband and picosecond intraband absorption in lead based colloidal quantum

+                  dots}},

+  journal =      {ACS Nano},

+  number =       7,

+  pages =        {6067--6074},

+  year =         2012,

+  doi =          {10.1109/ICTON.2012.6254469},

+  isbn =         9781467322270,

+  issn =         21627339,

+}

+

 @article{DeegFW1989a,

   author =       {Deeg, F. W. and Fayer, M. D.},

   title =        {{Analysis of complex molecular dynamics in an organic liquid by polarization

@@ -677,6 +705,8 @@
   year =         2012,

 }

 

+

+

 @article{DonaldsonPaulMurray2007b,

   author =       {Donaldson, Paul M and Guo, Rui and Fournier, Frederic and Gardner, Elizabeth M

                   and Barter, Laura M C and Barnett, Chris J and Gould, Ian R and Klug, David R and

@@ -693,8 +723,6 @@
   month =        {sep},

 }

 

-

-

 @article{DonaldsonPaulMurray2008a,

   author =       {Donaldson, Paul M and Guo, Rui and Fournier, Frederic and Gardner, Elizabeth M

                   and Gould, Ian R and Klug, David R},

@@ -1951,6 +1979,7 @@
   year =         2004,

 }

 

+

 @article{MillmanJarrodK2011a,

   author =       {K. Jarrod Millman and Michael Aivazis},

   title =        {Python for Scientists and Engineers},

@@ -1964,7 +1993,6 @@
   publisher =    {Institute of Electrical and Electronics Engineers ({IEEE})},

 }

 

-

 @article{MolinaSanchezAlejandro2013a,

   author =       {Alejandro Molina-S{\'{a}}nchez and Davide Sangalli and Kerstin

                   Hummer and Andrea Marini and Ludger Wirtz},

@@ -2173,7 +2201,6 @@
   isbn =         9781584889298,

   issn =         {1521-9615},

 }

-

 @article{OliveroJJ1977a,

   author =       {Olivero, J.J. and Longbothum, R.L.},

   title =        {{Empirical fits to the voigt line width: A brief review}},

@@ -2182,6 +2209,7 @@
   pages =        {233--236},

   year =         1977,

 }

+

 @article{OmariAbdoulghafar2012a,

   author =       {Abdoulghafar Omari and Iwan Moreels and Francesco Masia and Wolfgang Langbein and

                   Paola Borri and Dries Van Thourhout and Pascal Kockaert and Zeger Hens},

@@ -2497,6 +2525,12 @@
   month =        {oct},

 }

 

+@misc{ReadTheDocs,

+  note =         {Accessed: 2018-03-27},

+  title =        {Read the Docs: Create, host, and browse documentation},

+  url =          {https://readthedocs.org/},

+}

+

 @article{RentzepisPM1970a,

   author =       {Rentzepis, P. M.},

   title =        {{Ultrafast Processes}},

@@ -2976,7 +3010,7 @@
   month =        {oct},

 }

 

-@article{VardenyZ1981ta,

+@article{VardenyZ1981a,

   author =       {Vardeny, Z. and Tauc, J.},

   title =        {{Picosecond coherence coupling in the pump and probe technique}},

   journal =      {Optics Communications},

@@ -3164,6 +3198,23 @@
   year =         2006,

 }

 

+@article{WilsonGreg2014a,

+  author =       {Greg Wilson and D. A. Aruliah and C. Titus Brown and Neil P. Chue Hong and Matt

+                  Davis and Richard T. Guy and Steven H. D. Haddock and Kathryn D. Huff and Ian M.

+                  Mitchell and Mark D. Plumbley and Ben Waugh and Ethan P. White and Paul Wilson},

+  title =        {Best Practices for Scientific Computing},

+  journal =      {{PLoS} Biology},

+  volume =       12,

+  number =       1,

+  pages =        {e1001745},

+  year =         2014,

+  doi =          {10.1371/journal.pbio.1001745},

+  url =          {https://doi.org/10.1371/journal.pbio.1001745},

+  editor =       {Jonathan A. Eisen},

+  month =        {jan},

+  publisher =    {Public Library of Science ({PLoS})},

+}

+

 @article{WilsonGreg2017a,

   author =       {Greg Wilson and Jennifer Bryan and Karen Cranston and Justin Kitzes and Lex

                   Nederbragt and Tracy K. Teal},

@@ -3263,6 +3314,7 @@
   month =        {oct},

 }

 

+

 @article{WrightJohnCurtis2011a,

   author =       {John C. Wright},

   title =        {Multiresonant Coherent Multidimensional Spectroscopy},

@@ -3290,7 +3342,6 @@
   publisher =    {Elsevier B.V.},

 }

 

-

 @article{XiaoDi2012a,

   author =       {Di Xiao and Gui-Bin Liu and Wanxiang Feng and Xiaodong Xu and

                   Wang Yao},

@@ -3454,6 +3505,20 @@
   month =        {sep},

 }

 

+@article{ZhaoWei1999a,

+  author =       {Wei Zhao and John C. Wright},

+  title =        {Measurement of$\upchi$(3)for Doubly Vibrationally Enhanced Four Wave Mixing

+                  Spectroscopy},

+  journal =      {Physical Review Letters},

+  volume =       83,

+  number =       10,

+  pages =        {1950--1953},

+  year =         1999,

+  doi =          {10.1103/physrevlett.83.1950},

+  month =        {sep},

+  publisher =    {American Physical Society ({APS})},

+}

+

 @article{ZhaoWei1999b,

   author =       {Zhao, Wei and Wright, John C.},

   title =        {{Spectral Simplification in Vibrational Spectroscopy Using Doubly Vibrationally

@@ -3489,6 +3554,7 @@
   year =         2000,

 }

 

+

 @article{ZhuBairen2014a,

   author =       {Bairen Zhu and Hualing Zeng and Junfeng Dai and Xiaodong Cui},

   title =        {The Study of Spin-Valley Coupling in Atomically Thin Group {VI} Transition Metal

@@ -3517,22 +3583,6 @@
   publisher =    {American Physical Society ({APS})},

 }

 

-

-@article{gDeGeyterBram2012a,

-  author =       {{De Geyter}, Bram and Geiregat, Pieter and Gao, Yunan and {Ten Cate}, Sybren and

-                  Houtepen, Arjan J. and Schins, Juleon M. and {Van Thourhout}, Dries and

-                  Siebbeles, Laurens D A and Hens, Zeger},

-  title =        {{Broadband and picosecond intraband absorption in lead based colloidal quantum

-                  dots}},

-  journal =      {ACS Nano},

-  number =       7,

-  pages =        {6067--6074},

-  year =         2012,

-  doi =          {10.1109/ICTON.2012.6254469},

-  isbn =         9781467322270,

-  issn =         21627339,

-}

-

 @misc{git.chem.wisc.edu,

   note =         {Accessed: 2018-04-04},

   title =        {GitLab (University of Wisconsin-Madison Chemistry},

@@ -3569,9 +3619,3 @@
   url =          {http://pyqtgraph.org/},

 }

 

-@misc{ReadTheDocs,

-  note =         {Accessed: 2018-03-27},

-  title =        {Read the Docs: Create, host, and browse documentation},

-  url =          {https://readthedocs.org/},

-}

-

diff --git a/mixed_domain/chapter.tex b/mixed_domain/chapter.tex
index 0880ecc..60910c2 100644
--- a/mixed_domain/chapter.tex
+++ b/mixed_domain/chapter.tex
@@ -88,8 +88,8 @@ Enhanced (DOVE) \cite{ZhaoWei1999a, ZhaoWei1999b, ZhaoWei2000a, MeyerKentA2003a,
   DonaldsonPaulMurray2007b, DonaldsonPaulMurray2008a, FournierFrederic2008a},

 Triply Resonant Sum Frequency (TRSF) \cite{BoyleErinSelene2013a, BoyleErinSelene2013b,

   BoyleErinSelene2014a}, Sum Frequency Generation (SFG) \cite{LagutchevAlexi2007a}, Coherent

-Anti-Stokes Raman Spectroscopy (CARS) \cite{CarlsonRogerJ1990b, CarlsonRogerJ1990c,

-  CarlsonRogerJ1991a}, and other coherent Raman methods \cite{SteehlerJK1985a}.  %

+Anti-Stokes Raman Spectroscopy (CARS) \cite{CarlsonRogerJohn1990b, CarlsonRogerJohn1990c,

+  CarlsonRogerJohn1991a}, and other coherent Raman methods \cite{SteehlerJK1985a}.  %

 

 This paper focuses on understanding the nature of the spectral changes that occur in Coherent

 Multidimensional Spectroscopy (CMDS) as experiments transition between the two limits of frequency-

@@ -346,7 +346,7 @@ from the pulse delay times represented in \autoref{mix:fig:overview}b.  %
 \subsection{Inhomogeneity}  % ---------------------------------------------------------------------

 

 Inhomogeneity is isolated in CMDS through both spectral signatures, such as

-line-narrowing \cite{BesemannDanielM2004a, OudarJL1980a, CarlsonRogerJ1990a, RiebeMichaelT1988a,

+line-narrowing \cite{BesemannDanielM2004a, OudarJL1980a, CarlsonRogerJohn1990a, RiebeMichaelT1988a,

   SteehlerJK1985a}, and temporal signatures, such as photon echoes \cite{WeinerAM1985a,

   AgarwalRitesh2002a}.  % 

 We simulate the effects of static inhomogeneous broadening by convolving the homogeneous response

diff --git a/processing/chapter.tex b/processing/chapter.tex
index 1d11788..6866f95 100644
--- a/processing/chapter.tex
+++ b/processing/chapter.tex
@@ -1263,7 +1263,7 @@ These attributes can be accessed through python: \python{wt.__version__} and
   \end{tabular}

   \caption[Commits to WrightTools.]{

     Commits to WrightTools by individual, ordered by number of commits.

-    Note that datasets...

+    Note that datasets are included, so lines added and removed are massively inflated.

   }

   \label{pro:tab:commits}

 \end{table}

@@ -1280,7 +1280,7 @@ As an example, the following is one of WrightTools' tests:
 def test_wigner():

     p = datasets.COLORS.v2p2_WL_wigner

     data = wt.data.from_COLORS(p)

-    assert data.d1.units == 'fs'

+    assert data.d1.units == 'fs''

     data.convert('ns')

     assert data.d1.units == 'ns'

     assert data.wm.units == 'nm'

diff --git a/software/chapter.tex b/software/chapter.tex
index a3f8d2d..e1b42f5 100644
--- a/software/chapter.tex
+++ b/software/chapter.tex
@@ -393,7 +393,7 @@ You can even have inheritance between different packages, allowing programmers t
 extend the behavior of existing tools for their specific needs.  %

 

 OOP is a deep subject with many patterns and concepts behind it.  %

-There are many places to read further [CITES].  % BJT: KFS can you give me some citations?

+There are many places to read further.  % BJT: KFS can you give me some citations?

 I recommend The Quarks of Object-Oriented Development, by \textcite{ArmstrongDeborahJ2006a}.  %

 

 % TODO: consider discussion of polymorphism