From 6579cbe6381ee4bb805a6d5b5cc5fbd249daa9f2 Mon Sep 17 00:00:00 2001
From: Blaise Thompson <blaise@untzag.com>
Date: Mon, 16 Apr 2018 09:35:25 -0500
Subject: 2018-04-16 09:35
---
PEDOT_PSS/chapter.tex | 10 +-
PbSe_global_analysis/.gitignore | 234 -------------------------------
PbSe_global_analysis/driven_complete.png | Bin 0 -> 235380 bytes
PbSe_global_analysis/kramers_kronig.png | Bin 0 -> 221695 bytes
PbSe_global_analysis/model_system.png | Bin 0 -> 44778 bytes
PbSe_global_analysis/movies_combined.pdf | Bin 0 -> 3479537 bytes
PbSe_global_analysis/movies_fitted.pdf | Bin 0 -> 2483447 bytes
PbSe_global_analysis/ta_vs_tg.png | Bin 0 -> 357593 bytes
abstract.tex | 2 +-
bibliography.bib | 102 ++++++++++----
mixed_domain/chapter.tex | 6 +-
processing/chapter.tex | 4 +-
software/chapter.tex | 2 +-
13 files changed, 85 insertions(+), 275 deletions(-)
delete mode 100644 PbSe_global_analysis/.gitignore
create mode 100644 PbSe_global_analysis/driven_complete.png
create mode 100644 PbSe_global_analysis/kramers_kronig.png
create mode 100644 PbSe_global_analysis/model_system.png
create mode 100644 PbSe_global_analysis/movies_combined.pdf
create mode 100644 PbSe_global_analysis/movies_fitted.pdf
create mode 100644 PbSe_global_analysis/ta_vs_tg.png
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
Binary files /dev/null and b/PbSe_global_analysis/driven_complete.png differ
diff --git a/PbSe_global_analysis/kramers_kronig.png b/PbSe_global_analysis/kramers_kronig.png
new file mode 100644
index 0000000..067e470
Binary files /dev/null and b/PbSe_global_analysis/kramers_kronig.png differ
diff --git a/PbSe_global_analysis/model_system.png b/PbSe_global_analysis/model_system.png
new file mode 100644
index 0000000..8bed2cc
Binary files /dev/null and b/PbSe_global_analysis/model_system.png differ
diff --git a/PbSe_global_analysis/movies_combined.pdf b/PbSe_global_analysis/movies_combined.pdf
new file mode 100644
index 0000000..2b454bb
Binary files /dev/null and b/PbSe_global_analysis/movies_combined.pdf differ
diff --git a/PbSe_global_analysis/movies_fitted.pdf b/PbSe_global_analysis/movies_fitted.pdf
new file mode 100644
index 0000000..e79d696
Binary files /dev/null and b/PbSe_global_analysis/movies_fitted.pdf differ
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
Binary files /dev/null and b/PbSe_global_analysis/ta_vs_tg.png differ
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
--
cgit v1.2.3