diff options
| -rw-r--r-- | PEDOT_PSS/chapter.tex | 10 | ||||
| -rw-r--r-- | PbSe_global_analysis/.gitignore | 234 | ||||
| -rw-r--r-- | PbSe_global_analysis/driven_complete.png | bin | 0 -> 235380 bytes | |||
| -rw-r--r-- | PbSe_global_analysis/kramers_kronig.png | bin | 0 -> 221695 bytes | |||
| -rw-r--r-- | PbSe_global_analysis/model_system.png | bin | 0 -> 44778 bytes | |||
| -rw-r--r-- | PbSe_global_analysis/movies_combined.pdf | bin | 0 -> 3479537 bytes | |||
| -rw-r--r-- | PbSe_global_analysis/movies_fitted.pdf | bin | 0 -> 2483447 bytes | |||
| -rw-r--r-- | PbSe_global_analysis/ta_vs_tg.png | bin | 0 -> 357593 bytes | |||
| -rw-r--r-- | abstract.tex | 2 | ||||
| -rw-r--r-- | bibliography.bib | 102 | ||||
| -rw-r--r-- | mixed_domain/chapter.tex | 6 | ||||
| -rw-r--r-- | processing/chapter.tex | 4 | ||||
| -rw-r--r-- | software/chapter.tex | 2 |
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 Binary files differnew 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 Binary files differnew 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 Binary files differnew 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 Binary files differnew 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 Binary files differnew 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 Binary files differnew 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
|
