From 6579cbe6381ee4bb805a6d5b5cc5fbd249daa9f2 Mon Sep 17 00:00:00 2001 From: Blaise Thompson 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