saving work

Reviewed-on: loos/QUESTDB#5

Manuscript/QUESTDB.bib

@@ -1,13 +1,42 @@
 %% This BibTeX bibliography file was created using BibDesk.
 %% http://bibdesk.sourceforge.net/
 
-%% Created for Pierre-Francois Loos at 2020-11-25 13:44:50 +0100 
+%% Created for Pierre-Francois Loos at 2020-11-27 22:23:32 +0100 
 
 
 %% Saved with string encoding Unicode (UTF-8) 
 
 
 
+@book{Robb_2018,
+	author = {Robb, Michael A},
+	date-added = {2020-11-27 22:23:19 +0100},
+	date-modified = {2020-11-27 22:23:27 +0100},
+	doi = {10.1039/9781788013642},
+	isbn = {978-1-78262-864-4},
+	pages = {P001-225},
+	publisher = {The Royal Society of Chemistry},
+	series = {Theoretical and Computational Chemistry Series},
+	title = {Theoretical Chemistry for Electronic Excited States},
+	url = {http://dx.doi.org/10.1039/9781788013642},
+	year = {2018},
+	Bdsk-Url-1 = {http://dx.doi.org/10.1039/9781788013642}}
+
+@article{Mai_2020,
+	abstract = {Abstract Photochemistry is a fascinating branch of chemistry that is concerned with molecules and light. However, the importance of simulating light-induced processes is reflected also in fields as diverse as biology, material science, and medicine. This Minireview highlights recent progress achieved in theoretical chemistry to calculate electronically excited states of molecules and simulate their photoinduced dynamics, with the aim of reaching experimental accuracy. We focus on emergent methods and give selected examples that illustrate the progress in recent years towards predicting complex electronic structures with strong correlation, calculations on large molecules, describing multichromophoric systems, and simulating non-adiabatic molecular dynamics over long time scales, for molecules in the gas phase or in complex biological environments.},
+	author = {Mai, Sebastian and Gonz{\'a}lez, Leticia},
+	date-added = {2020-11-27 22:21:08 +0100},
+	date-modified = {2020-11-27 22:21:51 +0100},
+	doi = {https://doi.org/10.1002/anie.201916381},
+	journal = {Angew. Chem. Int. Ed.},
+	keywords = {excited states, molecular chemistry, non-adiabatic dynamics, photochemistry, quantum chemistry},
+	pages = {16832-16846},
+	title = {Molecular Photochemistry: Recent Developments in Theory},
+	volume = {59},
+	year = {2020},
+	Bdsk-Url-1 = {https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.201916381},
+	Bdsk-Url-2 = {https://doi.org/10.1002/anie.201916381}}
+
 @article{Lee_2020,
 	author = {Joonho Lee and Fionn D. Malone and David R. Reichman},
 	date-added = {2020-11-25 13:44:34 +0100},

Manuscript/SI/QUEST_WIREs-SI.tex

@@ -110,7 +110,7 @@ and the $^1B_{3u}$ states) being considered as ``unsafe''  in the database.
 Comparisons to experimental 0-0 energies in condensed medium and CNDO calculations can be found in the Table, but are not very helpful to assess our TBEs. 
 To the best of our knowledge, the present work is the first to report triplet excited states, and we list in Table \ref{tab:azanaph} eight valence transitions obtained at the CC3/{\AVTZ} level. As we were not able to 
 perform CCSDT calculations for the triplets, all these transition energies are labeled ``unsafe'' in the QUEST database. 
-Nevertheless, given the large  \%$T_1$ values, one can likely consider them accurate (for a given basis set at least). 
+Nevertheless, given the large  \%$T_1$ values, one can likely consider them accurate (for the basis set used at least). 
 
 %
 %%% TABLE %%%
@@ -365,7 +365,7 @@ The $A_g$ transitions are known to be much more challenging: the states are dark
 On a positive note, the basis set effects are very limited for the $A_g$ state, {\Pop} being apparently sufficient. 
 In contrast, as expected for such transition, there is a significant drop of the theoretical estimate in going from CC3 to CCSDT. 
 From the analysis performed for double excitations in Ref.~\cite{Loos_2019}, it is unclear if NEVPT2 or CASPT2 would in fact outperform CCSDT for such ``mixed-character'' state, so that we cannot define a trustworthy TBE on this basis.
-However, based on our experience for butadiene \cite{Loos_2020b}, one can widely estimate the transition energies to be in the range 5.55--5.60 eV for hexatriene and in the range 4.80--4.85 eV for octratetraene. 
+However, based on our experience for butadiene \cite{Loos_2020b}, one can widely estimate the transition energy to be in the range 5.55--5.60 eV for hexatriene and in the range 4.80--4.85 eV for octratetraene. 
 Interestingly the FCI value of Chien \textit{et al.}~with a small basis set for hexatriene (5.59 eV) is compatible with such an estimate. 
 Experimentally, for hexatriene, multiphoton experiments estimate the $A_g$ state to be slightly above the $B_u$ transition \cite{Fujii_1985}, an outcome that theory reproduces.
 

Manuscript/fig2/data_gaussian_histogram_paper

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+  -5.8181818181818182E-002   1.0503392263823726E-013
+  -5.4545454545454543E-002   3.1979374437806884E-012
+  -5.0909090909090911E-002   7.8108457347063320E-011
+  -4.7272727272727272E-002   1.5304314242122915E-009
+  -4.3636363636363640E-002   2.4055667144690598E-008
+  -4.0000000000000001E-002   3.0332531323628614E-007
+  -3.6363636363636362E-002   3.0682279452286258E-006
+  -3.2727272727272730E-002   2.4897417674801438E-005
+  -2.9090909090909087E-002   1.6207226680756907E-004
+  -2.5454545454545448E-002   8.4635161104256395E-004
+  -2.1818181818181816E-002   3.5455258945109665E-003
+  -1.8181818181818177E-002   1.1915114370157230E-002
+  -1.4545454545454540E-002   3.2122067227954430E-002
+  -1.0909090909090908E-002   6.9469868291055614E-002
+  -7.2727272727272693E-003  0.12052501154967402     
+  -3.6363636363636368E-003  0.16774346335684942     
+   2.1684043449710089E-018  0.18728446158700213     
+   3.6363636363636411E-003  0.16774346335685103     
+   7.2727272727272797E-003  0.12052501154967629     
+   1.0909090909090912E-002   6.9469868291057640E-002
+   1.4545454545454544E-002   3.2122067227955672E-002
+   1.8181818181818191E-002   1.1915114370157782E-002
+   2.1818181818181823E-002   3.5455258945111712E-003
+   2.5454545454545455E-002   8.4635161104262119E-004
+   2.9090909090909101E-002   1.6207226680758102E-004
+   3.2727272727272730E-002   2.4897417674803691E-005
+   3.6363636363636362E-002   3.0682279452289367E-006
+   3.9999999999999994E-002   3.0332531323632113E-007
+   4.3636363636363640E-002   2.4055667144693550E-008
+   4.7272727272727272E-002   1.5304314242124981E-009
+   5.0909090909090904E-002   7.8108457347074978E-011
+   5.4545454545454550E-002   3.1979374437811545E-012
+   5.8181818181818182E-002   1.0503392263825442E-013

Manuscript/fig2/data_histogram_paper

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Manuscript/fig2/fig2.org

@@ -0,0 +1,59 @@
+** Initialize R packages
+   #+begin_src R :results output :session *R* :exports code                                   
+library(ggplot2)                                                                              
+library(latex2exp)                                                                            
+library(extrafont)                                                                            
+library(RColorBrewer)                                                                         
+loadfonts()                                                                                   
+   #+end_src 
+
+   #+RESULTS:
+   : 
+   : Registering fonts with R
+
+** Read data
+   #+begin_src R :results output :session *R* :exports both
+df <- read.table("data_histogram_paper");
+df$x <- df$V1
+df$y <- df$V2
+df2 <- read.table("data_gaussian_histogram_paper");
+spline.d <- as.data.frame(spline(df2$V1, df2$V2))
+summary(spline.d)
+   #+end_src
+
+   #+RESULTS:
+   : 
+   :        x                  y            
+   :  Min.   :-0.05818   Min.   :0.000e+00  
+   :  1st Qu.:-0.02909   1st Qu.:2.000e-08  
+   :  Median : 0.00000   Median :1.213e-04  
+   :  Mean   : 0.00000   Mean   :3.093e-02  
+   :  3rd Qu.: 0.02909   3rd Qu.:3.011e-02  
+   :  Max.   : 0.05818   Max.   :1.873e-01
+
+#+begin_src R :results output graphics :file (org-babel-temp-file "figure" ".png") :exports both :width 600 :height 400 :session *R* 
+p <- ggplot(data=df, aes(x, y)) +
+  geom_bar(stat="identity", fill="steelblue")
+p <- p+ geom_line(data=spline.d, lwd=1, linetype="dashed")
+p <- p + scale_x_continuous(name=TeX("$X^{(m)}$"))
+p <- p + scale_y_continuous(name=TeX("Frequency"))
+p <- p + theme(text = element_text(size = 20, family="Times"),                                
+               legend.position = c(.20, .20),                                                 
+               legend.title = element_blank())
+p
+   #+end_src     
+
+   #+RESULTS:
+   [[file:/tmp/babel-nBBwmV/figureJJu58N.png]]
+
+* Export to pdf                                                                              
+   #+begin_src R :results output :session *R* :exports code                                   
+pdf("fig2.pdf", family="Times", width=8, height=5)                           
+p                                                                                             
+dev.off()                                                                                     
+   #+end_src      
+
+   #+RESULTS:
+   : 
+   : png 
+   :   2