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@ -4854,151 +4854,156 @@ G 1
* Work
** R
*** Initialize packages
#+begin_src R :results output :session *R* :exports both
#+begin_src R :results output :session *R* :exports both
to_kcal <- 627.502164882
library(ggplot2)
library(latex2exp)
library(extrafont)
loadfonts()
#+end_src
#+end_src
#+RESULTS:
#+begin_example
#+RESULTS:
#+begin_example
More than one version of regular/bold/italic found for Cannam Codec Fixed. Skipping setup for this font.
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Kalapi already registered with pdfFonts().
Kalimati already registered with pdfFonts().
Karumbi already registered with pdfFonts().
No regular (non-bold, non-italic) version of Keraleeyam. Skipping setup for this font.
Khmer OS already registered with pdfFonts().
Khmer OS System already registered with pdfFonts().
More than one version of regular/bold/italic found for Kinnari. Skipping setup for this font.
Laksaman already registered with pdfFonts().
Lato Black already registered with pdfFonts().
Lato already registered with pdfFonts().
Lato Hairline already registered with pdfFonts().
Lato Heavy already registered with pdfFonts().
Lato Light already registered with pdfFonts().
Lato Medium already registered with pdfFonts().
Lato Semibold already registered with pdfFonts().
Lato Thin already registered with pdfFonts().
More than one version of regular/bold/italic found for Liberation Mono. Skipping setup for this font.
More than one version of regular/bold/italic found for Liberation Sans. Skipping setup for this font.
Liberation Sans Narrow already registered with pdfFonts().
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Likhan already registered with pdfFonts().
LKLUG already registered with pdfFonts().
Lohit Assamese already registered with pdfFonts().
Lohit Bengali already registered with pdfFonts().
Lohit Devanagari already registered with pdfFonts().
Lohit Gujarati already registered with pdfFonts().
Lohit Gurmukhi already registered with pdfFonts().
Lohit Kannada already registered with pdfFonts().
Lohit Malayalam already registered with pdfFonts().
Lohit Odia already registered with pdfFonts().
Lohit Tamil already registered with pdfFonts().
Lohit Tamil Classical already registered with pdfFonts().
Lohit Telugu already registered with pdfFonts().
Loma already registered with pdfFonts().
Material Design Icons already registered with pdfFonts().
Meera already registered with pdfFonts().
Mitra Mono already registered with pdfFonts().
mry_KacstQurn already registered with pdfFonts().
Mukti Narrow already registered with pdfFonts().
Nakula already registered with pdfFonts().
Navilu already registered with pdfFonts().
More than one version of regular/bold/italic found for Norasi. Skipping setup for this font.
Noto Mono already registered with pdfFonts().
OpenSymbol already registered with pdfFonts().
Padauk already registered with pdfFonts().
Padauk Book already registered with pdfFonts().
More than one version of regular/bold/italic found for padmaa. Skipping setup for this font.
No regular (non-bold, non-italic) version of padmaa-Bold.1.1. Skipping setup for this font.
Pagul already registered with pdfFonts().
Phetsarath OT already registered with pdfFonts().
Pothana2000 already registered with pdfFonts().
Purisa already registered with pdfFonts().
Rachana already registered with pdfFonts().
RaghuMalayalam already registered with pdfFonts().
Rekha already registered with pdfFonts().
Saab already registered with pdfFonts().
Sahadeva already registered with pdfFonts().
Samanata already registered with pdfFonts().
Samyak Devanagari already registered with pdfFonts().
Samyak Gujarati already registered with pdfFonts().
Samyak Malayalam already registered with pdfFonts().
Samyak Tamil already registered with pdfFonts().
Sarai already registered with pdfFonts().
Sawasdee already registered with pdfFonts().
Source Code Pro Black already registered with pdfFonts().
Source Code Pro already registered with pdfFonts().
Source Code Pro ExtraLight already registered with pdfFonts().
Source Code Pro Light already registered with pdfFonts().
Source Code Pro Medium already registered with pdfFonts().
Source Code Pro Semibold already registered with pdfFonts().
Suruma already registered with pdfFonts().
Tibetan Machine Uni already registered with pdfFonts().
TlwgMono already registered with pdfFonts().
TlwgTypewriter already registered with pdfFonts().
Tlwg Typist already registered with pdfFonts().
Tlwg Typo already registered with pdfFonts().
Ubuntu already registered with pdfFonts().
Ubuntu Light already registered with pdfFonts().
Ubuntu Condensed already registered with pdfFonts().
Ubuntu Mono already registered with pdfFonts().
More than one version of regular/bold/italic found for Umpush. Skipping setup for this font.
No regular (non-bold, non-italic) version of Uroob. Skipping setup for this font.
utkal already registered with pdfFonts().
Vemana2000 already registered with pdfFonts().
Waree already registered with pdfFonts().
#+end_example
RStudio Community is a great place to get help:
https://community.rstudio.com/c/tidyverse
Registering fonts with R
More than one version of regular/bold/italic found for Cannam Codec Fixed. Skipping setup for this font.
More than one version of regular/bold/italic found for Cannam Codec Proportional. Skipping setup for this font.
aakar already registered with pdfFonts().
Abyssinica SIL already registered with pdfFonts().
Ani already registered with pdfFonts().
AnjaliOldLipi already registered with pdfFonts().
Chandas already registered with pdfFonts().
Chilanka already registered with pdfFonts().
DejaVu Math TeX Gyre already registered with pdfFonts().
DejaVu Sans already registered with pdfFonts().
DejaVu Sans Light already registered with pdfFonts().
DejaVu Sans Condensed already registered with pdfFonts().
DejaVu Sans Mono already registered with pdfFonts().
DejaVu Serif already registered with pdfFonts().
DejaVu Serif Condensed already registered with pdfFonts().
Droid Sans Fallback already registered with pdfFonts().
Dyuthi already registered with pdfFonts().
FontAwesome already registered with pdfFonts().
FreeMono already registered with pdfFonts().
FreeSans already registered with pdfFonts().
FreeSerif already registered with pdfFonts().
Gargi already registered with pdfFonts().
Garuda already registered with pdfFonts().
Gubbi already registered with pdfFonts().
Jamrul already registered with pdfFonts().
JetBrains Mono already registered with pdfFonts().
JetBrains Mono ExtraBold already registered with pdfFonts().
JetBrains Mono Medium already registered with pdfFonts().
JetBrains Mono NL already registered with pdfFonts().
JetBrains Mono NL ExtraBold already registered with pdfFonts().
JetBrains Mono NL Medium already registered with pdfFonts().
KacstArt already registered with pdfFonts().
KacstBook already registered with pdfFonts().
KacstDecorative already registered with pdfFonts().
KacstDigital already registered with pdfFonts().
KacstFarsi already registered with pdfFonts().
KacstLetter already registered with pdfFonts().
KacstNaskh already registered with pdfFonts().
KacstOffice already registered with pdfFonts().
KacstOne already registered with pdfFonts().
KacstPen already registered with pdfFonts().
KacstPoster already registered with pdfFonts().
KacstQurn already registered with pdfFonts().
KacstScreen already registered with pdfFonts().
KacstTitle already registered with pdfFonts().
KacstTitleL already registered with pdfFonts().
Kalapi already registered with pdfFonts().
Kalimati already registered with pdfFonts().
Karumbi already registered with pdfFonts().
No regular (non-bold, non-italic) version of Keraleeyam. Skipping setup for this font.
Khmer OS already registered with pdfFonts().
Khmer OS System already registered with pdfFonts().
More than one version of regular/bold/italic found for Kinnari. Skipping setup for this font.
Laksaman already registered with pdfFonts().
Lato Black already registered with pdfFonts().
Lato already registered with pdfFonts().
Lato Hairline already registered with pdfFonts().
Lato Heavy already registered with pdfFonts().
Lato Light already registered with pdfFonts().
Lato Medium already registered with pdfFonts().
Lato Semibold already registered with pdfFonts().
Lato Thin already registered with pdfFonts().
More than one version of regular/bold/italic found for Liberation Mono. Skipping setup for this font.
More than one version of regular/bold/italic found for Liberation Sans. Skipping setup for this font.
Liberation Sans Narrow already registered with pdfFonts().
More than one version of regular/bold/italic found for Liberation Serif. Skipping setup for this font.
Likhan already registered with pdfFonts().
LKLUG already registered with pdfFonts().
Lohit Assamese already registered with pdfFonts().
Lohit Bengali already registered with pdfFonts().
Lohit Devanagari already registered with pdfFonts().
Lohit Gujarati already registered with pdfFonts().
Lohit Gurmukhi already registered with pdfFonts().
Lohit Kannada already registered with pdfFonts().
Lohit Malayalam already registered with pdfFonts().
Lohit Odia already registered with pdfFonts().
Lohit Tamil already registered with pdfFonts().
Lohit Tamil Classical already registered with pdfFonts().
Lohit Telugu already registered with pdfFonts().
Loma already registered with pdfFonts().
Material Design Icons already registered with pdfFonts().
Meera already registered with pdfFonts().
Mitra Mono already registered with pdfFonts().
mry_KacstQurn already registered with pdfFonts().
Mukti Narrow already registered with pdfFonts().
Nakula already registered with pdfFonts().
Navilu already registered with pdfFonts().
More than one version of regular/bold/italic found for Norasi. Skipping setup for this font.
Noto Mono already registered with pdfFonts().
OpenSymbol already registered with pdfFonts().
Padauk already registered with pdfFonts().
Padauk Book already registered with pdfFonts().
More than one version of regular/bold/italic found for padmaa. Skipping setup for this font.
No regular (non-bold, non-italic) version of padmaa-Bold.1.1. Skipping setup for this font.
Pagul already registered with pdfFonts().
Phetsarath OT already registered with pdfFonts().
Pothana2000 already registered with pdfFonts().
Purisa already registered with pdfFonts().
Rachana already registered with pdfFonts().
RaghuMalayalam already registered with pdfFonts().
Rekha already registered with pdfFonts().
Saab already registered with pdfFonts().
Sahadeva already registered with pdfFonts().
Samanata already registered with pdfFonts().
Samyak Devanagari already registered with pdfFonts().
Samyak Gujarati already registered with pdfFonts().
Samyak Malayalam already registered with pdfFonts().
Samyak Tamil already registered with pdfFonts().
Sarai already registered with pdfFonts().
Sawasdee already registered with pdfFonts().
Source Code Pro Black already registered with pdfFonts().
Source Code Pro already registered with pdfFonts().
Source Code Pro ExtraLight already registered with pdfFonts().
Source Code Pro Light already registered with pdfFonts().
Source Code Pro Medium already registered with pdfFonts().
Source Code Pro Semibold already registered with pdfFonts().
Suruma already registered with pdfFonts().
Tibetan Machine Uni already registered with pdfFonts().
TlwgMono already registered with pdfFonts().
TlwgTypewriter already registered with pdfFonts().
Tlwg Typist already registered with pdfFonts().
Tlwg Typo already registered with pdfFonts().
Ubuntu already registered with pdfFonts().
Ubuntu Light already registered with pdfFonts().
Ubuntu Condensed already registered with pdfFonts().
Ubuntu Mono already registered with pdfFonts().
More than one version of regular/bold/italic found for Umpush. Skipping setup for this font.
No regular (non-bold, non-italic) version of Uroob. Skipping setup for this font.
utkal already registered with pdfFonts().
Vemana2000 already registered with pdfFonts().
Waree already registered with pdfFonts().
#+end_example
*** Read csv
#+begin_src R :results output :session *R* :exports both
#+begin_src R :results output :session *R* :exports both
mad = function(x) { mean(abs(x)) }
raw_data <- read.csv("rsdft.csv")
ref <- subset(raw_data, Method == "Reference")[c("Molecule","AtomizationEnergy")]
@ -5006,94 +5011,125 @@ ref <- subset(raw_data, Method == "Reference")[c("Molecule","AtomizationEnergy")
tmp <- subset(raw_data, (Method == "DMC" & Basis == "cc-pVTZ" & AtomizationEnergy != 0.))[c("Molecule","AtomizationEnergy")]
get_ref = function(name) {
l <- subset(ref,(Molecule == name))$"AtomizationEnergy"
ifelse( length(l) == 0, 0.,l[1])
l <- subset(ref,(Molecule == name))$"AtomizationEnergy"
ifelse( length(l) == 0, 0.,l[1])
}
raw_data$ref <- sapply(raw_data$"Molecule", get_ref)
raw_data$ae.diff <- (raw_data$"AtomizationEnergy" - raw_data$ref) * to_kcal
summary(raw_data)
#+end_src
#+RESULTS:
#+begin_example
Basis Method Mu Molecule
: 55 DMC :1005 :1127 BeH : 46
CBS : 67 CIPSI : 938 0.00 : 402 C2H2 : 46
cc-pVDZ:1340 B3LYP : 201 0.25 : 402 C2H4 : 46
cc-pVQZ: 737 BLYP : 201 0.50 : 402 C2H6 : 46
cc-pVTZ: 871 CCSD(T): 201 1.00 : 268 CH : 46
PBE : 201 2.00 : 134 CH2_1A1: 46
(Other): 323 (Other): 335 (Other):2794
TotalEnergy TotalEnergyErr AtomizationEnergy AtomizationEnergyErr
Min. :-919.5146 Min. :0.0000 Min. :0.0000 Min. :-75.1781
1st Qu.: -22.9064 1st Qu.:0.0003 1st Qu.:0.1543 1st Qu.: -4.9786
Median : -14.9620 Median :0.0015 Median :0.2740 Median : 0.0002
Mean : -20.5532 Mean :0.1480 Mean :0.3306 Mean : -3.5419
3rd Qu.: -6.7178 3rd Qu.:0.2385 3rd Qu.:0.4679 3rd Qu.: 0.0007
Max. : -0.0226 Max. :1.1423 Max. :1.1520 Max. :198.3121
NA's :55 NA's :1295 NA's :408 NA's :1343
Ndet ref ae.diff
Min. : 0 Min. :0.00000 Min. :-70.699
1st Qu.: 31 1st Qu.:0.09243 1st Qu.: -5.196
Median : 899 Median :0.24300 Median : 0.000
Mean : 1229087 Mean :0.29096 Mean : -3.109
3rd Qu.: 78705 3rd Qu.:0.42940 3rd Qu.: 0.000
Max. :19555662 Max. :1.13690 Max. : 12.632
NA's :1139 NA's :408
#+end_example
*** Overlap with Jastrow optimized wf
#+begin_src R :results output :session *R* :exports both
normalize <- function(x) {x / sqrt(sum(x^2))}
FCI <- normalize(scan("coef_fci.dat"))
mu_0 <- normalize(scan("coef_00.dat"))
mu_025 <- normalize(scan("coef_25.dat"))
mu_05 <- normalize(scan("coef_05.dat"))
mu_1 <- normalize(scan("coef_10.dat"))
mu_2 <- normalize(scan("coef_20.dat"))
mu_5 <- normalize(scan("coef_50.dat"))
mu_inf<- normalize(scan("coef_inf.dat"))
jast <- normalize(scan("coef_jast.dat"))
mat <- matrix( c(mu_0, mu_025, mu_05, mu_1, mu_2, mu_5, mu_inf, FCI, jast), nrow = length(FCI))
x <- t(mat)%*%jast
x
#+end_src
#+RESULTS:
#+begin_example
Read 5110 items
Read 5110 items
Read 5110 items
Read 5110 items
Read 5110 items
Read 5110 items
Read 5110 items
Read 5110 items
Read 5110 items
[,1]
[1,] 0.9462236
[2,] 0.9466957
[3,] 0.9562485
[4,] 0.9584139
[5,] 0.9573543
[6,] 0.9570250
[7,] 0.9923257
[8,] 0.9924144
[9,] 1.0000000
Basis Method Mu Molecule
: 55 DMC :1005 :1127 BeH : 46
CBS : 67 CIPSI : 938 0.00 : 402 C2H2 : 46
cc-pVDZ:1340 B3LYP : 201 0.25 : 402 C2H4 : 46
cc-pVQZ: 737 BLYP : 201 0.50 : 402 C2H6 : 46
cc-pVTZ: 871 CCSD(T): 201 1.00 : 268 CH : 46
PBE : 201 2.00 : 134 CH2_1A1: 46
(Other): 323 (Other): 335 (Other):2794
TotalEnergy TotalEnergyErr AtomizationEnergy AtomizationEnergyErr
Min. :-919.5146 Min. :0.0000 Min. :0.0000 Min. :-75.1781
1st Qu.: -22.9064 1st Qu.:0.0003 1st Qu.:0.1543 1st Qu.: -4.9786
Median : -14.9620 Median :0.0015 Median :0.2740 Median : 0.0002
Mean : -20.5532 Mean :0.1480 Mean :0.3306 Mean : -3.5419
3rd Qu.: -6.7178 3rd Qu.:0.2385 3rd Qu.:0.4679 3rd Qu.: 0.0007
Max. : -0.0226 Max. :1.1423 Max. :1.1520 Max. :198.3121
NA's :55 NA's :1295 NA's :408 NA's :1343
Ndet ref ae.diff
Min. : 0 Min. :0.00000 Min. :-70.699
1st Qu.: 31 1st Qu.:0.09243 1st Qu.: -5.196
Median : 899 Median :0.24300 Median : 0.000
Mean : 1229087 Mean :0.29096 Mean : -3.109
3rd Qu.: 78705 3rd Qu.:0.42940 3rd Qu.: 0.000
Max. :19555662 Max. :1.13690 Max. : 12.632
NA's :1139 NA's :408
#+end_example
*** Overlap with Jastrow optimized wf
Parameters of the Jastrow:
a r_{12} / (1 + b r_{12})
p r_{12}^2 / (1 + p r_{12}^2)
a = 1/2 b = 1/2(sqrt(pi)) = 0.886226925453
p_H = 0.3467 p_O = 1.1485 (energy minimization)
#+begin_src R :results output graphics :file (org-babel-temp-file "figure" ".png") :exports both :width 600 :height 400 :session *R*
p <- ggplot(data = data.frame(x = 0), mapping = aes(x = x))
fun.0 <- function(x) (1.1485 * x^2) / (1 + 1.1485* x^2)
fun.1 <- function(x) (0.3467 * x^2) / (1 + 0.3467* x^2)
fun.2 <- function(x) (0.5 * x) / (1 + 0.5*sqrt(pi) * x)
p <- p + stat_function(fun = fun.0) + xlim(0,5)
p <- p + stat_function(fun = fun.1) + xlim(0,5)
p <- p + stat_function(fun = fun.2) + xlim(0,5)
p
#+end_src
#+RESULTS:
[[file:/tmp/babel-0OtcKh/figurePGHfN9.png]]
#+begin_src R :results output :session *R* :exports both
normalize <- function(x) {x / sqrt(sum(x^2))}
FCI <- normalize(scan("fci.dat"))
d = data.frame(FCI)
d$mu_0 <- normalize(scan("mu00.dat"))
d$mu_025 <- normalize(scan("mu25.dat"))
d$mu_05 <- normalize(scan("mu05.dat"))
d$mu_1 <- normalize(scan("mu10.dat"))
d$mu_2 <- normalize(scan("mu20.dat"))
d$mu_5 <- normalize(scan("mu50.dat"))
d$mu_inf<- normalize(scan("diag.dat"))
d$jast <- normalize(scan("jast.dat"))
overlap <- function(x) {x <- abs(crossprod(x,jast)[1]) }
ov <- apply(d,2,overlap)
ov
#+end_src
#+RESULTS:
#+begin_example
Read 200 items
Read 200 items
Read 200 items
Read 200 items
Read 200 items
Read 200 items
Read 200 items
Read 200 items
Read 200 items
Named num [1:9] 0.991 0.988 0.989 0.992 0.994 ...
- attr(*, "names")= chr [1:9] "FCI" "mu_0" "mu_025" "mu_05" ...
#+end_example
#+begin_src R :results output graphics :file (org-babel-temp-file "figure" ".png") :exports both :width 600 :height 400 :session *R*
ov <- subset(ov, names(ov) != "jast" & names(ov) != "FCI")
mu <- c(0., 0.25, 0.5, 1., 2., 5., 1.e6)
X <- mu/(mu+1.)
mu <- as.character(mu)
mu[7] <- TeX("$\\infty$")
p <- ggplot(data.frame(ov, X), aes(y=ov, x=X))
p <- p + geom_point()
p <- p + scale_x_continuous(name=TeX("$\\mu$"), breaks=X, labels=mu)
p <- p + scale_y_continuous(name = TeX("Overlap") )
p <- p + theme(text = element_text(size = 20, family="Times"), legend.position = c(.15, .15))
p
#+end_src
#+RESULTS:
[[file:/tmp/babel-0OtcKh/figure6cb0ql.png]]
*** Optimal mu
**** Table
Find the optimal $\mu$ in cc-pVDZ for each molecule and atom, making
@ -5104,13 +5140,14 @@ rows <- list()
j <- 0
for (mol in levels(ref$"Molecule") )
{
data <- subset(raw_data, (Method == "DMC" & Basis == "cc-pVDZ" & Molecule == mol))
vdz = data["Mu"]
vdz$"X" = data$"Mu"/(data$"Mu"+1.)
vdz$"E" = data$"TotalEnergy"
vdz$"E.lo" = data$"TotalEnergy" - data$"TotalEnergyErr"
vdz$"E.hi" = data$"TotalEnergy" + data$"TotalEnergyErr"
vdz$"Basis" = "VDZ-BFD"
data <- subset(raw_data, (Method == "DMC" & Basis == "cc-pVDZ" & Molecule == mol & Mu != "opt"))
data$"Mu" <- as.numeric(data$"Mu")
vdz <- data["Mu"]
vdz$"X" <- data$"Mu"/(data$"Mu"+1.)
vdz$"E" <- data$"TotalEnergy"
vdz$"E.lo" <- data$"TotalEnergy" - data$"TotalEnergyErr"
vdz$"E.hi" <- data$"TotalEnergy" + data$"TotalEnergyErr"
vdz$"Basis" <- "VDZ-BFD"
vdz$"X"[7] <- 1.
vdz$"Mu"[7] <- TeX("$\\infty$")
vdz.spline_int <- as.data.frame(spline(vdz$"X", vdz$"E", n=101))
@ -5133,74 +5170,74 @@ mu_opt
#+RESULTS:
#+begin_example
Molecule Mu TotalEnergy TotalEnergyErr
1 Be 0.9607843 -1.0079615 2.171751e-05
2 BeH 0.5625000 -1.5805129 4.067433e-04
3 C 2.8461538 -5.4320134 2.060275e-04
4 C2H2 2.1250000 -12.4978013 1.693933e-03
5 C2H4 2.0303030 -13.7496646 3.523327e-03
6 C2H6 2.0303030 -14.9862616 3.724381e-03
7 CH 2.1250000 -6.0641416 4.574267e-04
8 CH2_1A1 3.3478261 -6.7168950 1.009825e-03
9 CH2_3B1 3.1666667 -6.7315434 8.764920e-04
10 CH3 1.2727273 -7.4162327 5.305483e-04
11 CH3Cl 3.5454545 -22.5123924 4.245374e-03
12 CH4 1.7777778 -8.0950231 7.121452e-04
13 Cl Inf -14.9623070 5.120000e-04
14 Cl2 2.5714286 -30.0152826 4.435378e-03
15 ClF Inf -39.2471030 2.942000e-03
16 ClO 2.7037037 -30.9557213 3.402424e-03
17 CN 2.3333333 -15.5136342 1.488321e-03
18 CO 2.4482759 -21.7422903 1.696224e-03
19 CO2 Inf -37.8388280 3.554000e-03
20 CS 3.7619048 -15.8228210 2.003188e-03
21 F 3.1666667 -24.1949312 7.391838e-04
22 F2 4.8823529 -48.4453257 4.050079e-03
23 H 0.0000000 -0.5000220 3.200000e-05
24 H2CO 2.7037037 -22.9171510 3.311087e-03
25 H2O 2.2258065 -17.2591426 1.461246e-03
26 H2O2 13.2857143 -33.2120183 4.669473e-03
27 H2S 2.4482759 -11.4106147 3.903350e-04
28 H3COH Inf -24.1332880 2.934000e-03
29 H3CSH 2.4482759 -18.2993308 4.557326e-03
30 HCl 3.3478261 -15.6303714 1.893189e-03
31 HCN 2.3333333 -16.2207533 1.825787e-03
32 HCO 2.0303030 -22.2673034 3.309921e-03
33 HF 2.3333333 -24.9104643 1.191760e-03
34 HOCl 4.5555556 -31.6166964 4.824703e-03
35 Li 1.0000000 -0.1963480 2.000000e-05
36 Li2 0.7241379 -0.4314662 3.585501e-05
37 LiF 2.5714286 -24.6088303 1.550810e-03
38 LiH 2.4482759 -0.7887656 3.052112e-05
39 N 3.0000000 -9.7986421 3.121059e-04
40 N2 2.1250000 -19.9524868 1.048942e-03
41 N2H4 2.1250000 -22.2699022 4.249663e-03
42 Na 0.6129032 -0.1821443 2.754961e-05
43 Na2 0.0000000 -0.3910930 1.660000e-04
44 NaCl 1.1276596 -15.3111605 5.178434e-03
45 NH 2.3333333 -10.4264840 7.976368e-04
46 NH2 2.1250000 -11.0809890 1.362137e-03
47 NH3 1.8571429 -11.7605192 3.873223e-04
48 NO 2.3333333 -25.9345356 2.074537e-03
49 O 2.7037037 -15.9017110 5.380787e-04
50 O2 4.2631579 -31.9858778 2.794643e-03
51 OH 2.8461538 -16.5657615 1.069651e-03
52 P 2.5714286 -6.4727490 3.693525e-04
53 P2 2.8461538 -13.1215885 2.097094e-03
54 PH2 Inf -7.7124550 8.060000e-04
55 PH3 Inf -8.3503240 1.756000e-03
56 S Inf -10.1249220 3.820000e-04
57 S2 6.6923077 -20.4034043 3.266119e-03
58 Si Inf -3.7651370 1.260000e-04
59 Si2 4.0000000 -7.6457238 9.502980e-04
60 Si2H6 3.5454545 -11.3730818 3.867320e-03
61 SiH2_1A1 6.1428571 -5.0079101 8.651101e-04
62 SiH2_3B1 7.3333333 -4.9746405 7.553165e-04
63 SiH3 Inf -5.6243160 1.250000e-03
64 SiH4 2.5714286 -6.2776913 9.957806e-04
65 SiO 3.7619048 -19.9634155 1.961388e-03
66 SO Inf -26.2122290 4.822000e-03
67 SO2 3.0000000 -42.2998957 6.613564e-03
Molecule Mu TotalEnergy TotalEnergyErr
1 Be 22.076923 -1.0104925 5.769640e-06
2 BeH 3.918033 -1.5804522 -3.092773e-05
3 C 6.500000 -5.4320500 1.999488e-04
4 C2H2 5.976744 -12.4977890 1.631542e-03
5 C2H4 5.976744 -13.7496692 3.475880e-03
6 C2H6 5.976744 -14.9862763 3.649831e-03
7 CH 6.142857 -6.0641447 4.604460e-04
8 CH2_1A1 6.500000 -6.7168723 9.408143e-04
9 CH2_3B1 6.500000 -6.7315386 8.420592e-04
10 CH3 5.250000 -7.4161384 4.575831e-04
11 CH3Cl 6.692308 -22.5123351 4.313597e-03
12 CH4 5.818182 -8.0950439 6.943745e-04
13 Cl Inf -14.9623070 5.120000e-04
14 Cl2 6.317073 -30.0149662 4.286545e-03
15 ClF Inf -39.2471030 2.942000e-03
16 ClO 6.317073 -30.9553639 3.379987e-03
17 CN 6.142857 -15.5135815 1.475441e-03
18 CO 6.317073 -21.7422093 1.746556e-03
19 CO2 Inf -37.8388280 3.554000e-03
20 CS 8.090909 -15.8227883 2.261302e-03
21 F 6.692308 -24.1947898 7.291550e-04
22 F2 10.538462 -48.4486772 1.191581e-02
23 H 2.000000 -0.5000220 3.200000e-05
24 H2CO 6.317073 -22.9170478 3.280498e-03
25 H2O 6.142857 -17.2591198 1.451158e-03
26 H2O2 19.000000 -33.2358899 -4.071474e-03
27 H2S 6.317073 -11.4106220 4.174444e-04
28 H3COH Inf -24.1332880 2.934000e-03
29 H3CSH 6.142857 -18.2991121 4.432337e-03
30 HCl 6.692308 -15.6303653 1.821596e-03
31 HCN 6.142857 -16.2206750 1.801664e-03
32 HCO 5.976744 -22.2672833 3.238134e-03
33 HF 6.142857 -24.9103839 1.130866e-03
34 HOCl 8.677419 -31.6179815 2.879019e-03
35 Li 22.076923 -0.1963761 3.904561e-05
36 Li2 22.076923 -0.4317381 1.040406e-04
37 LiF 6.317073 -24.6087084 1.505761e-03
38 LiH 6.142857 -0.7887410 3.993582e-05
39 N 6.500000 -9.7986241 2.993923e-04
40 N2 6.142857 -19.9524462 1.089443e-03
41 N2H4 5.976744 -22.2697720 4.213610e-03
42 Na 26.272727 -0.1822304 1.180745e-04
43 Na2 22.076923 -0.3915674 2.174183e-04
44 NaCl 19.000000 -15.3131353 9.113055e-03
45 NH 6.142857 -10.4264783 7.713270e-04
46 NH2 6.142857 -11.0809754 1.375113e-03
47 NH3 5.818182 -11.7605110 3.663185e-04
48 NO 6.142857 -25.9343787 2.038331e-03
49 O 6.317073 -15.9016039 5.110339e-04
50 O2 8.090909 -31.9863532 -1.189911e-03
51 OH 6.500000 -16.5656422 1.038452e-03
52 P 6.317073 -6.4727574 3.574169e-04
53 P2 6.317073 -13.1211638 2.071087e-03
54 PH2 Inf -7.7124550 8.060000e-04
55 PH3 Inf -8.3503240 1.756000e-03
56 S Inf -10.1249220 3.820000e-04
57 S2 16.647059 -20.4112519 -1.963031e-03
58 Si Inf -3.7651370 1.260000e-04
59 Si2 10.538462 -7.6463418 1.778160e-04
60 Si2H6 8.677419 -11.3730775 3.703778e-04
61 SiH2_1A1 17.750000 -5.0122525 5.573410e-04
62 SiH2_3B1 19.000000 -4.9762802 -8.064654e-04
63 SiH3 22.076923 -5.6262336 -6.690674e-03
64 SiH4 6.142857 -6.2776229 9.405144e-04
65 SiO 7.571429 -19.9632204 2.175365e-03
66 SO Inf -26.2122290 4.822000e-03
67 SO2 6.500000 -42.2992438 6.376208e-03
#+end_example
**** Atoms
@ -5217,6 +5254,7 @@ x <- rep(0.,7)
for (atom in atoms) {
data <- subset(raw_data, (Method == "DMC" & Basis == "cc-pVDZ" & Molecule == atom))
vdz = data["Mu"]
data$"Mu" <- as.numeric(data$"Mu")
vdz$"X" = data$"Mu"/(data$"Mu"+1.)
vdz$"E" = data$"TotalEnergy"
vdz$"E.lo" = data$"TotalEnergy" - data$"TotalEnergyErr"
@ -5224,18 +5262,18 @@ for (atom in atoms) {
vdz$"Basis" = "VDZ-BFD"
vdz$"X"[7] <- 1.
vdz$"Mu"[7] <- TeX("$\\infty$")
# vdz.spline_int <- as.data.frame(spline(vdz$"X", vdz$"E", n=101))
# vdz.spline_int_lo <- as.data.frame(spline(vdz$"X", vdz$"E.lo", n=101))
# vdz.spline_int_hi <- as.data.frame(spline(vdz$"X", vdz$"E.hi", n=101))
# vdz.spline_int <- as.data.frame(spline(vdz$"X", vdz$"E", n=101))
# vdz.spline_int_lo <- as.data.frame(spline(vdz$"X", vdz$"E.lo", n=101))
# vdz.spline_int_hi <- as.data.frame(spline(vdz$"X", vdz$"E.hi", n=101))
# vdz.spline_int_lo$y <- (vdz.spline_int_lo$y - vdz.spline_int$y[101])/(vdz.spline_int$y[1]-vdz.spline_int$y[101])
# vdz.spline_int_hi$y <- (vdz.spline_int_hi$y - vdz.spline_int$y[101])/(vdz.spline_int$y[1]-vdz.spline_int$y[101])
# vdz.spline_int$y <- (vdz.spline_int$y - vdz.spline_int$y[101])/(vdz.spline_int$y[1]-vdz.spline_int$y[101])
# vdz.spline_int_lo$y <- (vdz.spline_int_lo$y - vdz.spline_int$y[101])/(vdz.spline_int$y[1]-vdz.spline_int$y[101])
# vdz.spline_int_hi$y <- (vdz.spline_int_hi$y - vdz.spline_int$y[101])/(vdz.spline_int$y[1]-vdz.spline_int$y[101])
# vdz.spline_int$y <- (vdz.spline_int$y - vdz.spline_int$y[101])/(vdz.spline_int$y[1]-vdz.spline_int$y[101])
# mid <- mid + vdz.spline_int$y
# hi <- hi + vdz.spline_int_hi$y
# lo <- lo + vdz.spline_int_lo$y
# x <- vdz.spline_int$x
# mid <- mid + vdz.spline_int$y
# hi <- hi + vdz.spline_int_hi$y
# lo <- lo + vdz.spline_int_lo$y
# x <- vdz.spline_int$x
mid <- mid + (vdz$"E" - vdz$"E"[7])/(vdz$"E"[1] - vdz$"E"[7])
hi <- hi + (vdz$"E.hi" - vdz$"E"[7])/(vdz$"E"[1] - vdz$"E"[7])
@ -5263,26 +5301,27 @@ p
#+end_src
#+RESULTS:
[[file:/tmp/babel-cHKMq8/figureMRtles.png]]
[[file:/tmp/babel-8WVd9w/figureBMs1Mr.png]]
**** Molecules
#+begin_src R :results output graphics :file (org-babel-temp-file "figure" ".png") :exports both :width 600 :height 400 :session *R*
molecules = c("BeH", "C2H2", "C2H4", "C2H6", "CH", "CH2_1A1", "CH2_3B1", "CH3", "CH3Cl", "CH4", "CN", "CO", "CO2", "CS", "Cl2", "ClF", "ClO", "F2", "H2CO", "H2O", "H2O2", "H2S", "H3COH", "H3CSH", "HCN", "HCO", "HCl", "HF", "HOCl", "Li2", "LiF", "LiH", "N2", "N2H4", "NH", "NH2", "NH3", "NO", "Na2", "NaCl", "O2", "OH", "P2", "PH2", "PH3", "S2", "SO", "SO2", "Si2", "Si2H6", "SiH2_1A1", "SiH2_3B1", "SiH3", "SiH4", "SiO")
molecules <- c("BeH", "C2H2", "C2H4", "C2H6", "CH", "CH2_1A1", "CH2_3B1", "CH3", "CH3Cl", "CH4", "CN", "CO", "CO2", "CS", "Cl2", "ClF", "ClO", "F2", "H2CO", "H2O", "H2O2", "H2S", "H3COH", "H3CSH", "HCN", "HCO", "HCl", "HF", "HOCl", "Li2", "LiF", "LiH", "N2", "N2H4", "NH", "NH2", "NH3", "NO", "Na2", "NaCl", "O2", "OH", "P2", "PH2", "PH3", "S2", "SO", "SO2", "Si2", "Si2H6", "SiH2_1A1", "SiH2_3B1", "SiH3", "SiH4", "SiO")
molecules <- c("H2O")
mid <- rep(0.,101)
hi <- rep(0.,101)
lo <- rep(0.,101)
x <- rep(0.,101)
#mid <- rep(0.,7)
#hi <- rep(0.,7)
#lo <- rep(0.,7)
#x <- rep(0.,7)
#mid <- rep(0.,7)
#hi <- rep(0.,7)
#lo <- rep(0.,7)
#x <- rep(0.,7)
for (molecule in molecules) {
data <- subset(raw_data, (Method == "DMC" & Basis == "cc-pVDZ" & Molecule == molecule ))
data <- subset(raw_data, (Method == "DMC" & Basis == "cc-pVDZ" & Molecule == molecule & Mu != "opt"))
vdz = data["Mu"]
data$"Mu" <- na.omit(as.numeric(data$"Mu"))
vdz$"X" = data$"Mu"/(data$"Mu"+1.)
vdz$"E" = data$"TotalEnergy"
vdz$"E.lo" = data$"TotalEnergy" - data$"TotalEnergyErr"
@ -5303,10 +5342,10 @@ for (molecule in molecules) {
lo <- lo + vdz.spline_int_lo$y
x <- vdz.spline_int$x
# mid <- mid + (vdz$"E" - vdz$"E"[7])/(vdz$"E"[1] - vdz$"E"[7])
# hi <- hi + (vdz$"E.hi" - vdz$"E"[7])/(vdz$"E"[1] - vdz$"E"[7])
# lo <- lo + (vdz$"E.lo" - vdz$"E"[7])/(vdz$"E"[1] - vdz$"E"[7])
# x <- vdz$"X"
# mid <- mid + (vdz$"E" - vdz$"E"[7])/(vdz$"E"[1] - vdz$"E"[7])
# hi <- hi + (vdz$"E.hi" - vdz$"E"[7])/(vdz$"E"[1] - vdz$"E"[7])
# lo <- lo + (vdz$"E.lo" - vdz$"E"[7])/(vdz$"E"[1] - vdz$"E"[7])
# x <- vdz$"X"
}
out = data.frame(mid)
@ -5329,7 +5368,7 @@ p
#+end_src
#+RESULTS:
[[file:/tmp/babel-cHKMq8/figureQXBk5n.png]]
[[file:/tmp/babel-8WVd9w/figureRuNz9o.png]]
*** Figure H2O R
#+begin_src R :var data=tab1 :results output :session *R* :exports both
@ -5409,15 +5448,14 @@ dev.off()
: 1
*** Figure MAD R DZ
#+begin_src R :results output :session *R* :exports both
#+begin_src R :results output :session *R* :exports both
data <- data.frame(ref["Molecule"])
data <- subset(raw_data, (Method == "DMC" & Basis == "cc-pVDZ" & AtomizationEnergy != 0.))
aggregate(ae.diff~Mu, na.omit(data), mad)
#+end_src
#+end_src
#+RESULTS:
#+begin_example
#+RESULTS:
#+begin_example
Mu ae.diff
1 0.00 5.069784
@ -5428,9 +5466,9 @@ aggregate(ae.diff~Mu, na.omit(data), mad)
6 5.00 6.176869
7 inf 7.380395
8 opt 5.839398
#+end_example
#+end_example
#+begin_src R :results output graphics :file (org-babel-temp-file "figure" ".png") :exports both :width 600 :height 400 :session *R*
#+begin_src R :results output graphics :file (org-babel-temp-file "figure" ".png") :exports both :width 600 :height 400 :session *R*
fill <- "#4271AE"
line <- "#1F3552"
d = data[c("Mu","ae.diff","Molecule")]
@ -5447,25 +5485,25 @@ p <- p + geom_jitter(width=0.1,size=1.,aes(color=Molecule), show.legend=FALSE)
p <- p + theme(text = element_text(size = 20, family="Times"))
p
#+end_src
#+end_src
#+RESULTS:
[[file:/tmp/babel-8WVd9w/figurePbpfm7.png]]
#+RESULTS:
[[file:/tmp/babel-8WVd9w/figurePbpfm7.png]]
#+begin_src R :results output :session *R* :exports both
#+begin_src R :results output :session *R* :exports both
pdf("../Manuscript/g2-dmc-dz.pdf", family="Times", width=8, height=5)
p
dev.off()
#+end_src
#+RESULTS:
:
: null device
: 1
#+end_src
#+RESULTS:
:
: null device
: 1
*** Figure MAD R TZ
#+begin_src R :results output :session *R* :exports both
#+begin_src R :results output :session *R* :exports both
data <- data.frame(ref["Molecule"])
data <- subset(raw_data, (Method == "DMC" & Basis == "cc-pVTZ" & AtomizationEnergy != 0.))
aggregate(ae.diff~Mu, na.omit(data), mad)
@ -5488,7 +5526,7 @@ d$Mu <- factor(d$Mu)
labels <- as.character(c("0.00", "0.25", "0.50", "1.00" ) )
p <- ggplot(d, aes(x=Mu, y=ae.diff)) + geom_boxplot()
p <- p + scale_x_discrete(name=TeX("$\\mu$"),
breaks=c("0", "0.25", "0.5", "1" ), labels=labels)
breaks=c("0", "0.25", "0.5", "1" ), labels=labels)
p <- p + scale_y_continuous(name = TeX("Error (kcal/mol)"))
p <- p + geom_boxplot(fill = fill, colour = line, alpha = 0.7, outlier.colour = "#1F3552", outlier.shape = 20)
p <- p + geom_jitter(width=0.1,size=1.,aes(color=Molecule), show.legend=FALSE)
@ -5500,20 +5538,20 @@ p
#+RESULTS:
[[file:/tmp/babel-cHKMq8/figurebHUlqc.png]]
#+begin_src R :results output :session *R* :exports both
#+begin_src R :results output :session *R* :exports both
pdf("../Manuscript/g2-dmc-tz.pdf", family="Times", width=8, height=5)
p
dev.off()
#+end_src
#+end_src
#+RESULTS:
:
: null device
: 1
#+RESULTS:
:
: null device
: 1
*** Figure MAD R QZ
#+begin_src R :results output :session *R* :exports both
#+begin_src R :results output :session *R* :exports both
data <- data.frame(ref["Molecule"])
data <- subset(raw_data, (Method == "DMC" & Basis == "cc-pVQZ" & AtomizationEnergy != 0.))
aggregate(ae.diff~Mu, na.omit(data), mad)
@ -5534,8 +5572,8 @@ d$Mu <- factor(d$Mu)
p <- ggplot(d, aes(x=Mu, y=ae.diff)) + geom_boxplot()
p <- p + scale_x_discrete(name=TeX("$\\mu$"),
breaks=c("0", "0.25", "0.5" ),
labels=as.character(c("0.00", "0.25", "0.50" ) ))
breaks=c("0", "0.25", "0.5" ),
labels=as.character(c("0.00", "0.25", "0.50" ) ))
p <- p + scale_y_continuous(name = TeX("Error (kcal/mol)"))
p <- p + geom_boxplot(fill = fill, colour = line, alpha = 0.7, outlier.colour = "#1F3552", outlier.shape = 20)
p <- p + geom_jitter(width=0.05,size=2.,aes(color=Molecule), show.legend=FALSE)
@ -5546,16 +5584,16 @@ p
#+RESULTS:
[[file:/tmp/babel-cHKMq8/figureZUK13c.png]]
#+begin_src R :results output :session *R* :exports both
#+begin_src R :results output :session *R* :exports both
pdf("../Manuscript/g2-dmc-qz.pdf", family="Times", width=8, height=5)
p
dev.off()
#+end_src
#+end_src
#+RESULTS:
:
: null device
: 1
#+RESULTS:
:
: null device
: 1
** Gnuplot
*** Figure H2O gnuplot

200
Data/diag.dat Normal file
View File

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