In AliSajid/molecular_modeling_lab03: Utility functions to generate molecular modelling

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(molecular_modeling_lab03)
library(tidyverse)

In this lab, we will compare the value of teh orbitals at different radii across three different conditions.

sto_h <- sto_generator(1.24)
gto_h <- gto_generator(0.4166)
sto_2g_h <- sto_2g_generator(element = "hydrogen")
sto_3g_h <- sto_3g_generator(element = "hydrogen")
sto_4g_h <- sto_4g_generator(element = "hydrogen")
sto_5g_h <- sto_5g_generator(element = "hydrogen")
sto_6g_h <- sto_6g_generator(element = "hydrogen")

Now we run the analysis.

df <- tibble(radius = seq(0, 6, 0.01)) |> 
  mutate(STO = map_dbl(radius, sto_h),
         GTO = map_dbl(radius, gto_h),
         `STO-2G` = map_dbl(radius, sto_2g_h),
         `STO-3G` = map_dbl(radius, sto_3g_h),
         `STO-4G` = map_dbl(radius, sto_4g_h),
         `STO-5G` = map_dbl(radius, sto_5g_h),
         `STO-6G` = map_dbl(radius, sto_6g_h)) |> 
  pivot_longer(cols = c(starts_with("STO"), GTO), names_to = "type") |> 
  write_csv("vignettes/dataset.csv")

Now we make the figures.

g <- ggplot(df, aes(x = radius, y = value, color = type, group = type))

p_base <- g + geom_line(size = 1.2) +
  theme_minimal() +
  scale_x_continuous(breaks = seq(0, 6, 0.5)) +
  scale_y_continuous(breaks = seq(0, 0.8, 0.1))

Comparing just the STO and GTO

p1 <- p_base +
  scale_color_brewer(palette = "Dark2", name = "Basis Set", limit = c("STO", "GTO"))

Comparing STO with GTO and STO-3G

p2 <- p_base +
  scale_color_brewer(palette = "Dark2", name = "Basis Set", limit = c("STO", "GTO", "STO-3G"))

Comparing STO with GTO and STO-2G

p3 <- p_base +
  scale_color_brewer(palette = "Dark2", name = "Basis Set", limit = c("STO", "GTO", "STO-2G"))

Comparing STO with GTO and STO-4G

p4 <- p_base +
  scale_color_brewer(palette = "Dark2", name = "Basis Set", limit = c("STO", "GTO", "STO-4G"))

Comparing STO with GTO and STO-5G

p5 <- p_base +
  scale_color_brewer(palette = "Dark2", name = "Basis Set", limit = c("STO", "GTO", "STO-5G"))

Comparing STO with GTO and STO-6G

p6 <- p_base +
  scale_color_brewer(palette = "Dark2", name = "Basis Set", limit = c("STO", "GTO", "STO-6G"))

Saving all figures.

figs <- list(p1, p2, p3, p4, p5, p6)

labels <- list("Simple", "STO-3G", "STO-2G", "STO-4G", "STO-5G", "STO-6G")

walk2(figs, labels, ~ ggsave(str_glue("{.y}-Figure.png"), plot = .x, path = "vignettes/figs", width = 11, height = 8, units = "in", bg = "white"))

AliSajid/molecular_modeling_lab03 documentation built on Dec. 17, 2021, 8:41 a.m.