smarties_batch.qmd

---
title: "Calculating many SMARTIES T-matrices"
author: "baptiste"
date: today
format: html
engine: knitr
---

Below is an example script to run many SMARTIES simulations and export the T-matrices in HDF5. The script is available as standalone script [smarties_batch.R](smarties_batch.R).

```{r, eval=TRUE, message=FALSE}
library(glue)
library(dplyr)
library(purrr)

# read in the template
template <- glue_collapse(readLines('smarties/_template.m'), sep = "\n")

parameters <- expand.grid(a = seq(10, 100, by=5), c = seq(10, 100, by=5),
                          material = c("Au", "Ag", "Si"), 
                          medium = c("vacuum", "water")) |> 
  filter(a != c) |> # use Mie for this
  mutate(shape = ifelse(a > c, "oblate", "prolate"),
         n = ifelse(medium == "water", 1.33, 1.0),
         source = case_when(material == "Au" ~ "Raschke et al 10.1103/PhysRevB.86.235147", 
                            material == "Ag" ~ "Raschke et al 10.1103/PhysRevB.91.235137",
                            material == "Si" ~ "Aspnes et al 10.1103/PhysRevB.27.985",
                            .default = "Unknown material!"))

parameters$step <- 1
nrow(parameters)
```

For initial testing, we'll run much fewer combinations

```{r, eval=TRUE}
parameters <- expand.grid(a = seq(20, 50, by=10), c = seq(20, 50, by=10),
                          material = c("Au", "Ag"), 
                          medium = c("water")) |> 
  filter(a != c) |> # use Mie for this
  mutate(shape = ifelse(a > c, "oblate", "prolate"),
         n = ifelse(medium == "water", 1.33, 1.0),
         source = case_when(material == "Au" ~ "Raschke et al 10.1103/PhysRevB.86.235147", 
                            material == "Ag" ~ "Raschke et al 10.1103/PhysRevB.91.235137",
                            material == "Si" ~ "Aspnes et al 10.1103/PhysRevB.27.985",
                            .default = "Unknown material!"))
parameters$step <- 5
```

Even with these restricted options, there's already `r nrow(parameters)` combinations.

```{r echo=FALSE}
gt::gt(parameters[,c("a","c","shape","material","medium")])
```

We use the "glue" package to inject the parameters into the template, where the variables are indicated between braces `{}`. The process loops over each parameter combination and outputs a new file with corresponding filename.

```{r}
write_script <- function(a, c, material, medium, shape, n, step, source){
 script <- glue(template)   
 cat(script, file = glue('smarties/run_{material}_{medium}_{a}_{c}.m'))
 cat(glue("run_{material}_{medium}_{a}_{c}\n\n"), 
     file = "smarties/batch.m", append = TRUE)
}
 cat("%% Running all the files below\n",file = "smarties/batch.m", append = FALSE)
pwalk(rowwise(parameters), write_script)
```

Running the batch script in Matlab results in `r nrow(parameters)` output T-matrix files of size between 4 and 6Mb each, with the 5nm step defined above. The value of Lmax needed for $10^{-10}$ accuracy in $\langle\sigma_\text{ext}\rangle$ appears to be around 11.

`r library(knitr);library(xfun);f=knitr::current_input();`
`r invisible(purl(with_ext(f, "qmd"),output=with_ext(f, "R")))`