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14-silica.Rmd
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# Silica
## Contributors
Matthew R. Hipsey
<!-- ## Overview -->
<!-- ## Model Description -->
<!-- ### Process Descriptions -->
<!-- ### Optional Module Links -->
<!-- ### Feedbacks to the Host Model -->
<!-- The silica module has no feedbacks to the host hydrodynamic model. -->
### Variable Summary
The default variables created by this module, and the optionally required linked variables needed for full functionality of this module are summarised in Table \@ref(tab:14-statetable). The diagnostic outputs able to be output are summarised in Table \@ref(tab:14-diagtable).
#### State variables {-}
```{r 14-statetable, echo=FALSE, message=FALSE, warning=FALSE}
library(knitr)
library(kableExtra)
library(readxl)
library(rmarkdown)
theSheet <- read_excel('tables/aed_variable_tables.xlsx', sheet = 9)
theSheet <- theSheet[theSheet$Table == "State variable",]
theSheetGroups <- unique(theSheet$Group)
theSheet$`AED name` <- paste0("`",theSheet$`AED name`,"`")
for(i in seq_along(theSheet$Symbol)){
if(!is.na(theSheet$Symbol[i])==TRUE){
theSheet$Symbol[i] <- paste0("$$",theSheet$Symbol[i],"$$")
} else {
theSheet$Symbol[i] <- NA
}
}
for(i in seq_along(theSheet$Unit)){
if(!is.na(theSheet$Unit[i])==TRUE){
theSheet$Unit[i] <- paste0("$$\\small{",theSheet$Unit[i],"}$$")
} else {
theSheet$Unit[i] <- NA
}
}
for(i in seq_along(theSheet$Comments)){
if(!is.na(theSheet$Comments[i])==TRUE){
theSheet$Comments[i] <- paste0("",theSheet$Comments[i],"")
} else {
theSheet$Comments[i] <- " "
}
}
kbl(theSheet[,3:NCOL(theSheet)], caption = "Silica - *state* variables", align = "l",) %>%
pack_rows(theSheetGroups[1],
min(which(theSheet$Group == theSheetGroups[1])),
max(which(theSheet$Group == theSheetGroups[1])),
background = '#ebebeb') %>%
pack_rows(theSheetGroups[2],
min(which(theSheet$Group == theSheetGroups[2])),
max(which(theSheet$Group == theSheetGroups[2])),
background = '#ebebeb') %>%
row_spec(0, background = "#14759e", bold = TRUE, color = "white") %>%
kable_styling(full_width = F,font_size = 11) %>%
column_spec(2, width_min = "7em") %>%
column_spec(3, width_max = "18em") %>%
column_spec(4, width_min = "10em") %>%
column_spec(5, width_min = "5em") %>%
column_spec(7, width_min = "10em") %>%
column_spec(7, width_max = "20em") %>%
scroll_box(width = "770px", height = "200px",
fixed_thead = FALSE)
```
#### Diagnostics{-}
```{r 14-diagtable, echo=FALSE, message=FALSE, warning=FALSE}
library(knitr)
library(kableExtra)
library(readxl)
library(rmarkdown)
theSheet <- read_excel('tables/aed_variable_tables.xlsx', sheet = 9)
theSheet <- theSheet[theSheet$Table == "Diagnostics",]
theSheetGroups <- unique(theSheet$Group)
theSheet$`AED name` <- paste0("`",theSheet$`AED name`,"`")
for(i in seq_along(theSheet$Symbol)){
if(!is.na(theSheet$Symbol[i])==TRUE){
theSheet$Symbol[i] <- paste0("$$",theSheet$Symbol[i],"$$")
} else {
theSheet$Symbol[i] <- NA
}
}
for(i in seq_along(theSheet$Unit)){
if(!is.na(theSheet$Unit[i])==TRUE){
theSheet$Unit[i] <- paste0("$$\\small{",theSheet$Unit[i],"}$$")
} else {
theSheet$Unit[i] <- NA
}
}
for(i in seq_along(theSheet$Comments)){
if(!is.na(theSheet$Comments[i])==TRUE){
theSheet$Comments[i] <- paste0("",theSheet$Comments[i],"")
} else {
theSheet$Comments[i] <- " "
}
}
kbl(theSheet[,3:NCOL(theSheet)], caption = "Silica - *diagnostic* variables", align = "l",) %>%
pack_rows(theSheetGroups[1],
min(which(theSheet$Group == theSheetGroups[1])),
max(which(theSheet$Group == theSheetGroups[1])),
background = '#ebebeb') %>%
row_spec(0, background = "#14759e", bold = TRUE, color = "white") %>%
kable_styling(full_width = F,font_size = 11) %>%
column_spec(2, width_min = "7em") %>%
column_spec(3, width_max = "18em") %>%
column_spec(4, width_min = "10em") %>%
column_spec(5, width_min = "6em") %>%
column_spec(7, width_min = "10em") %>%
scroll_box(width = "770px", height = "120px",
fixed_thead = FALSE)
```
<br>
### Parameter Summary
The parameters and settings used by this module are summarised in Table \@ref(tab:14-parstable).
```{r 14-parstable, echo=FALSE, message=FALSE, warning=FALSE}
library(knitr)
library(kableExtra)
library(readxl)
library(rmarkdown)
theSheet <- read_excel('tables/aed_variable_tables.xlsx', sheet = 9)
theSheet <- theSheet[theSheet$Table == "Parameter",]
theSheetGroups <- unique(theSheet$Group)
theSheet$`AED name` <- paste0("`",theSheet$`AED name`,"`")
for(i in seq_along(theSheet$Symbol)){
if(!is.na(theSheet$Symbol[i])==TRUE){
theSheet$Symbol[i] <- paste0("$$",theSheet$Symbol[i],"$$")
} else {
theSheet$Symbol[i] <- " "
}
}
for(i in seq_along(theSheet$Unit)){
if(!is.na(theSheet$Unit[i])==TRUE){
theSheet$Unit[i] <- paste0("$$\\small{",theSheet$Unit[i],"}$$")
} else {
theSheet$Unit[i] <- NA
}
}
for(i in seq_along(theSheet$Comments)){
if(!is.na(theSheet$Comments[i])==TRUE){
theSheet$Comments[i] <- paste0("",theSheet$Comments[i],"")
} else {
theSheet$Comments[i] <- "-"
}
}
kbl(theSheet[,3:NCOL(theSheet)], caption = "Silica module parameters and configuration options", align = "l",) %>%
pack_rows(theSheetGroups[1],
min(which(theSheet$Group == theSheetGroups[1])),
max(which(theSheet$Group == theSheetGroups[1])),
background = '#ebebeb') %>%
pack_rows(theSheetGroups[2],
min(which(theSheet$Group == theSheetGroups[2])),
max(which(theSheet$Group == theSheetGroups[2])),
background = '#ebebeb') %>%
row_spec(0, background = "#14759e", bold = TRUE, color = "white") %>%
kable_styling(full_width = F,font_size = 11) %>%
column_spec(2, width_min = "7em") %>%
column_spec(3, width_max = "19em") %>%
column_spec(4, width_min = "10em") %>%
column_spec(5, width_min = "5em") %>%
column_spec(7, width_min = "10em") %>%
scroll_box(width = "770px", height = "500px",
fixed_thead = FALSE)
```
<br>
## Setup & Configuration
An example `aed.nml` parameter specification block for the `aed_silica` module is shown below:
```{fortran, eval = FALSE}
&aed_silica
!-- Initial value
rsi_initial = 12.5
!-- Sediment flux
Fsed_rsi = 1.8
Ksed_rsi = 50.0
theta_sed_rsi = 1.08
silica_reactant_variable = 'OXY_oxy'
Fsed_rsi_variable = 'SDF_Fsed_rsi'
/
```
<!-- ## Case Studies & Examples -->
<!-- ### Case Study -->
<!-- ### Publications -->