A simple example of using the Daisy wrapper for remote execution. Daisy files are included in the script, so theres no external dependencies.
See https://github.com/nitrogensensor/daisywrapper for more information.
First download the wrapper (daisy.jar) so we can run simulations remotely, if we don’t have it already
if (!file.exists("daisy.jar"))
download.file("https://daisy.nitrogensensor.eu/resultat/diverse/daisy.jar", "daisy.jar")Create input directory and a Daisy script file
unlink("daisyInput", recursive = TRUE)
dir.create("daisyInput")
script='
;; Including external library-files
(input file "tillage.dai")
(input file "crop.dai")
(input file "fertilizer.dai")
(input file "log.dai")
;; Weather data
(weather default "dk-taastrup.dwf")
;; Defining soil horizons of a fine sandy loam
(defhorizon "Ap F.S.L." FAO3
"Data from Jacobsen 1983"
(dry_bulk_density 1.53 [g/cm^3])
(clay 0.113 [])
(silt 0.277 [])
(sand 0.584 [])
(humus 0.026 [])
(C_per_N 11.0 [g C/g N]))
(defhorizon "B F.S.L." FAO3
(dry_bulk_density 1.51 [g/cm^3])
(clay 0.235 [])
(silt 0.253 [])
(sand 0.507 [])
(humus 0.005 [])
(C_per_N 11.0 [g C/g N]))
(defhorizon "C F.S.L." FAO3
(dry_bulk_density 1.57 [g/cm^3])
(clay 0.244 [])
(silt 0.283 [])
(sand 0.471 [])
(humus 0.002 [])
(C_per_N 11.0)) ; Note that the dimension is omittet
;; Parameterisation of column (Fine sandy loam)
(defcolumn "Fine sandy loam" default
(Soil (MaxRootingDepth 100 [cm])
(horizons ( -30 [cm] "Ap F.S.L.")
( -80 [cm] "B F.S.L.")
( -400 [cm] "C F.S.L.")))
(Groundwater deep)
(OrganicMatter original (init (input 3000 [kg C/ha/y]))))
;; Spring Barley setup.
(defaction "SBarley_management" activity
(wait_mm_dd 3 20)
(plowing)
(wait_mm_dd 4 15)
(seed_bed_preparation)
(sow "Spring Barley")
(wait_mm_dd 4 20)
(fertilize (N25S (weight 95 [kg N/ha])))
(wait (or (crop_ds_after "Spring Barley" 2.0) ;Ripe
(mm_dd 9 1))) (harvest "Spring Barley"))
;; Selecting column
(column "Fine sandy loam")
;; Start and end of simulation.
(time 1993 1 1)
(stop 1995 1 1)
;; Selecting management
(manager activity
"SBarley_management"
)
;; Selecting output
;; Description that will occur in all output files
(description "Spring Barley; Soil: Fine sandy loam; Weather: Taastrup")
;(activate_output (after 1993 03 31 23))
(log_prefix "Ex1/")
(output harvest
("Crop Production" (when daily))
;; Water balance 0-100 cm
("Field water" (to -400 [cm])(when daily)
(where "Daily_FWB.csv") (print_header false) (print_dimension false))
;; Nitrogen balance 0-100 cm
("Field nitrogen" (to -400 [cm])(when daily)
(where "Daily_FNB.dlf"))
;; Soil profile data
("Soil Water Content" (when daily))
("Soil Water Potential (pF)"(when daily))
("Soil NO3 Concentration" (when daily))
)
'
write(script,"daisyInput/Exercise01.dai")
dir.create("daisyInput/Ex1/")Run a single daisy simulation.
This chunk runs daisy on Exercise01.dai. Make sure that you have that file in the same directory as this script.
getwd()## [1] "/cloud/project"# unlink("daisyOutput", recursive = TRUE)
system2("java", "-jar daisy.jar client -d daisyInput Exercise01.dai -o daisyOutput")Load daisy results into a dataframe
Daily_FWB <- read.delim("daisyOutput/Exercise01/Ex1/Daily_FWB.csv")
Daily_FWB$date <- as.Date(paste(Daily_FWB$year, Daily_FWB$month, Daily_FWB$mday, sep = '-'), format = '%Y-%m-%d')
head(Daily_FWB)## year month mday hour Precipitation Irrigation Potential.evapotranspiration
## 1 1993 1 1 0 0 0 0
## 2 1993 1 2 0 0 0 0
## 3 1993 1 3 0 0 0 0
## 4 1993 1 4 0 0 0 0
## 5 1993 1 5 0 0 0 0
## 6 1993 1 6 0 0 0 0
## Actual.evapotranspiration Matrix.percolation Biopore.percolation
## 1 0 0.0000000 0
## 2 0 0.0778966 0
## 3 0 0.0778069 0
## 4 0 0.0776550 0
## 5 0 0.0775995 0
## 6 0 0.0775350 0
## Matrix.drain.flow Biopore.drain.flow Runoff Biopore.water Soil.matrix.water
## 1 0 0 0 0 1200.70
## 2 0 0 0 0 1200.62
## 3 0 0 0 0 1200.54
## 4 0 0 0 0 1200.47
## 5 0 0 0 0 1200.39
## 6 0 0 0 0 1200.31
## Surface.water date
## 1 0 1993-01-01
## 2 0 1993-01-02
## 3 0 1993-01-03
## 4 0 1993-01-04
## 5 0 1993-01-05
## 6 0 1993-01-06Plot the results
plot(Daily_FWB$date, Daily_FWB$Actual.evapotranspiration)