;;; chemestry-base.dai --- Standard definitions.

(defchemical solid default
  "Non-dissolvable chemicals"
  (crop_uptake_reflection_factor 1 [])
  (canopy_dissipation rate 0 [h^-1])
  (canopy_washoff_coefficient 1 [])
  (diffusion_coefficient 1 [cm^2/s])
  (adsorption full)
  (decompose rate 0 [h^-1]))
  
(defchemical classic default
  "For chemicals where we know no better."
  (cite focusgw2002)
  ;; decompose depth factor is from FOCUS 2002.
  (decompose_depth_factor (-105 [cm] 0.0 [])
                          ( -95 [cm] 0.3 []) ;FOCUS lim 100 cm
                          ( -65 [cm] 0.3 [])
                          ( -55 [cm] 0.5 []) ;FOCUS lim 60 cm
                          ( -35 [cm] 0.5 [])
                          ( -25 [cm] 1.0 []) ;FOCUS lim 30 cm
                          (   0 [cm] 1.0 []))
  (canopy_dissipation rate 0.0083 [h^-1]) ;Source?
  (canopy_washoff_coefficient 1.0 [])
  (crop_uptake_reflection_factor 1 [])
  (diffusion_coefficient 4.6e-6 [cm^2/s]) ; Source?
  )

(defchemical pesticide FOCUS
  "This stuff protects plants.")
  
(defchemical fungicide pesticide
  "This stuff kills swamps.")

(defchemical herbicide pesticide
  "This stuff kills plants.")

(defchemical insecticide pesticide
  "This stuff kills insects.")

(defchemical metabolite FOCUS
  "Degraded pesticide.")

(defchemical Tracer default
"No adsorption, plante uptake or degredation"
  (canopy_dissipation rate 0.00 [h^-1])       
  (canopy_washoff_coefficient 1.0)            
  (crop_uptake_reflection_factor 1.0)         
  (decompose rate 0 [h^-1])                   
  (diffusion_coefficient 1.8e-5 [cm^2/s]) ; For bromide at 20°C (Leistra & Boesten, 2010)
  (adsorption none))     			

; source: Leistram, M. & Boesten, J (2010): Measurement and computation of movement of bromide ions and carbofuran in ridged humic-sandy soil. Arch Environ Contam Toxicol. 59(1),39-48. doi: 10.1007/s00244-009-9442-4

 ;; defining colloid 
(defchemical colloid default ; must be named colloid to use the log made for colloids called "Colloids"
   "Mobile colloids."
   (canopy_dissipation rate 0.00 [h^-1])   ; must be specified, even though colloids is formed on the soil surface
   (canopy_washoff_coefficient 1.0)  ; must be specified
   (diffusion_coefficient 1.0e-12 [cm^2/s]) ; Calculated using 0.1 µm as particle size (Laegdsmand et al, 2006).
   (decompose rate 0 [h^-1]))
 
(defreaction colloid-filter filter_velocity
   "Filtration of colloids in the soil matrix." ; Since matrix domain in Daisy is divided into two domains, 80 and 40 was chosen to stay near 50m^-1 used in Jarvis99 (Hansen et al, 2012).
   (fc_primary 80 [m^-1])              ;Filter coefficient in primary domain.
   (fc_secondary 40 [m^-1])            ;Filter coefficient in secondary domain. 
   (mobile "colloid"))		       
   
 ;; colloid generation model
(defreaction colloid-generation colgen_Jarvis99 
   "Release of colloids in soil surface from heavy rain. Simulated with Jarvis99. Does not take vegetation into account"
   (kd 15 [g/J])                        ;Detachment rate coefficient (Jarvis & Ulén, 2008)
   (kr 0.1 [g/m^2/h]) 			;Replenishment rate coefficient (Jarvis & Ulén, 2008)
   (colloid "colloid")) 

;; Sources:
;; Laegdsmand, M., Moldrup, P, De Jonge, L (2006): Modelling of colloid leaching from unsaturated, aggregated soil. European Journal of Soil Sceince. 58(3),692-703. https://doi.org/10.1111/j.1365-2389.2006.00854.x
;; Hansen, S., Petersen, C., Mollerup, M., Abrahamsen, P., Gjettermann, B., Nielsen, M., Styczen, M., Poulsen, R., Lørup, J., Yamagata, K., Butts, M. (2012). Flerdimensional modellering af vandstrømning 
;;   og stoftransport i de øverste 1-2m af jorden i systemer med markdræn. Bekæmpelsesmiddelforskning fra Miljøstyrelsen. ISBN: 978-87-92779-52-6
;; Jarvis, N. & Ulén, K. (2008): Modelling particle mobilization and leaching in macroporous soil. European Journal of Soil Sceince. 50(4),621-632. https://doi.org/10.1046/j.1365-2389.1999.00269.x

;;; chemestry-base.dai ends here.
