function_prototype.h File Reference

#include "AuxBioCro.h"
#include "crocent.h"
#include "soilwater.h"

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Functions
void	Copy_SoilWater_BioCro_To_CropCent (struct soilML_str *soilMLS, struct cropcentlayer *CROPCENT)
void	CalculateBiogeochem (struct miscanthus *miscanthus, struct cropcentlayer *CROPCENT, struct dailyclimate *dailyclimate)
void	Filling_BioCro_SoilStructure (struct soilML_str *soilMLS, struct soilText_str *soTexS, int soillayers, double *depths)
void	Calculate_Soil_Layer_Temperature (double soiltavg[], int num_layers, struct dailyclimate *dailyclimate)
void	Copy_CropCent_To_DayCent_Structures (struct cropcentlayer *CROPCENT, SITEPAR_SPT sitepar, LAYERPAR_SPT layers, SOIL_SPT soil)

Function Documentation

void Calculate_Soil_Layer_Temperature	(	double	soiltavg[],
		int	num_layers,
		struct dailyclimate *	dailyclimate
	)

{
  /************************************************************************
   * Purpose:
   * To calculate average  temperature of multiple soil layer
   * Input
   * daily climate structure
   * number of layers in soil profile num_layers
   * Output
   * soiltavg[num_layers]
   * 
   * Currently I am assuming temperature of all the soil layers is same as air temperature
   * This is similar to what i got in the version Melaniie gave me.
   * I need to change it to make it more sophisticated, 
   * Also, perhaps I will need to include maxm and minm temperature of layers too 
   * *********************************************************************/
  int i;
  for (i=0; i<num_layers; i++)
  {
    soiltavg[i]=dailyclimate->temp;
  }
  return;
}

void CalculateBiogeochem	(	struct miscanthus *	miscanthus,
		struct cropcentlayer *	CROPCENT,
		struct dailyclimate *	dailyclimate
	)

{
 
  /**********************************************************************************************************************
   * Purpose:
   * To Evaluate biogeochemical cycle for the current day
   * 
   * Inputs/Outputs:
   * 
   * (1)
   * A pointer to a structure miscanthus. This is defineed in crocent.h 
   * This structure contain standing biomass of different plant organs and also litter components.
   * Idea is to use these litter component, create structures that can be send as input to soil decomposition
   * and update the standing biomass pool
   * 
   * (2)
   * A pointer to structure cropcentlayer. This is defined in crocent.h 
   * This contain all the parameters and input/output required to perform soil biogeochemistry calculations which is a function of
   * incoming litter, environmental conditions, soil properties. 
   * This structures contain all the input/output pool and after function call, all pools are updated for today.
   * 
   * (3)
   * A pointer to a structure dailyclimate. This is defined in crocent.h
   *This is a structure for storing daily climate. This is required to perform decomposition of SOC/ and calculations of trace gas 
   *which are done daily and require daily climate data 
   * 
   * Summary/Main output of interest:-
   *     (a)  Updated plant structure (after taking care of fall rate of leaf litter).
   *     (b)  Updated SOC pools
   *     (c)  Updated NH4 pool
   *     (d)  Updated NO3 in Layers
   *     (e)  Updated Flux of N from different Layers
   *     (f)  gaseous flux from soil, CH4, N20, N2, CO2
   *     (g)  Leaching of Organic matter and Nitrogen 
   * ***************************************************************************************************************************/
  // Structure Definition from DayCent Code Provided by Melanie that will be used in function call to trace gas calculations
  SITEPAR_SPT sitepar;
  LAYERPAR_SPT layers;
  SOIL_SPT soil;
  
  // these variable are in argument to trace_gas_model but are not used, I am defining them for consistency. I can remove them later on.
  double time,sand,silt,clay,nreduce,NOabsorp_grass,NOabsorp_tree,tree_lai;
  int texture;
  time= 0.0;
  texture=2;
  nreduce=1.0;
  CROPCENT->ENV.nit_amt=0.0;
  tree_lai=0.0;
  NOabsorp_grass=0.0;// These are outputs
  NOabsorp_tree=0.0;// These are outputs
  
  
  // These are local variables, some of them need to move them somewhere else later
   struct InputToCropcent leaflitter,stemlitter,rootlitter,rhizomelitter;
   struct minerals leaflitterE,stemlitterE,rootlitterE,rhizomelitterE;
   int woody, Eflag;
   double *fake;
   woody = 0 ; // No woody Material for now
   Eflag = 1; // For N simulations only
 // The below parameters aee RCESTR from fix.100 representing CE Ratio of structural material
   leaflitterE.CN=200.0;
   leaflitterE.CP=500.0;
   leaflitterE.CS=500.0;
   leaflitterE.CS=500.0;
   stemlitterE = leaflitterE;
   rootlitterE=  leaflitterE;
   rhizomelitterE=leaflitterE;
   
//***********WE CAN DEFINE ALL THE FALL RATES & OTHER PARAMETERS IN MISCANTHUS STRUCTURE THEN  SEND ALL OF THIS IN A SEPARATE FUNCTION *******  //
   //Now here We are simpyl taking litter vector and creating new structures to send to soil biogeochemistry simulations
  
    BiocroToCrocent(&miscanthus->leaf.litter,1.0,0.2, &leaflitterE, 1.0, 1, 0,&leaflitter);
    BiocroToCrocent(&miscanthus->stem.litter,1.0,0.2, &stemlitterE, 1.0, 1, 0,&stemlitter);
    BiocroToCrocent(&miscanthus->root.litter,1.0,0.2, &rootlitterE, 1.0, 0, 0,&rootlitter);
    BiocroToCrocent(&miscanthus->rhizome.litter,1.0,0.2, &rhizomelitterE, 1.0, 0, 0,&rhizomelitter);

   
   
   
//********* THIS CAN GO INTO A SEPARATE FUNCTION*********************************************************/
   
    if(leaflitter.C.totalC >0.0) 
     {
      UpdateCropcentPoolsFromBioCro(&CROPCENT, &leaflitter);
     }
      if(stemlitter.C.totalC >0.0) 
     {
      UpdateCropcentPoolsFromBioCro(&CROPCENT, &stemlitter);
     }
      if(rootlitter.C.totalC >0.0) 
     {
      UpdateCropcentPoolsFromBioCro(&CROPCENT, &rootlitter);
     }
      if(rhizomelitter.C.totalC >0.0) 
     {
      UpdateCropcentPoolsFromBioCro(&CROPCENT, &rhizomelitter);
     }

 

     // Calculate Top Layer 0-15 cm Properties based on Multi-layer soil Structure
     //**************FILL IN THE FUNCTION****************************************/
     Calculate_Soil_Layer_Temperature(CROPCENT->soilprofile.properties.soiltavg,CROPCENT->soilprofile.number_layers, dailyclimate);
     
     //Call Function to Assign Environmental Variables in the top 0-15 cm depth for Decomposition
     assignENV(&CROPCENT,fake,fake,fake,fake,fake,fake,fake);
       
     // When Management is Implemented, Use this space two modify decomposition rates (tillage) and Soil N (fertilization)
     //************INSERT IMPLEMENT MANAGEMENT FUNCTION HERE***********************
     
     // Call Function  to Assign Flux Ratios for movement between different Pools  
     assignFluxRatios(&CROPCENT);
     
     // Call Function to Decompose SOC in the top 0-15 cm layer
     decomposeCROPCENT(&CROPCENT, woody,Eflag);
       
    // Call Function to Update All the Pools
      updatecropcentpools(&CROPCENT);
    
  // Copying to DayCent Structures from CropCent multilayer Soil Structure Before Calling Trace_gas_Model
   Copy_CropCent_To_DayCent_Structures(&CROPCENT->soilprofile, sitepar,layers, soil);
    
     
  // call the tracegas model
 
   trace_gas_model(&dailyclimate->doy,&time, &CROPCENT->ENV.newminN,&CROPCENT->ENV.ammonium,CROPCENT->soilprofile.pools.nitrate,
                  &texture,&sand,&silt,&clay,
                  &CROPCENT->ENV.SOILTEX.fieldc,&CROPCENT->ENV.SOILTEX.bulkd,&CROPCENT->sitepar.maxt,&dailyclimate->precip,
                  &dailyclimate->snow,&CROPCENT->ENV.SOILTEX.avgwfps,&CROPCENT->Emission.stormf,
                  &CROPCENT->Emission.basef, CROPCENT->soilprofile.flux.frlechd,CROPCENT->soilprofile.flux.stream,
                  &CROPCENT->Emission.inorglch, &CROPCENT->soilprofile.critflow,CROPCENT->soilprofile.flux.waterflux,
                  &CROPCENT->Emission.newCO2, &CROPCENT->Emission.NOflux, &CROPCENT->Emission.Nn20flux,&CROPCENT->Emission.Dn20flux,
                  &CROPCENT->Emission.Dn2flux,&CROPCENT->Emission.CH4,&CROPCENT->sitepar.isdecid, 
                  &CROPCENT->sitepar.isagri, &miscanthus->LAI,&tree_lai,
                  &NOabsorp_grass,&NOabsorp_tree,
                  &CROPCENT->ENV.nit_amt,&nreduce,
                  CROPCENT->soilprofile.flux.dN2lyr,CROPCENT->soilprofile.flux.dN2Olyr,sitepar,layers,soil);
                  
                  
   /*
   trace_gas_model(int *jday, double *time, double *newminrl, double *ammonium, double nitrate[],
                         int *texture, double *sand, double *silt, double *clay,
                         double *afiel, double *bulkd, double *maxt, double *ppt,
                         double *snow, double *avgwfps, double *stormf,
                         double *basef, double frlechd[], double stream[],
                         double *inorglch, double *critflow, double wfluxout[],
                         double *newCO2, double *NOflux, double *Nn2oflux, double *Dn2oflux,
                         double *Dn2flux, double *CH4, int *isdecid,
                         int *isagri, double *grass_lai, double *tree_lai,
                         double *NOabsorp_grass, double *NOabsorp_tree,
                         double *nit_amt, double *nreduce, 
                         double dN2lyr[], double dN2Olyr[],SITEPAR_SPT sitepar,LAYERPAR_SPT layers,SOIL_SPT soil);
                         
 */ 
  // Write All the Variables of Interest in the Cropcentlayer structure
  
  //***********Update CROPCENT********************************************
 
}

void Copy_CropCent_To_DayCent_Structures	(	struct cropcentlayer *	CROPCENT,
		SITEPAR_SPT	sitepar,
		LAYERPAR_SPT	layers,
		SOIL_SPT	soil
	)

{
  int i;
      
      layers->numlyrs=CROPCENT->soilprofile.number_layers;
      for (i=0; i<CROPCENT->soilprofile.number_layers; i++)
      {
        layers->width[i]= CROPCENT->soilprofile.properties.width[i];
        layers->swc[i]= CROPCENT->soilprofile.pools.swc[i];
        layers->swclimit[i]= CROPCENT->soilprofile.properties.swclimit[i];
        layers->pH[i]= CROPCENT->soilprofile.properties.pH[i];
        layers->bulkd[i]= CROPCENT->soilprofile.properties.bulkd[i];
        layers->fieldc[i]= CROPCENT->soilprofile.properties.fieldc[i];
        layers->dpthmx[i]= CROPCENT->soilprofile.properties.dpthmx[i];
        layers->dpthmn[i]= CROPCENT->soilprofile.properties.dpthmn[i];
        layers->tcoeff[i]=CROPCENT->soilprofile.pools.rootbiomass[i];
        soil->soiltavg[i]=CROPCENT->soilprofile.properties.soiltavg[i];
      }
      sitepar->Ncoeff=CROPCENT->sitepar.Ncoeff;
      sitepar->jdayStart=CROPCENT->sitepar.jdayStart;
      sitepar->jdayEnd=CROPCENT->sitepar.jdayEnd;
      sitepar->N2Oadjust=CROPCENT->sitepar.N2Oadjust;
}

void Copy_SoilWater_BioCro_To_CropCent	(	struct soilML_str *	soilMLS,
		struct cropcentlayer *	CROPCENT
	)

{
  /***************************************************************************************
   * File Name:Copy_SoilWater_BioCro_To_CropCent.c
   * 
   * Function Name: Copy_SoilWater_BioCro_To_CropCent
   * 
   * Purpose: Soil Water Module of BioCro is used to update multilayer soil structure of cropcent layer,
   *          which will be eventually used for the calculation of soil biogeochemistry cycling
   * 
   * Input:
   * struct soilML_str *soilMLS:  pointer to structure soilMLS defined in AuxBioCro.h This structure 
   *                   contains calculations of soul hydrology 
   * int soillayers:  Number of soil layers being used in the calculations
   * struct cropcentlayer *CROPCENT: Pointer to structure cropcent defined in crocent.h
   * 
   * Output:
   * soilprofile of CROPCENT is updated
   * ************************************************************************************/
    int i;
     CROPCENT->soilprofile.number_layers = soilMLS->Num_BioCro_soil_layers;
      for (i = 0; i < CROPCENT->soilprofile.number_layers; i++)
        {
        CROPCENT->soilprofile.pools.rootbiomass[i]=soilMLS->rootDist[i];
        CROPCENT->soilprofile.pools.swc[i]=soilMLS->cws[i];
        CROPCENT->soilprofile.flux.waterflux[i]=soilMLS->dailyWflux[i]; 
        CROPCENT->soilprofile.properties.width[i]=soilMLS->width[i];
        CROPCENT->soilprofile.properties.dpthmx[i]=soilMLS->dpthmx[i];
        CROPCENT->soilprofile.properties.dpthmn[i]=soilMLS->dpthmn[i];
        CROPCENT->soilprofile.properties.pH[i]=soilMLS->pH[i];
        CROPCENT->soilprofile.properties.bulkd[i]=soilMLS->bulkd[i];
        CROPCENT->soilprofile.properties.swclimit[i]=soilMLS->swclimit[i];
        CROPCENT->soilprofile.properties.fieldc[i]=soilMLS->fieldc[i];
        }      
      return;
}

void Filling_BioCro_SoilStructure	(	struct soilML_str *	soilMLS,
		struct soilText_str *	soTexS,
		int	soillayers,
		double *	depths
	)

 {
    /*************************************************************************************
    *Purpose
    * 
    * Surrently Soil water module of BioCro is very simple, using a multi-layer concept but
    * average soil properties and all layers must be of same size.
    * 
    * We have added additional elements in soil multilayer structure used in BioCro where
    * each layer is explicitly defined and also additional properties which are required for
    * biogeochemical calculations are also defined for each layer
    * 
    * We are simply filling these additional elements in a way that it is consistent with the 
    * current BioCro-soil water module [average soil properties for all the layers, each layer is
    * about 5 cm depth] so that older function of soilML can be used.I have to ensure from R that each layer is 5 cm 
    * by defining  Nlayers such that Nlayers= round(Rooting depth/5 , 0).
    * 
    * Once Explicit definition of soil layers are used, Error associated with Rooting depth will disappear
    * 
    * IN future, I can use additional information to write more sophisticated soil water function
    * which cansiders effect of varying soil properties within a single soil profile and also
    * effect of using non-uniform discretization of the soil profile
    * 
    * Variables Initialized
    * soilMLS->
    * width
    * dpthmn
    * dpthmx
    * bulkd
    * fieldc
    * pH
    * swclimit
    * ***********************************************************************************/
    int i;
    soilMLS->Num_BioCro_soil_layers= soillayers;
    
    for (i=0; i <soillayers;i++)
      {
                if(i == 0)
                {
                 soilMLS->width[i] = depths[1];
                 soilMLS->dpthmn[i]=0.0;
                 soilMLS->dpthmx[i]=depths[1];
                 
                } 
                else
                {
                 soilMLS->width[i] = depths[i] - depths[i-1];
                 soilMLS->dpthmn[i]=depths[i-1];
                 soilMLS->dpthmx[i]=depths[i];
                }
          soilMLS->pH[i]=7.0;
          soilMLS->swclimit[i]=soTexS->wiltp-0.0008; // soil/in file says swc limit = wiltpoint - deltamin, which is 0.0008 in example file
          soilMLS->bulkd[i]=soTexS->bulkd;
          soilMLS->fieldc[i]=soTexS->fieldc;
          soilMLS->sand[i]=soTexS->sand;
          soilMLS->silt[i]=soTexS->silt;
          soilMLS->clay[i]=soTexS->clay;
      }
   return;
 }

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• function_prototype.h
• Generated on Fri Apr 3 2015 15:41:07 for BioCro by 1.8.6