maizeGro.h File Reference

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Functions
struct Can_Str	CanAC (double LAI, int DOY, int hr, double solarR, double Temp, double RH, double WindSpeed, double lat, int nlayers, double Vmax, double Alpha, double Kparm, double theta, double beta, double Rd, double Catm, double b0, double b1, double StomataWS, int ws, double kd, double chil, double heightf, double leafN, double kpLN, double lnb0, double lnb1, int lnfun, double upperT, double lowerT, struct nitroParms nitroP)
struct lai_str	laiLizasoFun (double thermalt, double phenostage, double phyllochron1, double phyllochron2, double Ax, double LT, double k0, double a1, double a2, double L0, double LLx, double Lx, double LNl)
struct lai_str	laiBirchdiscontinuousFun (double phenostage, double Lt, double Amax, double c1, double c2, double c3, double c4)
struct lai_str	laiBirchcontinuousFun (double phenostage, double a, double b, double Amax, double x0, double f, double g, double TT, double LT)

Function Documentation

struct Can_Str CanAC	(	double	LAI,
		int	DOY,
		int	hr,
		double	solarR,
		double	Temp,
		double	RH,
		double	WindSpeed,
		double	lat,
		int	nlayers,
		double	Vmax,
		double	Alpha,
		double	Kparm,
		double	theta,
		double	beta,
		double	Rd,
		double	Catm,
		double	b0,
		double	b1,
		double	StomataWS,
		int	ws,
		double	kd,
		double	chil,
		double	heightf,
		double	leafN,
		double	kpLN,
		double	lnb0,
		double	lnb1,
		int	lnfun,
		double	upperT,
		double	lowerT,
		struct nitroParms	nitroP
	)

{

        struct ET_Str tmp5_ET, tmp6_ET;
        struct Can_Str ans;
        struct c4_str tmpc4;
        struct c4_str tmpc42;

        int i;
        double Idir, Idiff, cosTh;
        double LAIc;
        double IDir, IDiff, Itot, rh, WS;
        double pLeafsun, pLeafshade;
        double Leafsun, Leafshade;
        double CanHeight;

        double vmax1, leafN_lay;
        double TempIdir,TempIdiff,AssIdir,AssIdiff,GAssIdir,GAssIdiff;

        double CanopyA, CanopyT,GCanopyA;

        const double cf = 3600 * 1e-6 * 30 * 1e-6 * 10000;
        const double cf2 = 3600 * 1e-3 * 18 * 1e-6 * 10000; 

        /* For Assimilation */
        /* 3600 converts seconds to hours */
        /* 1e-6 converts micro mols to mols */
        /* 30 is the grams in one mol of CO2 */
        /* 1e-6 converts g to Mg */
        /* 10000 scales from meter squared to hectare */

        /* For Transpiration */
        /* 3600 converts seconds to hours */
        /* 1e-3 converts mili mols to mols */
        /* 18 is the grams in one mol of H20 */
        /* 1e-6 converts g to Mg */
        /* 10000 scales from meter squared to hectare */

        lightME(lat,DOY,hr);

        Idir = tmp1[0] * solarR;
        Idiff = tmp1[1] * solarR;
        cosTh = tmp1[2];
    
        sunML(Idir,Idiff,LAI,nlayers,cosTh, kd, chil, heightf);

        /* results from multilayer model */
        LAIc = LAI / nlayers;
        /* Next I need the RH and wind profile */
        RHprof(RH,nlayers);
        WINDprof(WindSpeed,LAI,nlayers);

        LNprof(leafN, LAI, nlayers, kpLN);
        /* It populates tmp5 */

        /* Next use the EvapoTrans function */
        CanopyA=0.0;
        GCanopyA=0.0;
        CanopyT=0.0;
        for(i=0;i<nlayers;i++)
        {
                leafN_lay = tmp5[--tp5];
                if(lnfun == 0){
                        vmax1 = Vmax;
                }else{
                        vmax1=nitroP.Vmaxb1*leafN_lay+nitroP.Vmaxb0;
                                              if(vmax1<0) vmax1=0.0;
                                                      Alpha=nitroP.alphab1*leafN_lay+nitroP.alphab0;
                                                       Rd=nitroP.Rdb1*leafN_lay+nitroP.Rdb0;
               /* For now alpha is not affected by leaf nitrogen */
                }

                IDir = layIdir[--sp1];
                Itot = layItotal[--sp3];

                rh = tmp4[--tp4];
                WS = tmp3[--tp3];
                pLeafsun = layFsun[--sp4];
                CanHeight = layHeight[--sp6];
                Leafsun = LAIc * pLeafsun;
                tmp5_ET = EvapoTrans(IDir,Itot,Temp,rh,WS,LAIc,CanHeight,StomataWS,ws,vmax1,Alpha,Kparm,theta,beta,Rd,b0,b1,upperT,lowerT,Catm);
                TempIdir = Temp + tmp5_ET.Deltat;
                tmpc4 = c4photoC(IDir,TempIdir,rh,vmax1,Alpha,Kparm,theta,beta,Rd,b0,b1,StomataWS, Catm, ws,upperT,lowerT);
                AssIdir = tmpc4.Assim;
                GAssIdir =tmpc4.GrossAssim;

                IDiff = layIdiff[--sp2];
                pLeafshade = layFshade[--sp5];
                Leafshade = LAIc * pLeafshade;
                tmp6_ET = EvapoTrans(IDiff,Itot,Temp,rh,WS,LAIc,CanHeight,StomataWS,ws,vmax1,Alpha,Kparm,theta,beta,Rd,b0,b1,upperT,lowerT,Catm);
                TempIdiff = Temp + tmp6_ET.Deltat;
                tmpc42 = c4photoC(IDiff,TempIdiff,rh,vmax1,Alpha,Kparm,theta,beta,Rd,b0,b1,StomataWS, Catm, ws,upperT,lowerT);
                AssIdiff = tmpc42.Assim;
                GAssIdiff = tmpc42.GrossAssim;
                CanopyA += Leafsun * AssIdir + Leafshade * AssIdiff;
                GCanopyA += Leafsun * GAssIdir + Leafshade * GAssIdiff;
// I am evaluating CanopyT using Penman Method because it gives realistic results
// IN future canopyT needs to be fixed
//                CanopyT += Leafsun * tmp5_ET.TransR + Leafshade * tmp6_ET.TransR;
                CanopyT += Leafsun * tmp5_ET.EPenman + Leafshade * tmp6_ET.EPenman;
        }
        /*## These are micro mols of CO2 per m2 per sec for Assimilation
          ## and mili mols of H2O per m2 per sec for Transpiration
          ## Need to convert to 
          ## 3600 converts seconds to hours
          ## 10^-6 converts micro mols to mols
          ## 30 converts mols of CO2 to grams
          ## (1/10^6) converts grams to Mg
          ## 10000 scales up to ha */
/* A similar conversion is made for water but
   replacing 30 by 18 and mili mols are converted to
   mols (instead of micro) */
        ans.Assim = cf * CanopyA ;
        ans.Trans = cf2 * CanopyT; 
        ans.GrossAssim=cf*GCanopyA;
        return(ans);
}

struct lai_str laiBirchcontinuousFun	(	double	phenostage,
		double	a,
		double	b,
		double	Amax,
		double	x0,
		double	f,
		double	g,
		double	TT,
		double	LT
	)

                                               {
        struct lai_str tmp;
        double leafnumber = 0.0, totalLAI = 0.0, SLA = 0.0, TPLAmax = 0.0;

        int i, i2, i3, ln, ln2;

        for(i2 = 0; i2 < MAXLEAFNUMBER; i2++){
                tmp.leafarea[i2] = 0.0;
        }

        if (phenostage <= 0) {
          leafnumber = 0;
        }else{
          if (phenostage < 1){
            leafnumber = phenostage* 100;
          }else{
            leafnumber = LT;
          }
        }         
        if (Amax == -1){
                /* Eq 13 in Birch*/
                Amax = 1000 * exp(-1.17 + 0.047 * LT);
        }
        if (a == -1){
                /* Eq 18 in Birch */
                a = -0.009 - exp(-0.2 * LT);
        }
        if (b == -1){
                /* Eq 19 in Birch */
                b = 0.0006 - exp(-0.43 * LT);
        }
        if (x0 == -1){
                /* Eq 14 in Birch */
                x0 = 0.67 * LT;
        }
        if (g == -1){
                /* Eq 20 in Birch */
                g = 107.9 * LT - 327;
        }

        for(i3 = 0; i3 < LT; i3++){
                ln2 = i3 + 1;
                TPLAmax += Amax * exp(a * (ln2 - x0) * (ln2 - x0) + b *
                             (ln2 - x0) * (ln2 - x0) * (ln2 - x0));
        }

        /* Birch Eq 11*/
        SLA = TPLAmax / (1 + exp(-f * (TT - g)));

        for (i = 0; i < leafnumber; i++){
          ln = i + 1;
          tmp.leafarea[i] = Amax * exp(a * (ln - x0) * (ln - x0) + b *
                             (ln - x0) * (ln - x0) * (ln - x0));

           totalLAI += tmp.leafarea[i];
         }
         tmp.totalLeafArea = totalLAI - SLA;
         return (tmp);
}

struct lai_str laiBirchdiscontinuousFun	(	double	phenostage,
		double	Lt,
		double	Amax,
		double	c1,
		double	c2,
		double	c3,
		double	c4
	)

                                                             {
        struct lai_str tmp;
        double leafnumber, totalLAI = 0.0;
        if (phenostage <= 0) {
          leafnumber = 0;
        }else{
          if (phenostage < 1){
            leafnumber = phenostage* 100;
          }else{
            leafnumber = LT;
          }
        }         
        if (Amax == -1){
          /* Eq 13 in Birch*/
          Amax = 1000 * exp(-1.17 + 0.047 * LT);
        }
        int i, i2, ln;
        for(i2=0;i2<MAXLEAFNUMBER;i2++){
          tmp.leafarea[i2] = 0.0;
        }
        for (i = 0; i<leafnumber; i++){
          ln = i + 1;
          if (ln <= 3){
            /* Eq 14 in Birch */
            tmp.leafarea[i] = c1 * ln;
          }else{
            if (ln <= 11){
              /* Eq 15 in Birch */
              tmp.leafarea[i] = c2* ln * ln;
            }else{
              /* Eq 16 in Birch */
              tmp.leafarea[i] = c3 * Amax + c4 * ln * ln;
            }
          }
          totalLAI += tmp.leafarea[i];
        }
        tmp.totalLeafArea = totalLAI;
        return (tmp);
}

struct lai_str laiLizasoFun	(	double	thermalt,
		double	phenostage,
		double	phyllochron1,
		double	phyllochron2,
		double	Ax,
		double	LT,
		double	k0,
		double	a1,
		double	a2,
		double	L0,
		double	LLx,
		double	Lx,
		double	LNl
	)

                                                                                    {

        struct lai_str tmp;
        double A, kei, tei;
        double LNx = 0.67 * LT;
        double te1 = 25;
        double te2 = 50;
        double tti;
        double tsi;
        double leafnumber ;
        double totalLAI = 0.0;

        if (phenostage <= 0) {
          leafnumber = 0;
        }else{
          if (phenostage < 1){
            leafnumber = phenostage* 100;
          }else{
            leafnumber = LT;
          }
        }

/* Longevity */

        /* Eq 11 in Lisazo 2003 */
        if (LNl == -1){ 
            LNl = 3.59 + 0.498 * LT;
        }
        /* Eq 12 in Lisazo 2003 */
        /* double Wl = 0.333333 * LT; not used ? */
        double LLi;

        double Wk = LT / 8.18;

        int i, i2, ln = 0;

        for(i2=0;i2<MAXLEAFNUMBER;i2++){
                tmp.leafarea[i2] = 0.0;
        }

        for(i=0;i<leafnumber;i++){

                /* Eq 7 in Lizaso 2003 */
                ln = i + 1;
                tti = (ln - 2) * phyllochron1 + te2;

                /* Eq 8 in Lizaso 2003 */
                kei = k0 + 0.174 * exp( - ((ln - 1)*(ln - 1))/(2 * Wk * Wk));

                /* Eq 10 in Lizaso 2003 */
                LLi = L0 + Lx * exp( - (ln - LNl)*(ln - LNl)/ (2*Wk*Wk));
                

                /* Eq 6 in Lizaso 2003 */
                if(ln == 1) tei = te1;
                if(ln == 2){
                        tei = te2;
                }else{
                        tei = tti + (2.197 /kei);
                }
                
                /* calculating time of 50% senescence from time of 50%
                 * expansion and leaf longevity */
                tsi = LLi + tei;

                /* Applying Eq 4 in Lizaso 2003 */
                A = Aei(ln, Ax, LNx, a1, a2);

                /* Applying Eq 2 in Lizaso 2003 */
                tmp.leafarea[i] = Alogistic(thermalt, A, kei, tei);

                /* calculating senesced area for this leaf */
                tmp.leafarea[i] -= Alogistic(thermalt, A, kei, tsi);

                /* Rprintf("leaf area %.1f \n", tmp.leafarea[i]);  */
                totalLAI += tmp.leafarea[i];
        }

        tmp.totalLeafArea = totalLAI;
        return(tmp);


}