/**
 *  @file Reactor.cpp
 *
 *  A zero-dimensional reactor
 */
 
// Copyright 2001  California Institute of Technology


#ifdef WIN32
#pragma warning(disable:4786)
#pragma warning(disable:4503)
#endif

#include "ConstPressureReactor.h"
#include "FlowDevice.h"
#include "Wall.h"
#include "InterfaceKinetics.h"
#include "SurfPhase.h"

using namespace Cantera;
using namespace std;

namespace CanteraZeroD {

    ConstPressureReactor::ConstPressureReactor() : Reactor() {}

    void ConstPressureReactor::
    getInitialConditions(double t0, size_t leny, double* y) 
    {
        m_init = true;
        if (m_thermo == 0) {
            throw CanteraError("getInitialConditions",
                "Error: reactor is empty.");
        }  
        m_time = t0;
        m_thermo->restoreState(m_state);

        // total mass
        doublereal mass = m_thermo->density() * m_vol;
        
        // set components y + 2 ... y + K + 1 to the  
        // mass M_k of each species
        m_thermo->getMassFractions(y+2);
        scale(y + 2, y + m_nsp + 2, y + 2, mass);
            
        // set the first component to the total enthalpy
        y[0] = m_thermo->enthalpy_mass() * mass;
        
        // set the second component to the total volume
        y[1] = m_vol;

        // set the remaining components to the surface species
        // coverages on the walls
        int loc = m_nsp + 2;
        SurfPhase* surf;
        for (int m = 0; m < m_nwalls; m++) {
            surf = m_wall[m]->surface(m_lr[m]);
            if (surf) {
                m_wall[m]->getCoverages(m_lr[m], y + loc);
                loc += surf->nSpecies();
            }
        }
    }

    void ConstPressureReactor::initialize(doublereal t0) {
        m_thermo->restoreState(m_state);
        m_sdot.resize(m_nsp, 0.0);
        m_nv = m_nsp + 2;
        for (int w = 0; w < m_nwalls; w++)
            if (m_wall[w]->surface(m_lr[w]))
                m_nv += m_wall[w]->surface(m_lr[w])->nSpecies();
        m_enthalpy = m_thermo->enthalpy_mass();
        m_pressure = m_thermo->pressure();
        m_intEnergy = m_thermo->intEnergy_mass();

        int m, nt = 0, maxnt = 0;
        for (m = 0; m < m_nwalls; m++) {
            if (m_wall[m]->kinetics(m_lr[m])) {
                nt = m_wall[m]->kinetics(m_lr[m])->nTotalSpecies();
                if (nt > maxnt) maxnt = nt;
                if (m_wall[m]->kinetics(m_lr[m])) {
                    if (&m_kin->thermo(0) != 
                        &m_wall[m]->kinetics(m_lr[m])->thermo(0)) {
                        throw CanteraError("ConstPressureReactor::initialize",
                            "First phase of all kinetics managers must be"
                            " the gas.");
                    }
                }
            }   
        }
        m_work.resize(maxnt);
        m_init = true;
    }
    
    void ConstPressureReactor::updateState(doublereal* y) {

        // The components of y are the total enthalpy,
        // the total volume, and the mass of each species.
        doublereal h   = y[0];
        doublereal* mss = y + 2;
        doublereal mass = accumulate(y+2, y+2+m_nsp, 0.0);
        m_thermo->setMassFractions(mss);

        if (m_energy) {
            m_thermo->setState_HP(h/mass, m_pressure, 1.0e-4); 
        }
        else {
            m_thermo->setPressure(m_pressure); 
        }            
        m_vol = mass / m_thermo->density();

        int loc = m_nsp + 2;
        SurfPhase* surf;
        for (int m = 0; m < m_nwalls; m++) {
            surf = m_wall[m]->surface(m_lr[m]);
            if (surf) {
                m_wall[m]->setCoverages(m_lr[m], y+loc);
                loc += surf->nSpecies();
            }
        }

        // save parameters needed by other connected reactors
        m_enthalpy = m_thermo->enthalpy_mass();
        m_intEnergy = m_thermo->intEnergy_mass();
        m_thermo->saveState(m_state);
    }


    /*
     * Called by the integrator to evaluate ydot given y at time 'time'.
     */
    void ConstPressureReactor::evalEqs(doublereal time, doublereal* y, 
        doublereal* ydot, doublereal* params) 
    {
        int i, k, nk;
        m_time = time;
        m_thermo->restoreState(m_state);

        Kinetics* kin;
        int m, n, npar, ploc;
        double mult;

        // process sensitivity parameters
        if (params) {
            
            npar = m_pnum.size();
            for (n = 0; n < npar; n++) {
                mult = m_kin->multiplier(m_pnum[n]);
                m_kin->setMultiplier(m_pnum[n], mult*params[n]);
            }
            ploc = npar;
            for (m = 0; m < m_nwalls; m++) {
                if (m_nsens_wall[m] > 0) {
                    m_wall[m]->setSensitivityParameters(m_lr[m], params + ploc);
                    ploc += m_nsens_wall[m];
                }
            }
        }

        m_vdot = 0.0;
        m_Q    = 0.0;

        // compute wall terms
        doublereal rs0, sum, wallarea;

        SurfPhase* surf;
        int lr, ns, loc = m_nsp+2, surfloc;
        fill(m_sdot.begin(), m_sdot.end(), 0.0);
        for (i = 0; i < m_nwalls; i++) {
            lr = 1 - 2*m_lr[i];
            m_Q += lr*m_wall[i]->Q(time);
            kin = m_wall[i]->kinetics(m_lr[i]);
            surf = m_wall[i]->surface(m_lr[i]);
            if (surf && kin) {
                rs0 = 1.0/surf->siteDensity();
                nk = surf->nSpecies();
                sum = 0.0;
                surf->setTemperature(m_state[0]);
                m_wall[i]->syncCoverages(m_lr[i]);
                kin->getNetProductionRates(DATA_PTR(m_work));
                ns = kin->surfacePhaseIndex();
                surfloc = kin->kineticsSpeciesIndex(0,ns);
                for (k = 1; k < nk; k++) {
                    ydot[loc + k] = m_work[surfloc+k]*rs0*surf->size(k);
                    sum -= ydot[loc + k];
                }
                ydot[loc] = sum;
                loc += nk;

                wallarea = m_wall[i]->area();
                for (k = 0; k < m_nsp; k++) {
                    m_sdot[k] += m_work[k]*wallarea;
                }
            }
        } 

        // dummy equation
        ydot[1] = 0.0;

        /* species equations
         *  Equation is:
         *  \dot M_k = \hat W_k \dot\omega_k + \dot m_{in} Y_{k,in}
         *             - \dot m_{out} Y_{k} + A \dot s_k.
         */
        const doublereal* mw = DATA_PTR(m_thermo->molecularWeights());
        if (m_chem) {
            m_kin->getNetProductionRates(ydot+2);   // "omega dot"
        }
        else {
            fill(ydot + 2, ydot + 2 + m_nsp, 0.0);
        }
        for (n = 0; n < m_nsp; n++) {
            ydot[n+2] *= m_vol;     //           moles/s/m^3 -> moles/s
            ydot[n+2] += m_sdot[n]; 
            ydot[n+2] *= mw[n];
        }


        /*
         *  Energy equation.
         *  \f[
         *  \dot U = -P\dot V + A \dot q + \dot m_{in} h_{in}
         * - \dot m_{out} h.
         * \f]
         */
        if (m_energy) {
            ydot[0] = - m_Q;
        }
        else {
            ydot[0] = 0.0;
        }

        // add terms for open system
        if (m_open) {

            const doublereal* mf = m_thermo->massFractions();
            doublereal enthalpy = m_thermo->enthalpy_mass();

            // outlets 

            int n;
            doublereal mdot_out;
            for (i = 0; i < m_nOutlets; i++) {
                mdot_out = m_outlet[i]->massFlowRate(time);
                for (n = 0; n < m_nsp; n++) {
                    ydot[2+n] -= mdot_out * mf[n];
                }
                if (m_energy) {
                    ydot[0] -= mdot_out * enthalpy;
                }
            }


            // inlets

            doublereal mdot_in;
            for (i = 0; i < m_nInlets; i++) {
                mdot_in = m_inlet[i]->massFlowRate(time);
                for (n = 0; n < m_nsp; n++) {
                    ydot[2+n] += m_inlet[i]->outletSpeciesMassFlowRate(n);
                }
                if (m_energy) {
                    ydot[0] += mdot_in * m_inlet[i]->enthalpy_mass();
                }
            }
        }

        // reset sensitivity parameters
        if (params) {
            npar = m_pnum.size();
            for (n = 0; n < npar; n++) {
                mult = m_kin->multiplier(m_pnum[n]);
                m_kin->setMultiplier(m_pnum[n], mult/params[n]);
            }
            ploc = npar;
            for (m = 0; m < m_nwalls; m++) {
                if (m_nsens_wall[m] > 0) {
                    m_wall[m]->resetSensitivityParameters(m_lr[m]);
                    ploc += m_nsens_wall[m];
                }
            }
        }
    }

    int ConstPressureReactor::componentIndex(string nm) const {
        if (nm == "H") return 0;
        if (nm == "V") return 1;
        // check for a gas species name
        int k = m_thermo->speciesIndex(nm);
        if (k >= 0) return k + 2;

        // check for a wall species
        int walloffset = 0, kp = 0;
        thermo_t* th;
        for (int m = 0; m < m_nwalls; m++) {
            if (m_wall[m]->kinetics(m_lr[m])) {
                kp = m_wall[m]->kinetics(m_lr[m])->reactionPhaseIndex();
                th = &m_wall[m]->kinetics(m_lr[m])->thermo(kp);
                k = th->speciesIndex(nm);
                if (k >= 0) {
                    return k + 2 + m_nsp + walloffset;
                }
                else {
                    walloffset += th->nSpecies();
                }
            }   
        }
        return -1;
    }

}