//Evaluate any routines prior to solving the system
int SCOPSOWL_preprocesses(SCOPSOWL_DATA *owl_dat)
{
int success = 0;
//Establish boundary conditions before simulation starts
owl_dat->magpie_dat.sys_dat.T = owl_dat->gas_temperature;
owl_dat->magpie_dat.sys_dat.PT = owl_dat->total_pressure;
for (int i=0; i<owl_dat->magpie_dat.sys_dat.N; i++)
{
if (owl_dat->SurfDiff == true && owl_dat->Heterogeneous == true)
{
for (int l=0; l<owl_dat->finch_dat[i].LN; l++)
{
double p_out = owl_dat->y[i]*owl_dat->total_pressure;
if (p_out >= owl_dat->param_dat[i].ref_pressure) owl_dat->param_dat[i].ref_pressure = p_out;
owl_dat->skua_dat[l].param_dat[i].ref_diffusion = D_inf(owl_dat->param_dat[i].ref_diffusion, owl_dat->param_dat[i].ref_temperature, owl_dat->param_dat[i].affinity, owl_dat->param_dat[i].ref_pressure, owl_dat->gas_temperature);
owl_dat->skua_dat[l].param_dat[i].activation_energy = owl_dat->param_dat[i].activation_energy;
owl_dat->skua_dat[l].param_dat[i].ref_temperature = 0.0;
owl_dat->skua_dat[l].param_dat[i].affinity = 0.0;
}
}
owl_dat->finch_dat[i].uo = Cstd(owl_dat->magpie_dat.sys_dat.PT*owl_dat->y[i], owl_dat->magpie_dat.sys_dat.T);
owl_dat->finch_dat[i].Ro = (*owl_dat->eval_retard) (i,-1,owl_dat);
if (owl_dat->finch_dat[i].Ro < 0.0)
{
mError(simulation_fail);
return -1;
}
owl_dat->finch_dat[i].Do = (*owl_dat->eval_diff) (i,-1,owl_dat);
owl_dat->finch_dat[i].kfnp1 = (*owl_dat->eval_kf) (i,owl_dat);
}
return success;
}
Real
MAGPIE_Perturbation::computeValue()
{
MAGPIE_DATA magpie_copy;
magpie_copy = _magpie_dat[_qp];
//Check for adsorption
if (_magpie_dat[_qp].gsta_dat[_index].qmax > 0.0)
{
//perturn the copy's _index y
double pi = _magpie_dat[_qp].gpast_dat[_index].y * _magpie_dat[_qp].sys_dat.PT;
double ci = Cstd(pi,_magpie_dat[_qp].sys_dat.T) + sqrt(DBL_EPSILON);
double yi = Pstd(ci,_magpie_dat[_qp].sys_dat.T) / _magpie_dat[_qp].sys_dat.PT;
magpie_copy.gpast_dat[_index].y = yi;
int success = 0;
success = MAGPIE( (void *)&magpie_copy );
if (success < 0 || success > 3) {mError(simulation_fail);}
else success = 0;
return magpie_copy.gpast_dat[_index].q;
//This override was used to demonstrate that we can do perturbation with kinetics
//double k = magpie_copy.gpast_dat[_index].q * 0.008;
//double qe = magpie_copy.gpast_dat[_index].q;
//return (_u_old[_qp] + (_dt*k*qe))/(1.0+(_dt*k));
}
else
{
return 0.0;
}
}
//Set up the ICs for the problem
int set_SCOPSOWL_ICs(SCOPSOWL_DATA *owl_dat)
{
int success = 0;
//Print file header
if (owl_dat->Print2File == true)
print2file_SCOPSOWL_header(owl_dat);
owl_dat->magpie_dat.sys_dat.PT = owl_dat->total_pressure;
owl_dat->magpie_dat.sys_dat.T = owl_dat->gas_temperature;
if (owl_dat->SurfDiff == true && owl_dat->Heterogeneous == true)
{
//Call SKUA ICs to establish SCOPSOWL ICs
for (int l=0; l<owl_dat->finch_dat[0].LN; l++)
{
owl_dat->skua_dat[l].total_steps = 0;
owl_dat->skua_dat[l].magpie_dat.sys_dat.T = owl_dat->gas_temperature;
owl_dat->skua_dat[l].magpie_dat.sys_dat.PT = owl_dat->total_pressure;
for (int i=0; i<owl_dat->magpie_dat.sys_dat.N; i++)
{
owl_dat->skua_dat[l].param_dat[i].ref_diffusion = D_inf(owl_dat->param_dat[i].ref_diffusion, owl_dat->param_dat[i].ref_temperature, owl_dat->param_dat[i].affinity, owl_dat->y[i]*owl_dat->total_pressure, owl_dat->gas_temperature);
owl_dat->skua_dat[l].param_dat[i].activation_energy = owl_dat->param_dat[i].activation_energy;
owl_dat->skua_dat[l].param_dat[i].ref_temperature = 0.0;
owl_dat->skua_dat[l].param_dat[i].affinity = 0.0;
owl_dat->skua_dat[l].param_dat[i].xIC = owl_dat->param_dat[i].xIC;
}
success = set_SKUA_ICs(&owl_dat->skua_dat[l]);
if (success != 0) {mError(simulation_fail); return -1;}
owl_dat->total_steps = owl_dat->total_steps + owl_dat->skua_dat[l].total_steps;
//Loop for species
for (int i=0; i<owl_dat->magpie_dat.sys_dat.N; i++)
{
owl_dat->param_dat[i].qAvg.edit(l, 0, owl_dat->skua_dat[l].finch_dat[i].uAvg);
owl_dat->param_dat[i].Qst.edit(l, 0, owl_dat->skua_dat[l].param_dat[i].Qstn);
owl_dat->param_dat[i].qAvg_old.edit(l, 0, owl_dat->param_dat[i].qAvg(l,0));
owl_dat->param_dat[i].Qst_old.edit(l, 0, owl_dat->param_dat[i].Qst(l,0));
owl_dat->magpie_dat.gpast_dat[i].y = owl_dat->skua_dat[l].magpie_dat.gpast_dat[i].y;
}
}
//Outer species loop
double yad_sum = 0.0;
for (int i=0; i<owl_dat->magpie_dat.sys_dat.N; i++)
{
//Now form averages and totals
owl_dat->param_dat[i].Qsto = owl_dat->param_dat[i].Qst(0,0);
owl_dat->param_dat[i].qo = owl_dat->param_dat[i].qAvg(owl_dat->finch_dat[i].LN-1,0);
owl_dat->param_dat[i].qIntegralAvg = owl_dat->param_dat[i].qAvg.sphericalAvg(owl_dat->finch_dat[i].L,owl_dat->finch_dat[i].dz,owl_dat->param_dat[i].qo,owl_dat->DirichletBC);
owl_dat->param_dat[i].QstAvg = owl_dat->param_dat[i].Qst.sphericalAvg(owl_dat->finch_dat[i].L, owl_dat->finch_dat[i].dz,owl_dat->param_dat[i].Qsto,owl_dat->DirichletBC);
owl_dat->param_dat[i].QstAvg_old = owl_dat->param_dat[i].QstAvg;
owl_dat->param_dat[i].qIntegralAvg_old = owl_dat->param_dat[i].qIntegralAvg;
//SCOPSOWL ICs
owl_dat->finch_dat[i].Sn.ConstantICFill(0.0);
owl_dat->finch_dat[i].Snp1.ConstantICFill(0.0);
owl_dat->finch_dat[i].vn.ConstantICFill(0.0);
owl_dat->finch_dat[i].vnp1.ConstantICFill(0.0);
owl_dat->finch_dat[i].kn.ConstantICFill(0.0);
owl_dat->finch_dat[i].knp1.ConstantICFill(0.0);
owl_dat->finch_dat[i].ko = 0.0;
owl_dat->finch_dat[i].vo = 0.0;
owl_dat->finch_dat[i].kfn = (*owl_dat->eval_kf) (i,owl_dat);
owl_dat->finch_dat[i].kfnp1 = owl_dat->finch_dat[i].kfn;
if (owl_dat->finch_dat[i].kfn < 0.0)
{
mError(simulation_fail);
return -1;
}
if (owl_dat->param_dat[i].Adsorbable == true)
{
owl_dat->finch_dat[i].un.ConstantICFill(Cstd(owl_dat->magpie_dat.sys_dat.PT*owl_dat->magpie_dat.gpast_dat[i].y,owl_dat->magpie_dat.sys_dat.T));
}
if (owl_dat->param_dat[i].Adsorbable == true)
yad_sum = yad_sum + owl_dat->magpie_dat.gpast_dat[i].y;
}
//Need to re-adjust the initial conditions for non-adsorbing species
double rat_frac = 0.0;
int first = 0;
bool changed = false;
for (int i=0; i<owl_dat->magpie_dat.sys_dat.N; i++)
{
if (owl_dat->param_dat[i].Adsorbable == false)
{
if (changed == false)
{
first = i; changed = true;
rat_frac = rat_frac + (owl_dat->y[i] / owl_dat->y[first]);
}
else
{
rat_frac = rat_frac + (owl_dat->y[i] / owl_dat->y[first]);
}
}
}
double yFirst = (1.0 - yad_sum) / rat_frac;
for (int i=0; i<owl_dat->magpie_dat.sys_dat.N; i++)
{
double yi = 0.0;
if (owl_dat->param_dat[i].Adsorbable == false)
{
yi = yFirst * (owl_dat->y[i] / owl_dat->y[first]);
owl_dat->finch_dat[i].un.ConstantICFill(Cstd(owl_dat->magpie_dat.sys_dat.PT*yi,owl_dat->magpie_dat.sys_dat.T));
}
owl_dat->finch_dat[i].uo = owl_dat->finch_dat[i].un(0,0);
owl_dat->finch_dat[i].unp1 = owl_dat->finch_dat[i].un;
owl_dat->finch_dat[i].unm1 = owl_dat->finch_dat[i].un;
//Form Totals
success = uTotal(&owl_dat->finch_dat[i]);
if (success != 0) {mError(simulation_fail); return -1;}
//Form Averages
success = uAverage(&owl_dat->finch_dat[i]);
if (success != 0) {mError(simulation_fail); return -1;}
}
//Print out ICs
if (owl_dat->Print2File == true)
print2file_SCOPSOWL_result_old(owl_dat);
//Call parameter functions
for (int i=0; i<owl_dat->magpie_dat.sys_dat.N; i++)
{
for (int l=0; l<owl_dat->finch_dat[i].LN; l++)
{
double p_out = owl_dat->y[i]*owl_dat->total_pressure;
double p_in = Pstd(owl_dat->finch_dat[i].un(l,0), owl_dat->gas_temperature);
if (p_out >= p_in) owl_dat->param_dat[i].ref_pressure = p_out;
else owl_dat->param_dat[i].ref_pressure = p_in;
owl_dat->skua_dat[l].param_dat[i].ref_diffusion = D_inf(owl_dat->param_dat[i].ref_diffusion, owl_dat->param_dat[i].ref_temperature, owl_dat->param_dat[i].affinity, owl_dat->param_dat[i].ref_pressure, owl_dat->gas_temperature);
owl_dat->skua_dat[l].param_dat[i].activation_energy = owl_dat->param_dat[i].activation_energy;
owl_dat->skua_dat[l].param_dat[i].ref_temperature = 0.0;
owl_dat->skua_dat[l].param_dat[i].affinity = 0.0;
//Now Recall skua parameter functions to apply corrections
owl_dat->skua_dat[l].finch_dat[i].Do = (*owl_dat->skua_dat[l].eval_diff) (i, -1, (void *)&owl_dat->skua_dat[l]);
owl_dat->skua_dat[l].finch_dat[i].Dn.ConstantICFill(owl_dat->skua_dat[l].finch_dat[i].Do);
owl_dat->skua_dat[l].finch_dat[i].Dnp1.ConstantICFill(owl_dat->skua_dat[l].finch_dat[i].Do);
owl_dat->finch_dat[i].Rn.edit(l, 0, (*owl_dat->eval_retard) (i,l,owl_dat));
owl_dat->finch_dat[i].Dn.edit(l, 0, (*owl_dat->eval_diff) (i,l,owl_dat));
}
owl_dat->finch_dat[i].Ro = (*owl_dat->eval_retard) (i,-1,owl_dat);
owl_dat->finch_dat[i].Do = (*owl_dat->eval_diff) (i,-1,owl_dat);
owl_dat->finch_dat[i].Rnp1 = owl_dat->finch_dat[i].Rn;
owl_dat->finch_dat[i].Dnp1 = owl_dat->finch_dat[i].Dn;
//Update averages and totals
owl_dat->finch_dat[i].uT_old = owl_dat->finch_dat[i].uT;
owl_dat->finch_dat[i].uAvg_old = owl_dat->finch_dat[i].uAvg;
}
}
else
{
//Call MAGPIE to establish SCOPSOWL ICs
owl_dat->magpie_dat.sys_dat.Recover = true;
owl_dat->magpie_dat.sys_dat.Carrier = false;
for (int i=0; i<owl_dat->magpie_dat.sys_dat.N; i++)
{
if (owl_dat->param_dat[i].Adsorbable == false)
{
owl_dat->magpie_dat.sys_dat.Carrier = true;
break;
}
}
for (int i=0; i<owl_dat->magpie_dat.sys_dat.N; i++)
owl_dat->magpie_dat.gpast_dat[i].x = owl_dat->param_dat[i].xIC;
//Temperature, pressure, total adsorption, and x's are set: Call MAGPIE
success = MAGPIE((void *)&owl_dat->magpie_dat);
if (success < 0 || success > 3) {mError(simulation_fail); return -1;}
else success = 0;
owl_dat->total_steps = owl_dat->total_steps + owl_dat->magpie_dat.sys_dat.total_eval;
//Reset the MAGPIE parameters before continuing
owl_dat->magpie_dat.sys_dat.Recover = false;
owl_dat->magpie_dat.sys_dat.Carrier = false;
//The GPAST structure of MAGPIE now holds the y's which establish the SCOPSOWL ICs
double yad_sum = 0.0;
for (int i=0; i<owl_dat->magpie_dat.sys_dat.N; i++)
{
owl_dat->param_dat[i].qAvg.ConstantICFill(owl_dat->magpie_dat.sys_dat.qT * owl_dat->magpie_dat.gpast_dat[i].x);
owl_dat->param_dat[i].qAvg_old = owl_dat->param_dat[i].qAvg;
owl_dat->param_dat[i].qo = owl_dat->magpie_dat.sys_dat.qT * owl_dat->magpie_dat.gpast_dat[i].x;
owl_dat->finch_dat[i].Sn.ConstantICFill(0.0);
owl_dat->finch_dat[i].Snp1.ConstantICFill(0.0);
owl_dat->finch_dat[i].vn.ConstantICFill(0.0);
owl_dat->finch_dat[i].vnp1.ConstantICFill(0.0);
owl_dat->finch_dat[i].kn.ConstantICFill(0.0);
owl_dat->finch_dat[i].knp1.ConstantICFill(0.0);
owl_dat->finch_dat[i].ko = 0.0;
owl_dat->finch_dat[i].vo = 0.0;
owl_dat->finch_dat[i].kfn = (*owl_dat->eval_kf) (i,owl_dat);
owl_dat->finch_dat[i].kfnp1 = owl_dat->finch_dat[i].kfn;
if (owl_dat->finch_dat[i].kfn < 0.0)
{
mError(simulation_fail);
return -1;
}
if (owl_dat->param_dat[i].Adsorbable == true)
{
owl_dat->finch_dat[i].un.ConstantICFill(Cstd(owl_dat->magpie_dat.sys_dat.PT*owl_dat->magpie_dat.gpast_dat[i].y,owl_dat->magpie_dat.sys_dat.T));
}
if (owl_dat->param_dat[i].Adsorbable == true)
yad_sum = yad_sum + owl_dat->magpie_dat.gpast_dat[i].y;
}
//Need to re-adjust the initial conditions for non-adsorbing species
double rat_frac = 0.0;
int first = 0;
bool changed = false;
for (int i=0; i<owl_dat->magpie_dat.sys_dat.N; i++)
{
if (owl_dat->param_dat[i].Adsorbable == false)
{
if (changed == false)
{
first = i; changed = true;
rat_frac = rat_frac + (owl_dat->y[i] / owl_dat->y[first]);
}
else
{
rat_frac = rat_frac + (owl_dat->y[i] / owl_dat->y[first]);
}
}
}
double yFirst = (1.0 - yad_sum) / rat_frac;
for (int i=0; i<owl_dat->magpie_dat.sys_dat.N; i++)
{
double yi = 0.0;
if (owl_dat->param_dat[i].Adsorbable == false)
{
yi = yFirst * (owl_dat->y[i] / owl_dat->y[first]);
owl_dat->finch_dat[i].un.ConstantICFill(Cstd(owl_dat->magpie_dat.sys_dat.PT*yi,owl_dat->magpie_dat.sys_dat.T));
}
owl_dat->finch_dat[i].uo = owl_dat->finch_dat[i].un(0,0);
owl_dat->finch_dat[i].unp1 = owl_dat->finch_dat[i].un;
owl_dat->finch_dat[i].unm1 = owl_dat->finch_dat[i].un;
//Form Totals
success = uTotal(&owl_dat->finch_dat[i]);
if (success != 0) {mError(simulation_fail); return -1;}
//Form Averages
success = uAverage(&owl_dat->finch_dat[i]);
if (success != 0) {mError(simulation_fail); return -1;}
}
//Use established info to call the retardation and diffusion functions as well as heats of adsorption
for (int i=0; i<owl_dat->magpie_dat.sys_dat.N; i++)
{
if (owl_dat->param_dat[i].Adsorbable == true)
{
owl_dat->param_dat[i].Qst.ConstantICFill(Qst(Pstd(owl_dat->finch_dat[i].un(0,0),owl_dat->magpie_dat.sys_dat.T), (void *)&owl_dat->magpie_dat, i));
}
else
{
owl_dat->param_dat[i].Qst.ConstantICFill(0.0);
}
owl_dat->param_dat[i].Qst_old = owl_dat->param_dat[i].Qst;
owl_dat->param_dat[i].Qsto = owl_dat->param_dat[i].Qst(0,0);
//Now form averages and totals
owl_dat->param_dat[i].qIntegralAvg = owl_dat->param_dat[i].qAvg.sphericalAvg(owl_dat->finch_dat[i].L,owl_dat->finch_dat[i].dz,owl_dat->param_dat[i].qo,owl_dat->DirichletBC);
owl_dat->param_dat[i].QstAvg = owl_dat->param_dat[i].Qst.sphericalAvg(owl_dat->finch_dat[i].L, owl_dat->finch_dat[i].dz,owl_dat->param_dat[i].Qsto,owl_dat->DirichletBC);
//Update adsorption info
owl_dat->param_dat[i].QstAvg_old = owl_dat->param_dat[i].QstAvg;
owl_dat->param_dat[i].qIntegralAvg_old = owl_dat->param_dat[i].qIntegralAvg;
}
//Print out ICs
if (owl_dat->Print2File == true)
print2file_SCOPSOWL_result_old(owl_dat);
//Call the parameter functions
for (int i=0; i<owl_dat->magpie_dat.sys_dat.N; i++)
{
//Set the reference pressure
for (int l=0; l<owl_dat->finch_dat[i].LN; l++)
{
double p_out = owl_dat->y[i]*owl_dat->total_pressure;
double p_in = Pstd(owl_dat->finch_dat[i].un(l,0), owl_dat->gas_temperature);
if (p_out >= p_in) owl_dat->param_dat[i].ref_pressure = p_out;
else owl_dat->param_dat[i].ref_pressure = p_in;
}
for (int l=0; l<owl_dat->finch_dat[i].LN; l++)
{
owl_dat->finch_dat[i].Rn.edit(l, 0, (*owl_dat->eval_retard) (i,l,owl_dat));
owl_dat->finch_dat[i].Dn.edit(l, 0, (*owl_dat->eval_diff) (i,l,owl_dat));
}
owl_dat->finch_dat[i].Ro = (*owl_dat->eval_retard) (i,-1,owl_dat);
owl_dat->finch_dat[i].Do = (*owl_dat->eval_diff) (i,-1,owl_dat);
owl_dat->finch_dat[i].Rnp1 = owl_dat->finch_dat[i].Rn;
owl_dat->finch_dat[i].Dnp1 = owl_dat->finch_dat[i].Dn;
//Update averages and totals
owl_dat->finch_dat[i].uT_old = owl_dat->finch_dat[i].uT;
owl_dat->finch_dat[i].uAvg_old = owl_dat->finch_dat[i].uAvg;
}
}
return success;
}
//Default Adsorption Strength function is based on input args
double default_adsorption(int i, int l, const void *user_data)
{
SCOPSOWL_DATA *dat = (SCOPSOWL_DATA *) user_data;
double dq_dc = 0.0;
double eps = sqrt(DBL_EPSILON);
double qEPS = 0.0;
double uo = 0.0;
int success = 0;
//Check if any work needs to be done
if (dat->param_dat[i].Adsorbable == false)
{
if (l < 0)
dat->param_dat[i].dq_dco = 0.0;
else
dat->param_dat[i].dq_dc.edit(l, 0, 0.0);
return 0.0;
}
//Boundary value of dq/dc
if (l < 0)
{
//Based on MAGPIE simulations ONLY!
uo = Cstd(dat->magpie_dat.sys_dat.PT*dat->y[i], dat->magpie_dat.sys_dat.T);
//Perturb the ith concentration
for (int j=0; j<dat->magpie_dat.sys_dat.N; j++)
{
if (j == i)
dat->magpie_dat.gpast_dat[j].y = Pstd(uo+eps,dat->magpie_dat.sys_dat.T)/dat->magpie_dat.sys_dat.PT;
else if (dat->param_dat[j].Adsorbable == true)
dat->magpie_dat.gpast_dat[j].y = Pstd(uo,dat->magpie_dat.sys_dat.T)/dat->magpie_dat.sys_dat.PT;
else
dat->magpie_dat.gpast_dat[j].y = 0.0;
}
//Call MAGPIE to evaluate perturbed adsorption
success = MAGPIE((void *)&dat->magpie_dat);
if (success < 0 || success > 3) {mError(simulation_fail); return -1;}
else success = 0;
dat->total_steps = dat->total_steps + dat->magpie_dat.sys_dat.total_eval;
//Store perturbed result in temp location
qEPS = dat->magpie_dat.sys_dat.qT * dat->magpie_dat.gpast_dat[i].x;
//Restore original info
for (int j=0; j<dat->magpie_dat.sys_dat.N; j++)
{
if (dat->param_dat[j].Adsorbable == true)
dat->magpie_dat.gpast_dat[j].y = dat->y[j];
else
dat->magpie_dat.gpast_dat[j].y = 0.0;
}
//Call MAGPIE to evaluate adsorption
success = MAGPIE((void *)&dat->magpie_dat);
if (success < 0 || success > 3) {mError(simulation_fail); return -1;}
else success = 0;
dat->total_steps = dat->total_steps + dat->magpie_dat.sys_dat.total_eval;
//Store the solution
if (dat->param_dat[i].Adsorbable == true)
{
dat->param_dat[i].qo = dat->magpie_dat.sys_dat.qT * dat->magpie_dat.gpast_dat[i].x;
dat->param_dat[i].Qsto = Qst(Pstd(uo,dat->magpie_dat.sys_dat.T), (void *)&dat->magpie_dat, i);
}
else
{
dat->param_dat[i].qo = 0.0;
dat->param_dat[i].Qsto = 0.0;
}
dq_dc = ( qEPS - dat->param_dat[i].qo ) / eps;
dat->param_dat[i].dq_dco = dq_dc;
}
//Nodal values of dq/dc
else
{
if (dat->SurfDiff == true && dat->Heterogeneous == true)
{
//Adjust interior pressure with perturbation
double tempPT = 0.0;
for (int j=0; j<dat->skua_dat[l].magpie_dat.sys_dat.N; j++)
{
if (i == j)
tempPT = tempPT + Pstd(dat->finch_dat[j].unp1(l,0)+eps, dat->skua_dat[l].magpie_dat.sys_dat.T);
else
tempPT = tempPT + Pstd(dat->finch_dat[j].unp1(l,0), dat->skua_dat[l].magpie_dat.sys_dat.T);
}
dat->skua_dat[l].magpie_dat.sys_dat.PT = tempPT;
//Perform SKUA simulation
dat->skua_dat[l].finch_dat[i].dt = dat->finch_dat[i].dt;
dat->skua_dat[l].finch_dat[i].dt_old = dat->finch_dat[i].dt_old;
dat->skua_dat[l].finch_dat[i].t = dat->finch_dat[i].t;
dat->skua_dat[l].finch_dat[i].t_old = dat->finch_dat[i].t_old;
dat->skua_dat[l].t = dat->skua_dat[l].finch_dat[i].t;
dat->skua_dat[l].t_old = dat->skua_dat[l].finch_dat[i].t_old;
//Set up SKUA data
dat->skua_dat[l].magpie_dat.sys_dat.T = dat->magpie_dat.sys_dat.T;
for (int j=0; j<dat->skua_dat[l].magpie_dat.sys_dat.N; j++)
{
if (i == j)
dat->skua_dat[l].y[j] = Pstd(dat->finch_dat[j].unp1(l,0)+eps,dat->skua_dat[l].magpie_dat.sys_dat.T)/dat->skua_dat[l].magpie_dat.sys_dat.PT;
else
dat->skua_dat[l].y[j] = Pstd(dat->finch_dat[j].unp1(l,0),dat->skua_dat[l].magpie_dat.sys_dat.T)/dat->skua_dat[l].magpie_dat.sys_dat.PT;
}
//Call SKUA executioner to evaluate adsorption
dat->skua_dat[l].total_steps = 0;
success = SKUA_Executioner(&dat->skua_dat[l]);
if (success != 0) {mError(simulation_fail); return -1;}
dat->total_steps = dat->total_steps + dat->skua_dat[l].total_steps;
//Store the results temporarily
qEPS = dat->skua_dat[l].finch_dat[i].uAvg;
//Adjust again without perturbation
tempPT = 0.0;
for (int j=0; j<dat->skua_dat[l].magpie_dat.sys_dat.N; j++)
tempPT = tempPT + Pstd(dat->finch_dat[j].unp1(l,0), dat->skua_dat[l].magpie_dat.sys_dat.T);
dat->skua_dat[l].magpie_dat.sys_dat.PT = tempPT;
//Undo perturbation
for (int j=0; j<dat->magpie_dat.sys_dat.N; j++)
{
dat->skua_dat[l].y[j] = Pstd(dat->finch_dat[j].unp1(l,0),dat->magpie_dat.sys_dat.T)/dat->skua_dat[l].magpie_dat.sys_dat.PT;
}
//Call SKUA again to evaluate perturbation
dat->skua_dat[l].total_steps = 0;
success = SKUA_Executioner(&dat->skua_dat[l]);
if (success != 0) {mError(simulation_fail); return -1;}
dat->total_steps = dat->total_steps + dat->skua_dat[l].total_steps;
//Store perturbed result in temp location
dat->param_dat[i].qAvg.edit(l, 0, dat->skua_dat[l].finch_dat[i].uAvg);
dat->param_dat[i].Qst.edit(l, 0, dat->skua_dat[l].param_dat[i].Qstnp1);
dq_dc = ( qEPS - dat->param_dat[i].qAvg(l,0) ) / eps;
dat->param_dat[i].dq_dc.edit(l, 0, dq_dc);
}
else
{
//Perturb the ith value and form the total pressure
double tempPT = 0.0;
for (int j=0; j<dat->magpie_dat.sys_dat.N; j++)
{
if (i == j)
tempPT = tempPT + Pstd(dat->finch_dat[j].unp1(l,0)+eps, dat->magpie_dat.sys_dat.T);
else
tempPT = tempPT + Pstd(dat->finch_dat[j].unp1(l,0), dat->magpie_dat.sys_dat.T);
}
dat->magpie_dat.sys_dat.PT = tempPT;
//Perturb the ith concentration
for (int j=0; j<dat->magpie_dat.sys_dat.N; j++)
{
if (j == i)
dat->magpie_dat.gpast_dat[j].y = Pstd(dat->finch_dat[j].unp1(l,0)+eps,dat->magpie_dat.sys_dat.T)/dat->magpie_dat.sys_dat.PT;
else if (dat->param_dat[j].Adsorbable == true)
dat->magpie_dat.gpast_dat[j].y = Pstd(dat->finch_dat[j].unp1(l,0),dat->magpie_dat.sys_dat.T)/dat->magpie_dat.sys_dat.PT;
else
dat->magpie_dat.gpast_dat[j].y = 0.0;
}
//Call MAGPIE to evaluate perturbed adsorption
success = MAGPIE((void *)&dat->magpie_dat);
if (success < 0 || success > 3) {mError(simulation_fail); return -1;}
else success = 0;
dat->total_steps = dat->total_steps + dat->magpie_dat.sys_dat.total_eval;
//Store perturbed result in temp location
qEPS = dat->magpie_dat.sys_dat.qT * dat->magpie_dat.gpast_dat[i].x;
//Adjust interior pressure back to true values
tempPT = 0.0;
for (int j=0; j<dat->magpie_dat.sys_dat.N; j++)
tempPT = tempPT + Pstd(dat->finch_dat[j].unp1(l,0), dat->magpie_dat.sys_dat.T);
dat->magpie_dat.sys_dat.PT = tempPT;
//Perform MAGPIE simulation
for (int j=0; j<dat->magpie_dat.sys_dat.N; j++)
{
if (dat->param_dat[j].Adsorbable == true)
dat->magpie_dat.gpast_dat[j].y = Pstd(dat->finch_dat[j].unp1(l,0),dat->magpie_dat.sys_dat.T)/dat->magpie_dat.sys_dat.PT;
else
dat->magpie_dat.gpast_dat[j].y = 0.0;
}
//Call MAGPIE to evaluate adsorption
success = MAGPIE((void *)&dat->magpie_dat);
if (success < 0 || success > 3) {mError(simulation_fail); return -1;}
else success = 0;
dat->total_steps = dat->total_steps + dat->magpie_dat.sys_dat.total_eval;
//Store the solutions
if (dat->param_dat[i].Adsorbable == true)
{
dat->param_dat[i].qAvg.edit(l, 0, dat->magpie_dat.sys_dat.qT * dat->magpie_dat.gpast_dat[i].x);
dat->param_dat[i].Qst.edit(l,0,Qst(Pstd(dat->finch_dat[i].unp1(l,0),dat->magpie_dat.sys_dat.T), (void *)&dat->magpie_dat, i));
}
else
{
dat->param_dat[i].qAvg.edit(l, 0, 0.0);
dat->param_dat[i].Qst.edit(l,0,0.0);
}
dq_dc = ( qEPS - dat->param_dat[i].qAvg(l,0) ) / eps;
dat->param_dat[i].dq_dc.edit(l, 0, dq_dc);
}
}
return dq_dc;
}