void AbstractTetrahedralElement<ELEMENT_DIM, SPACE_DIM>::CalculateInverseJacobian(c_matrix<double, SPACE_DIM, ELEMENT_DIM>& rJacobian, double& rJacobianDeterminant, c_matrix<double, ELEMENT_DIM, SPACE_DIM>& rInverseJacobian)
{
assert(ELEMENT_DIM <= SPACE_DIM);
CalculateJacobian(rJacobian, rJacobianDeterminant);
// CalculateJacobian should make sure that the determinant is not close to zero (or, in fact, negative)
assert(rJacobianDeterminant > 0.0);
rInverseJacobian = Inverse(rJacobian);
}
AbstractTetrahedralElement<ELEMENT_DIM, SPACE_DIM>::AbstractTetrahedralElement(unsigned index, const std::vector<Node<SPACE_DIM>*>& rNodes)
: AbstractElement<ELEMENT_DIM, SPACE_DIM>(index, rNodes)
{
// Sanity checking
unsigned num_vectices = ELEMENT_DIM+1;
double det;
if (SPACE_DIM == ELEMENT_DIM)
{
// This is so we know it's the first time of asking
// Create Jacobian
c_matrix<double, SPACE_DIM, ELEMENT_DIM> jacobian;
try
{
CalculateJacobian(jacobian, det);
}
catch (Exception)
{
// if the Jacobian is negative the orientation of the element is probably
// wrong, so swap the last two nodes around.
this->mNodes[num_vectices-1] = rNodes[num_vectices-2];
this->mNodes[num_vectices-2] = rNodes[num_vectices-1];
CalculateJacobian(jacobian, det);
// If determinant < 0 then element nodes are listed clockwise.
// We want them anticlockwise.
assert(det > 0.0);
}
}
else
{
//This is not a full-dimensional element
c_vector<double, SPACE_DIM> weighted_direction;
CalculateWeightedDirection(weighted_direction, det);
}
}
void BoxChemStep(int i, int j, int k, long dt,
const Vector *sunpos, double *photorate)
{
double f[MAXSUBST], vv[MAXSUBST], fact, err, origh2o;
int indx[MAXSUBST], il, jl, nit;
ProductionDesc *p;
BOOL repeatit = FALSE;
gli.i = i; gli.j = j; gli.k = k; gli.loc = k*layer+i*row+j;
origh2o = g[HUMIDITY][gli.loc];
g[HUMIDITY][gli.loc] *= 1.608e9;
CalcRateConstants(AbsoluteTemp(g[TEMP][gli.loc], pp[k], origh2o),
dt, density[k], pp[k], sunpos->z, photorate);
for (il = nsubst; il--; ) {
/* if (CONZ(subst[il].subs) < 0.)
printf("Warning: Substance %s got negative: %le\n",
subst[il].name, CONZ(subst[il].subs)); */
if (CONZ(subst[il].subs) < 1.e-30) /* can't really handle such small concentrations */
CONZ(subst[il].subs) = 0.;
}
CalcRates();
for (il = nsubst; il--; ) {
subst[il].oldc = CONZ(subst[il].subs);
subst[il].take_as_fast = 0;
}
/* CalcSlowSubst(); Aenderung am 17.9.97! */
do {
nit = 0;
while (1) {
jcb = CalculateJacobian(jcb);
err = 0.;
for (il = nfast; il--; ) {
err += fabs((f[il] = CONZ(fast[il]->subs) - fast[il]->dcdt - fast[il]->oldc) /
(CONZ(fast[il]->subs) > 1.e-7 ? CONZ(fast[il]->subs) : 1.));
}
if (!repeatit && err < 1.e-5) break;
if (++nit > 500) {
printf("Chemistry is not converging at point %i/%i/%i\n", i, j, k);
PrintConcentrations();
PrintRates(REACTION_RATES);
break;
}
if (LUdecomp(nfast, jcb, indx, &fact, vv)) {
printf("Matrix is singular (in ChemicalTimeStep) at point %d/%d/%d!\n",
i, j, k);
plausible = FALSE;
return;
}
/* if (i == 10 && j == 4 && k == 1)
PrintRates(REACTION_RATES);
PrintMatrix(nfast, jcb, f); */
LUbackSub(nfast, jcb, indx, f);
repeatit = 0;
for (il = nfast; il--; ) {
CONZ(fast[il]->subs) -= f[il];
if (CONZ(fast[il]->subs) < 0.) {
/* printf("Warning: Substance %s got negative: %le\n",
fast[il]->name, CONZ(fast[il]->subs)); */
CONZ(fast[il]->subs) = 0.;
repeatit = 1;
}
}
}
repeatit = 0;
CalcSlowSubst();
for (il = nfast; il--; ) {
if (!fast[il]->oldc ||
fabs(CONZ(fast[il]->subs) - fast[il]->oldc) < 0.1 * fast[il]->oldc) {
fast[il]->take_as_fast = 0;
}
}
for (il = nslow; il--; ) {
if (CONZ(slow[il]->subs) < 0.) {
slow[il]->take_as_fast = repeatit = 1;
}
}
if (repeatit) {
printf("repeating chemistry at point %i/%i/%i\n", i, j, k);
CalcRates();
}
} while (repeatit);
for (p = prodd; p; p = p->next)
p->pps[gli.loc] = (CONZ(p->subs) - subst[p->subs - SUBS + 1].oldc) /
(double)dt;
g[HUMIDITY][k*layer+i*row+j] = origh2o;
}
