static int bloch (realtype t, N_Vector y, N_Vector ydot, void *pWorld) {
World* pW = (World*) pWorld;
BMAux* m_bmaux = (BMAux*) pW->auxiliary;
int m_nprops = pW->m_noofspinprops;
int m_ncomp = pW->m_noofspincompartments;
int m_ncoprops = (m_nprops - 4) / m_ncomp;
double* m_exrates = m_bmaux->exrates;
bool m_single = m_bmaux->single;
// Magnetisation for each poosl
double* Mxy = new double [m_ncomp];
double* phi = new double [m_ncomp];
double* Mz = new double [m_ncomp];
double* s = new double [m_ncomp];
double* c = new double [m_ncomp];
double* Mx = new double [m_ncomp];
double* My = new double [m_ncomp];
double* Mx_dot = new double [m_ncomp];
double* My_dot = new double [m_ncomp];
double* Mz_dot = new double [m_ncomp];
for (int i = 0; i < m_ncomp; i++) {
Mx_dot[i] = 0.0;
My_dot[i] = 0.0;
Mz_dot[i] = 0.0;
Mxy [i] = 0.0;
phi [i] = 0.0;
Mx [i] = 0.0;
My [i] = 0.0;
Mz [i] = 0.0;
s [i] = 0.0;
c [i] = 0.0;
}
//get current B-field values from the sequence
if (t<=0.0 || t>pW->pAtom->GetDuration()) { // Kaveh, hier hab ich gemogelt
// this case can happen when searching for step size; in this area no solution is needed
// -> set ydot to any defined value.
for(int i = 0; i< m_ncomp*NEQ; i+=NEQ) {
NV_Ith_S(ydot,XC+i) = 0.0; NV_Ith_S(ydot,YC+i) = 0.0; NV_Ith_S(ydot,ZC+i) = 0.0;
}
return 0;
}
double d_SeqVal[5] = {0.0,0.0,0.0,0.0,0.0}; // [B1magn,B1phase,Gx,Gy,Gz]
pW->pAtom->GetValue( d_SeqVal, t ); // calculates also pW->NonLinGradField
if (pW->pStaticAtom != NULL) pW->pStaticAtom->GetValue( d_SeqVal, t ); // calculates also pW->NonLinGradField
double Bx=0.0, By=0.0, Bz=0.0;
double* BzPool = new double[m_ncomp];
//RF field
Bx = d_SeqVal[RF_AMP]*cos(d_SeqVal[RF_PHS]);
By = d_SeqVal[RF_AMP]*sin(d_SeqVal[RF_PHS]);
//Gradient field
Bz = pW->Values[XC]*d_SeqVal[GRAD_X]+ pW->Values[YC]*d_SeqVal[GRAD_Y]+ pW->Values[ZC]*d_SeqVal[GRAD_Z];
//other off-resonance contributions (differs for every pool)
for(int i = 0; i< m_ncomp; i++)
BzPool[i] = Bz + pW->Values[i*m_ncoprops+DB] + pW->ConcomitantField(&d_SeqVal[GRAD_X]) + pW->NonLinGradField;
//NV_Ith_S is the solution magn. vector with components AMPL,PHASE,ZC
//important: restrict phase to [0, 2*PI]
int pool =0;
/* for(int i = 0; i< m_ncomp*NEQ; i+=NEQ){ // loop over pools
NV_Ith_S(y,PHASE+i) = fmod(NV_Ith_S(y,PHASE+i),6.28318530717958);
Mxy[pool] = NV_Ith_S(y,AMPL+i); phi[pool] = NV_Ith_S(y,PHASE+i); Mz[pool] = NV_Ith_S(y,ZC+i);
pool++;
}*/
for (int i = 0; i< m_ncomp*NEQ; i+=NEQ) { // loop over pools
Mx[pool] = NV_Ith_S(y,XC+i);
My[pool] = NV_Ith_S(y,YC+i);
Mz[pool] = NV_Ith_S(y,ZC+i);
pool++;
}
pool = 0;
for (int eqpool = 0; eqpool< ((m_ncomp)*NEQ); eqpool+=NEQ) { // loop over pools, NEQ steps
//avoid CVODE warnings (does not change physics!)
if (pW->Values[pool*m_ncoprops + M0] == 0.0) {
// this pool is empty, the number of pools reduces
NV_Ith_S(y,XC+eqpool) = 0.0; NV_Ith_S(y,YC+eqpool) = 0.0;
NV_Ith_S(ydot,XC+eqpool) = 0.0; NV_Ith_S(ydot,YC+eqpool) = 0.0;
NV_Ith_S(y,ZC+eqpool) = 0.0;
NV_Ith_S(ydot,ZC+eqpool) = 0.0;
} else if ((Mx[pool]*Mx[pool] + My[pool]*My[pool]) < ATOL1 * pW->Values[pool*m_ncoprops+M0] && d_SeqVal[RF_AMP]<BEPS) {
//trivial case: no transv. magnetisation AND no excitation
NV_Ith_S(y,XC+eqpool) = 0.0; NV_Ith_S(y,YC+eqpool) = 0.0;
NV_Ith_S(ydot,XC+eqpool) = 0.0; NV_Ith_S(ydot,YC+eqpool) = 0.0;
//further, longit. magnetisation already fully relaxed
if (fabs(pW->Values[pool*m_ncoprops +M0] - Mz[pool])<ATOL3 *pW->Values[pool*m_ncoprops +M0]) {
NV_Ith_S(y,ZC+eqpool) = pW->Values[pool*m_ncoprops +M0];
NV_Ith_S(ydot,ZC+eqpool) = 0.0;
if(eqpool == (((m_ncomp)*NEQ)-1))
return 0;
}
} else {
//compute cartesian components of transverse magnetization
/*c[pool] = cos(phi[pool]);
s[pool] = sin(phi[pool]);
Mx[pool] = c[pool]*Mxy[pool];
My[pool] = s[pool]*Mxy[pool];*/
// Built the n-pool bloch equation, check if each pool exists
if (m_ncomp > 1 ){ // do this only if really necessary - time consuming!
if (m_single == false) {
Mx_dot[pool] = -(pW->Values[pool*m_ncoprops +R2] + exchangeConstants(m_ncomp,pool,m_exrates)) *Mx[pool] + BzPool[pool]*My[pool] - By*Mz[pool] + exchangeTerms(m_ncomp,pool,m_exrates,Mx);
My_dot[pool] = - BzPool[pool]*Mx[pool] - (pW->Values[pool*m_ncoprops +R2]+exchangeConstants(m_ncomp,pool,m_exrates)) *My[pool] + Bx*Mz[pool] + exchangeTerms(m_ncomp,pool,m_exrates,My);
Mz_dot[pool] = By*Mx[pool] - Bx*My[pool] ;
} else {
Mx_dot[pool] = -(pW->Values[pool*m_ncoprops +R2]) *Mx[pool] + BzPool[pool]*My[pool] - By*Mz[pool];
My_dot[pool] = - BzPool[pool]*Mx[pool] - (pW->Values[pool*m_ncoprops +R2]) *My[pool] + Bx*Mz[pool];
Mz_dot[pool] = By*Mx[pool] - Bx*My[pool] ;
}
} else {
// use single pool model, much faster
Mx_dot[pool] = - pW->Values[pool*m_ncoprops +R2] *Mx[pool] + BzPool[pool]*My[pool] - By*Mz[pool];
My_dot[pool] = - BzPool[pool]*Mx[pool] - pW->Values[pool*m_ncoprops +R2] *My[pool] + Bx*Mz[pool];
Mz_dot[pool] = By*Mx[pool] - Bx*My[pool] ;
}
//compute bloch equations old version
// Mx_dot = -pW->Values[R2]*Mx + Bz*My - By*Mz;
// My_dot = -Bz*Mx - pW->Values[R2]*My + Bx*Mz;
// Mz_dot = By*Mx - Bx*My ;
//compute derivatives in cylindrical coordinates
//NV_Ith_S(ydot,AMPL+eqpool) = c[pool]*Mx_dot[pool] + s[pool]*My_dot[pool];
//NV_Ith_S(ydot,PHASE+eqpool) = (c[pool]*My_dot[pool] - s[pool]*Mx_dot[pool]) / (Mxy[pool]>BEPS?Mxy[pool]:BEPS); //avoid division by zero
NV_Ith_S(ydot,XC+eqpool) = Mx_dot[pool];
NV_Ith_S(ydot,YC+eqpool) = My_dot[pool];
}
//longitudinal relaxation
if (m_ncomp > 1){
if(m_single == false){
Mz_dot[pool] += pW->Values[pool*m_ncoprops +R1]*(pW->Values[pool*m_ncoprops +M0] - Mz[pool]) - exchangeConstants(m_ncomp,pool,m_exrates)*Mz[pool] + exchangeTerms(m_ncomp,pool,m_exrates,Mz);
} else{
Mz_dot[pool] += pW->Values[pool*m_ncoprops +R1]*(pW->Values[pool*m_ncoprops +M0] - Mz[pool]);
}
} else
Mz_dot[pool] += pW->Values[pool*m_ncoprops +R1]*(pW->Values[pool*m_ncoprops +M0] - Mz[pool]);
NV_Ith_S(ydot,ZC+eqpool) = Mz_dot[pool];
pool++;
}
// Kaveh, hier stehen noch unterschiedliche Zahlen in den verschiedenen Pools
//cout<<NV_Ith_S(ydot,ZC+0) << " " <<NV_Ith_S(ydot,ZC+3) <<endl;
delete [] Mxy;
delete [] phi;
delete [] Mz;
delete [] s;
delete [] c;
delete [] Mx;
delete [] My;
delete [] Mx_dot;
delete [] My_dot;
delete [] Mz_dot;
delete [] BzPool;
return 0;
}
