int traceVBI(int i, int j) {
int VBIij_temp;
int ip, jp, el, v;
int ifinal, jfinal;
ifinal = 0;
jfinal = 0;
for (ip = i + 1; ip < j - 1; ip++) {
for (jp = ip + 1; jp < j; jp++) {
if (check_iloop(i,j,ip,jp)) continue;
el = eL(i, j, ip, jp);
v = V(ip, jp);
VBIij_temp = el + v;
if (VBIij_temp == VBI(i,j)) {
ifinal = ip;
jfinal = jp;
break;
}
}
if (jp != j)
break;
}
structure[ifinal] = jfinal;
structure[jfinal] = ifinal;
if (verbose==1)
printf(" %12.2f\n", eL(i, j, ifinal, jfinal)/100.00);
total_en += eL(i, j, ifinal, jfinal);
int eVI = traceV(ifinal, jfinal);
return eVI ;
}
void NSEDataTraceService::traceRegurlarGrid(
peano::applications::faxen::lbf::RegularGridBlockVertex** vertices,
peano::applications::faxen::lbf::RegularGridBlockCell& cell,
const tarch::la::Vector<DIMENSIONS,double>& centerPoint) {
if(_isInitialized) {
int indX = floor((centerPoint[0]-_xOffset)/_dx);
int indY = floor((centerPoint[1]-_yOffset)/_dy);
// std::cout << "cell center point: " << centerPoint << std::endl;
// std::cout << "indX & indY: " << indX << ", " << indY << std::endl;
// std::cout << "is trace u enabled: " << _traceU << std::endl;
// std::cout << "is trace v enabled: " << _traceV << std::endl;
// std::cout << "is trace p enabled: " << _traceP << std::endl;
traceU(indX,indY,cell);
traceV(indX,indY,cell);
traceRHS(indX,indY,cell);
traceP(indX,indY,cell);
}
}
int traceV(int i, int j) {
int a, b, c, d, Vij;
if (j-i < TURN) return INFINITY_;
a = eH(i, j);
b = eS(i, j) + V(i + 1, j - 1);
if (eS(i, j) == 0) b = INFINITY_;
c = VBI(i,j);
d = VM(i,j);
Vij = MIN(MIN(a, b), MIN(c, d));
if (Vij == a && Vij != b && Vij != c && Vij != d) {
if (verbose == 1)
printf("i %5d j %5d Hairpin %12.2f\n", i, j, eH(i, j)/100.00);
total_en += eH(i,j);
return Vij;
} else if (Vij == b) {
if (verbose == 1)
printf("i %5d j %5d Stack %12.2f\n", i, j, eS(i, j)/100.00);
total_en += eS(i,j);
structure[i + 1] = j - 1;
structure[j - 1] = i + 1;
traceV(i + 1, j - 1);
return Vij;
} else if (Vij == c) {
if (verbose == 1)
printf("i %5d j %5d IntLoop ", i, j);
traceVBI(i, j);
return Vij;
} else if (Vij == d && Vij != a && Vij != b && Vij != c) {
int eVM = traceVM(i, j);
if (verbose ==1)
printf("i %5d j %5d MultiLoop %12.2f\n", i, j, (Vij-eVM)/100.0);
total_en += (Vij-eVM);
return Vij;
}
return 0;
}
void traceW(int j) {
int done = 0, i;
int wim1, flag = 1 ;
if (j == 0 || j == 1)
return;
for (i = 1; i < j && !done; i++) {
if (j-i < TURN) continue;
wim1 = MIN(0, W[i-1]);
flag = 1;
if ( wim1 != W[i-1] && canSSregion(0,i)) flag = 0;
if (g_unamode||g_mismatch) {
if ((W[j] == V(i,j) + auPenalty(i, j) + wim1 && canStack(i,j)) || forcePair(i,j)) {
done = 1;
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d ExtLoop %12.2f\n", i, j, auPenalty(i, j)/100.00);
total_ex += auPenalty(i, j);
traceV(i, j);
if (flag ) traceW(i - 1);
break;
} else if ((W[j] == V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1 && canSS(j) && canStack(i,j-1)) || forcePair(i, j-1)) {
done = 1;
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d ExtLoop %12.2f\n", i, j-1, (auPenalty(i,j-1) + Ed5(j-1,i,j))/100.00);
total_ex += (auPenalty(i,j-1) + Ed5(j-1,i,j));
traceV(i, j - 1);
if (flag ) traceW(i - 1);
break;
} else if ((W[j] == V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1 && canSS(i) && canStack(i+1,j)) || forcePair(i+1,j)){
done = 1;
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d ExtLoop %12.2f\n", i+1, j, (auPenalty(i+1,j) + Ed3(j,i+1,i))/100.00);
total_ex += (auPenalty(i+1,j) + Ed3(j,i+1,i));
traceV(i + 1, j);
if (flag ) traceW(i - 1);
break;
} else if ((W[j] == V(i+1,j-1) + auPenalty(i+1, j-1) + Estacke(j-1,i+1) + wim1 && canSS(i) && canSS(j) && canStack(i+1,j-1)) || forcePair(i+1,j-1)) {
done = 1;
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d ExtLoop %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Estacke(j-1,i+1))/100.00);
total_ex += (auPenalty(i+1, j-1) + Estacke(j-1,i+1));
traceV(i + 1, j - 1);
if (flag ) traceW(i - 1);
break;
}
} else if (g_dangles == 2) {
int e_dangles = 0;
if (i>1) e_dangles += Ed3(j,i,i-1);
if (j<length) e_dangles += Ed5(j,i,j+1);
if ((W[j] == V(i,j) + auPenalty(i, j) + e_dangles + wim1 && canSS(i) && canSS(j) && canStack(i+1,j-1)) || forcePair(i+1,j-1)) {
done = 1;
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d ExtLoop %12.2f\n", i+1, j-1, (auPenalty(i, j) + e_dangles)/100.00);
total_ex += (auPenalty(i, j) + e_dangles);
traceV(i, j);
if (flag ) traceW(i - 1);
break;
}
} else if (g_dangles == 0) {
if ((W[j] == V(i,j) + auPenalty(i, j) + wim1 && canStack(i,j)) || forcePair(i,j)) {
done = 1;
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d ExtLoop %12.2f\n", i, j, auPenalty(i, j)/100.00);
total_ex += auPenalty(i, j);
traceV(i, j);
if (flag ) traceW(i - 1);
break;
}
} else { // default
if ((W[j] == V(i,j) + auPenalty(i, j) + wim1 && canStack(i,j)) || forcePair(i,j)) {
done = 1;
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d ExtLoop %12.2f\n", i, j, auPenalty(i, j)/100.00);
total_ex += auPenalty(i, j);
traceV(i, j);
if (flag ) traceW(i - 1);
break;
} else if ((W[j] == V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1 && canSS(j) && canStack(i,j-1)) || forcePair(i, j-1)) {
done = 1;
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d ExtLoop %12.2f\n", i, j-1, (auPenalty(i,j-1) + Ed5(j-1,i,j))/100.00);
total_ex += (auPenalty(i,j-1) + Ed5(j-1,i,j));
traceV(i, j - 1);
if (flag ) traceW(i - 1);
break;
} else if ((W[j] == V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1 && canSS(i) && canStack(i+1,j)) || forcePair(i+1,j)){
done = 1;
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d ExtLoop %12.2f\n", i+1, j, (auPenalty(i+1,j) + Ed3(j,i+1,i))/100.00);
total_ex += (auPenalty(i+1,j) + Ed3(j,i+1,i));
traceV(i + 1, j);
if (flag ) traceW(i - 1);
break;
} else if ((W[j] == V(i+1,j-1) + auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + wim1 && canSS(i) && canSS(j) && canStack(i+1,j-1)) || forcePair(i+1,j-1)) {
done = 1;
if (print_energy_decompose == 1) fprintf(energy_decompose_outfile, "i %5d j %5d ExtLoop %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j))/100.00);
total_ex += (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j));
traceV(i + 1, j - 1);
if (flag ) traceW(i - 1);
break;
}
}
}
if (W[j] == W[j - 1] && !done) traceW(j-1);
//if (!done) {
// fprintf(stderr, "ERROR: W(%d) could not be traced\n", j);
//}
return;
}
int traceWM(int i, int j) {
assert(i < j);
int done=0, eWM=0;
if (!done && WM(i,j) == WMPrime[i][j]) {
eWM += traceWMPrime(i,j);
done = 1;
}
if (!done){
if (g_unamode||g_mismatch) {
if (WM(i,j) == V(i,j) + auPenalty(i, j) + Eb && canStack(i,j)) {
eWM += traceV(i, j);
done = 1;
} else if (WM(i,j) == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec && canSS(i) && canStack(i+1,j)) {
eWM += traceV(i + 1, j);
done = 1;
} else if (WM(i,j) == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec && canSS(j) && canStack(i,j-1)) {
done = 1;
eWM += traceV(i, j - 1);
} else if (WM(i,j) == V(i+1,j-1) + Estackm(j-1,i+1) + auPenalty(i+1, j-1) + Eb + 2*Ec && canSS(i) && canSS(j) && canStack(i+1,j-1)) {
done = 1;
eWM += traceV(i + 1, j - 1);
}
} else if (g_dangles == 2) {
int energy = V(i,j) + auPenalty(i, j) + Eb;
energy += (i==1)?Ed3(j,i,length):Ed3(j,i,i-1);
/*if (j<len)*/ energy += Ed5(j,i,j+1);
if (WM(i,j) == energy && canSS(i) && canSS(j) && canStack(i+1,j-1)) {
eWM += traceV(i, j);
done = 1;
}
} else if (g_dangles == 0) {
if (WM(i,j) == V(i,j) + auPenalty(i, j) + Eb && canStack(i,j)) {
eWM += traceV(i, j);
done = 1;
}
} else {
if (WM(i,j) == V(i,j) + auPenalty(i, j) + Eb && canStack(i,j)) {
eWM += traceV(i, j);
done = 1;
} else if (WM(i,j) == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec && canSS(i) && canStack(i+1,j)) {
eWM += traceV(i + 1, j);
done = 1;
} else if (WM(i,j) == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec && canSS(j) && canStack(i,j-1)) {
eWM += traceV(i, j - 1);
done = 1;
} else if (WM(i,j) == V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1, j-1) + Eb + 2*Ec && canSS(i) && canSS(j) && canStack(i+1,j-1)) {
eWM += traceV(i + 1, j - 1);
done = 1;
}
}
}
if (!done){
if (WM(i,j) == WM(i + 1,j) + Ec && canSS(i)) {
done = 1;
eWM += traceWM(i + 1, j);
} else if (WM(i,j) == WM(i,j - 1) + Ec && canSS(j)) {
done = 1;
eWM += traceWM(i, j - 1);
}
}
if(!done) {
fprintf(stderr, "ERROR: WM(%d,%d) could not be traced\n", i,j);
}
return eWM;
}
void traceW(int j) {
int done, i, Wj,Wj_temp;
int wim1, flag, Widjd, Wijd, Widj, Wij;
Wj = INFINITY_;
flag = 1;
done = 0;
if (j == 0 || j == 1) return;
for (i = 1; i < j && !done; i++) {
if (j-i < TURN) continue;
wim1 = MIN(0, W[i-1]);
flag = 1;
if (wim1 != W[i-1]) flag = 0;
Widjd = Wijd = Widj = INFINITY_;
Wij = V(i,j) + auPenalty(i, j) + wim1;
Widjd =(check_base(i)&&check_base(j))?(V(i+1,j-1) + auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + wim1): INFINITY_;
Wijd = (check_base(j))?(V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1):INFINITY_;
Widj = (check_base(i))?(V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1):INFINITY_;
Wj_temp=Wj;
Wj = MIN(MIN(MIN(Wij, Widjd), MIN(Wijd, Widj)), Wj);
if (W[j] == Wj) {
if (W[j] == Wij) {
done = 1;
if (verbose == 1)
printf("i %5d j %5d ExtLoop %12.2f\n", i, j, auPenalty(i, j)/100.00);
total_ex += auPenalty(i, j);
structure[i] = j;
structure[j] = i;
traceV(i, j);
if (flag || is_ss(1,i)) traceW(i - 1);
break;
} else if (W[j] == Widjd && check_base(i) && check_base(j)) {
done = 1;
if (verbose == 1)
printf("i %5d j %5d ExtLoop %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j))/100.00);
total_ex += (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j));
structure[i + 1] = j - 1;
structure[j - 1] = i + 1;
traceV(i + 1, j - 1);
if (flag || is_ss(1,i)) traceW(i - 1);
break;
} else if (W[j] == Wijd && check_base(j)) {
done = 1;
if (verbose == 1)
printf("i %5d j %5d ExtLoop %12.2f\n", i, j-1, (auPenalty(i,j-1) + Ed5(j-1,i,j))/100.00);
total_ex += (auPenalty(i,j-1) + Ed5(j-1,i,j));
structure[i] = j - 1;
structure[j - 1] = i;
traceV(i, j - 1);
if (flag || is_ss(1,i)) traceW(i - 1);
break;
} else if (W[j] == Widj && check_base(i)) {
done = 1;
if (verbose == 1)
printf("i %5d j %5d ExtLoop %12.2f\n", i+1, j, (auPenalty(i+1,j) + Ed3(j,i+1,i))/100.00);
total_ex += (auPenalty(i+1,j) + Ed3(j,i+1,i));
structure[i + 1] = j;
structure[j] = i + 1;
traceV(i + 1, j);
if (flag || is_ss(1,i)) traceW(i - 1);
break;
}
}
}
if (W[j] == W[j - 1] && !done) traceW(j-1);
return;
}
