void update_ion_temp(recomb_t *thisRecombRates, double dens_old, double dens, double *Xe_old, double *Xe, double *temp_old, double *temp, double z_old, double z, double gamma, double n, double xray_heating, double Hubble)
{
int temp_index = temp_recomb_index(thisRecombRates, *temp_old);
double recomb = thisRecombRates->recHII[temp_index];
*Xe = update_ion_smallXe(n*dens, *Xe_old, recomb, z, z_old, gamma, Hubble);
*temp = update_temp(dens_old, dens, *Xe_old, *Xe, *temp_old, z, z_old, xray_heating, Hubble);
// printf("Xe_old = %e\t Xe = %e\t z_old = %e\t z = %e\n", *Xe_old, *Xe, z_old, 0.5*(z_old+z));
// if((*Xe)-(*Xe_old) > 0.1)
// {
// update_ion_temp(thisRecombRates, dens_old, dens, Xe_old, Xe, temp_old, temp, z_old, 0.5*(z_old+z), gamma, n, xray_heating, Hubble);
// update_ion_temp(thisRecombRates, dens_old, dens, Xe_old, Xe, temp_old, temp, 0.5*(z_old+z), z, gamma, n, xray_heating, Hubble);
// }
if((*Xe) > 0.01)
{
*Xe = update_ion_constdens(n*dens*CUB(1.+z_old), *Xe_old, recomb, z, z_old, gamma, Hubble);
*temp = update_temp(dens_old, dens, *Xe_old, *Xe, *temp_old, z, z_old, xray_heating, Hubble);
}
if(isnan(*Xe))
{
printf("NAN alarm! Xe = %e\t Xe_old = %e\t gamma = %e\t n = %e\t dens = %e\t temp = %e\t recomb = %e\t Hubble = %e\n", *Xe, *Xe_old, gamma, n, dens, *temp_old, recomb, Hubble);
}
Xe_old = Xe;
temp_old = temp;
}
double update_ion_constdens(double dens, double Xe_old, double recomb, double z, double z_old, double gamma, double Hubble)
{
double z_old_CUB = sqrt(CUB(1.+z_old));
double z_CUB = sqrt(CUB(1.+z));
double tmp = gamma/(2.*dens*recomb);
double tmp2 = sqrt(1.+2./tmp);
double atanh_argument = (Xe_old+tmp)/(tmp*tmp2);
double tanh_argument = gamma*tmp2*(1./z_old_CUB - 1./z_CUB)/(3.*Hubble) - atanh(atanh_argument);
double Xe_new = - tmp * (1. + tmp2 * tanh(tanh_argument));
if(isnan(Xe_new))
{
printf("tmp = %e\t tmp2 = %e\t tanh_argument = %e (%e)\t atanh_argument = %e\n", tmp, tmp2, tanh_argument, gamma*tmp2*(1./z_old_CUB - 1./z_CUB)/(3.*Hubble), atanh_argument);
}
return Xe_new;
}
double update_ion_smallXe(double dens, double Xe_old, double recomb, double z, double z_old, double gamma, double Hubble)
{
double z_old_CUB = sqrt(CUB(1.+z_old));
double exponent = sqrt(4.*dens*recomb*gamma/SQR(Hubble) + 2.25);
double a_div_b = pow((1.+z)/(1.+z_old), exponent);
double factor = exponent*2.*Hubble;
double tmp = (1.+ a_div_b)*factor;
double tmp2 = 1.-a_div_b;
double numerator = tmp + tmp2 * (-3.*Hubble + 4.*gamma/(Xe_old*z_old_CUB));
double denominator = tmp + tmp2 * (3.*Hubble + 4.*dens*recomb*Xe_old*z_old_CUB);
double Xe_new = Xe_old/sqrt(CUB(1.+z))*z_old_CUB * numerator/denominator;
return Xe_new;
}
double z_calc_numdensity_He_at_redshift(double h, double omega_b, double z, double Y)
{
return 3.*SQR(h*100.*km_cm/Mpc_cm)/(8.*M_PI*G)/mp_g*omega_b*CUB(1.+z)*Y*0.25;
}
double z_calc_numdensity_per_mp_at_redshift(double h, double omega_b, double z)
{
return 3.*SQR(h*100.*km_cm/Mpc_cm)/(8.*M_PI*G)/mp_g*omega_b*CUB(1.+z);
}
void Forces::WriteTens(char *FTens,int Comp,double InvNFile){
double InvValues = 1. / Tens.NSlab;
double InvVolume = prho()*CUBE(Tens.NSlab)/pVol();
if(VAR_IF_TYPE(Tens.CalcMode,CALC_2d)){
#ifdef OMPI_MPI_H
MPI_Allreduce(MPI_IN_PLACE,Tens.Pre[Comp],SQR(Tens.NSlab),MPI_DOUBLE,MPI_SUM,Proc->CommGrid);
for(int t=0;t<2;t++){
MPI_Allreduce(MPI_IN_PLACE,Tens.Dens[t],SQR(Tens.NSlab),MPI_DOUBLE,MPI_SUM,Proc->CommGrid);
}
int Rank=0;
MPI_Comm_rank(Proc->CommGrid, &Rank);
if(Rank==0){
#endif
FILE *FWrite = fopen(FTens,"w");
WriteTens2d(FWrite,Comp,InvNFile);
fclose(FWrite);
for(int s=0;s<SQR(Tens.NSlab);s++){
Tens.Pre[Comp][s] = 0.;
Tens.Dens[0][s] = 0.;
Tens.Dens[1][s] = 0.;
}
#ifdef OMPI_MPI_H
}
#endif
}
if(VAR_IF_TYPE(Tens.CalcMode,CALC_3d)){
#ifdef OMPI_MPI_H
MPI_Allreduce(MPI_IN_PLACE,Tens.Pre[Comp],CUB(Tens.NSlab),MPI_DOUBLE,MPI_SUM,Proc->CommGrid);
for(int t=0;t<2;t++){
MPI_Allreduce(MPI_IN_PLACE,Tens.Dens[t],CUB(Tens.NSlab),MPI_DOUBLE,MPI_SUM,Proc->CommGrid);
}
int Rank=0;
MPI_Comm_rank(Proc->CommGrid, &Rank);
if(Rank==0){
#endif
FILE *FWrite = fopen(FTens,"w");
fprintf(FWrite,"# l(%.1f %.1f %.1f) r(%.2f %.2f %.2f) v[%d] d[color]\n",pEdge(0),pEdge(1),pEdge(2),Tens.RefPos[0],Tens.RefPos[1],Tens.RefPos[2],Tens.NSlab);
for(int sx=0;sx<Tens.NSlab;sx++){
double x = sx*InvValues*pEdge(CLat1);
for(int sy=0;sy<Tens.NSlab;sy++){
double y = sy*InvValues*pEdge(CLat2);
for(int sz=0;sz<Tens.NSlab;sz++){
double z = sz*InvValues*pEdge(CNorm);
int v = (sx*Tens.NSlab+sy)*Tens.NSlab+sz;
if(Tens.Dens[0][v] <= 0 && Tens.Dens[1][v] <= 0 && ABS(Tens.Pre[Comp][v]) <= 0) continue;
fprintf(FWrite,"{x(%.3f %.3f %.3f)",x,y,z);
fprintf(FWrite," v( %lf %.2f %.2f)}\n",
-Tens.Pre[Comp][v]*InvNFile*InvVolume,
Tens.Dens[0][v]*InvNFile*InvVolume,
Tens.Dens[1][v]*InvNFile*InvVolume);
}
}
}
fclose(FWrite);
for(int s=0;s<CUB(Tens.NSlab);s++){
Tens.Pre[Comp][s] = 0.;
Tens.Dens[0][s] = 0.;
Tens.Dens[1][s] = 0.;
}
}
#ifdef OMPI_MPI_H
}
#endif
}
void reinitcmintegration(const SlaterDet* Q, const SlaterDet* Qp,
cmintegrationpara* par)
{
alpha = 0.5/(_estimateacm(Q)+_estimateacm(Qp));
if (par->type == CMNone) {
par->w[0] = 1.0;
par->x[0][0] = 0.0; par->x[0][1] = 0.0; par->x[0][2] = 0.0;
}
else if (par->type == CMSimple) {
par->w[0] = 0.125*pow(M_PI*alpha,-1.5);
par->x[0][0] = 0.0; par->x[0][1] = 0.0; par->x[0][2] = 0.0;
}
else if (par->type == CMProd) {
int nr=par->prod.nr;
int nx=par->prod.ntheta; int nphi=par->prod.nphi;
double pointr[nr], weightr[nr];
GaussSqrHermitePoints(nr, alpha, pointr, weightr);
double pointx[nx], weightx[nx];
GaussLegendrePoints(nx, -1.0, 1.0, pointx, weightx);
double pointphi[nphi], weightphi[nphi];
ShiftedPeriodicTrapezoidalPoints(nphi, 0, 2*M_PI, 0.00,
pointphi, weightphi);
int i=0;
int ir, ix, iphi;
for (ir=0; ir<nr; ir++)
for (ix=0; ix<nx; ix++)
for (iphi=0; iphi<nphi; iphi++) {
par->x[i][0] = pointr[ir]*sqrt(1-SQR(pointx[ix]))*cos(pointphi[iphi]);
par->x[i][1] = pointr[ir]*sqrt(1-SQR(pointx[ix]))*sin(pointphi[iphi]);
par->x[i][2] = pointr[ir]*pointx[ix];
par->w[i] = 1/CUB(2*M_PI)*
weightr[ir]*weightx[ix]*weightphi[iphi];
i++;
}
}
else if (par->type == CMPoly) {
int nr=par->poly.nr;
int npoly=par->poly.npoly;
double pointr[nr], weightr[nr];
GaussSqrHermitePoints(nr, alpha, pointr, weightr);
int i=0;
int ir, ipoly, j;
for (ir=0; ir<nr; ir++)
for (ipoly=0; ipoly<npoly; ipoly++) {
for (j=0; j<3; j++)
par->x[i][j] = pointr[ir]*polyhedron[npoly][ipoly][j];
par->w[i] = 1/CUB(2*M_PI)*
weightr[ir]*(4*M_PI/npoly);
i++;
}
}
}
void _initcmintegration(const Projection* P,
double alpha,
cmintegrationpara* par)
{
if (P->cm == CMNone) {
par->n = 1;
par->x = malloc(3*sizeof(double));
par->w = malloc(1*sizeof(double));
par->x[0][0] = 0.0; par->x[0][1] = 0.0; par->x[0][2] = 0.0;
par->w[0] = 1.0;
}
else if (P->cm == CMSimple) {
par->n = 1;
par->x = malloc(3*sizeof(double));
par->w = malloc(1*sizeof(double));
par->x[0][0] = 0.0; par->x[0][1] = 0.0; par->x[0][2] = 0.0;
par->w[0] = 0.125*pow(M_PI*alpha,-1.5);
}
else if (P->cm == CMProd) {
int nr=P->cmprod.nr;
int nx=P->cmprod.ntheta; int nphi=P->cmprod.nphi;
double pointr[nr], weightr[nr];
GaussSqrHermitePoints(nr, alpha, pointr, weightr);
double pointx[nx], weightx[nx];
GaussLegendrePoints(nx, -1.0, 1.0, pointx, weightx);
double pointphi[nphi], weightphi[nphi];
ShiftedPeriodicTrapezoidalPoints(nphi, 0, 2*M_PI, 0.00,
pointphi, weightphi);
par->n = nr*nx*nphi;
par->x = malloc(3*par->n*sizeof(double));
par->w = malloc(par->n*sizeof(double));
int i=0;
int ir, ix, iphi;
for (ir=0; ir<nr; ir++)
for (ix=0; ix<nx; ix++)
for (iphi=0; iphi<nphi; iphi++) {
par->x[i][0] = pointr[ir]*sqrt(1-SQR(pointx[ix]))*cos(pointphi[iphi]);
par->x[i][1] = pointr[ir]*sqrt(1-SQR(pointx[ix]))*sin(pointphi[iphi]);
par->x[i][2] = pointr[ir]*pointx[ix];
par->w[i] = 1/CUB(2*M_PI)*
weightr[ir]*weightx[ix]*weightphi[iphi];
i++;
}
}
else if (P->cm == CMPoly) {
int nr=P->cmpoly.nr;
int npoly=P->cmpoly.npoly;
double pointr[nr], weightr[nr];
GaussSqrHermitePoints(nr, alpha, pointr, weightr);
par->n = nr*npoly;
par->x = malloc(3*par->n*sizeof(double));
par->w = malloc(par->n*sizeof(double));
int i=0;
int ir, ipoly, j;
for (ir=0; ir<nr; ir++)
for (ipoly=0; ipoly<npoly; ipoly++) {
for (j=0; j<3; j++)
par->x[i][j] = pointr[ir]*polyhedron[npoly][ipoly][j];
par->w[i] = 1/CUB(2*M_PI)*
weightr[ir]*(4*M_PI/npoly);
i++;
}
}
}
void ElPoly::IsoSurf(int NSample,double *IsoLevel,int NIso){
int NPairF = NFile[1]-NFile[0];
double OldPos[3] = {pNanoPos(0,0),pNanoPos(0,1),pNanoPos(0,2)};
double DensEl = CUB(NSample)/(pVol()*NPairF);
double Dens = 13.3;
FILE *FNano = fopen("NanoPos.txt","w");
//IsoLevel *= NPairF;
for(int ff=NFile[0];ff<NFile[1];ff+=NPairF){
double *Plot = (double *)calloc(CUBE(NSample),sizeof(double));
double Min = 0.;
double Max = 0.;
VAR_TRIANGLE *Triang = NULL;
double Pos[3];
for(int f=ff;f<ff+NPairF&&f<NFile[1];f++){
Processing(f);
if(OpenRisk(cFile[f],BF_PART))return;
for(int b=0;b<pNBlock();b++){
for(int p=Block[b].InitIdx;p<Block[b].EndIdx;p++){
if(pType(p) != 0)continue;
for(int d=0;d<3;d++){
Pos[d] = pPos(p,d) - (pNanoPos(0,d)-.5*pEdge(d));
Pos[d] -= floor(Pos[d]*pInvEdge(d))*pEdge(d);
}
int sx = (int)(Pos[0]*pInvEdge(0)*NSample);
int sy = (int)(Pos[1]*pInvEdge(1)*NSample);
int sz = (int)(Pos[2]*pInvEdge(2)*NSample);
int sTot = (sx*NSample+sy)*NSample+sz;
Plot[sTot] += DensEl;
if(Max < Plot[sTot]) Max = Plot[sTot];
if(Min > Plot[sTot]) Min = Plot[sTot];
}
}
}
Matrice Mask(3,3,3);
Mask.FillGaussian(.5,3.);
Mask.Print();
int NDim = 3;
int IfMinImConv = 1;
Mask.ConvoluteMatrix(Plot,NSample,NDim,IfMinImConv);
Mask.ConvoluteMatrix(Plot,NSample,NDim,IfMinImConv);
// ConvoluteMatrix(Plot,NSample,&Mask,3);
// ConvoluteMatrix(Plot,NSample,&Mask,3);
char FString[256];
sprintf(FString,"IsoSurf%05d.dat",ff);
FILE *F2Write = fopen(FString,"w");
fprintf(F2Write,"#l(%lf %lf %lf) v[%d] d[polygon]\n",pEdge(0),pEdge(1),pEdge(2),NSample);
HeaderNano(F2Write);
int NTri = 0;
for(int i=0;i<NIso;i++){
printf("Min %lf Max %lf IsoLevel %lf DensEl %lf\n",Min,Max,IsoLevel[i],DensEl);
Triang = MarchingCubes(Plot,NSample,IsoLevel[i],&NTri);
for(int t=0;t<NTri;t++){
for(int i=0;i<3;i++){
int l1 = t*3 + (i+1)%3;
int l2 = t*3 + (i+2)%3;
for(int d=0;d<3;d++) Pos[d] = Triang[t].p[i].x[d];
int sx = (int)(Pos[0]*pInvEdge(0)*NSample);
int sy = (int)(Pos[1]*pInvEdge(1)*NSample);
int sz = (int)(Pos[2]*pInvEdge(2)*NSample);
int sTot = (sx*NSample+sy)*NSample+sz;
fprintf(F2Write,"{t[%d %d %d] ",sTot,t,0);
fprintf(F2Write,"x(%lf %lf %lf) ",Pos[0],Pos[1],Pos[2]);
fprintf(F2Write,"v(%lf %lf %lf) ",Triang[t].n[i].x[0],Triang[t].n[i].x[1],Triang[t].n[i].x[2]);
fprintf(F2Write,"l[%d] l[%d]}\n",l1,l2);
}
}
}
fclose(F2Write);
free(Plot);
free(Triang);continue;
int NVertex = CUBE(2*NSample-1);
double *WeightL = (double *) calloc(NVertex,sizeof(double));
NormalWeight(Triang,WeightL,NSample,NTri);
double CmStalk[3] = {0.,0.,0.};//OldPos[0],OldPos[1],OldPos[2]};
double CountStalk = 0.;
for(int t=0;t<NTri;t++){
for(int v=0;v<3;v++){
int vRef = Triang[t].v[v];
for(int d=0;d<3;d++){
CmStalk[d] = Triang[t].p[v].x[d]*WeightL[vRef];
}
CountStalk += WeightL[vRef];
}
}
free(WeightL);
free(Triang);
if(CountStalk <= 0.) CountStalk = 1.;
for(int d=0;d<3;d++){
CmStalk[d] /= CountStalk;
}
pPos(CmStalk);
SetNNano(1);
for(int d=0;d<3;d++){
Nano->Pos[d] = CmStalk[d];
OldPos[d] = Nano->Pos[d];
}
SetNanoBkf(0);
Nano->Axis[0] = 0.;
Nano->Axis[1] = 0.;
Nano->Axis[2] = 1.;
Nano->Rad = .5;
Nano->Height = 4.;
Nano->Hamaker = 1.;
Nano->OffSet = 1.;
Nano->Shape = SHAPE_STALK;
for(int f=ff;f<ff+NPairF&&f<NFile[1];f++){
char String[120];
StringNano(String,0);
fprintf(FNano,"sed '/Rigid/c\\%s' %s > Ciccia.dat\n",String,cFile[f]);
fprintf(FNano,"mv Ciccia.dat %s\n",cFile[f]);
//command("chmod u+x %s\n","NanoPos.txt");
//SubNanoHeader(cFile[f]);
}
printf("\n");
}
fclose(FNano);
}
