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model_iharm3d.c
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model_iharm3d.c
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#include "decs.h"
#include <string.h>
//chose coordinates
#define FMKS 1
#define MKS 0
//function from IL group, coefficents needed to set up metric corrections for modified coodtinates
#define MUNULOOP for(int mu=0;mu<NDIM;mu++) for(int nu=0;nu<NDIM;nu++)
void set_dxdX(double X[NDIM], double dxdX[NDIM][NDIM])
{
// Jacobian with respect to KS basis where X is given in
// non-KS basis
MUNULOOP dxdX[mu][nu] = 0.;
#if(FMKS)
dxdX[0][0] = 1.;
dxdX[1][1] = exp(X[1]);
dxdX[2][1] = -exp(mks_smooth * (startx[1] - X[1])) * mks_smooth
* (
M_PI / 2. -
M_PI * X[2]
+ poly_norm * (2. * X[2] - 1.)
* (1
+ (pow((-1. + 2 * X[2]) / poly_xt, poly_alpha))
/ (1 + poly_alpha))
- 1. / 2. * (1. - hslope) * sin(2. * M_PI * X[2]));
dxdX[2][2] = M_PI + (1. - hslope) * M_PI * cos(2. * M_PI * X[2])
+ exp(mks_smooth * (startx[1] - X[1]))
* (-M_PI
+ 2. * poly_norm
* (1.
+ pow((2. * X[2] - 1.) / poly_xt, poly_alpha)
/ (poly_alpha + 1.))
+ (2. * poly_alpha * poly_norm * (2. * X[2] - 1.)
* pow((2. * X[2] - 1.) / poly_xt, poly_alpha - 1.))
/ ((1. + poly_alpha) * poly_xt)
- (1. - hslope) * M_PI * cos(2. * M_PI * X[2]));
dxdX[3][3] = 1.;
#endif
//sane test
#if(MKS)
dxdX[0][0] = 1.;
dxdX[1][1] = exp(X[1]);
dxdX[2][2] = M_PI + 2*M_PI*0.5*(1-hslope)*cos(2. * M_PI * X[2]);
dxdX[3][3] = 1.;
#endif
}
/*
Current metric: modified Kerr-Schild, squashed in theta
to give higher resolution at the equator
*/
void gcov_func(double *X, double gcov[][NDIM])
{
double sth, cth, s2, rho2;
double r, th;
double gcov_ks[NDIM][NDIM];
MUNULOOP gcov_ks[mu][nu] = 0.;
bl_coord(X,&r,&th);
cth = cos(th);
sth = sin(th);
s2 = sth * sth;
rho2 = r * r + a * a * cth * cth;
gcov_ks[0][0] = -1. + 2. * r / rho2 ;
gcov_ks[0][1] = 2. * r / rho2 ;
gcov_ks[0][3] = -2. * a * r * s2 / rho2;
gcov_ks[1][0] = gcov_ks[0][1];
gcov_ks[1][1] = 1. + 2. * r / rho2 ;
gcov_ks[1][3] = -a * s2 * (1. + 2. * r / rho2);
gcov_ks[2][2] = rho2 ;
gcov_ks[3][0] = gcov_ks[0][3];
gcov_ks[3][1] = gcov_ks[1][3];
gcov_ks[3][3] = s2 * (rho2 + a * a * s2 * (1. + 2. * r / rho2));
// convert from ks metric to a modified one using Jacobian
double dxdX[NDIM][NDIM];
set_dxdX(X, dxdX);
MUNULOOP
{
gcov[mu][nu] = 0;
for (int lam = 0; lam < NDIM; lam++) {
for (int kap = 0; kap < NDIM; kap++) {
gcov[mu][nu] += gcov_ks[lam][kap] * dxdX[lam][mu] * dxdX[kap][nu];
}
}
if( isnan(gcov[mu][nu])){
fprintf(stdout," gcov is nan here: r=%g th=%g X1=%g X2=%g -->> %g %g \n",r,th,X[1],X[2],dxdX[2][1],dxdX[2][2]);
exit(1);
}
}
}
#undef MUNULOOP
void get_connection(double X[NDIM], double lconn[NDIM][NDIM][NDIM])
{
/* for these coordinates it is safer to go numerically */
#if(FMKS)
get_connection_num(X,lconn);
#endif
#if(MKS)
double r1,r2,r3,r4,sx,cx;
double th,dthdx2,dthdx22,d2thdx22,sth,cth,sth2,cth2,sth4,cth4,s2th,c2th;
double a2,a3,a4,rho2,irho2,rho22,irho22,rho23,irho23,irho23_dthdx2;
double fac1,fac1_rho23,fac2,fac3,a2cth2,a2sth2,r1sth2,a4cth4;
r1 = exp(X[1]);
r2 = r1*r1;
r3 = r2*r1;
r4 = r3*r1;
sx = sin(2.*M_PI*X[2]);
cx = cos(2.*M_PI*X[2]);
th = M_PI*X[2] + hslope*sx;
dthdx2 = M_PI + 2.*M_PI*hslope*cx;
d2thdx22 = -4.*M_PI*M_PI*hslope*sx; /* d^2(th)/dx2^2 */
dthdx22 = dthdx2*dthdx2;
sth = sin(th);
cth = cos(th);
sth2 = sth*sth;
r1sth2 = r1*sth2;
sth4 = sth2*sth2;
cth2 = cth*cth;
cth4 = cth2*cth2;
s2th = 2.*sth*cth;
c2th = 2*cth2 - 1.;
a2 = a*a;
a2sth2 = a2*sth2;
a2cth2 = a2*cth2;
a3 = a2*a;
a4 = a3*a;
a4cth4 = a4*cth4;
rho2 = r2 + a2cth2;
rho22 = rho2*rho2;
rho23 = rho22*rho2;
irho2 = 1./rho2;
irho22 = irho2*irho2;
irho23 = irho22*irho2;
irho23_dthdx2 = irho23/dthdx2;
fac1 = r2 - a2cth2;
fac1_rho23 = fac1*irho23;
fac2 = a2 + 2*r2 + a2*c2th;
fac3 = a2 + r1*(-2. + r1);
lconn[0][0][0] = 2.*r1*fac1_rho23;
lconn[0][0][1] = r1*(2.*r1+rho2)*fac1_rho23;
lconn[0][0][2] = -a2*r1*s2th*dthdx2*irho22;
lconn[0][0][3] = -2.*a*r1sth2*fac1_rho23;
lconn[0][1][0] = lconn[0][0][1];
lconn[0][1][1] = 2.*r2*(r4 + r1*fac1 - a4cth4)*irho23;
lconn[0][1][2] = -a2*r2*s2th*dthdx2*irho22;
lconn[0][1][3] = a*r1*(-r1*(r3 + 2*fac1) + a4cth4)*sth2*irho23;
lconn[0][2][0] = lconn[0][0][2];
lconn[0][2][1] = lconn[0][1][2];
lconn[0][2][2] = -2.*r2*dthdx22*irho2;
lconn[0][2][3] = a3*r1sth2*s2th*dthdx2*irho22;
lconn[0][3][0] = lconn[0][0][3];
lconn[0][3][1] = lconn[0][1][3];
lconn[0][3][2] = lconn[0][2][3];
lconn[0][3][3] = 2.*r1sth2*(-r1*rho22 + a2sth2*fac1)*irho23;
lconn[1][0][0] = fac3*fac1/(r1*rho23);
lconn[1][0][1] = fac1*(-2.*r1 + a2sth2)*irho23;
lconn[1][0][2] = 0.;
lconn[1][0][3] = -a*sth2*fac3*fac1/(r1*rho23);
lconn[1][1][0] = lconn[1][0][1];
lconn[1][1][1] = (r4*(-2. + r1)*(1. + r1) + a2*(a2*r1*(1. + 3.*r1)*cth4 + a4cth4*cth2 + r3*sth2 + r1*cth2*(2.*r1 + 3.*r3 - a2sth2)))*irho23;
lconn[1][1][2] = -a2*dthdx2*s2th/fac2;
lconn[1][1][3] = a*sth2*(a4*r1*cth4 + r2*(2*r1 + r3 - a2sth2) + a2cth2*(2.*r1*(-1. + r2) + a2sth2))*irho23;
lconn[1][2][0] = lconn[1][0][2];
lconn[1][2][1] = lconn[1][1][2];
lconn[1][2][2] = -fac3*dthdx22*irho2;
lconn[1][2][3] = 0.;
lconn[1][3][0] = lconn[1][0][3];
lconn[1][3][1] = lconn[1][1][3];
lconn[1][3][2] = lconn[1][2][3];
lconn[1][3][3] = -fac3*sth2*(r1*rho22 - a2*fac1*sth2)/(r1*rho23);
lconn[2][0][0] = -a2*r1*s2th*irho23_dthdx2;
lconn[2][0][1] = r1*lconn[2][0][0];
lconn[2][0][2] = 0.;
lconn[2][0][3] = a*r1*(a2+r2)*s2th*irho23_dthdx2;
lconn[2][1][0] = lconn[2][0][1];
lconn[2][1][1] = r2*lconn[2][0][0];
lconn[2][1][2] = r2*irho2;
lconn[2][1][3] = (a*r1*cth*sth*(r3*(2. + r1) + a2*(2.*r1*(1. + r1)*cth2 + a2*cth4 + 2*r1sth2)))*irho23_dthdx2;
lconn[2][2][0] = lconn[2][0][2];
lconn[2][2][1] = lconn[2][1][2];
lconn[2][2][2] = -a2*cth*sth*dthdx2*irho2 + d2thdx22/dthdx2;
lconn[2][2][3] = 0.;
lconn[2][3][0] = lconn[2][0][3];
lconn[2][3][1] = lconn[2][1][3];
lconn[2][3][2] = lconn[2][2][3];
lconn[2][3][3] = -cth*sth*(rho23 + a2sth2*rho2*(r1*(4. + r1) + a2cth2) + 2.*r1*a4*sth4)*irho23_dthdx2;
lconn[3][0][0] = a*fac1_rho23;
lconn[3][0][1] = r1*lconn[3][0][0];
lconn[3][0][2] = -2.*a*r1*cth*dthdx2/(sth*rho22);
lconn[3][0][3] = -a2sth2*fac1_rho23;
lconn[3][1][0] = lconn[3][0][1];
lconn[3][1][1] = a*r2*fac1_rho23;
lconn[3][1][2] = -2*a*r1*(a2 + 2*r1*(2. + r1) + a2*c2th)*cth*dthdx2/(sth*fac2*fac2);
lconn[3][1][3] = r1*(r1*rho22 - a2sth2*fac1)*irho23;
lconn[3][2][0] = lconn[3][0][2];
lconn[3][2][1] = lconn[3][1][2];
lconn[3][2][2] = -a*r1*dthdx22*irho2;
lconn[3][2][3] = dthdx2*(0.25*fac2*fac2*cth/sth + a2*r1*s2th)*irho22;
lconn[3][3][0] = lconn[3][0][3];
lconn[3][3][1] = lconn[3][1][3];
lconn[3][3][2] = lconn[3][2][3];
lconn[3][3][3] = (-a*r1sth2*rho22 + a3*sth4*fac1)*irho23;
#endif
}
void interp_fourv(double X[NDIM], double ****fourv, double Fourv[NDIM]) ;
double interp_scalar(double X[NDIM], double ***var) ;
void init_model(char *args[])
{
void init_harm3d_grid(char *);
void init_harm3d_data(char *);
fprintf(stderr, "reading data header...\n");
/* Read in header and allocate space for grid data */
init_harm3d_grid(args[3]);
fprintf(stderr, "success\n");
/* find dimensional quantities from black hole
mass and its accretion rate */
set_units(args[4]);
fprintf(stderr, "reading data...\n");
/* Read in the grid data */
init_harm3d_data(args[3]);
fprintf(stderr, "success\n");
/* pre-compute densities, field strengths, etc. */
init_physical_quantities() ;
/* horizon radius */
Rh = 1 + sqrt(1. - a * a) ;
}
/*
these supply basic model data to grmonty
*/
void get_model_ucov(double X[NDIM], double Ucov[NDIM])
{
double gcov[NDIM][NDIM];
gcov_func(X, gcov);
if(X[1] < startx[1] ||
X[1] > stopx[1] ||
X[2] < startx[2] ||
X[2] > stopx[2]) {
/* sensible default value */
Ucov[0] = -1./sqrt(-gcov[0][0]) ;
Ucov[1] = 0. ;
Ucov[2] = 0. ;
Ucov[3] = 0. ;
return ;
}
interp_fourv(X, ucov, Ucov) ;
}
void get_model_ucon(double X[NDIM], double Ucon[NDIM])
{
double gcov[NDIM][NDIM] ;
double gcon[NDIM][NDIM] ;
double tmp[NDIM] ;
if(X[1] < startx[1] ||
X[1] > stopx[1] ||
X[2] < startx[2] ||
X[2] > stopx[2]) {
/* sensible default value */
gcov_func(X, gcov) ;
gcon_func(gcov, gcon) ;
tmp[0] = -1./sqrt(-gcon[0][0]) ;
tmp[1] = 0. ;
tmp[2] = 0. ;
tmp[3] = 0. ;
Ucon[0] =
tmp[0]*gcon[0][0] +
tmp[1]*gcon[0][1] +
tmp[2]*gcon[0][2] +
tmp[3]*gcon[0][3] ;
Ucon[1] =
tmp[0]*gcon[1][0] +
tmp[1]*gcon[1][1] +
tmp[2]*gcon[1][2] +
tmp[3]*gcon[1][3] ;
Ucon[2] =
tmp[0]*gcon[2][0] +
tmp[1]*gcon[2][1] +
tmp[2]*gcon[2][2] +
tmp[3]*gcon[2][3] ;
Ucon[3] =
tmp[0]*gcon[3][0] +
tmp[1]*gcon[3][1] +
tmp[2]*gcon[3][2] +
tmp[3]*gcon[3][3] ;
return ;
}
interp_fourv(X, ucon, Ucon) ;
}
void get_model_bcov(double X[NDIM], double Bcov[NDIM])
{
if(X[1] < startx[1] ||
X[1] > stopx[1] ||
X[2] < startx[2] ||
X[2] > stopx[2]) {
Bcov[0] = 0. ;
Bcov[1] = 0. ;
Bcov[2] = 0. ;
Bcov[3] = 0. ;
return ;
}
interp_fourv(X, bcov, Bcov) ;
}
void get_model_bcon(double X[NDIM], double Bcon[NDIM])
{
if(X[1] < startx[1] ||
X[1] > stopx[1] ||
X[2] < startx[2] ||
X[2] > stopx[2]) {
Bcon[0] = 0. ;
Bcon[1] = 0. ;
Bcon[2] = 0. ;
Bcon[3] = 0. ;
return ;
}
interp_fourv(X, bcon, Bcon) ;
}
double get_model_thetae(double X[NDIM])
{
if(X[1] < startx[1] ||
X[1] > stopx[1] ||
X[2] < startx[2] ||
X[2] > stopx[2]) {
return(0.) ;
}
return(interp_scalar(X, thetae)) ;
}
double get_model_uu(double X[NDIM])
{
if(X[1] < startx[1] ||
X[1] > stopx[1] ||
X[2] < startx[2] ||
X[2] > stopx[2]) {
return(0.) ;
}
return(interp_scalar(X, uu)) ;
}
//b field strength in Gauss
double get_model_b(double X[NDIM])
{
if(X[1] < startx[1] ||
X[1] > stopx[1] ||
X[2] < startx[2] ||
X[2] > stopx[2]) {
return(0.) ;
}
return(interp_scalar(X, b)) ;
}
double get_model_ne(double X[NDIM])
{
if(X[1] < startx[1] ||
X[1] > stopx[1] ||
X[2] < startx[2] ||
X[2] > stopx[2]) {
return(0.) ;
}
return(interp_scalar(X, ne)) ;
}
/** HARM utilities **/
void Xtoijk(double X[NDIM], int *i, int *j, int *k, double del[NDIM]) ;
/********************************************************************
Interpolation routines
********************************************************************/
/* return fluid four-vector in simulation units */
void interp_fourv(double X[NDIM], double ****fourv, double Fourv[NDIM]){
double del[NDIM],b1,b2,b3,d1,d2,d3,d4;
int i, j, k, ip1, jp1, kp1;
/* find the current zone location and offsets del[0], del[1] */
Xtoijk(X, &i, &j, &k, del);
ip1 = i + 1;
jp1 = j + 1;
kp1 = k + 1;
if(k==(N3-1)) kp1=0; //periodic
b1 = 1.-del[1];
b2 = 1.-del[2];
b3 = 1.-del[3];
d1 = b1*b2;
d3 = del[1] * b2;
d2 = del[2] * b1;
d4 = del[1] * del[2];
/* Interpolate along x1,x2 first */
Fourv[0] = d1*fourv[i][j][k][0] + d2*fourv[i][jp1][k][0] + d3*fourv[ip1][j][k][0] + d4*fourv[ip1][jp1][k][0];
Fourv[1] = d1*fourv[i][j][k][1] + d2*fourv[i][jp1][k][1] + d3*fourv[ip1][j][k][1] + d4*fourv[ip1][jp1][k][1];
Fourv[2] = d1*fourv[i][j][k][2] + d2*fourv[i][jp1][k][2] + d3*fourv[ip1][j][k][2] + d4*fourv[ip1][jp1][k][2];
Fourv[3] = d1*fourv[i][j][k][3] + d2*fourv[i][jp1][k][3] + d3*fourv[ip1][j][k][3] + d4*fourv[ip1][jp1][k][3];
/* Now interpolate above in x3 */
Fourv[0] = b3*Fourv[0] + del[3]*(d1*fourv[i][j][kp1][0] + d2*fourv[i][jp1][kp1][0] + d3*fourv[ip1][j][kp1][0] + d4*fourv[ip1][jp1][kp1][0]);
Fourv[1] = b3*Fourv[1] + del[3]*(d1*fourv[i][j][kp1][1] + d2*fourv[i][jp1][kp1][1] + d3*fourv[ip1][j][kp1][1] + d4*fourv[ip1][jp1][kp1][1]);
Fourv[2] = b3*Fourv[2] + del[3]*(d1*fourv[i][j][kp1][2] + d2*fourv[i][jp1][kp1][2] + d3*fourv[ip1][j][kp1][2] + d4*fourv[ip1][jp1][kp1][2]);
Fourv[3] = b3*Fourv[3] + del[3]*(d1*fourv[i][j][kp1][3] + d2*fourv[i][jp1][kp1][3] + d3*fourv[ip1][j][kp1][3] + d4*fourv[ip1][jp1][kp1][3]);
}
/* return scalar in cgs units */
double interp_scalar(double X[NDIM], double ***var)
{
double del[NDIM],b1,b2,interp;
int i, j, k, ip1, jp1, kp1;
/* find the current zone location and offsets del[0], del[1] */
Xtoijk(X, &i, &j, &k, del);
ip1 = i+1;
jp1 = j+1;
kp1 = k+1;
if(k==(N3-1)) kp1=0; //periodic
b1 = 1.-del[1];
b2 = 1.-del[2];
/* Interpolate in x1,x2 first */
interp = var[i][j][k]*b1*b2 +
var[i][jp1][k]*b1*del[2] +
var[ip1][j][k]*del[1]*b2 +
var[ip1][jp1][k]*del[1]*del[2];
/* Now interpolate above in x3 */
interp = (1.-del[3])*interp +
del[3]*(var[i ][j ][kp1]*b1*b2 +
var[i ][jp1][kp1]*del[2]*b1 +
var[ip1][j ][kp1]*del[1]*b2 +
var[ip1][jp1][kp1]*del[1]*del[2]);
return(interp);
}
/***********************************************************************************
End interpolation routines
***********************************************************************************/
void Xtoijk(double X[NDIM], int *i, int *j, int *k, double del[NDIM])
{
double phi;
/* Map X[3] into sim range, assume startx[3] = 0 */
phi = fmod(X[3], stopx[3]);
if(phi < 0.0) phi = stopx[3]+phi;
*i = (int) ((X[1] - startx[1]) / dx[1] - 0.5 + 1000) - 1000;
*j = (int) ((X[2] - startx[2]) / dx[2] - 0.5 + 1000) - 1000;
*k = (int) ((phi - startx[3]) / dx[3] - 0.5 + 1000) - 1000;
if(*i < 0) {
*i = 0 ;
del[1] = 0. ;
}
else if(*i > N1-2) { //OK because del[1]=1 and only terms with ip1=N1-1 will be important in interpolation
*i = N1-2 ;
del[1] = 1. ;
}
else {
del[1] = (X[1] - ((*i + 0.5) * dx[1] + startx[1])) / dx[1];
}
if(*j < 0) {
*j = 0 ;
del[2] = 0. ;
}
else if(*j > N2-2) {
*j = N2-2 ;
del[2] = 1. ;
}
else {
del[2] = (X[2] - ((*j + 0.5) * dx[2] + startx[2])) / dx[2];
}
if(*k < 0) {
*k = 0 ;
del[3] = 0. ;
}
else if(*k > N3-1) {
*k = N3-1;
del[3] = 1. ;
}
else {
del[3] = (phi - ((*k + 0.5) * dx[3] + startx[3])) / dx[3];
}
return;
}
void bl_coord(double *X, double *r, double *th)
{
*r = exp(X[1]) ;
#if(FMKS)
double thG = M_PI * X[2] + ((1. - hslope) / 2.) * sin(2. * M_PI * X[2]);
double y = 2 * X[2] - 1.;
double thJ = poly_norm * y
* (1. + pow(y / poly_xt, poly_alpha) / (poly_alpha + 1.)) + 0.5 * M_PI;
*th = thG + exp(mks_smooth * (startx[1] - X[1])) * (thJ - thG);
return;
#endif
#if(MKS)
*th = M_PI * X[2] + 0.5*(1-hslope)*sin(2. * M_PI * X[2]);
return;
#endif
}
void coord(int i, int j, int k, double *X)
{
/* returns zone-centered values for coordinates */
X[0] = startx[0];
X[1] = startx[1] + (i + 0.5) * dx[1];
X[2] = startx[2] + (j + 0.5) * dx[2];
X[3] = startx[3] + (k + 0.5) * dx[3];
return;
}
void set_units(char *munitstr)
{
double MBH ;
#if(SOURCE_SGRA)
MBH = MSGRA;
#endif
#if(SOURCE_M87)
MBH = MM87;
#endif
#if(SOURCE_DABHB)
MBH = MABHB;
#endif
#if(SOURCE_NT)
MBH = 10;
#endif
sscanf(munitstr,"%lf",&M_unit) ;
MBH *= MSUN ;
/** from this, calculate units of length, time, mass,
and derivative units **/
L_unit = GNEWT * MBH / (CL * CL);
T_unit = L_unit / CL;
RHO_unit = M_unit / pow(L_unit, 3);
U_unit = RHO_unit * CL * CL;
B_unit = CL * sqrt(4.*M_PI*RHO_unit);
fprintf(stderr,"L,T,M units: %g [cm] %g [sec] %g [g]\n",L_unit,T_unit,M_unit) ;
fprintf(stderr,"rho,u,B units: %g [g cm^-3] %g [g cm^-1 sec^-2] %g [G] \n",RHO_unit,U_unit,B_unit) ;
}
void init_physical_quantities(void)
{
int i, j, k;
double bsq,Thetae_unit,beta,b2,trat,sigma_m;
for (i = 0; i < N1; i++) {
for (j = 0; j < N2; j++) {
for (k = 0; k < N3; k++) {
uu[i][j][k] = p[UU][i][j][k];
bsq= bcon[i][j][k][0] * bcov[i][j][k][0] +
bcon[i][j][k][1] * bcov[i][j][k][1] +
bcon[i][j][k][2] * bcov[i][j][k][2] +
bcon[i][j][k][3] * bcov[i][j][k][3] ;
b[i][j][k] = sqrt(bsq)*B_unit ;
sigma_m=bsq/p[KRHO][i][j][k] ;
beta=p[UU][i][j][k]*(gam-1.)/0.5/bsq;
b2=beta*beta;
trat = trat_d * b2/(1. + b2) + trat_j /(1. + b2);
Thetae_unit = (MP/ME) * (game-1.) * (gamp-1.) / ( (gamp-1.) + (game-1.)*trat );
//Thetae_unit=2.*MP/15./ME;
thetae[i][j][k] = (p[UU][i][j][k]/p[KRHO][i][j][k])* Thetae_unit;
thetae[i][j][k] = MAX(thetae[i][j][k], THETAE_MIN);
ne[i][j][k] = p[KRHO][i][j][k] * RHO_unit/(MP+ME) ;
if(sigma_m > sigma_cut) {
ne[i][j][k]=0.0;
}
}
}
}
return ;
}
void *malloc_rank1(int n1, int size)
{
void *A;
if((A = malloc(n1*size)) == NULL){
fprintf(stderr,"malloc failure in malloc_rank1\n");
exit(123);
}
return A;
}
double **malloc_rank2(int n1, int n2)
{
double **A;
double *space;
int i;
space = malloc_rank1(n1*n2, sizeof(double));
A = malloc_rank1(n1, sizeof(double *));
for(i = 0; i < n1; i++) A[i] = &(space[i*n2]);
return A;
}
double ***malloc_rank3(int n1, int n2, int n3)
{
double ***A;
double *space;
int i,j;
space = malloc_rank1(n1*n2*n3, sizeof(double));
A = malloc_rank1(n1, sizeof(double *));
for(i = 0; i < n1; i++){
A[i] = malloc_rank1(n2,sizeof(double *));
for(j = 0; j < n2; j++){
A[i][j] = &(space[n3*(j + n2*i)]);
}
}
return A;
}
double ****malloc_rank4(int n1, int n2, int n3, int n4)
{
double ****A;
double *space;
int i,j,k;
space = malloc_rank1(n1*n2*n3*n4, sizeof(double));
A = malloc_rank1(n1, sizeof(double *));
for(i=0;i<n1;i++){
A[i] = malloc_rank1(n2,sizeof(double *));
for(j=0;j<n2;j++){
A[i][j] = malloc_rank1(n3,sizeof(double *));
for(k=0;k<n3;k++){
A[i][j][k] = &(space[n4*(k + n3*(j + n2*i))]);
}
}
}
return A;
}
double *****malloc_rank5(int n1, int n2, int n3, int n4, int n5)
{
double *****A;
double *space;
int i,j,k,l;
space = malloc_rank1(n1*n2*n3*n4*n5, sizeof(double));
A = malloc_rank1(n1, sizeof(double *));
for(i=0;i<n1;i++){
A[i] = malloc_rank1(n2, sizeof(double *));
for(j=0;j<n2;j++){
A[i][j] = malloc_rank1(n3, sizeof(double *));
for(k=0;k<n3;k++){
A[i][j][k] = malloc_rank1(n4, sizeof(double *));
for(l=0;l<n4;l++){
A[i][j][k][l] = &(space[n5*(l + n4*(k + n3*(j + n2*i)))]);
}
}
}
}
return A;
}
void init_storage(void)
{
int i;
bcon = malloc_rank4(N1,N2,N3,NDIM);
bcov = malloc_rank4(N1,N2,N3,NDIM);
ucon = malloc_rank4(N1,N2,N3,NDIM);
ucov = malloc_rank4(N1,N2,N3,NDIM);
p = (double ****)malloc_rank1(NPRIM,sizeof(double *));
for(i = 0; i < NPRIM; i++) p[i] = malloc_rank3(N1,N2,N3);
ne = malloc_rank3(N1,N2,N3);
uu = malloc_rank3(N1,N2,N3);
thetae = malloc_rank3(N1,N2,N3);
b = malloc_rank3(N1,N2,N3);
return;
}
#include <hdf5.h>
#include <hdf5_hl.h>
void init_harm3d_grid(char *fname)
{
hid_t file_id;
double th_cutout,t;
file_id = H5Fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT);
if(file_id < 0){
fprintf(stderr,"file %s does not exist, aborting...\n",fname);
exit(1234);
}
H5LTread_dataset_int(file_id, "/header/n1", &N1);
H5LTread_dataset_int(file_id, "/header/n2", &N2);
H5LTread_dataset_int(file_id, "/header/n3", &N3);
H5LTread_dataset_double(file_id, "/header/gam", &gam);
H5LTread_dataset_double(file_id, "/header/geom/startx1", &(startx[1]));
H5LTread_dataset_double(file_id, "/header/geom/startx2", &(startx[2]));
H5LTread_dataset_double(file_id, "/header/geom/startx3", &(startx[3]));
H5LTread_dataset_double(file_id, "/header/geom/dx1", &(dx[1]));
H5LTread_dataset_double(file_id, "/header/geom/dx2", &(dx[2]));
H5LTread_dataset_double(file_id, "/header/geom/dx3", &(dx[3]));
#if(MKS)
H5LTread_dataset_double(file_id, "/header/geom/mks/a", &a);
H5LTread_dataset_double(file_id, "/header/geom/mks/r_in", &Rin);
H5LTread_dataset_double(file_id, "/header/geom/mks/r_out", &Rout);
H5LTread_dataset_double(file_id, "/header/geom/mks/hslope", &hslope);
#endif
#if(FMKS)
H5LTread_dataset_double(file_id, "/header/geom/mmks/a", &a);
H5LTread_dataset_double(file_id, "/header/gam_e", &game);
H5LTread_dataset_double(file_id, "/header/gam_p", &gamp);
H5LTread_dataset_double(file_id, "/header/geom/mmks/hslope", &hslope);
/*additional parameter that describe theta*/
/* mks_smooth,poly_alpha,poly_xt */
H5LTread_dataset_double(file_id, "/header/geom/mmks/mks_smooth", &mks_smooth);
H5LTread_dataset_double(file_id, "/header/geom/mmks/poly_alpha", &poly_alpha);
H5LTread_dataset_double(file_id, "/header/geom/mmks/poly_xt", &poly_xt);
poly_norm = 0.5*M_PI*1./(1. + 1./(poly_alpha + 1.)*1./pow(poly_xt, poly_alpha));
#endif
stopx[0] = 1.;
stopx[1] = startx[1]+N1*dx[1];
stopx[2] = startx[2]+N2*dx[2];
stopx[3] = startx[3]+N3*dx[3];
th_cutout=0.02;//0.0;
//th_cutout=0.0174;
th_beg=th_cutout;
fprintf(stdout,"size: %d %d %d M gam=%g game=%g gamp=%g t=%g M mks_smooth=%g\n",N1,N2,N3,gam,game,gamp,t,mks_smooth);
fprintf(stdout,"a=%g Rout=%g hslope=%g th_cutout=%g\n",a,Rout,hslope,th_cutout);
fprintf(stdout,"start: %g %g %g \n",startx[1],startx[2],startx[3]);
fprintf(stdout,"stop: %g %g %g \n",stopx[1],stopx[2],stopx[3]);
init_storage();
H5Fclose(file_id);
}
int hdf5_read_array(void *data, const char *name, size_t rank,
hsize_t *fdims, hsize_t *fstart, hsize_t *fcount, hsize_t *mdims, hsize_t *mstart, hsize_t hdf5_type, char *fname)
{
hid_t filespace = H5Screate_simple(rank, fdims, NULL);
H5Sselect_hyperslab(filespace, H5S_SELECT_SET, fstart, NULL, fcount,NULL);
hid_t memspace = H5Screate_simple(rank, mdims, NULL);
H5Sselect_hyperslab(memspace, H5S_SELECT_SET, mstart, NULL, fcount,NULL);
hid_t file_id ;
file_id = H5Fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT);
hid_t dset_id = H5Dopen(file_id, "prims");
hid_t plist_id = H5Pcreate(H5P_DATASET_XFER);
herr_t err = H5Dread(dset_id, hdf5_type, memspace, filespace, plist_id, data);
H5Dclose(dset_id);
H5Pclose(plist_id);
H5Sclose(filespace);
H5Sclose(memspace);
return 0;
}
void init_harm3d_data(char *fname)
{
int i,j,k,l,m;
double X[NDIM],UdotU,ufac,udotB;
double gcov[NDIM][NDIM],gcon[NDIM][NDIM], g;
double dMact, Ladv, MBH;
double r,th;
FILE *fp;
#if(SOURCE_SGRA)
MBH = MSGRA;
#endif
#if(SOURCE_M87)
MBH = MM87;
#endif
#if(SOURCE_DABHB)
MBH = MABHB;
#endif
#if(SOURCE_NT)
MBH = 10;
#endif
MBH *= MSUN;
L_unit = GNEWT * MBH / (CL * CL);
T_unit = L_unit / CL;
hid_t file_id;
file_id = H5Fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT);
if(file_id < 0){
fprintf(stderr,"file %s does not exist, aborting...\n",fname);
exit(12345);
}
fprintf(stderr,"data incoming from --------> %s \n",fname);
int n_prims;
H5LTread_dataset_int(file_id, "/header/n_prim", &n_prims);
hsize_t fdims[] = { N1, N2, N3, n_prims };
hsize_t fstart[] = { 0, 0, 0, 0 };
hsize_t fcount[] = { N1, N2, N3, 1 };
hsize_t mdims[] = { N1, N2, N3, 1 };
hsize_t mstart[] = { 0, 0, 0, 0 };
fstart[3] = 0;
hdf5_read_array(p[KRHO][0][0], "prims", 4, fdims, fstart, fcount, mdims, mstart, H5T_IEEE_F64LE,fname);
fstart[3] = 1;
hdf5_read_array(p[UU][0][0], "prims", 4, fdims, fstart, fcount, mdims, mstart, H5T_IEEE_F64LE,fname);
fstart[3] = 2;
hdf5_read_array(p[U1][0][0], "prims", 4, fdims, fstart, fcount, mdims, mstart, H5T_IEEE_F64LE,fname);
fstart[3] = 3;
hdf5_read_array(p[U2][0][0], "prims", 4, fdims, fstart, fcount, mdims, mstart, H5T_IEEE_F64LE,fname);
fstart[3] = 4;
hdf5_read_array(p[U3][0][0], "prims", 4, fdims, fstart, fcount, mdims, mstart, H5T_IEEE_F64LE,fname);
fstart[3] = 5;
hdf5_read_array(p[B1][0][0], "prims", 4, fdims, fstart, fcount, mdims, mstart, H5T_IEEE_F64LE,fname);
fstart[3] = 6;
hdf5_read_array(p[B2][0][0], "prims", 4, fdims, fstart, fcount, mdims, mstart, H5T_IEEE_F64LE,fname);
fstart[3] = 7;
hdf5_read_array(p[B3][0][0], "prims", 4, fdims, fstart, fcount, mdims, mstart, H5T_IEEE_F64LE,fname);
H5Fclose(file_id);
X[0] = 0.;
X[3] = 0.;
fprintf(stderr,"reconstructing 4-vectors...\n");
dMact = Ladv = 0.;
for(i = 0; i < N1; i++){
for(j = 0; j < N2; j++){
coord(i,j,0,X);
gcov_func(X, gcov);
gcon_func(gcov, gcon);
g = gdet_func(gcov);
for(k = 0; k < N3; k++){
coord(i,j,k,X);
//the four-vector reconstruction should have gcov and gcon and gdet using the modified coordinates
//interpolating the four vectors to the zone center !!!!
UdotU = 0.;
for(l = 1; l < NDIM; l++) for(m = 1; m < NDIM; m++) UdotU += gcov[l][m]*p[U1+l-1][i][j][k]*p[U1+m-1][i][j][k];
ufac = sqrt(-1./gcon[0][0]*(1 + fabs(UdotU)));
ucon[i][j][k][0] = -ufac*gcon[0][0];
for(l = 1; l < NDIM; l++) ucon[i][j][k][l] = p[U1+l-1][i][j][k] - ufac*gcon[0][l];
lower(ucon[i][j][k], gcov, ucov[i][j][k]);
//reconstruct the magnetic field three vectors
udotB = 0.;
for(l = 1; l < NDIM; l++) udotB += ucov[i][j][k][l]*p[B1+l-1][i][j][k];
bcon[i][j][k][0] = udotB;
for(l = 1; l < NDIM; l++) bcon[i][j][k][l] = (p[B1+l-1][i][j][k] + ucon[i][j][k][l]*udotB)/ucon[i][j][k][0];