void addMatrixAsVectorVector(Pool& p, const string& key, const TNT::Array2D<Real>& mat) {
for (int i=0; i<int(mat.dim1()); ++i) {
vector<Real> v(mat.dim1());
for (int j=0; j<int(mat.dim2()); ++j) {
v[j] = mat[i][j];
}
p.add(key, v);
}
}
// Processing routine for the pca with one input cube
void Transform(Buffer &in, Buffer &out) {
for(int i = 0; i < in.SampleDimension(); i++) {
for(int j = 0; j < in.LineDimension(); j++) {
TNT::Array2D<double> pre(1, in.BandDimension());
for(int k = 0; k < pre.dim2(); k++) {
int index = i + j * in.SampleDimension() + k * in.SampleDimension() * in.LineDimension();
pre[0][k] = in[index];
}
TNT::Array2D<double> post = pca.Transform(pre);
for(int k = 0; k < post.dim2(); k++) {
int index = i + j * in.SampleDimension() + k * in.SampleDimension() * in.LineDimension();
out[index] = post[0][k];
}
}
}
}
// Processing routine for the pca with two input cubes
void NormalizeAndInvert(Buffer &in, Buffer &out) {
for(int i = 0; i < in.SampleDimension(); i++) {
for(int j = 0; j < in.LineDimension(); j++) {
TNT::Array2D<double> pre(1, in.BandDimension());
for(int k = 0; k < pre.dim2(); k++) {
int index = i + j * in.SampleDimension() + k * in.SampleDimension() * in.LineDimension();
// Stretch the data before inverting it
// NOTE: this needs to be modified to use a GAUSSIAN STRETCH
//pre[0][k] = (in[index]-bandStats[k]->Average())/bandStats[k]->StandardDeviation();
pre[0][k] = stretches[k]->Map(in[index]);
}
TNT::Array2D<double> post = pca.Inverse(pre);
for(int k = 0; k < post.dim2(); k++) {
int index = i + j * in.SampleDimension() + k * in.SampleDimension() * in.LineDimension();
out[index] = post[0][k];
}
}
}
}
void* VectorMatrixReal::fromPythonCopy(PyObject* obj) {
if (!PyList_Check(obj)) {
throw EssentiaException("VectorMatrixReal::fromPythonCopy: input is not a list");
}
int size = PyList_Size(obj);
vector<TNT::Array2D<Real> >* v = new vector<TNT::Array2D<Real> >(size);
for (int i=0; i<size; ++i) {
TNT::Array2D<Real>* mat;
try {
mat = reinterpret_cast<TNT::Array2D<Real>*>(MatrixReal::fromPythonCopy(PyList_GET_ITEM(obj, i)));
}
catch (const exception&) {
delete v;
throw;
}
(*v)[i] = mat->copy();
}
return v;
}
int
initialise_maes (TNT::Array2D < unk > mesh,
TNT::Array2D < double >faceBx,
TNT::Array2D < double >faceBy,
MPI_Comm new_comm, int ndims, int *dim_size,
double *xsize, double *ysize)
{
double minpressure = 9e99;
double mindensity = 9e99;
double maxdensity = (-9e99);
std::cout << "Initialise Magnetised Accretion-Ejection Structure " << std::
endl;
const int nx = mesh.dim1 ();
const int ny = mesh.dim2 ();
const double gammam1i = 1 / (PhysConsts::gamma - 1);
const double gammam1 = (PhysConsts::gamma - 1);
double r0, r, z, h;
double r2, z2, h2;
double r02;
// ms is a parameter smaller than unity
// which then ensures an initial subsonic poloidal
// inflow
double ms = 0.3;
double rho, vtheta, vz, vr, bz, br, btheta;
// plasma beta parameter measuring the ratio of the
// thermal pressure to the magnetic pressure at Z = 0
double beta = 1.0;
double pressure = 0;
// Disk Aspect Ratio
double eps = 0.1;
int coords[] = { 0, 0 };
int myid = 99;
MPI_Comm_rank (MPI_COMM_WORLD, &myid);
MPI_Cart_coords (new_comm, myid, ndims, coords);
int dims[] = { 0, 0 };
MPI_Cartdim_get (new_comm, dims);
int xmax = 0;
int ymax = 0;
MPI_Allreduce (coords, &xmax, 1, MPI_INT, MPI_MAX, new_comm);
MPI_Allreduce (coords + 1, &ymax, 1, MPI_INT, MPI_MAX, new_comm);
xmax++;
ymax++;
std::cout << "Proc" << myid << " " << xmax << " " << ymax << std::endl;
int myaddress[] = { 0, 0 };
myaddress[0] = (nx - 2 * NGC) * coords[0];
myaddress[1] = (ny - 2 * NGC) * coords[1];
*xsize = 40;
// Initialise the face-centred magnetic field
for (int jj = 0; jj < ny + 1; jj++)
for (int ii = 0; ii < nx + 1; ii++)
{
//
int gg = std::max (ii - NGC, 0);
float myx = 0;
float myy = 0;
myx = (float) myaddress[0] + gg;
float delta_x = *xsize / ((nx - 2 * NGC) * xmax);
//std::cout << delta_x << " " <<delta_y << std::endl;
r = (40.0 * myx) / (dim_size[0] * nx) + delta_x * 0.5;
h = eps * r;
h2 = h * h;
r2 = r * r;
r0 = 4;
r02 = r0 * r0;
bz = pow (r0, 2.5) / (pow ((r02 + r2), 1.25) * sqrt (beta));
faceBx[ii][jj] = 0.0;
faceBy[ii][jj] = bz;
if (isnan (bz))
{
MPI_Abort (MPI_COMM_WORLD, 33333333);
exit (0);
}
// faceBy[ii][jj] = 3.0;
}
for (int jj = 0; jj < ny + 1; jj++)
{
faceBy[nx][jj] =
faceBy[nx-1][jj] =
faceBy[nx-2][jj] ;
}
#undef PROBS_WITH_B
#ifdef PROBS_WITH_B
for (int hh = 0; hh < ny + 1; hh++)
for (int gg = 0; gg < nx + 1; gg++)
{
faceBy[hh][gg] = 3.0;
}
#endif
*xsize = 40;
*ysize = 80;
for (int jj = 2; jj < ny; jj++)
for (int ii = 2; ii < nx; ii++)
{
// Mass Density
int gg = ii - NGC;
int hh = jj - NGC;
float myx = 0;
float myy = 0;
myx = (float) myaddress[0] + gg;
myy = (float) myaddress[1] + hh;
float delta_x = *xsize / ((nx - 2 * NGC) * xmax);
float delta_y = *ysize / ((ny - 2 * NGC) * ymax);
//std::cout << delta_x << " " <<delta_y << std::endl;
z = (80.0 * myy) / (dim_size[1] * ny) + delta_y * 0.5;
r = (40.0 * myx) / (dim_size[0] * nx) + delta_x * 0.5;
r = std::max (r, delta_x * 0.5);
z = std::max (z, delta_y * 0.5);
h = eps * r;
h2 = h * h;
z2 = z * z;
r2 = r * r;
/* R0 is a constant set equal to 4 in our runs.
* This offset radius in the denominator makes the
* density regular up to R = 0.
*/
r0 = 4;
r02 = r0 * r0;
rho =
std::max (1e-6, (pow (r0, 1.5) / pow ((r0 * r0 + r * r), 0.75))) *
std::pow (std::max (1e-6, (1 - 0.5 * (gammam1) * z2 / h2)), gammam1i);
//mesh[ii][jj] _MASS= (pow(r0,1.5)/pow((r0*r0+r*r),0.75))*pow (max(1e-6, (1- 0.5* (gammam1) * z2/h2 )), gammam1i ) ;
rho = std::max (1e-6, rho);
/*
std::cout
<< rho
<< " " << ii << " " << jj
<< " " << r
<< " " <<
std::pow (std::max (1e-6, (1 - 0.5 * (gammam1) * z2 / h2)), gammam1i)
<< std::endl;
*/
mesh[ii][jj] _MASS = rho;
/*
mesh[ii][jj] _MASS = 0.2 * (
mesh[ii][jj] _MASS +
mesh[ std::min(ii+1,nx-1) ][jj] _MASS +
mesh[ std::max(ii-1,0) ][jj] _MASS +
mesh[ii ][std::min (jj+1, ny-1) ] _MASS +
mesh[ii ][std ::max(jj-1,0)] _MASS
);
*/
// Rotation Profile
vtheta =
(1 -
eps * eps) * sqrt (r0) * exp (-2 * z2 / h2) / (eps *
pow ((r02 + r2),
0.25));
mesh[ii][jj] _MOMZ = mesh[ii][jj] _MASS *vtheta;
if (isnan (mesh[ii][jj] _MOMZ))
{
std::cout << "z-momentum is nan" << std::endl;
MPI_Abort (MPI_COMM_WORLD, 0);
exit (0);
}
// Poloidal Velocity
vr =
(-ms) * sqrt (r0) * exp (-2 * z2 / h2) / (pow ((r02 + r2), 0.25));
mesh[ii][jj] _MOMX = mesh[ii][jj] _MASS *vr;
if (isnan (mesh[ii][jj] _MOMX))
{
std::cout << "x-momentum is nan" << std::endl;
MPI_Abort (MPI_COMM_WORLD, 99);
exit (0);
}
vz = vr * z / r;
mesh[ii][jj] _MOMY = mesh[ii][jj] _MOMX *z / r;
if (isnan (mesh[ii][jj] _MOMY))
{
std::cout << "y-momentum is nan" << std::endl;
MPI_Abort (MPI_COMM_WORLD, 101);
exit (0);
}
// Magnetic Field
bz = pow (r0, 2.5) / (pow ((r02 + r2), 1.25) * sqrt (beta));
bz = 0.5 * (faceBy[ii][jj] + faceBy[ii][jj + 1]);
br = 0;
btheta = 0;
// Pressure = rho ^ gamma
pressure = pow (rho, PhysConsts::gamma);
// Energy
mesh[ii][jj] _B_X = 0.;
mesh[ii][jj] _B_Y = bz;
mesh[ii][jj] _B_Z = 0.;
double vv2 = vz * vz + vr * vr + vtheta * vtheta;
double b2 = bz * bz + br * br + btheta * btheta;
mesh[ii][jj] _ENER =
(0.5 * rho * vv2) + (0.5 * b2) + pressure * gammam1i
;
if (mesh[ii][jj] _ENER < 0)
{
std::cout
<< " Neg init energy"
<< " (" << ii << " , " << jj << " )" << std::endl;
}
mesh[ii][jj].temperature = myid;
minpressure = std::min (pressure, minpressure);
mindensity = std::min (rho, mindensity);
maxdensity = std::max (rho, maxdensity);
}
std::cout << "Min pressure " << minpressure << std::endl;
std::cout << "Min density " << mindensity << std::endl;
std::cout << "Max density " << maxdensity << std::endl;
//
}
int
emf_exchange (TNT::Array2D < double >faceEx,
TNT::Array2D < double >faceEy,
int myNorth, int mySouth, int myEast, int myWest, int myid)
{
int nx=faceEx.dim1();
int ny=faceEy.dim2();
MPI_Status stat;
int fnx = faceEx.dim1 ();
int fny = faceEy.dim2 ();
int xfnx = faceEx.dim1 ();
int xfny = faceEx.dim2 ();
int yfnx = faceEy.dim1 ();
int yfny = faceEy.dim2 ();
int ne = NE;
unk test;
double gammam1 = PhysConsts::gamma - 1;
double gammam1i = 1.0 / gammam1;
MPI_Datatype FaceCol;
MPI_Datatype FaceRowt;
MPI_Datatype xFaceCol;
MPI_Datatype xFaceRow;
MPI_Datatype yFaceCol;
MPI_Datatype yFaceRow;
MPI_Type_vector (fnx, /* # column elements */
1, /* 1 column only */
fny, /* skip ny elements */
MPI_DOUBLE, /* elements are double */
&FaceCol); /* MPI derived datatype */
MPI_Type_vector (1, /* # row elements */
fny, /* 1 row only */
0, /* skip ny elements */
// myrow, /* elements are double */
MPI_DOUBLE, /* elements are double */
&FaceRowt); /* MPI derived datatype */
MPI_Type_vector (xfnx, /* # column elements */
1, /* 1 column only */
xfny, /* skip ny elements */
MPI_DOUBLE, /* elements are double */
&xFaceCol); /* MPI derived datatype */
MPI_Type_vector (1, /* # row elements */
xfny, /* 1 row only */
0, /* skip ny elements */
// myrow, /* elements are double */
MPI_DOUBLE, /* elements are double */
&xFaceRow); /* MPI derived datatype */
MPI_Type_vector (yfnx, /* # column elements */
1, /* 1 column only */
yfny, /* skip ny elements */
MPI_DOUBLE, /* elements are double */
&yFaceCol); /* MPI derived datatype */
MPI_Type_vector (1, /* # row elements */
yfny, /* 1 row only */
0, /* skip ny elements */
// myrow, /* elements are double */
MPI_DOUBLE, /* elements are double */
&yFaceRow); /* MPI derived datatype */
MPI_Type_commit (&FaceCol);
MPI_Type_commit (&FaceRowt);
MPI_Type_commit (&yFaceCol);
MPI_Type_commit (&yFaceRow);
MPI_Type_commit (&xFaceCol);
MPI_Type_commit (&xFaceRow);
#define DEBUG
#ifdef DEBUG1
std::cout << "Proc " << myid << " okay to here " << std::endl;
#endif
//========== FACE CENTRED ELECTRIC FIELD EXCHANGE ===============
// Send Columns
#define OLDWAY
#ifdef OLDWAY
MPI_Send (&faceEx[0][xfny - 3], 1, xFaceCol, myNorth, myid, MWULD);
MPI_Recv (&faceEx[0][1], 1, xFaceCol, mySouth, mySouth, MWULD, &stat);
MPI_Barrier (MWULD);
MPI_Send (&faceEx[0][2], 1, xFaceCol, mySouth, myid, MWULD);
MPI_Recv (&faceEx[0][xfny - 2], 1, xFaceCol, myNorth, myNorth, MWULD, &stat);
MPI_Barrier (MWULD);
MPI_Send (&faceEy[2][0], 1, yFaceRow, myWest, myid, MWULD);
MPI_Recv (&faceEy[yfnx - 2][0], 1, yFaceRow, myEast, myEast, MWULD, &stat);
MPI_Barrier (MWULD);
MPI_Send (&faceEy[yfnx - 3][0], 1, yFaceRow, myEast, myid, MWULD);
MPI_Recv (&faceEy[1][0], 1, yFaceRow, myWest, myWest, MWULD, &stat);
MPI_Barrier (MWULD);
#else
#ifdef PERIODIC
for (int i = 2; i < nx-1 ; ++i)
{
faceEx[i][ny-2]=faceEx[i][2] ;
faceEx[i][1]= (faceEx[i][ny-3]) ;
}
for (int j = 2; j < ny - 1; ++j)
{
faceEy[nx-2][j]= faceEy[2][j];
faceEy[1][j]= (faceEy[nx-3][j]) ;
}
#else
for (int i = 2; i < nx-1 ; ++i)
{
faceEx[i][ny-2]=faceEx[i][ny-3] ;
faceEx[i][1]= (faceEx[i][2]) ;
}
for (int j = 2; j < ny - 1; ++j)
{
faceEy[nx-2][j]= faceEy[nx-3][j];
faceEy[1][j]= (-faceEy[2][j]) ;
}
#endif
#endif
#ifdef CYLINDRICAL
if (myNorth == MPI_PROC_NULL)
{
for (int i = 0; i < nx ; ++i)
{
faceEx[i][ny-2]=faceEx[i][ny-3] ;
}
}
if (mySouth == MPI_PROC_NULL)
{
for (int i = 0; i < nx ; ++i)
{
faceEx[i][1]= (faceEx[i][2]) ;
}
}
if (myEast == MPI_PROC_NULL)
{
for (int j = 0; j < ny ; ++j)
{
faceEy[nx-2][j]= faceEy[nx-3][j];
}
}
if (myWest == MPI_PROC_NULL)
{
for (int j = 0; j < ny ; ++j)
{
faceEy[1][j]= (-faceEy[2][j]) ;
}
}
#endif
#ifdef MAES
if (mySouth == MPI_PROC_NULL)
{
if (myWest == MPI_PROC_NULL)
{
int diskheight=8;
int boxwidth=8;
for (int j = 0; j < diskheight; ++j)
{
for (int i = 0; i < boxwidth; ++i)
{
faceEx[i][diskheight-1] = faceEx[i][diskheight];
faceEx[i][j] = faceEx[i][diskheight];
faceEy[i][j] = faceEy[i][diskheight];
}
}
for (int j = 0; j < diskheight; ++j)
{
faceEy[boxwidth-1][j] = faceEy[boxwidth][j];
}
}
}
#endif
return 0;
}
int
initialise_jet (TNT::Array2D < unk > mesh,
TNT::Array2D < double >faceBx,
TNT::Array2D < double >faceBy,
MPI_Comm new_comm, int ndims, int *dim_size,
double *xsize, double *ysize)
{
std::cout << "Initialise Jet Problem" << std::endl;
const int nx = mesh.dim1 ();
const int ny = mesh.dim2 ();
const double gammam1i = 1 / (PhysConsts::gamma - 1);
const double gammam1 = (PhysConsts::gamma - 1);
double r0, r, z, h;
double r2, z2, h2;
double r02;
// ms is a parameter smaller than unity
// which then ensures an initial subsonic poloidal
// inflow
double ms = 0.3;
double rho, vtheta, vz, vr, bz, br, btheta;
// plasma beta parameter measuring the ratio of the thermal pressure to the magnetic pressure at Z = 0
double beta = 1.0;
double pressure = 0;
// Disk Aspect Ratio
double eps = 0.1;
double bx = 10;
double by = 10;
int coords[] = { 0, 0 };
int myid = 99;
MPI_Comm_rank (MPI_COMM_WORLD, &myid);
MPI_Cart_coords (new_comm, myid, ndims, coords);
int dims[] = { 0, 0 };
MPI_Cartdim_get (new_comm, dims);
int xmax = 0;
int ymax = 0;
MPI_Allreduce (coords, &xmax, 1, MPI_INT, MPI_MAX, new_comm);
MPI_Allreduce (coords + 1, &ymax, 1, MPI_INT, MPI_MAX, new_comm);
xmax++;
ymax++;
std::cout << "Proc" << myid << " " << xmax << " " << ymax << std::endl;
int myaddress[] = { 0, 0 };
myaddress[0] = (nx - 2 * NGC) * coords[0];
myaddress[1] = (ny - 2 * NGC) * coords[1];
xmax *= (nx - 2 * NGC);
ymax *= (ny - 2 * NGC);
*xsize = 100.0;
*ysize = 200.0;
// Initialise face-centered B fields
for (int ii = 0; ii < nx + 1; ii++)
for (int jj = 0; jj < ny + 1; jj++)
{
int gg = ii - NGC;
int hh = jj - NGC;
double myx = (float) myaddress[0] + (ii - NGC);
double myy = (float) myaddress[1] + (jj - NGC);
//faceBx[ii][jj] = -sin( 2*PhysConsts::pi * myy / ymax) ;
//faceBy[ii][jj] = sin( 4*PhysConsts::pi * myx / xmax);
faceBx[ii][jj] = 0.0;
faceBy[ii][jj] = 1.0;
}
for (int jj = 0; jj < ny; jj++)
for (int ii = 0; ii < nx; ii++)
{
// Mass Density
bx = 0.5 * (faceBx[ii][jj] + faceBx[ii + 1][jj]);
by = 0.5 * (faceBy[ii][jj] + faceBy[ii][jj + 1]);
bz = 0.0;
rho = 0.25;
double myx = (float) myaddress[0] + (ii - NGC);
double myy = (float) myaddress[1] + (jj - NGC);
double vx = 0.0;
double vy = 0.0;
double vz = 0.0;
if ( 0 && myx <40 && myy<40)
{
vy=10.0;
if ( myx >30)
{
vy= (40 - 30 )*(myx - 40)/(0-10);
}
}
//if ( myy<40) vy=10.0;
double bsqr = 0.5 * (bx * bx + by * by + bz * bz);
double ke = 0.5 * rho * (vx * vx + vy * vy + vz * vz);
double rmax2=nx*nx;
pressure = 0.5+(1.- myx*myx / rmax2);
pressure = 0.0004;
mesh[ii][jj] _MASS = rho;
mesh[ii][jj] _MOMX = rho * vx;
mesh[ii][jj] _MOMY = rho * vy;
mesh[ii][jj] _MOMZ = rho * vz;
mesh[ii][jj] _ENER = pressure * gammam1i + bsqr + ke;
mesh[ii][jj] _B_X = bx;
mesh[ii][jj] _B_Y = by;
mesh[ii][jj] _B_Z = bz*myx/nx;
mesh[ii][jj].temperature = myid;
}
}
int
parflux (TNT::Array2D < unk > mesh,
TNT::Array2D < flux > fx,
TNT::Array2D < flux > fy,
TNT::Array2D < double >xjx,
TNT::Array2D < double >xjy,
TNT::Array2D < double >xjz,
TNT::Array2D < double >yjx,
TNT::Array2D < double >yjy,
TNT::Array2D < double >yjz,
double *delta_x, double *delta_y, int *myaddress, MPI_Comm Cart_comm)
{
double eps = 0.1;
double gammam1 = PhysConsts::gamma - 1.;
double gammam1i = 1. / gammam1;
int nx = mesh.dim1 ();
int ny = mesh.dim2 ();
// Current arrays
int myid = 99999;
MPI_Comm_rank (MPI_COMM_WORLD, &myid);
int ndims = 2;
int coords[2];
int remain_dims[] = { 0, 1 };
MPI_Comm Sub_comm;
MPI_Cart_sub (Cart_comm, remain_dims, &Sub_comm);
int lowest = 99999;
coords[1] = 1;
MPI_Cart_coords (Cart_comm, myid, ndims, coords);
MPI_Cart_rank (Cart_comm, coords, &lowest);
// Check my position in the Cartesian grid
// Then bcast my id to the Sub_comm
// Then all print out the id
// Grab the coords of the processor
double tmpbuf;
tmpbuf = myid;
TNT::Array1D < double >pressure_buf (nx);
MPI_Bcast (&tmpbuf, 1, MPI_DOUBLE, 0, Sub_comm);
#ifdef DEBUG_SUB_COMM
std::cout
<< "myid = " << myid
<< "coords = (" << coords[0] << "," << coords[1] << ")"
<< " lowest = " << tmpbuf << std::endl;
#endif
// Sweep for fluxes
for (int ii = 1; ii <= nx - 2; ii++)
{
for (int jj = 1; jj <= ny - 2; jj++)
{
double rr = mesh[ii][jj] _MASS;
if (rr < 0)
{
std::cout
<< __FUNCTION__ << ": "
<< "Negative density at"
<< " (" << ii << " , " << jj <<" )"
<<std::endl;
MPI_Abort(MPI_COMM_WORLD, 1234);
exit(0);
}
double px = mesh[ii][jj] _MOMX;
double py = mesh[ii][jj] _MOMY;
double pz = mesh[ii][jj] _MOMZ;
double et = mesh[ii][jj] _ENER;
double bx = mesh[ii][jj] _B_X;
double by = mesh[ii][jj] _B_Y;
double bz = mesh[ii][jj] _B_Z;
double ri = 1.0 / rr;
double vx = px * ri;
double vy = py * ri;
double vz = pz * ri;
double ke = 0.5 * rr * (vx * vx + vy * vy);
double b2 = 0.5 * (bx * bx + by * by + bz * bz);
double vdotb = (vx * bx + vy * by + vz * bz);
double p = et - ke - b2;
double ptot = et - ke;
p = p * gammam1;
if (isnan (p))
{
std::cout
<< __FUNCTION__
<< " ("
<< ii << "," << jj
<< ") bx " << bx << " by " << by << " bz " << bz << std::endl;
MPI_Abort (MPI_COMM_WORLD, 44444);
exit(0);
}
// Work out current at each cell face and add to energy flux
// xflux current
double idx = 1.0 / (*delta_x);
double idy = 1.0 / (*delta_y);
xjx[ii][jj] =
0.5 * idy * ((mesh[ii][jj + 1] _B_Z + mesh[ii - 1][jj + 1] _B_Z) -
(mesh[ii][jj - 1] _B_Z + mesh[ii - 1][jj - 1] _B_Z));
if (isnan (xjx[ii][jj]))
{
std::cout
<< "xjx"
<< " " << *delta_y
<< " " << idy
<< " " << *delta_x
<< " " << idx
<< " " << mesh[ii][jj + 1] _B_Z
<< " " << mesh[ii - 1][jj + 1] _B_Z << std::endl;
MPI_Abort (MPI_COMM_WORLD, 666666);
exit (0);
}
xjy[ii][jj] =
(-idx) * ((mesh[ii][jj] _B_Z - mesh[ii - 1][jj] _B_Z));
xjz[ii][jj] =
(idx) * ((mesh[ii][jj] _B_Y - mesh[ii - 1][jj] _B_Y)) -
0.5 * idy * ((mesh[ii][jj + 1] _B_X + mesh[ii - 1][jj + 1] _B_X) -
(mesh[ii][jj - 1] _B_X + mesh[ii - 1][jj - 1] _B_X));
// yflux current
yjx[ii][jj] = idy * (mesh[ii][jj] _B_Z - mesh[ii][jj - 1] _B_Z);
yjy[ii][jj] =
0.5 * (-idx) *
((mesh[ii + 1][jj] _B_Z + mesh[ii + 1][jj - 1] _B_Z) -
(mesh[ii - 1][jj] _B_Z + mesh[ii - 1][jj - 1] _B_Z));
yjz[ii][jj] =
0.5 * (idx) *
((mesh[ii + 1][jj] _B_Y + mesh[ii + 1][jj - 1] _B_Y) -
(mesh[ii - 1][jj] _B_Y + mesh[ii - 1][jj - 1] _B_Y)) -
idy * (mesh[ii][jj] _B_X - mesh[ii][jj - 1] _B_X);
fx[ii][jj] _MASS = rr * vx;
fx[ii][jj] _MOMX = rr * vx * vx + ptot - bx * bx;
fx[ii][jj] _MOMY = rr * vx * vy - bx * by;
fx[ii][jj] _MOMZ = rr * vx * vz - bx * bz;
fx[ii][jj] _ENER = (et + ptot) * vx - bx * vdotb;
fx[ii][jj] _B_X = 0;
fx[ii][jj] _B_Y = by * bx - bx * vy;
fx[ii][jj] _B_Z = bz * vx - bx * vz;
fy[ii][jj] _MASS = rr * vy;
fy[ii][jj] _MOMX = rr * vx * vy - by * bx;
fy[ii][jj] _MOMY = rr * vy * vy + ptot - by * by;
fy[ii][jj] _MOMZ = rr * vz * vy - by * bz;
fy[ii][jj] _ENER = (et + ptot) * vy - by * vdotb;
fy[ii][jj] _B_X = bx * vy - by * vx;
fy[ii][jj] _B_Y = 0;
fy[ii][jj] _B_Z = bz * vy - by * vz;
if (isnan (fy[ii][jj] _ENER))
{
std::cout
<< __FUNCTION__
<< " Flux ("
<< ii << "," << jj
<< ") et " << et
<< " ptot " << ptot
<< " p " << p
<< " vy " << vy
<< " by " << by
<< " vdotb " << vdotb << " rr " << rr << std::endl;
MPI_Abort (MPI_COMM_WORLD, 1222);
exit (0);
}
// Gravity Term
// r and z are distances from (0,0) in global grid
double myx = (double) myaddress[0] + ii;
double myy = (double) myaddress[1] + jj;
double r = myx * *delta_x;
double z = myy * *delta_y;
#define GRAVITY
#ifdef GRAVITY
double GM = 1.0 / (eps * eps);
double gravity =
(-GM) / std::sqrt (std::pow (r, 2.0) + std::pow (z, 2.0));
double grav_en = mesh[ii][jj] _MOMX * gravity;
// std::cout << " r " << r << " z " << z << std::endl;
gravity = mesh[ii][jj] _MASS *gravity;
fx[ii][jj] _MOMX += gravity;
fx[ii][jj] _ENER += grav_en;
grav_en = mesh[ii][jj] _MOMY *gravity;
gravity = mesh[ii][jj] _MASS *gravity;
fy[ii][jj] _MOMY += gravity;
fy[ii][jj] _ENER += grav_en;
#else
std::cout << "Gravity disabled" << std::endl;
#endif
//double etam=alpham * Va * H *exp(-2*zz*zz/(H*H));
double etam = 0.1;
double alpham = 0.1;
// H is the thermal heightscale of the disk
// cs is soundspeed at disk midplane
// cs = sqrt (gamma *P/ rho);
// double cs=0;
// omegaK is keplerian velocity at disk midplane
double omegaK = 0;
omegaK = sqrt (GM / r * r * r);
double H = eps * r;
double Va =
std::sqrt (bx * bx + by * by + bz * bz) / std::sqrt (rr);
etam = alpham * H * Va * exp (-2 * z * z / (H * H));
double chim = 1.0;
double etamdash = chim * etam;
double etaR = etamdash;
double etaZ = etamdash;
double etaPhi = etam;
// Resistive Terms (See Toth 2000)
// add a -B X (eta J)
fx[ii][jj] _ENER +=
(by * etaPhi * xjz[ii][jj] - bz * etaZ * xjy[ii][jj]);
fy[ii][jj] _ENER +=
(-bx * etaPhi * yjz[ii][jj] + bz * etaR * yjx[ii][jj]);
if (isnan (fy[ii][jj] _ENER))
{
std::cout
<< __FUNCTION__
<< " Flux ("
<< ii << "," << jj
<< ")"
<< " bx " << bx
<< " by " << by
<< " bz " << bz
<< " rr " << rr
<< " etaPhi " << etaPhi
<< " yjz " << yjz[ii][jj]
<< " etaR " << etaR << " yjx " << yjx[ii][jj] << std::endl;
MPI_Abort (MPI_COMM_WORLD, 1222);
exit (0);
}
}
}
}
/////////////////////////////////////////////////////////////////////////////////////
// We now calculate the diffusion tensor and its eigenvalues and eigenvectors
// The method and the following explanation is from dSimFitTensor.m:
// Fit the Stejskal-Tanner equation: S(b) = S(0) exp(-b ADC),
// where S(b) is the image acquired at non-zero b-value, and S(0) is
// the image acquired at b=0. Thus, we can find ADC with the
// following:
// ADC = -1/b * log( S(b) / S(0) )
// But, to avoid divide-by-zero, we need to add a small offset to
// S(0). We also need to add a small offset to avoid log(0).
//
// Note: Using floats in JAMA::SVD causes numerical inaccuracies, so we compute
// everything in double format.
/////////////////////////////////////////////////////////////////////////////////////
void computeTensor(uint index, double tensors[][3][3], double eigenvecs[][3][3], float lambdas[][3], float mds[], float fas[], float rds[]){
double* gradDir = new double[3*numGrads]; // gradDir will contain the gradient components, scaled to have norm 1
double* bVals = new double[numGrads]; // bVals will contain the b-values
double offset = 0.000001; // This offset will be used to avoid divide-by-zero errors
double norm; // Will contain the norm of each gradient - used for scaling to norm 1
double logB0 = 0; // Will contain the average log value of the measured signal for zero gradients
double* logDw = new double[numGrads]; // Will contain the log values of the measured signal for non-zero gradients
uint numZeroGrads = 0, numNonZeroGrads = 0; // Counters for the number of zero and non-zero gradients
uint* nonZeroGradsInd = new uint[numGrads];
///////////////////////////////////////////////////////////////////
// Compute gradDir, bVals, logDw and logB0
///////////////////////////////////////////////////////////////////
for (uint j=0; j<numGrads; j++){
norm = sqrt(gradientDataResults[j*numOutputs+3]*gradientDataResults[j*numOutputs+3]+gradientDataResults[j*numOutputs+4]*gradientDataResults[j*numOutputs+4]+gradientDataResults[j*numOutputs+5]*gradientDataResults[j*numOutputs+5]);
printf("Signal for gradient %u and compartment %i: %g\n", j+1, index-1, gradientDataResults[j*numOutputs+6+index]);
if (norm==0){
gradDir[j*3+0] = 0;
gradDir[j*3+1] = 0;
gradDir[j*3+2] = 0;
logB0 += log(gradientDataResults[j*numOutputs+6+index]+offset);
numZeroGrads++;
} else {
gradDir[j*3+0] = (double) gradientDataResults[j*numOutputs+3]/norm;
gradDir[j*3+1] = (double) gradientDataResults[j*numOutputs+4]/norm;
gradDir[j*3+2] = (double) gradientDataResults[j*numOutputs+5]/norm;
logDw[numNonZeroGrads] = log(gradientDataResults[j*numOutputs+6+index]+offset);
nonZeroGradsInd[numNonZeroGrads] = j;
numNonZeroGrads++;
}
bVals[j] = pow((2.0*3.1415926535*42576.0)*norm/1000000000*gradientDataResults[j*numOutputs+0],2)*(gradientDataResults[j*numOutputs+1]-gradientDataResults[j*numOutputs+0]/3.0);
}
logB0 = logB0/numZeroGrads;
double* bv = new double[numNonZeroGrads*3]; // bv will contain the normalized components of all non-zero gradients
double errorMargin = 0.000001; // We will round off matrices to precision errormargin, to avoid small-value numerical errors
TNT::Array2D<double> adc(numNonZeroGrads,1); // ADC for each non-zero gradient according to ADC = -1/b * log( S(b) / S(0) )
TNT::Array2D<double> m(numNonZeroGrads,6); // Rearrangement of normalized non-zero gradient components
for (uint k=0; k<numNonZeroGrads; k++){
adc[k][0] = -1/bVals[nonZeroGradsInd[k]]*(logDw[k]-logB0);
bv[k*3+0] = gradDir[nonZeroGradsInd[k]*3+0];
bv[k*3+1] = gradDir[nonZeroGradsInd[k]*3+1];
bv[k*3+2] = gradDir[nonZeroGradsInd[k]*3+2];
m[k][0] = bv[k*3+0]*bv[k*3+0];
m[k][1] = bv[k*3+1]*bv[k*3+1];
m[k][2] = bv[k*3+2]*bv[k*3+2];
m[k][3] = 2*bv[k*3+0]*bv[k*3+1];
m[k][4] = 2*bv[k*3+0]*bv[k*3+2];
m[k][5] = 2*bv[k*3+1]*bv[k*3+2];
}
// Round off m to avoid small-value numerical errors
for (int n=0; n<m.dim1(); n++){
for(int m1=0; m1<m.dim2(); m1++){
m[n][m1] = floor(m[n][m1]*1000000.0f + 0.5)/1000000.0f;
}
}
////////////////////////////////////////////////////////////////////////////////////////
// We now find the pseudo-inverse of m by doing an SVD decomposition
///////////////////////////////////////////////////////////////////////////////////////
JAMA::SVD<double> svd(m);
TNT::Array2D<double> S;
TNT::Array2D<double> U;
TNT::Array2D<double> V;
svd.getS(S);
svd.getU(U);
svd.getV(V);
// Round off S, U and V to avoid small-value numerical errors
for (int p=0; p<S.dim1(); p++){
for(int q=0; q<S.dim2(); q++){
S[p][q] = floor(S[p][q]*1000000.0f + 0.5)/1000000.0f;
}
}
for (int p=0; p<U.dim1(); p++){
for(int q=0; q<U.dim2(); q++){
U[p][q] = floor(U[p][q]*1000000.0f + 0.5)/1000000.0f;
}
}
for (int p=0; p<V.dim1(); p++){
for(int q=0; q<V.dim2(); q++){
V[p][q] = floor(V[p][q]*1000000.0f + 0.5)/1000000.0f;
}
}
// Find the inverse matrix of S
TNT::Array2D<double> S_inv(S.dim2(),S.dim1());
for (int n=0; n<S.dim1(); n++){
for (int m=0; m<S.dim2(); m++){
if (S[n][m] == 0){
S_inv[m][n] = 0;
} else {
S_inv[m][n] = 1/S[n][m];
}
}
}
// Transpose U and V (they are real, so we don't need to take complex conjugates)
TNT::Array2D<double> Ustar(U.dim2(),U.dim1());
for (int n=0; n<U.dim1(); n++){
for (int m=0; m<U.dim2(); m++){
Ustar[m][n] = U[n][m];
}
}
TNT::Array2D<double> Vstar(V.dim2(),V.dim1());
for (int n=0; n<V.dim1(); n++){
for (int m=0; m<V.dim2(); m++){
Vstar[m][n] = V[n][m];
}
}
// Now calculate the pseudo-inverse of m by m_inv = V*S_inv*Ustar
TNT::Array2D<double> m_inv(m.dim2(),m.dim1());
TNT::Array2D<double> S_invUstar(S_inv.dim1(),U.dim1());
S_invUstar = matmult(S_inv,Ustar);
m_inv = matmult(V,S_invUstar);
// Round off m_inv to avoid small-value numerical errors
for (int p=0; p<m_inv.dim1(); p++){
for(int q=0; q<m_inv.dim2(); q++){
m_inv[p][q] = floor(m_inv[p][q]*1000000.0f + 0.5)/1000000.0f;
}
}
// Use the pseudo-inverse to compute the diffusion tensor D
TNT::Array2D<double> coef(m_inv.dim1(),1);
TNT::Array2D<double> D(3,3);
coef = matmult(m_inv,adc);
D[0][0] = coef[0][0]; D[0][1] = coef[3][0]; D[0][2] = coef[4][0];
D[1][0] = coef[3][0]; D[1][1] = coef[1][0]; D[1][2] = coef[5][0];
D[2][0] = coef[4][0]; D[2][1] = coef[5][0]; D[2][2] = coef[2][0];
// Get the eigenvalues and eigenvectors of the diffusion tensor D
JAMA::Eigenvalue<double> eig(D);
TNT::Array1D<double> eigenvalues;
TNT::Array2D<double> eigenvectors;
eig.getRealEigenvalues(eigenvalues);
eig.getV(eigenvectors);
// l1 to l3 are the largest to the smallest eigenvalues of the diffusion tensor
float l1 = (float) eigenvalues[2];
float l2 = (float) eigenvalues[1];
float l3 = (float) eigenvalues[0];
// Compute the mean diffusivity, fractional anisotropy and radial diffusivity
float md = (l1+l2+l3)/3.0f;
float fa = sqrt(3.0/2.0)*sqrt(pow(l1-md,2)+pow(l2-md,2)+pow(l3-md,2))/sqrt(pow(l1,2)+pow(l2,2)+pow(l3,2));
float rd = (l2+l3)/2.0f;
printf("*\n");
// Compute parameters for plotting ellipsoid if we are looking at total signal
if (index==0){
// [ex,ey,ez] is the eigenvector corresponding to the largest eigenvalue (should be pointed in the main diffusion direction)
ex = (float) eigenvectors[0][2];
ey = (float) eigenvectors[1][2];
ez = (float) eigenvectors[2][2];
printf("Main eigenvector: [%g, %g, %g]\n", ex,ey,ez);
// Theta is the angle between [ex,ey,ez] and the x-axis
theta = acos(ex/sqrt(ex*ex+ey*ey+ez*ez))*180/3.1415926535;
printf("Theta: %g\n", theta);
// We will plot the ellipsoid with axes ell1, ell2 and ell3, scales by ellipse_scalefactor
float ellipse_scalefactor = 0.7;
ell1 = ellipse_scalefactor*1;
ell2 = ellipse_scalefactor*sqrt(l2/l1);
ell3 = ellipse_scalefactor*sqrt(l3/l1);
printf("ell1, ell2, ell3: %g, %g, %g\n", ell1, ell2, ell3);
}
// Print out the results
printf("Eigenvector matrix : \n");
for (int n=0; n<eigenvectors.dim1(); n++){
for(int m=0; m<eigenvectors.dim2(); m++){
printf("%g ",eigenvectors[n][m]);
eigenvecs[index][n][m] = eigenvectors[n][m];
}
printf("\n");
}
printf("D = \n");
for (int n=0; n<3; n++){
for(int m=0; m<3; m++){
printf("%g ",D[n][m]);
tensors[index][n][m] = D[n][m];
}
printf("\n");
}
printf("l1: %g\n", l1);
printf("l2: %g\n", l2);
printf("l3: %g\n", l3);
printf("md (mean diffusivity): %g\n", md);
printf("fa (fractional anisotropy): %g\n", fa);
printf("rd (radial diffusivity): %g\n", rd);
printf("*\n");
lambdas[index][0] = (float) eigenvalues[0];
lambdas[index][1] = (float) eigenvalues[1];
lambdas[index][2] = (float) eigenvalues[2];
mds[index] = (lambdas[index][0]+lambdas[index][1]+lambdas[index][2])/3.0f;
fas[index] = sqrt(3.0/2.0)*sqrt(pow(lambdas[index][0]-mds[index],2)+pow(lambdas[index][1]-mds[index],2)+pow(lambdas[index][2]-mds[index],2))/sqrt(pow(lambdas[index][0],2)+pow(lambdas[index][1],2)+pow(lambdas[index][2],2));
rds[index] = (lambdas[index][0]+lambdas[index][1])/2.0f;
delete [] gradDir;
delete [] bVals;
delete [] logDw;
}