static inline jl_value_t *jl_iintrinsic_2(jl_value_t *a, jl_value_t *b, const char *name, char (*getsign)(void*, unsigned),
jl_value_t* (*lambda2)(jl_value_t*, void*, void*, unsigned, unsigned, void*),
void *list, int cvtb)
{
jl_value_t *ty = jl_typeof(a);
jl_value_t *tyb = jl_typeof(b);
if (tyb != ty) {
if (!cvtb)
jl_errorf("%s: types of a and b must match", name);
if (!jl_is_bitstype(tyb))
jl_errorf("%s: b is not a bitstypes", name);
}
if (!jl_is_bitstype(ty))
jl_errorf("%s: a is not a bitstypes", name);
void *pa = jl_data_ptr(a), *pb = jl_data_ptr(b);
unsigned sz = jl_datatype_size(ty);
unsigned sz2 = next_power_of_two(sz);
unsigned szb = jl_datatype_size(tyb);
if (sz2 > sz) {
/* round type up to the appropriate c-type and set/clear the unused bits */
void *pa2 = alloca(sz2);
memcpy(pa2, pa, sz);
memset((char*)pa2 + sz, getsign(pa, sz), sz2 - sz);
pa = pa2;
}
if (sz2 > szb) {
/* round type up to the appropriate c-type and set/clear/truncate the unused bits */
void *pb2 = alloca(sz2);
memcpy(pb2, pb, szb);
memset((char*)pb2 + szb, getsign(pb, sz), sz2 - szb);
pb = pb2;
}
jl_value_t *newv = lambda2(ty, pa, pb, sz, sz2, list);
return newv;
}
int main (int argc,
char** argv)
// ---------------------------------------------------------------------------
// Driver.
// ---------------------------------------------------------------------------
{
Geometry::CoordSys system;
char *session, *dump, *func, fields[StrMax];
int_t i, j, k, p, q;
int_t np, nz, nel, allocSize, NCOM, NDIM;
int_t iAdd = 0;
bool add[FLAG_MAX], need[FLAG_MAX], gradient;
ifstream file;
FEML* F;
Mesh* M;
BCmgr* B;
Domain* D;
vector<Element*> elmt;
AuxField *Ens, *Hel, *Div, *Disc, *Strain;
AuxField *Func, *Vtx, *DivL, *Nrg, *work;
vector<AuxField*> velocity, vorticity, lamb, addField(FLDS_MAX);
vector<vector<AuxField*> > Vij; // -- Usually computed, for internal use.
vector<vector<real_t*> > VijData; // -- For pointwise access in Vij.
vector<real_t*> VorData; // -- Ditto in vorticity.
vector<real_t*> LamData; // -- Ditto in Lamb vector.
real_t *DisData, *DivData, *StrData, *VtxData, *HelData, *EnsData;
real_t vel[3], vort[3], tensor[9];
Femlib::initialize (&argc, &argv);
for (i = 0; i < FLAG_MAX; i++) add [i] = need [i] = false;
// -- Read command line.
getargs (argc, argv, session, dump, func, add);
file.open (dump);
if (!file) message (prog, "can't open input field file", ERROR);
// -- Set up domain.
F = new FEML (session);
M = new Mesh (F);
nel = M -> nEl ();
np = Femlib::ivalue ("N_P");
nz = Femlib::ivalue ("N_Z");
system = (Femlib::ivalue ("CYLINDRICAL") ) ?
Geometry::Cylindrical : Geometry::Cartesian;
Geometry::set (np, nz, nel, system);
allocSize = Geometry::nTotal();
elmt.resize (nel);
for (i = 0; i < nel; i++) elmt[i] = new Element (i, np, M);
B = new BCmgr (F, elmt);
D = new Domain (F, elmt, B);
if (strstr (D -> field, "uvw")) NCOM = 3;
else if (strstr (D -> field, "uv")) NCOM = 2;
else message (prog, "lacking velocity components: is session valid?", ERROR);
NDIM = Geometry::nDim();
velocity.resize (NCOM);
vorticity.resize ((NDIM == 2) ? 1 : 3);
for (i = 0; i < NCOM; i++) velocity[i] = D -> u[i];
// -- From the requested fields, flag dependencies.
// -- First, only allow the "coherent structures" measures for flows
// that are 3D.
if (NDIM == 2)
add[HELICITY]=add[DISCRIMINANT]=add[VORTEXCORE]=add[DIVLAMB] = false;
for (p = 0, i = 0; i < FLAG_MAX; i++) p += (add[i]) ? 1 : 0;
if (p == 0) message (prog, "nothing to be done", ERROR);
// -- Check if we just have the (first two) cases not requiring derivatives.
for (p = 0, i = 0; i < FLAG_MAX; i++) p += (add[i]) ? (i + 1) : 0;
if (p <= 2) gradient = false; else gradient = true;
for (i = 0; i < FLAG_MAX; i++) need[i] = add[i];
// -- If any gradients need to be computed, we make all of them.
// Vij = du_j/dx_i. So j labels velocity component and i labels
// spatial dimension.
// -- Despite the fact that it's overkill we will take the
// simple-minded approach and always make Vij as a 3x3 tensor.
// That's a wasteful for anything which is 2D but presumably for
// those cases the memory can be afforded.
// -- The velocity gradient tensor is initially just a naive matrix
// of derivatives. In cylindrical coordinates we need to make
// modifications.
if (gradient) {
Vij .resize (3);
VijData.resize (3);
for (i = 0; i < 3; i++) {
Vij [i].resize (3);
VijData[i].resize (3);
for (j = 0; j < 3; j++) {
VijData[i][j] = new real_t [allocSize];
Vij [i][j] = new AuxField (VijData[i][j], nz, elmt);
*Vij [i][j] = 0.0;
}
}
}
// -- Fields without dependants.
if (need[ENERGY]) {
Nrg = new AuxField (new real_t[allocSize], nz, elmt, 'q');
addField[iAdd++] = Nrg;
}
if (need[FUNCTION]) {
Func = new AuxField (new real_t[allocSize], nz, elmt, 'f');
addField[iAdd++] = Func;
}
if (need[DIVERGENCE]) {
DivData = new real_t [allocSize];
*(Div = new AuxField (DivData, nz, elmt, 'd')) = 0.0;
addField[iAdd++] = Div;
}
if (need[DISCRIMINANT]) {
DisData = new real_t [allocSize];
*(Disc = new AuxField (DisData, nz, elmt, 'D')) = 0.0;
addField[iAdd++] = Disc;
}
if (need[STRAINRATE]) {
StrData = new real_t [allocSize];
Strain = new AuxField (StrData, nz, elmt, 'g');
addField[iAdd++] = Strain;
}
if (need[VORTEXCORE]) {
VtxData = new real_t [allocSize];
Vtx = new AuxField (VtxData, nz, elmt, 'J');
addField[iAdd++] = Vtx;
}
if (need[VORTICITY])
if (NDIM == 2) {
vorticity.resize (1);
VorData .resize (1);
VorData[0] = new real_t [allocSize];
vorticity[0] = new AuxField (VorData[0], nz, elmt, 't');
addField[iAdd++] = vorticity[0];
} else {
vorticity.resize (3);
VorData .resize (3);
for (i = 0; i < 3; i++) {
VorData[i] = new real_t [allocSize];
vorticity[i] = new AuxField (VorData[i], nz, elmt, 'r' + i);
addField[iAdd++] = vorticity[i];
}
}
if (add[DIVLAMB]) { // -- Know also NDIM == 3.
lamb .resize (3);
LamData.resize (3);
for (i = 0; i < 3; i++) {
LamData[i] = new real_t [allocSize];
lamb[i] = new AuxField (LamData[i], nz, elmt, 'L');
}
addField[iAdd++] = lamb[0]; // -- Where divergence will get stored.
}
if (need[ENSTROPHY]) {
EnsData = new real_t[allocSize];
Ens = new AuxField (EnsData, nz, elmt, 'e');
if (add[ENSTROPHY]) addField[iAdd++] = Ens;
}
if (need[HELICITY]) {
HelData = new real_t [allocSize];
Hel = new AuxField (HelData, nz, elmt, 'H');
if (add[HELICITY]) addField[iAdd++] = Hel;
}
// -- Cycle through field dump, first (if required) making the only
// two things which just need the velocity and no gradients, then
// if needed computing the full VG tensor and work forward from
// there. The order of computation is determined by
// dependencies. Then write requested output, listed in
// addField.
while (getDump (D, file)) {
if (need[FUNCTION]) *Func = func;
if (need[ENERGY]) ((*Nrg) . innerProduct (velocity, velocity)) *= 0.5;
if (gradient) { // -- All other things.
// -- First make all VG components.
for (i = 0; i < NDIM ; i++)
for (j = 0; j < NCOM ; j++) {
*Vij[i][j] = *velocity[j];
if (i == 2) Vij[i][j] -> transform (FORWARD);
Vij[i][j] -> gradient (i);
if (i == 2) Vij[i][j] -> transform (INVERSE);
}
if (Geometry::cylindrical()) {
work = new AuxField (new real_t[allocSize], nz, elmt);
if (NDIM == 3) for (j = 0; j < NCOM; j++) Vij[2][j] -> divY();
(*work = *velocity[1]) . divY(); *Vij[2][2] += *work;
#if 1
if (NCOM == 3) { (*work = *velocity[2]) . divY(); *Vij[1][2] += *work; }
#else
if (NCOM == 3) { (*work = *velocity[2]) . divY(); *Vij[1][2] -= *work; }
#endif
}
#if 1
// -- Loop over every point in the mesh and compute everything
// from Vij. Quite likely this could be made more efficient
// but for now simplicity is the aim.
for (i = 0; i < allocSize; i++) {
for (k = 0, p = 0; p < 3; p++) {
for (q = 0; q < 3; q++, k++)
tensor [k] = VijData [p][q][i];
}
// -- These operations produce a simple scalar result from Vij.
if (need[DIVERGENCE]) DivData[i] = tensor3::trace (tensor);
if (need[ENSTROPHY]) EnsData[i] = tensor3::enstrophy (tensor);
if (need[DISCRIMINANT]) DisData[i] = tensor3::discrimi (tensor);
if (need[STRAINRATE]) StrData[i] = tensor3::strainrate (tensor);
if (need[VORTEXCORE]) VtxData[i] = tensor3::lambda2 (tensor);
// -- Vorticity could be considered scalar in 2D.
if (need[VORTICITY]) {
tensor3::vorticity (tensor, vort);
if (NDIM == 2)
VorData[0][i] = vort[2];
else {
VorData[0][i] = vort[0];
VorData[1][i] = vort[1];
VorData[2][i] = vort[2];
}
}
if (!(need[HELICITY] || need[DIVLAMB])) continue;
// -- Last two measures need velocity too, only made for NDIM = 3.
vel[0] = velocity[0] -> data()[i];
vel[1] = velocity[1] -> data()[i];
vel[2] = velocity[2] -> data()[i];
if (need[HELICITY]) HelData[i] = tensor3::helicity (tensor, vel);
if (need[DIVLAMB]) {
tensor3::lambvector (tensor, vel, vort); // -- vort is a dummy.
LamData[0][i] = vort[0];
LamData[1][i] = vort[1];
LamData[2][i] = vort[2];
}
}
// -- For this case, we still need to compute a divergence:
if (need[DIVLAMB]) {
lamb[0] -> gradient (0);
(*lamb[2]) . transform (FORWARD) . gradient (2) . transform(INVERSE);
if (Geometry::cylindrical()) lamb[2] -> divY();
*lamb[0] += *lamb[2];
if (Geometry::cylindrical()) *lamb[0] += (*lamb[2] = *lamb[1]) . divY();
*lamb[0] += (*lamb[1]) . gradient (1);
}
}
#else
if (need[DISCRIMINANT]) {
// -- 2nd invariant (Q from Chong et al.).
InvQ -> times (*Vij[0][0], *Vij[1][1]);
InvQ -> timesMinus (*Vij[0][1], *Vij[1][0]);
InvQ -> timesPlus (*Vij[0][0], *Vij[2][2]);
InvQ -> timesMinus (*Vij[0][2], *Vij[2][0]);
InvQ -> timesPlus (*Vij[1][1], *Vij[2][2]);
InvQ -> timesMinus (*Vij[1][2], *Vij[2][1]);
// -- 3rd invariant: determinant of Vij (R from Chong et al.).
work -> times (*Vij[1][1], *Vij[2][2]);
work -> timesMinus (*Vij[2][1], *Vij[1][2]);
InvR -> times (*work, *Vij[0][0]);
work -> times (*Vij[1][2], *Vij[2][0]);
work -> timesMinus (*Vij[2][2], *Vij[1][0]);
InvR -> timesPlus (*work, *Vij[0][1]);
work -> times (*Vij[2][1], *Vij[1][0]);
work -> timesMinus (*Vij[1][1], *Vij[2][0]);
InvR -> timesPlus (*work, *Vij[0][2]);
// -- Discriminant L of Vij.
// NB: DIVERGENCE (P from Chong et al.) ASSUMED = 0.
work -> times (*InvQ, *InvQ);
Disc -> times (*work, *InvQ);
work -> times (*InvR, *InvR);
*work *= 6.75;
*Disc += *work;
}
if (need[DIVERGENCE])
for (i = 0; i < nComponent; i++) *Div += *Vij[i][i];
if (need[VORTICITY]) {
if (nComponent == 2) {
*vorticity[0] = *Vij[1][0];
*vorticity[0] -= *Vij[0][1];
} else {
*vorticity[0] = *Vij[2][1];
*vorticity[0] -= *Vij[1][2];
*vorticity[1] = *Vij[0][2];
*vorticity[1] -= *Vij[2][0];
*vorticity[2] = *Vij[1][0];
*vorticity[2] -= *Vij[0][1];
}
}
if (need[DIVLAMB]) {
if (nComponent == 2) {
*lamb[0] = 0.0;
lamb[0] -> timesMinus (*D -> u[1], *vorticity[0]);
lamb[1] -> times (*D -> u[0], *vorticity[0]);
*DivL = (*work = *lamb[0]) . gradient (0);
*DivL += (*work = *lamb[1]) . gradient (1);
if (Geometry::cylindrical())
*DivL += (*work = *lamb[1]) . divY();
} else {
lamb[0] -> times (*D -> u[2], *vorticity[1]);
lamb[0] -> timesMinus (*D -> u[1], *vorticity[2]);
lamb[1] -> times (*D -> u[0], *vorticity[2]);
lamb[1] -> timesMinus (*D -> u[2], *vorticity[0]);
lamb[2] -> times (*D -> u[1], *vorticity[0]);
lamb[2] -> timesMinus (*D -> u[0], *vorticity[1]);
*DivL = (*work = *lamb[0]) . gradient (0);
*DivL += (*work = *lamb[1]) . gradient (1);
(*work = *lamb[2]).transform(FORWARD).gradient(2).transform(INVERSE);
if (Geometry::cylindrical()) {
*DivL += work -> divY();
*DivL += (*work = *lamb[1]) . divY();
} else
*DivL += *work;
}
}
if (need[ENSTROPHY])
Ens -> innerProduct (vorticity, vorticity) *= 0.5;
if (need[HELICITY])
Hel -> innerProduct (vorticity, velocity) *= 0.5;
if (need[STRAINTENSOR]) {
for (i = 0; i < nComponent; i++)
for (j = i; j < nComponent; j++) {
*Sij[i][j] = *Vij[i][j];
*Sij[i][j] += *Vij[j][i];
*Sij[i][j] *= 0.5;
}
}
if (need[STRAINRATE]) {
*Strain = 0.0;
for (i = 0; i < nComponent; i++)
for (j = 0; j < nComponent; j++)
Strain -> timesPlus (*Sij[i][j], *Sij[j][i]);
(*Strain *= 2.0) . sqroot();
}
if (need[VORTEXCORE]) // -- Only done for 3-component fields.
for (i = 0; i < allocSize; i++) {
for (k = 0, p = 0; p < 3; p++)
for (q = 0; q < 3; q++, k++)
tensor [k] = VijData[p][q][i];
VtxData[i] = lambda2 (tensor);
}
}
#endif
// -- Finally, add mass-projection smoothing on everything.
for (i = 0; i < iAdd; i++) D -> u[0] -> smooth (addField[i]);
putDump (D, addField, iAdd, cout);
}
SSVUT_EXPECT(SSVPP_TPL_ELEM(SSVPP_TPL_PUSH_BACK((1, 2), 3), 0) == 1);
SSVUT_EXPECT(SSVPP_TPL_ELEM(SSVPP_TPL_PUSH_BACK((1, 2), 3), 2) == 3);
}
{
SSVUT_EXPECT(SSVPP_TPL_SIZE(SSVPP_TPL_FILL(())) == SSVPP_TPL_MAX_SIZE);
SSVUT_EXPECT(SSVPP_TPL_SIZE(SSVPP_TPL_FILL((1))) == SSVPP_TPL_MAX_SIZE);
SSVUT_EXPECT(SSVPP_TPL_SIZE(SSVPP_TPL_FILL((1, 1))) == SSVPP_TPL_MAX_SIZE);
SSVUT_EXPECT(SSVPP_TPL_SIZE(SSVPP_TPL_FILL((1, 1, 1))) == SSVPP_TPL_MAX_SIZE);
}
{
#define SSVU_TEST_GEN_LMBD(mReturn, mName, mBody) auto mName = []() -> mReturn { mBody };
SSVU_TEST_GEN_LMBD(__R(std::pair<int, int>), __R(lambda1), __R(return std::make_pair(1, 5);));
SSVU_TEST_GEN_LMBD(__R(std::pair<int, std::pair<float, float>>), __R(lambda2), __R(return std::make_pair(2, std::pair<float, float>(1.5f, 2.5f));));
SSVUT_EXPECT(lambda1().first == 1);
SSVUT_EXPECT(lambda1().second == 5);
SSVUT_EXPECT(lambda2().first == 2);
SSVUT_EXPECT(lambda2().second.first == 1.5f);
SSVUT_EXPECT(lambda2().second.second == 2.5f);
#undef SSVU_TEST_GEN_LMBD
}
}
#endif
RcppExport SEXP nsem3b(SEXP data,
SEXP theta,
SEXP Sigma,
SEXP modelpar,
SEXP control
) {
// srand ( time(NULL) ); /* initialize random seed: */
Rcpp::NumericVector Theta(theta);
Rcpp::NumericMatrix D(data);
unsigned nobs = D.nrow(), k = D.ncol();
mat Data(D.begin(), nobs, k, false); // Avoid copying
Rcpp::NumericMatrix V(Sigma);
mat S(V.begin(), V.nrow(), V.ncol());
S(0,0) = 1;
mat iS = inv(S);
double detS = det(S);
Rcpp::List Modelpar(modelpar);
// Rcpp::IntegerVector _nlatent = Modelpar["nlatent"]; unsigned nlatent = _nlatent[0];
Rcpp::IntegerVector _ny0 = Modelpar["nvar0"]; unsigned ny0 = _ny0[0];
Rcpp::IntegerVector _ny1 = Modelpar["nvar1"]; unsigned ny1 = _ny1[0];
Rcpp::IntegerVector _ny2 = Modelpar["nvar2"]; unsigned ny2 = _ny2[0];
Rcpp::IntegerVector _npred0 = Modelpar["npred0"]; unsigned npred0 = _npred0[0];
Rcpp::IntegerVector _npred1 = Modelpar["npred1"]; unsigned npred1 = _npred1[0];
Rcpp::IntegerVector _npred2 = Modelpar["npred2"]; unsigned npred2 = _npred2[0];
Rcpp::List Control(control);
Rcpp::NumericVector _lambda = Control["lambda"]; double lambda = _lambda[0];
Rcpp::NumericVector _niter = Control["niter"]; double niter = _niter[0];
Rcpp::NumericVector _Dtol = Control["Dtol"]; double Dtol = _Dtol[0];
rowvec mu0(ny0), lambda0(ny0);
rowvec mu1(ny1), lambda1(ny1);
rowvec mu2(ny2), lambda2(ny2);
rowvec beta0(npred0);
rowvec beta1(npred1);
rowvec beta2(npred2);
rowvec gamma(2);
rowvec gamma2(2);
unsigned pos=0;
for (unsigned i=0; i<ny0; i++) {
mu0(i) = Theta[pos];
pos++;
}
for (unsigned i=0; i<ny1; i++) {
mu1(i) = Theta[pos];
pos++;
}
for (unsigned i=0; i<ny2; i++) {
mu2(i) = Theta[pos];
pos++;
}
for (unsigned i=0; i<ny0; i++) {
lambda0(i) = Theta[pos];
pos++;
}
lambda1(0) = 1;
for (unsigned i=1; i<ny1; i++) {
lambda1(i) = Theta[pos];
pos++;
}
lambda2(0) = 1;
for (unsigned i=1; i<ny2; i++) {
lambda2(i) = Theta[pos];
pos++;
}
for (unsigned i=0; i<npred0; i++) {
beta0(i) = Theta[pos];
pos++;
}
for (unsigned i=0; i<npred1; i++) {
beta1(i) = Theta[pos];
pos++;
}
for (unsigned i=0; i<npred2; i++) {
beta2(i) = Theta[pos];
pos++;
}
gamma(0) = Theta[pos]; gamma(1) = Theta[pos+1];
gamma2(0) = Theta[pos+2]; gamma2(1) = Theta[pos+3];
// cerr << "mu0=" << mu0 << endl;
// cerr << "mu1=" << mu1 << endl;
// cerr << "mu2=" << mu2 << endl;
// cerr << "lambda0=" << lambda0 << endl;
// cerr << "lambda1=" << lambda1 << endl;
// cerr << "lambda2=" << lambda2 << endl;
// cerr << "beta0=" << beta0 << endl;
// cerr << "beta1=" << beta1 << endl;
// cerr << "beta2=" << beta2 << endl;
// cerr << "gamma=" << gamma << endl;
// cerr << "gamma2=" << gamma2 << endl;
mat lap(nobs,4);
for (unsigned i=0; i<nobs; i++) {
rowvec newlap = laNRb(Data.row(i), iS, detS,
mu0, mu1, mu2,
lambda0, lambda1, lambda2,
beta0,beta1, beta2, gamma, gamma2,
Dtol,niter,lambda);
lap.row(i) = newlap;
}
List res;
res["indiv"] = lap;
res["logLik"] = sum(lap.col(0)) + (3-V.nrow())*log(2.0*datum::pi)*nobs/2;
res["norm0"] = (3-V.nrow())*log(2*datum::pi)/2;
return res;
}
static double refmap_tetra_f1(double x, double y, double z) { return lambda2(x, y, z); }
int main (int argc,
char** argv)
// ---------------------------------------------------------------------------
// Driver.
// ---------------------------------------------------------------------------
{
Geometry::CoordSys system;
char *session, *dump, *func, fields[StrMax];
int_t i, j, k, p, q;
int_t np, nz, nel, allocSize, nComponent;
int_t iAdd = 0;
bool add[FLAG_MAX], need[FLAG_MAX], gradient;
ifstream file;
FEML* F;
Mesh* M;
BCmgr* B;
Domain* D;
vector<Element*> elmt;
AuxField *Ens, *Hel, *Div, *InvQ, *InvR, *Disc, *Strain;
AuxField *Func, *Ell, *Egr, *Vtx, *work, *DivL, *Nrg;
vector<AuxField*> lamb, velocity, vorticity, addField(FLDS_MAX);
vector<vector<AuxField*> > Sij;
vector<vector<AuxField*> > Vij; // -- Usually computed, for internal use.
vector<vector<real_t*> > VijData; // -- For pointwise access.
real_t *egrow, *VtxData; // -- Ditto.
real_t tensor[9];
Femlib::initialize (&argc, &argv);
for (i = 0; i < FLAG_MAX; i++) add [i] = need [i] = false;
// -- Read command line.
getargs (argc, argv, session, dump, func, add);
file.open (dump);
if (!file) message (prog, "can't open input field file", ERROR);
// -- Set up domain.
F = new FEML (session);
M = new Mesh (F);
nel = M -> nEl ();
np = Femlib::ivalue ("N_P");
nz = Femlib::ivalue ("N_Z");
system = (Femlib::ivalue ("CYLINDRICAL") ) ?
Geometry::Cylindrical : Geometry::Cartesian;
Geometry::set (np, nz, nel, system);
if (nz > 1) strcpy (fields, "uvwp");
else strcpy (fields, "uvp");
nComponent = Geometry::nDim();
allocSize = Geometry::nTotal();
elmt.resize (nel);
for (i = 0; i < nel; i++) elmt[i] = new Element (i, np, M);
B = new BCmgr (F, elmt);
D = new Domain (F, elmt, B);
velocity.resize (nComponent);
vorticity.resize ((nComponent == 2) ? 1 : 3);
for (i = 0; i < nComponent; i++) velocity[i] = D -> u[i];
// -- From the requested fields, flag dependencies.
if (nComponent < 3)
add[HELICITY] = add[DISCRIMINANT] = add[VORTEXCORE] = false;
for (p = 0, i = 0; i < FLAG_MAX; i++) p += (add[i]) ? 1 : 0;
if (p == 0) message (prog, "nothing to be done", ERROR);
for (p = 0, i = 0; i < FLAG_MAX; i++)
p += (add[i]) ? (i + 1) : 0;
if (p <= 3) gradient = false; else gradient = true;
for (i = 0; i < FLAG_MAX; i++) need[i] = add[i];
if (add[ENSTROPHY]) {
need[VORTICITY] = true;
need[ENSTROPHY] = true;
}
if (add[HELICITY]) {
need[VORTICITY] = true;
}
if (add[ELLIPTICITY]) {
need[VORTICITY] = true;
need[ENSTROPHY] = true;
need[STRAINRATE] = true;
need[STRAINTENSOR] = true;
}
if (add[STRAINRATE]) {
need[STRAINTENSOR] = true;
}
if (add[EGROWTH]) {
need[VORTICITY] = true;
need[ENSTROPHY] = true;
need[STRAINRATE] = true;
need[STRAINTENSOR] = true;
need[ELLIPTICITY] = true;
}
if (add[LAMBVECTOR]) {
need[VORTICITY] = true;
need[LAMBVECTOR] = true;
}
// -- If any gradients need to be computed, we make all of them.
if (gradient) {
Vij .resize (nComponent);
VijData.resize (nComponent);
for (i = 0; i < nComponent; i++) {
Vij [i].resize (nComponent);
VijData[i].resize (nComponent);
for (j = 0; j < nComponent; j++) {
VijData[i][j] = new real_t [allocSize];
Vij [i][j] = new AuxField (VijData[i][j], nz, elmt);
*Vij [i][j] = 0.0;
}
}
}
// -- Fields without dependants.
work = new AuxField (new real_t[allocSize], nz, elmt);
if (need[ENERGY]) {
Nrg = new AuxField (new real_t[allocSize], nz, elmt, 'q');
addField[iAdd++] = Nrg;
}
if (need[FUNCTION]) {
Func = new AuxField (new real_t[allocSize], nz, elmt, 'f');
addField[iAdd++] = Func;
}
if (need[DIVERGENCE]) {
Div = new AuxField (new real_t[allocSize], nz, elmt, 'd');
*Div = 0.0;
addField[iAdd++] = Div;
}
if (need[DISCRIMINANT]) {
*(InvQ = new AuxField (new real_t[allocSize], nz, elmt, 'Q')) = 0.0;
*(InvR = new AuxField (new real_t[allocSize], nz, elmt, 'R')) = 0.0;
*(Disc = new AuxField (new real_t[allocSize], nz, elmt, 'L')) = 0.0;
addField[iAdd++] = Disc;
}
if (need[VORTEXCORE]) {
VtxData = new real_t [allocSize];
Vtx = new AuxField (VtxData, nz, elmt, 'J');
addField[iAdd++] = Vtx;
}
// -- Vorticity and its dependants.
if (need[VORTICITY])
if (nComponent == 2) {
vorticity[0] = new AuxField (new real_t[allocSize], nz, elmt, 't');
if (add[VORTICITY])
addField[iAdd++] = vorticity[0];
} else {
for (i = 0; i < nComponent; i++)
vorticity[i] = new AuxField (new real_t[allocSize], nz, elmt, 'r' + i);
if (add[VORTICITY])
for (i = 0; i < 3; i++) addField[iAdd++] = vorticity[i];
}
if (add[LAMBVECTOR]) {
if (nComponent == 2) {
lamb.resize(2);
for (i = 0; i < nComponent; i++)
lamb[i] = new AuxField (new real_t[allocSize], nz, elmt, 'm' + i);
for (i = 0; i < 2; i++) addField[iAdd++] = lamb[i];
} else {
lamb.resize(3);
for (i = 0; i < nComponent; i++)
lamb[i] = new AuxField (new real_t[allocSize], nz, elmt, 'm' + i);
for (i = 0; i < 3; i++) addField[iAdd++] = lamb[i];
}
DivL = new AuxField (new real_t[allocSize], nz, elmt, 'Q');
addField[iAdd++] = DivL;
}
if (need[ENSTROPHY]) {
Ens = new AuxField (new real_t[allocSize], nz, elmt, 'e');
if (add[ENSTROPHY]) addField[iAdd++] = Ens;
}
if (need[HELICITY]) {
Hel = new AuxField (new real_t[allocSize], nz, elmt, 'h');
if (add[HELICITY]) addField[iAdd++] = Hel;
}
if (need[ELLIPTICITY]) {
Ell = new AuxField (new real_t[allocSize], nz, elmt, 'b');
if (add[ELLIPTICITY]) addField[iAdd++] = Ell;
}
// -- Rate of strain tensor and its dependants.
if (need[STRAINTENSOR]) {
Sij.resize (nComponent);
for (k = 0, i = 0; i < nComponent; i++) {
Sij[i].resize (nComponent);
for (j = 0; j < nComponent; j++) {
if (j >= i) {
Sij[i][j] = new AuxField (new real_t[allocSize], nz, elmt, 'i'+k++);
} else
Sij[i][j] = Sij[j][i];
}
}
}
if (need[STRAINRATE]) {
*(Strain = new AuxField (new real_t[allocSize], nz, elmt, 'g')) = 0.0;
if (add[STRAINRATE]) addField[iAdd++] = Strain;
}
if (need[EGROWTH]) {
egrow = new real_t[allocSize]; // -- A handle for direct access to data.
Egr = new AuxField (egrow, nz, elmt, 'a');
if (add[EGROWTH]) addField[iAdd++] = Egr;
}
// -- Cycle through field dump, first computing the velocity
// gradient tensor and then the needed quantities -- vorticity
// etc. The order of computation is determined by dependencies.
// Then write requested output, listed in addField.
while (getDump (D, file)) {
if (need[FUNCTION]) *Func = func;
// -- Velocity gradient tensor; transform required for z (2) gradient.
if (nComponent > 2) D -> transform (FORWARD);
if (gradient)
for (i = 0; i < nComponent ; i++)
for (j = 0; j < nComponent ; j++) {
(*Vij[i][j] = *velocity[i]) . gradient (j);
Vij[i][j] -> transform (INVERSE);
}
if (need[ENERGY]) {
*Nrg = 0.0;
for (i = 0; i < nComponent ; i++)
Nrg -> timesPlus (*D -> u[i], *D -> u[i]);
*Nrg *= 0.5;
}
if (nComponent > 2) D -> transform (INVERSE);
if (Geometry::cylindrical() && nComponent == 3) {
for (i = 0; i < nComponent; i++) Vij[i][2] -> divY();
(*work = *D -> u[2]) . divY(); *Vij[1][2] -= *work;
(*work = *D -> u[1]) . divY(); *Vij[2][2] += *work;
}
if (need[DISCRIMINANT]) {
// -- 2nd invariant (Q from Chong et al.).
InvQ -> times (*Vij[0][0], *Vij[1][1]);
InvQ -> timesMinus (*Vij[0][1], *Vij[1][0]);
InvQ -> timesPlus (*Vij[0][0], *Vij[2][2]);
InvQ -> timesMinus (*Vij[0][2], *Vij[2][0]);
InvQ -> timesPlus (*Vij[1][1], *Vij[2][2]);
InvQ -> timesMinus (*Vij[1][2], *Vij[2][1]);
// -- 3rd invariant: determinant of Vij (R from Chong et al.).
work -> times (*Vij[1][1], *Vij[2][2]);
work -> timesMinus (*Vij[2][1], *Vij[1][2]);
InvR -> times (*work, *Vij[0][0]);
work -> times (*Vij[1][2], *Vij[2][0]);
work -> timesMinus (*Vij[2][2], *Vij[1][0]);
InvR -> timesPlus (*work, *Vij[0][1]);
work -> times (*Vij[2][1], *Vij[1][0]);
work -> timesMinus (*Vij[1][1], *Vij[2][0]);
InvR -> timesPlus (*work, *Vij[0][2]);
// -- Discriminant L of Vij.
// NB: DIVERGENCE (P from Chong et al.) ASSUMED = 0.
work -> times (*InvQ, *InvQ);
Disc -> times (*work, *InvQ);
work -> times (*InvR, *InvR);
*work *= 6.75;
*Disc += *work;
}
if (need[DIVERGENCE])
for (i = 0; i < nComponent; i++) *Div += *Vij[i][i];
if (need[VORTICITY]) {
if (nComponent == 2) {
*vorticity[0] = *Vij[1][0];
*vorticity[0] -= *Vij[0][1];
} else {
*vorticity[0] = *Vij[2][1];
*vorticity[0] -= *Vij[1][2];
*vorticity[1] = *Vij[0][2];
*vorticity[1] -= *Vij[2][0];
*vorticity[2] = *Vij[1][0];
*vorticity[2] -= *Vij[0][1];
}
}
if (need[LAMBVECTOR]) {
if (nComponent == 2) {
*lamb[0] = 0.0;
lamb[0] -> timesMinus (*D -> u[1], *vorticity[0]);
lamb[1] -> times (*D -> u[0], *vorticity[0]);
*DivL = (*work = *lamb[0]) . gradient (0);
*DivL += (*work = *lamb[1]) . gradient (1);
if (Geometry::cylindrical())
*DivL += (*work = *lamb[1]) . divY();
} else {
lamb[0] -> times (*D -> u[2], *vorticity[1]);
lamb[0] -> timesMinus (*D -> u[1], *vorticity[2]);
lamb[1] -> times (*D -> u[0], *vorticity[2]);
lamb[1] -> timesMinus (*D -> u[2], *vorticity[0]);
lamb[2] -> times (*D -> u[1], *vorticity[0]);
lamb[2] -> timesMinus (*D -> u[0], *vorticity[1]);
*DivL = (*work = *lamb[0]) . gradient (0);
*DivL += (*work = *lamb[1]) . gradient (1);
(*work = *lamb[2]).transform(FORWARD).gradient(2).transform(INVERSE);
if (Geometry::cylindrical()) {
*DivL += work -> divY();
*DivL += (*work = *lamb[1]) . divY();
} else
*DivL += *work;
}
}
if (need[ENSTROPHY])
Ens -> innerProduct (vorticity, vorticity) *= 0.5;
if (need[HELICITY])
Hel -> innerProduct (vorticity, velocity) *= 0.5;
if (need[STRAINTENSOR]) {
for (i = 0; i < nComponent; i++)
for (j = i; j < nComponent; j++) {
*Sij[i][j] = *Vij[i][j];
*Sij[i][j] += *Vij[j][i];
*Sij[i][j] *= 0.5;
}
}
if (need[STRAINRATE]) {
*Strain = 0.0;
for (i = 0; i < nComponent; i++)
for (j = 0; j < nComponent; j++)
Strain -> timesPlus (*Sij[i][j], *Sij[j][i]);
(*Strain *= 2.0) . sqroot();
}
if (need[ELLIPTICITY]) {
((*work = *Ens) . sqroot() *= 2.0) += 1.0e-1;
Ell -> divide (*Strain, *work);
}
if (need[EGROWTH]) {
*Egr = *Ell;
Veclib::clip (allocSize, 0.0, 1.0, egrow, 1, egrow, 1);
Veclib::spow (allocSize, 2.811, egrow, 1, egrow, 1);
Veclib::vneg (allocSize, egrow, 1, egrow, 1);
Veclib::sadd (allocSize, 1.0, egrow, 1, egrow, 1);
Veclib::spow (allocSize, 0.3914, egrow, 1, egrow, 1);
Veclib::smul (allocSize, 9.0/16.0, egrow, 1, egrow, 1);
(*work = *Strain) *= sqrt (1.0/8.0);
Egr -> times (*Egr, *work);
}
if (need[VORTEXCORE]) // -- Only done for 3-component fields.
for (i = 0; i < allocSize; i++)
for (k = 0, p = 0; p < 3; p++)
for (q = 0; q < 3; q++, k++) {
tensor [k] = VijData[p][q][i];
VtxData[i] = lambda2 (tensor);
}
// -- Finally, add mass-projection smoothing on everything.
for (i = 0; i < iAdd; i++) D -> u[0] -> smooth (addField[i]);
putDump (D, addField, iAdd, cout);
}
file.close();
Femlib::finalize();
return EXIT_SUCCESS;
}
