double Fields::computeADMMass() {
Basis* thetaBasis = basis.getBasis(SphericalBasis::COORD2);
const double* xi = thetaBasis->getAbscissas();
int nR = basis.getRank(SphericalBasis::COORD1);
const double* r = basis.getCoord(SphericalBasis::COORD1);
int nTheta = basis.getRank(SphericalBasis::COORD2);
const double* theta = basis.getCoord(SphericalBasis::COORD2);
double integrand[nTheta];
for (int iTheta = 0; iTheta < nTheta; iTheta++) {
// This formula holds because of the boundary condition.
double myPsi = psi(r[nR-1], theta[iTheta]);
integrand[iTheta] = (myPsi - 1.)*
r[nR-1]*sin(theta[iTheta]);
// Change to the spectral coordinate to integrate...
integrand[iTheta] *= 0.5*M_PI*sqrt(1.0 - xi[iTheta]*xi[iTheta]);
}
return thetaBasis->integrate(integrand);
}
int DefaultEvaluatorForIntegralOperators<BasisFunctionType, KernelType,
ResultType, GeometryFactory>::farFieldQuadOrder(
const Basis<BasisFunctionType>& basis) const
{
int elementOrder = (basis.order());
// Order required for exact quadrature on affine elements with kernel
// approximated by a polynomial of order identical with that of the basis
int defaultQuadratureOrder = 2 * elementOrder;
return m_quadratureOptions.quadratureOrder(defaultQuadratureOrder);
}
//constraint between two different rigidbodies
btVehicleJacobianEntry(
const Basis &world2A,
const Basis &world2B,
const Vector3 &rel_pos1,
const Vector3 &rel_pos2,
const Vector3 &jointAxis,
const Vector3 &inertiaInvA,
const real_t massInvA,
const Vector3 &inertiaInvB,
const real_t massInvB) :
m_linearJointAxis(jointAxis) {
m_aJ = world2A.xform(rel_pos1.cross(m_linearJointAxis));
m_bJ = world2B.xform(rel_pos2.cross(-m_linearJointAxis));
m_0MinvJt = inertiaInvA * m_aJ;
m_1MinvJt = inertiaInvB * m_bJ;
m_Adiag = massInvA + m_0MinvJt.dot(m_aJ) + massInvB + m_1MinvJt.dot(m_bJ);
//btAssert(m_Adiag > real_t(0.0));
}
NeutronDrop::NeutronDrop(Basis &_basis, Interaction &_inter, int _nbNeut, double _omega, int _nPoints) :
System(std::string("NeutronDrop"), _basis, arma::ivec(
{
_nbNeut
}), std::vector<std::string>({"neutron"}), _inter, _nPoints), omega(_omega),TBME(_basis.size, _basis.size)
{
if(basis->type == "SpBasis" || basis->type == "ReducedSpBasis")
{
for (int i = 0; i < basis->size; i++)
for (int j = 0; j < basis->size; j++)
{
TBME(i, j) = arma::zeros(_basis.size, basis->size);
for (int k = 0; k < basis->size; k++)
for (int l = 0; l < basis->size; l++)
{
arma::field<arma::mat> dummyR;
TBME(i, j)(k, l) = inter->get(dummyR, 0, i, 0, l, 0, j, 0, k);
}
}
}
else if (basis->type == "FullSpBasis")
{
for (int i = 0; i < basis->size; i++)
for (int j = 0; j < basis->size; j++)
{
if (_basis.qNumbers(i, 1) != _basis.qNumbers(j, 1)) continue;
if (_basis.qNumbers(i, 2) != _basis.qNumbers(j, 2)) continue;
TBME(i, j) = arma::zeros(_basis.size, basis->size);
for (int k = 0; k < basis->size; k++)
for (int l = 0; l < basis->size; l++)
{
if (_basis.qNumbers(k, 1) != _basis.qNumbers(l, 1)) continue;
if (_basis.qNumbers(k, 2) != _basis.qNumbers(l, 2)) continue;
arma::field<arma::mat> dummyR;
TBME(i, j)(k, l) = inter->get(dummyR, 0, i, 0, l, 0, j, 0, k);
}
}
}
}
void GridMapEditor::_update_duplicate_indicator() {
if (!selection.active || input_action!=INPUT_DUPLICATE) {
Transform xf;
xf.basis.set_zero();
VisualServer::get_singleton()->instance_set_transform(duplicate_instance,xf);
return;
}
Transform xf;
xf.scale(Vector3(1,1,1)*(Vector3(1,1,1)+(selection.end-selection.begin))*node->get_cell_size());
xf.origin=(selection.begin+(selection.current-selection.click))*node->get_cell_size();
Basis rot;
rot.set_orthogonal_index(selection.duplicate_rot);
xf.basis = rot * xf.basis;
VisualServer::get_singleton()->instance_set_transform(duplicate_instance,node->get_global_transform() * xf);
}
static void UE3_QuantizeBasis(Basis & basis)
{
float handness = basis.handness();
UE3_QuantizeVector(basis.normal);
UE3_QuantizeVector(basis.tangent);
// Reconstruct bitangent as done in the vertex shader:
basis.bitangent = cross(basis.normal, basis.tangent) * handness;
// @@ Does the vertex shader normalize normal, tangent, and bitangent?
}
FnMap minimizeLength(const FnWord &u, const Basis &basis)
{
/* Returns an automorphism phi such that phi(u) has minimal
length. */
int r = basis.getRank();
FnMap phi(r);
if (u == Id) return phi;
if (u.length() == 1) return phi;
int old_norm,new_norm;
FnWord u_min(u),tmp;
FnMap whAuto(r);
QList<WhiteheadData> whAutos = whiteheadAutos(basis);
QListIterator<WhiteheadData> move(whAutos);
bool reduced_norm = true;
while (reduced_norm) {
old_norm = u_min.length();
new_norm = old_norm;
move.toFront();
while (old_norm <= new_norm && move.hasNext()) {
whAuto = whitehead(move.next(),basis);
tmp = whAuto(u_min);
new_norm = tmp.length();
}
if (new_norm < old_norm) {
u_min = tmp;
phi = whAuto*phi;
} else
reduced_norm = false;
} // end while (reduced_norm)
// now u_min = phi(u)
return phi;
}
// This is doing a simple ear-clipping algorithm that skips invalid triangles. Ideally, we should
// also sort the ears by angle, start with the ones that have the smallest angle and proceed in order.
HalfEdge::Mesh * nv::triangulate(const HalfEdge::Mesh * inputMesh)
{
HalfEdge::Mesh * mesh = new HalfEdge::Mesh;
// Add all vertices.
const uint vertexCount = inputMesh->vertexCount();
for (uint v = 0; v < vertexCount; v++) {
const HalfEdge::Vertex * vertex = inputMesh->vertexAt(v);
mesh->addVertex(vertex->pos);
}
Array<int> polygonVertices;
Array<float> polygonAngles;
Array<Vector2> polygonPoints;
const uint faceCount = inputMesh->faceCount();
for (uint f = 0; f < faceCount; f++)
{
const HalfEdge::Face * face = inputMesh->faceAt(f);
nvDebugCheck(face != NULL);
const uint edgeCount = face->edgeCount();
nvDebugCheck(edgeCount >= 3);
polygonVertices.clear();
polygonVertices.reserve(edgeCount);
if (edgeCount == 3) {
// Simple case for triangles.
for (HalfEdge::Face::ConstEdgeIterator it(face->edges()); !it.isDone(); it.advance())
{
const HalfEdge::Edge * edge = it.current();
const HalfEdge::Vertex * vertex = edge->vertex;
polygonVertices.append(vertex->id);
}
int v0 = polygonVertices[0];
int v1 = polygonVertices[1];
int v2 = polygonVertices[2];
mesh->addFace(v0, v1, v2);
}
else {
// Build 2D polygon projecting vertices onto normal plane.
// Faces are not necesarily planar, this is for example the case, when the face comes from filling a hole. In such cases
// it's much better to use the best fit plane.
const Vector3 fn = face->normal();
Basis basis;
basis.buildFrameForDirection(fn);
polygonPoints.clear();
polygonPoints.reserve(edgeCount);
polygonAngles.clear();
polygonAngles.reserve(edgeCount);
for (HalfEdge::Face::ConstEdgeIterator it(face->edges()); !it.isDone(); it.advance())
{
const HalfEdge::Edge * edge = it.current();
const HalfEdge::Vertex * vertex = edge->vertex;
polygonVertices.append(vertex->id);
Vector2 p;
p.x = dot(basis.tangent, vertex->pos);
p.y = dot(basis.bitangent, vertex->pos);
polygonPoints.append(p);
}
polygonAngles.resize(edgeCount);
while (polygonVertices.size() > 2) {
uint size = polygonVertices.size();
// Update polygon angles. @@ Update only those that have changed.
float minAngle = 2 * PI;
uint bestEar = 0; // Use first one if none of them is valid.
bool bestIsValid = false;
for (uint i = 0; i < size; i++) {
uint i0 = i;
uint i1 = (i+1) % size; // Use Sean's polygon interation trick.
uint i2 = (i+2) % size;
Vector2 p0 = polygonPoints[i0];
Vector2 p1 = polygonPoints[i1];
Vector2 p2 = polygonPoints[i2];
float d = clamp(dot(p0-p1, p2-p1) / (length(p0-p1) * length(p2-p1)), -1.0f, 1.0f);
float angle = acosf(d);
float area = triangleArea(p0, p1, p2);
if (area < 0.0f) angle = 2.0f * PI - angle;
polygonAngles[i1] = angle;
if (angle < minAngle || !bestIsValid) {
// Make sure this is a valid ear, if not, skip this point.
bool valid = true;
for (uint j = 0; j < size; j++) {
if (j == i0 || j == i1 || j == i2) continue;
Vector2 p = polygonPoints[j];
if (pointInTriangle(p, p0, p1, p2)) {
valid = false;
break;
}
}
if (valid || !bestIsValid) {
minAngle = angle;
bestEar = i1;
bestIsValid = valid;
}
}
}
nvDebugCheck(minAngle <= 2 * PI);
// Clip best ear:
uint i0 = (bestEar+size-1) % size;
uint i1 = (bestEar+0) % size;
uint i2 = (bestEar+1) % size;
int v0 = polygonVertices[i0];
int v1 = polygonVertices[i1];
int v2 = polygonVertices[i2];
mesh->addFace(v0, v1, v2);
polygonVertices.removeAt(i1);
polygonPoints.removeAt(i1);
polygonAngles.removeAt(i1);
}
}
#if 0
uint i = 0;
while (polygonVertices.size() > 2 && i < polygonVertices.size()) {
uint size = polygonVertices.size();
uint i0 = (i+0) % size;
uint i1 = (i+1) % size;
uint i2 = (i+2) % size;
const HalfEdge::Vertex * v0 = polygonVertices[i0];
const HalfEdge::Vertex * v1 = polygonVertices[i1];
const HalfEdge::Vertex * v2 = polygonVertices[i2];
const Vector3 p0 = v0->pos;
const Vector3 p1 = v1->pos;
const Vector3 p2 = v2->pos;
const Vector3 e0 = p2 - p1;
const Vector3 e1 = p0 - p1;
// If this ear forms a valid triangle, setup relations, remove v1 and repeat.
Vector3 n = cross(e0, e1);
float len = dot(fn, n); // = sin(angle)
float angle = asin(len);
if (len > 0.0f) {
mesh->addFace(v0->id(), v1->id(), v2->id());
polygonVertices.removeAt(i1);
polygonAngles.removeAt(i1);
if (i2 > i1) i2--;
// @@ Update angles at i0 and i2
}
else {
i++;
}
}
// @@ Create a few degenerate triangles to avoid introducing holes.
i = 0;
const uint size = polygonVertices.size();
while (i < size - 2) {
uint i0 = (i+0) % size;
uint i1 = (i+1) % size;
uint i2 = (i+2) % size;
const HalfEdge::Vertex * v0 = polygonVertices[i0];
const HalfEdge::Vertex * v1 = polygonVertices[i1];
const HalfEdge::Vertex * v2 = polygonVertices[i2];
mesh->addFace(v0->id(), v1->id(), v2->id());
i++;
}
#endif
}
mesh->linkBoundary();
return mesh;
}
Basis Basis::transposed() const {
Basis tr = *this;
tr.transpose();
return tr;
}
// Matrix and Residual Fills
bool
HMX_PDE::evaluate(
NOX::Epetra::Interface::Required::FillType flag,
const Epetra_Vector* soln,
Epetra_Vector* tmp_rhs)
{
// Determine what to fill (F or Jacobian)
bool fillF = false;
bool fillMatrix = false;
if (tmp_rhs != 0) {
fillF = true;
rhs = tmp_rhs;
}
else {
fillMatrix = true;
}
// "flag" can be used to determine how accurate your fill of F should be
// depending on why we are calling evaluate (Could be using computeF to
// populate a Jacobian or Preconditioner).
if (flag == NOX::Epetra::Interface::Required::Residual) {
// Do nothing for now
}
else if (flag == NOX::Epetra::Interface::Required::Jac) {
// Do nothing for now
}
else if (flag == NOX::Epetra::Interface::Required::Prec) {
// Do nothing for now
}
else if (flag == NOX::Epetra::Interface::Required::User) {
// Do nothing for now
}
int numDep = depProblems.size();
// Create the overlapped solution and position vectors
Epetra_Vector u(*OverlapMap);
Epetra_Vector uold(*OverlapMap);
std::vector<Epetra_Vector*> dep(numDep);
for( int i = 0; i<numDep; i++)
dep[i] = new Epetra_Vector(*OverlapMap);
Epetra_Vector xvec(*OverlapMap);
// Export Solution to Overlap vector
// If the vector to be used in the fill is already in the Overlap form,
// we simply need to map on-processor from column-space indices to
// OverlapMap indices. Note that the old solution is simply fixed data that
// needs to be sent to an OverlapMap (ghosted) vector. The conditional
// treatment for the current soution vector arises from use of
// FD coloring in parallel.
uold.Import(*oldSolution, *Importer, Insert);
for( int i = 0; i<numDep; i++ )
(*dep[i]).Import(*( (*(depSolutions.find(depProblems[i]))).second ),
*Importer, Insert);
xvec.Import(*xptr, *Importer, Insert);
if( flag == NOX::Epetra::Interface::Required::FD_Res)
// Overlap vector for solution received from FD coloring, so simply reorder
// on processor
u.Export(*soln, *ColumnToOverlapImporter, Insert);
else // Communication to Overlap vector is needed
u.Import(*soln, *Importer, Insert);
// Declare required variables
int OverlapNumMyNodes = OverlapMap->NumMyElements();
int OverlapMinMyNodeGID;
if (MyPID==0) OverlapMinMyNodeGID = StandardMap->MinMyGID();
else OverlapMinMyNodeGID = StandardMap->MinMyGID()-1;
// Setup iterators for looping over each problem source term contribution
// to this one's PDE
map<string, double>::iterator srcTermIter;
map<string, double>::iterator srcTermEnd = SrcTermWeight.end();
// Bundle up the dependent variables in the way needed for computing
// the source terms of each reaction
/*
Epetra_Vector debugSrcTerm(*OverlapMap);
map<string, Epetra_Vector*> debugDepVars;
debugDepVars.insert( pair<string, Epetra_Vector*>(getName(), &u) );
for( int i = 0; i<numDep; i++ )
debugDepVars.insert( pair<string, Epetra_Vector*>
(myManager->getName(depProblems[i]), &dep[i]) );
for( srcTermIter = SrcTermWeight.begin();
srcTermIter != srcTermEnd; srcTermIter++) {
HMX_PDE &srcTermProb =
dynamic_cast<HMX_PDE&>(
myManager->getProblem(srcTermIter->first) );
std::cout << "Inside problem: \"" << getName() << "\" calling to get source term "
<< "from problem: \"" << srcTermIter->first << "\" :" << std::endl;
srcTermProb.computeSourceTerm(debugDepVars, debugSrcTerm);
std::cout << "Resulting source term :" << debugSrcTerm << std::endl;
}
*/
int row;
double alpha = 500.0;
double xx[2];
double uu[2];
double uuold[2];
std::vector<double*> ddep(numDep);
for( int i = 0; i<numDep; i++)
ddep[i] = new double[2];
double *srcTerm = new double[2];
Basis basis;
// Bundle up the dependent variables in the way needed for computing
// the source terms of each reaction
map<string, double*> depVars;
depVars.insert( pair<string, double*>(getName(), uu) );
for( int i = 0; i<numDep; i++ )
depVars.insert( pair<string, double*>
(myManager->getProblemName(depProblems[i]), ddep[i]) );
// Do a check on this fill
// map<string, double*>::iterator iter;
// for( iter = depVars.begin(); iter != depVars.end(); iter++)
// std::cout << "Inserted ... " << iter->first << "\t" << iter->second << std::endl;
// std::cout << "--------------------------------------------------" << std::endl;
// for( iter = depVars.begin(); iter != depVars.end(); iter++)
// std::cout << iter->first << "\t" << (iter->second)[0] << ", "
// << (iter->second)[1] << std::endl;
// std::cout << "--------------------------------------------------" << std::endl;
// Zero out the objects that will be filled
if ( fillMatrix ) A->PutScalar(0.0);
if ( fillF ) rhs->PutScalar(0.0);
// Loop Over # of Finite Elements on Processor
for (int ne=0; ne < OverlapNumMyNodes-1; ne++)
{
// Loop Over Gauss Points
for(int gp=0; gp < 2; gp++)
{
// Get the solution and coordinates at the nodes
xx[0]=xvec[ne];
xx[1]=xvec[ne+1];
uu[0] = u[ne];
uu[1] = u[ne+1];
uuold[0] = uold[ne];
uuold[1] = uold[ne+1];
for( int i = 0; i<numDep; i++ ) {
ddep[i][0] = (*dep[i])[ne];
ddep[i][1] = (*dep[i])[ne+1];
}
// Calculate the basis function and variables at the gauss points
basis.getBasis(gp, xx, uu, uuold, ddep);
// Loop over Nodes in Element
for (int i=0; i< 2; i++) {
row=OverlapMap->GID(ne+i);
if (StandardMap->MyGID(row)) {
if ( fillF ) {
// First do time derivative and diffusion operator
(*rhs)[StandardMap->LID(OverlapMap->GID(ne+i))]+=
+basis.wt*basis.dx
*((basis.uu - basis.uuold)/dt * basis.phi[i]
+(1.0/(basis.dx*basis.dx))*diffCoef*basis.duu*basis.dphide[i]);
// Then do source term contributions
//
for( srcTermIter = SrcTermWeight.begin();
srcTermIter != srcTermEnd; srcTermIter++) {
HMX_PDE &srcTermProb =
dynamic_cast<HMX_PDE&>(
myManager->getProblem((*srcTermIter).first) );
srcTermProb.computeSourceTerm(2, depVars, srcTerm);
(*rhs)[StandardMap->LID(OverlapMap->GID(ne+i))]+=
+basis.wt*basis.dx
*( basis.phi[i] * ( - (*srcTermIter).second * srcTerm[i] ));
}
//
}
}
// Loop over Trial Functions
if ( fillMatrix ) {
/*
for(j=0;j < 2; j++) {
if (StandardMap->MyGID(row)) {
column=OverlapMap->GID(ne+j);
jac=basis.wt*basis.dx*(
basis.phi[j]/dt*basis.phi[i]
+(1.0/(basis.dx*basis.dx))*diffCoef*basis.dphide[j]*
basis.dphide[i]
+ basis.phi[i] * ( (beta+1.0)*basis.phi[j]
- 2.0*basis.uu*basis.phi[j]*basis.ddep[id_spec]) );
ierr=A->SumIntoGlobalValues(row, 1, &jac, &column);
}
}
*/
}
}
}
}
// Apply Dirichlet BC for Temperature problem only (for now); this implies
// no-flux across domain boundary for all species.
if( getName() == tempFieldName )
{
// Insert Boundary Conditions and modify Jacobian and function (F)
// U(0)=1
if (MyPID==0)
{
if ( fillF )
(*rhs)[0]= (*soln)[0] - alpha;
if ( fillMatrix )
{
int column=0;
double jac=1.0;
A->ReplaceGlobalValues(0, 1, &jac, &column);
column=1;
jac=0.0;
A->ReplaceGlobalValues(0, 1, &jac, &column);
}
}
// U(1)=1
if ( StandardMap->LID(StandardMap->MaxAllGID()) >= 0 )
{
int lastDof = StandardMap->LID(StandardMap->MaxAllGID());
if ( fillF )
(*rhs)[lastDof] = (*soln)[lastDof] - alpha;
if ( fillMatrix )
{
int row=StandardMap->MaxAllGID();
int column = row;
double jac = 1.0;
A->ReplaceGlobalValues(row, 1, &jac, &column);
jac=0.0;
column--;
A->ReplaceGlobalValues(row, 1, &jac, &column);
}
}
}
// Sync up processors to be safe
Comm->Barrier();
A->FillComplete();
#ifdef DEBUG
A->Print(cout);
if( fillF )
std::cout << "For residual fill :" << std::endl << *rhs << std::endl;
if( fillMatrix )
{
std::cout << "For jacobian fill :" << std::endl;
A->Print(cout);
}
#endif
// Cleanup
for( int i = 0; i < numDep; ++i)
{
delete [] ddep[i];
delete dep[i];
}
delete [] srcTerm;
return true;
}
Basis Basis::orthonormalized() const {
Basis c = *this;
c.orthonormalize();
return c;
}
Basis Basis::inverse() const {
Basis inv = *this;
inv.invert();
return inv;
}
// Matrix and Residual Fills
bool
Pitchfork_FiniteElementProblem::evaluate(FillType f,
const Epetra_Vector* soln,
Epetra_Vector* tmp_rhs,
Epetra_RowMatrix* tmp_matrix,
double jac_coeff,
double mass_coeff)
{
flag = f;
// Set the incoming linear objects
if (flag == F_ONLY) {
rhs = tmp_rhs;
} else if (flag == MATRIX_ONLY) {
A = dynamic_cast<Epetra_CrsMatrix*> (tmp_matrix);
assert(A != NULL);
} else if (flag == ALL) {
rhs = tmp_rhs;
A = dynamic_cast<Epetra_CrsMatrix*> (tmp_matrix);
assert(A != NULL);
} else {
std::cout << "ERROR: Pitchfork_FiniteElementProblem::fillMatrix() - FillType flag is broken" << std::endl;
throw;
}
// Create the overlapped solution and position vectors
Epetra_Vector u(*OverlapMap);
Epetra_Vector x(*OverlapMap);
// Export Solution to Overlap vector
u.Import(*soln, *Importer, Insert);
// Declare required variables
int i,j,ierr;
int OverlapNumMyElements = OverlapMap->NumMyElements();
int OverlapMinMyGID;
if (MyPID==0) OverlapMinMyGID = StandardMap->MinMyGID();
else OverlapMinMyGID = StandardMap->MinMyGID()-1;
int row, column;
double jac;
double xx[2];
double uu[2];
Basis basis;
// Create the nodal coordinates
double Length=2.0;
double dx=Length/((double) NumGlobalElements-1);
for (i=0; i < OverlapNumMyElements; i++) {
x[i]=-1.0 + dx*((double) OverlapMinMyGID+i);
}
// Zero out the objects that will be filled
if ((flag == MATRIX_ONLY) || (flag == ALL)) {
i = A->PutScalar(0.0);
assert(i == 0);
}
if ((flag == F_ONLY) || (flag == ALL)) {
i = rhs->PutScalar(0.0);
assert(i == 0);
}
// Loop Over # of Finite Elements on Processor
for (int ne=0; ne < OverlapNumMyElements-1; ne++) {
// Loop Over Gauss Points
for(int gp=0; gp < 2; gp++) {
// Get the solution and coordinates at the nodes
xx[0]=x[ne];
xx[1]=x[ne+1];
uu[0]=u[ne];
uu[1]=u[ne+1];
// Calculate the basis function at the gauss point
basis.getBasis(gp, xx, uu);
// Loop over Nodes in Element
for (i=0; i< 2; i++) {
row=OverlapMap->GID(ne+i);
//printf("Proc=%d GlobalRow=%d LocalRow=%d Owned=%d\n",
// MyPID, row, ne+i,StandardMap.MyGID(row));
if (StandardMap->MyGID(row)) {
if ((flag == F_ONLY) || (flag == ALL)) {
(*rhs)[StandardMap->LID(OverlapMap->GID(ne+i))]+=
+basis.wt*basis.dx
*((-1.0/(basis.dx*basis.dx))*basis.duu*
basis.dphide[i]-source_term(basis.uu)*basis.phi[i]);
}
}
// Loop over Trial Functions
if ((flag == MATRIX_ONLY) || (flag == ALL)) {
for(j=0;j < 2; j++) {
if (StandardMap->MyGID(row)) {
column=OverlapMap->GID(ne+j);
jac=jac_coeff*basis.wt*basis.dx*
((-1.0/(basis.dx*basis.dx))*basis.dphide[j]*basis.dphide[i]
-source_deriv(basis.uu)*basis.phi[j]*basis.phi[i]) +
mass_coeff*basis.wt*basis.dx*basis.phi[j]*basis.phi[i];
ierr=A->SumIntoGlobalValues(row, 1, &jac, &column);
assert(ierr == 0);
}
}
}
}
}
}
// Insert Boundary Conditions and modify Jacobian and function (F)
// U(-1)=beta
if (MyPID==0) {
if ((flag == F_ONLY) || (flag == ALL))
(*rhs)[0]= (*soln)[0] - beta;
if ((flag == MATRIX_ONLY) || (flag == ALL)) {
column=0;
jac=1.0*jac_coeff;
A->ReplaceGlobalValues(0, 1, &jac, &column);
column=1;
jac=0.0*jac_coeff;
A->ReplaceGlobalValues(0, 1, &jac, &column);
}
}
// U(1)=beta
if ( StandardMap->LID(StandardMap->MaxAllGID()) >= 0 ) {
int lastDof = StandardMap->LID(StandardMap->MaxAllGID());
if ((flag == F_ONLY) || (flag == ALL))
(*rhs)[lastDof] = (*soln)[lastDof] - beta;
if ((flag == MATRIX_ONLY) || (flag == ALL)) {
int row = StandardMap->MaxAllGID();
column = row;
jac=1.0*jac_coeff;
A->ReplaceGlobalValues(row, 1, &jac, &column);
column=row-1;
jac=0.0*jac_coeff;
A->ReplaceGlobalValues(row, 1, &jac, &column);
}
}
// Sync up processors to be safe
Comm->Barrier();
A->FillComplete();
return true;
}
void GDAPI godot_basis_set_axis_angle_scale(godot_basis *p_self, const godot_vector3 *p_axis, godot_real p_phi, const godot_vector3 *p_scale) {
Basis *self = (Basis *)p_self;
const Vector3 *axis = (const Vector3 *)p_axis;
const Vector3 *scale = (const Vector3 *)p_scale;
self->set_axis_angle_scale(*axis, p_phi, *scale);
}
void MobileVRInterface::set_position_from_sensors() {
_THREAD_SAFE_METHOD_
// this is a helper function that attempts to adjust our transform using our 9dof sensors
// 9dof is a misleading marketing term coming from 3 accelerometer axis + 3 gyro axis + 3 magnetometer axis = 9 axis
// but in reality this only offers 3 dof (yaw, pitch, roll) orientation
uint64_t ticks = OS::get_singleton()->get_ticks_usec();
uint64_t ticks_elapsed = ticks - last_ticks;
float delta_time = (double)ticks_elapsed / 1000000.0;
// few things we need
Input *input = Input::get_singleton();
Vector3 down(0.0, -1.0, 0.0); // Down is Y negative
Vector3 north(0.0, 0.0, 1.0); // North is Z positive
// make copies of our inputs
bool has_grav = false;
Vector3 acc = input->get_accelerometer();
Vector3 gyro = input->get_gyroscope();
Vector3 grav = input->get_gravity();
Vector3 magneto = scale_magneto(input->get_magnetometer()); // this may be overkill on iOS because we're already getting a calibrated magnetometer reading
if (sensor_first) {
sensor_first = false;
} else {
acc = scrub(acc, last_accerometer_data, 2, 0.2);
magneto = scrub(magneto, last_magnetometer_data, 3, 0.3);
};
last_accerometer_data = acc;
last_magnetometer_data = magneto;
if (grav.length() < 0.1) {
// not ideal but use our accelerometer, this will contain shakey shakey user behaviour
// maybe look into some math but I'm guessing that if this isn't available, its because we lack the gyro sensor to actually work out
// what a stable gravity vector is
grav = acc;
if (grav.length() > 0.1) {
has_grav = true;
};
} else {
has_grav = true;
};
bool has_magneto = magneto.length() > 0.1;
if (gyro.length() > 0.1) {
/* this can return to 0.0 if the user doesn't move the phone, so once on, it's on */
has_gyro = true;
};
if (has_gyro) {
// start with applying our gyro (do NOT smooth our gyro!)
Basis rotate;
rotate.rotate(orientation.get_axis(0), gyro.x * delta_time);
rotate.rotate(orientation.get_axis(1), gyro.y * delta_time);
rotate.rotate(orientation.get_axis(2), gyro.z * delta_time);
orientation = rotate * orientation;
tracking_state = ARVRInterface::ARVR_NORMAL_TRACKING;
};
///@TODO improve this, the magnetometer is very fidgity sometimes flipping the axis for no apparent reason (probably a bug on my part)
// if you have a gyro + accelerometer that combo tends to be better then combining all three but without a gyro you need the magnetometer..
if (has_magneto && has_grav && !has_gyro) {
// convert to quaternions, easier to smooth those out
Quat transform_quat(orientation);
Quat acc_mag_quat(combine_acc_mag(grav, magneto));
transform_quat = transform_quat.slerp(acc_mag_quat, 0.1);
orientation = Basis(transform_quat);
tracking_state = ARVRInterface::ARVR_NORMAL_TRACKING;
} else if (has_grav) {
// use gravity vector to make sure down is down...
// transform gravity into our world space
grav.normalize();
Vector3 grav_adj = orientation.xform(grav);
float dot = grav_adj.dot(down);
if ((dot > -1.0) && (dot < 1.0)) {
// axis around which we have this rotation
Vector3 axis = grav_adj.cross(down);
axis.normalize();
Basis drift_compensation(axis, acos(dot) * delta_time * 10);
orientation = drift_compensation * orientation;
};
};
// JIC
orientation.orthonormalize();
last_ticks = ticks;
};
void setSchreyerMultipliers(const Basis& basis) {
MonoVector schreyer(monoid());
for (size_t gen = 0; gen < basis.size(); ++gen)
schreyer.push_back(basis.getPoly(gen)->getLeadMonomial());
setSchreyerMultipliers(std::move(schreyer));
}
void GDAPI godot_basis_set_quat(godot_basis *p_self, const godot_quat *p_quat) {
Basis *self = (Basis *)p_self;
const Quat *quat = (const Quat *)p_quat;
self->set_quat(*quat);
}
// Print out the basis set specification in the format:
// (example is C atom in 3-21G basis set)
// BASIS: 6-31G
// Total no. of cgbfs: 9
// Total no. of primitives: 9
// ===============
// Specification
// ===============
// Atom Shell #CGBFs #Prims
// ......................................
// C s 3 6
// p 6 3
// (if full = true, then continue with this)
// ===============
// Basis Functions
// ===============
// Atom Shell BF Coeff Exponent
// .................................................
// C s 1 0.0617669 172.2560
// 0.358794 25.91090
// 0.700713 5.533350
// etc...
void Logger::print(Basis& b, bool full) const
{
// Collect the data needed for printing
int nbfs = b.getNBFs(); // Store number of cgbfs and prims
int nprims = 0;
Vector qs = b.getCharges();
// Sort the qs and get rid of duplicates
qs.sort();
Vector qtemp(qs.size());
qtemp[0] = qs(0);
int k = 1;
for (int i = 1; i < qs.size(); i++){
if (qs(i) != qtemp[k-1]){
qtemp[k] = qs(i);
k++;
}
}
qs = qtemp;
qs.resizeCopy(k);
// Now sum over all basis functions to get the number of prims
Vector c(3); c[0] = 0.0; c[1] = 0.0; c[2] = 0.0;
BF bftemp(c, 0, 0, 0, c, c);
for (int i = 0; i < nbfs; i++){
bftemp = b.getBF(i);
nprims += bftemp.getNPrims();
}
// Start printing
title("Basis Set");
outfile << "BASIS: " << b.getName() << "\n";
outfile << "Total no. of cgbfs: " << nbfs << "\n";
outfile << "Total no. of prims: " << nprims << "\n";
title("Specification");
outfile << std::setw(8) << "Atom";
outfile << std::setw(8) << "Shell";
outfile << std::setw(8) << "#CGBFs";
outfile << std::setw(8) << "#Prims\n";
outfile << std::string(35, '.') << "\n";
// loop over the atom types
outfile << std::setprecision(2);
Vector subshells; Vector sublnums;
for (int i = 0; i < k; i++){
int nc = 0; int np = 0;
outfile << std::setw(8) << getAtomName(qs(i));
subshells = b.getShells(qs[i]);
sublnums = b.getLnums(qs[i]);
outfile << std::setw(8) << getShellName(sublnums[0]);
outfile << std::setw(8) << subshells[0];
for (int j = 0; j < subshells[0]; j++){
np += b.getBF(qs[i], j).getNPrims();
}
nc += subshells[0];
outfile << std::setw(8) << np << "\n";
for (int j = 1; j < subshells.size(); j++){
outfile << std::setw(8) << "";
outfile << std::setw(8) << getShellName(sublnums[j]);
outfile << std::setw(8) << subshells[j];
np = 0;
for (int l = 0; l < subshells[j]; l++){
np += b.getBF(qs[i], nc + l).getNPrims();
}
nc += subshells[j];
outfile << std::setw(8) << np << "\n";
}
}
outfile << std::setprecision(8);
// Now print out basis functions if required
if (full) {
title("Basis Functions");
outfile << std::setw(8) << "Atom";
outfile << std::setw(8) << "Shell";
outfile << std::setw(5) << "BF";
outfile << std::setw(18) << "Coeff";
outfile << std::setw(18) << "Exponent\n";
outfile << std::string(58, '.') << "\n";
// Loop over all the basis functions
Vector subshell; Vector sublnums;
Vector coeffs; Vector exps;
std::string filler = "";
for (int i = 0; i < k; i++){
subshell = b.getShells(qs(i));
sublnums = b.getLnums(qs(i));
// Loop over shells
int sum = 0;
for (int r = 0; r < subshell.size(); r++){
// Loop over bfs
for (int s = 0; s < subshell[r]; s++){
bftemp = b.getBF(qs(i), s+sum);
coeffs = bftemp.getCoeffs();
exps = bftemp.getExps();
// Loop over coeffs/exps
for (int t = 0; t < coeffs.size(); t++){
filler = ((r == 0 && s==0 && t==0) ? getAtomName(qs[i]) : "");
outfile << std::setw(8) << filler;
filler = ((s == 0 && t == 0) ? getShellName(sublnums[r]) : "");
outfile << std::setw(8) << filler;
filler = (t == 0 ? std::to_string(s+1) : "");
outfile << std::setw(5) << filler;
outfile << std::setw(18) << std::setprecision(8) << coeffs(t);
outfile << std::setw(18) << std::setprecision(8) << exps(t) << "\n";
}
}
sum += subshell[r];
}
}
}
}
// A fill specialized to the single node at the coupling interface
void
ConvDiff_PDE::computeHeatFlux( const Epetra_Vector * soln )
{
int numDep = depProblems.size();
// Create the overlapped solution and position vectors
Epetra_Vector u(*OverlapMap);
Epetra_Vector uold(*OverlapMap);
std::vector<Epetra_Vector*> dep(numDep);
for( int i = 0; i < numDep; ++i)
dep[i] = new Epetra_Vector(*OverlapMap);
Epetra_Vector xvec(*OverlapMap);
// Export Solution to Overlap vector
// If the vector to be used in the fill is already in the Overlap form,
// we simply need to map on-processor from column-space indices to
// OverlapMap indices. Note that the old solution is simply fixed data that
// needs to be sent to an OverlapMap (ghosted) vector. The conditional
// treatment for the current soution vector arises from use of
// FD coloring in parallel.
uold.Import(*oldSolution, *Importer, Insert);
for( int i = 0; i < numDep; ++i )
(*dep[i]).Import(*( (*(depSolutions.find(depProblems[i]))).second ), *Importer, Insert);
xvec.Import(*xptr, *Importer, Insert);
if( NULL == soln )
u.Import(*initialSolution, *Importer, Insert);
else
u.Import(*soln, *Importer, Insert);
// Declare required variables
int row;
double * xx = new double[2];
double * uu = new double[2];
double * uuold = new double[2];
std::vector<double*> ddep(numDep);
for( int i = 0; i < numDep; ++i)
ddep[i] = new double[2];
Basis basis;
// Bundle up the dependent variables in the way needed for computing
// the source terms of each reaction
map<string, double*> depVars;
depVars.insert( pair< std::string, double*>(getName(), uu) );
for( int i = 0; i < numDep; ++i )
depVars.insert( pair<string, double*>(myManager->getProblemName(depProblems[i]), ddep[i]) );
myFlux = 0.0;
// Loop Over Gauss Points
for( int gp = 0; gp < 2; ++gp )
{
// Get the solution and coordinates at the nodes
xx[0]=xvec[interface_elem];
xx[1]=xvec[interface_elem+1];
uu[0] = u[interface_elem];
uu[1] = u[interface_elem+1];
uuold[0] = uold[interface_elem];
uuold[1] = uold[interface_elem+1];
for( int i = 0; i < numDep; ++i )
{
ddep[i][0] = (*dep[i])[interface_elem];
ddep[i][1] = (*dep[i])[interface_elem+1];
}
// Calculate the basis function and variables at the gauss points
basis.getBasis(gp, xx, uu, uuold, ddep);
row = OverlapMap->GID( interface_elem + local_node );
if( StandardMap->MyGID(row) )
{
myFlux +=
+ basis.wt * basis.dx
* ( peclet * (basis.duu / basis.dx) * basis.phi[local_node]
+ kappa * (1.0/(basis.dx*basis.dx)) * basis.duu * basis.dphide[local_node] );
}
}
// Sync up processors to be safe
Comm->Barrier();
// Cleanup
for( int i = 0; i < numDep; ++i)
{
delete [] ddep[i];
delete dep[i];
}
delete [] xx ;
delete [] uu ;
delete [] uuold ;
//int lastDof = StandardMap->LID(StandardMap->MaxAllGID());
//cout << "\t\"" << myName << "\" u[0] = " << u[0]
// << "\tu[N] = " << u[lastDof] << std::endl;
//cout << u << std::endl;
//cout << "\t\"" << myName << "\" myFlux = " << myFlux << std::endl << std::endl;
// Scale domain integration according to interface position
myFlux *= dirScale;
// Now add radiation contribution to flux
myFlux += radiation * ( pow(u[interface_node], 4) - pow(u[opposite_node], 4) );
return;
}
// Matrix and Residual Fills
bool
ConvDiff_PDE::evaluate(
NOX::Epetra::Interface::Required::FillType flag,
const Epetra_Vector * soln,
Epetra_Vector * rhs)
{
if( rhs == 0 )
{
std::string msg = "ERROR: ConvDiff_PDE::evaluate : callback appears to be other than a residual fill. Others are not support for this type.";
throw msg;
}
int numDep = depProblems.size();
// Create the overlapped solution and position vectors
Epetra_Vector u(*OverlapMap);
Epetra_Vector uold(*OverlapMap);
std::vector<Epetra_Vector*> dep(numDep);
for( int i = 0; i < numDep; ++i)
dep[i] = new Epetra_Vector(*OverlapMap);
Epetra_Vector xvec(*OverlapMap);
// Export Solution to Overlap vector
// If the vector to be used in the fill is already in the Overlap form,
// we simply need to map on-processor from column-space indices to
// OverlapMap indices. Note that the old solution is simply fixed data that
// needs to be sent to an OverlapMap (ghosted) vector. The conditional
// treatment for the current soution vector arises from use of
// FD coloring in parallel.
uold.Import(*oldSolution, *Importer, Insert);
for( int i = 0; i < numDep; ++i )
(*dep[i]).Import(*( (*(depSolutions.find(depProblems[i]))).second ), *Importer, Insert);
xvec.Import(*xptr, *Importer, Insert);
if( flag == NOX::Epetra::Interface::Required::FD_Res)
// Overlap vector for solution received from FD coloring, so simply reorder
// on processor
u.Export(*soln, *ColumnToOverlapImporter, Insert);
else // Communication to Overlap vector is needed
u.Import(*soln, *Importer, Insert);
// Declare required variables
int OverlapNumMyNodes = OverlapMap->NumMyElements();
int OverlapMinMyNodeGID;
if (MyPID==0) OverlapMinMyNodeGID = StandardMap->MinMyGID();
else OverlapMinMyNodeGID = StandardMap->MinMyGID()-1;
int row;
double * xx = new double[2];
double * uu = new double[2];
double * uuold = new double[2];
std::vector<double*> ddep(numDep);
for( int i = 0; i < numDep; ++i)
ddep[i] = new double[2];
Basis basis;
// Bundle up the dependent variables in the way needed for computing
// the source terms of each reaction
map<string, double*> depVars;
depVars.insert( pair< std::string, double*>(getName(), uu) );
for( int i = 0; i < numDep; ++i )
depVars.insert( pair<string, double*>(myManager->getProblemName(depProblems[i]), ddep[i]) );
// Zero out the objects that will be filled
rhs->PutScalar(0.0);
// Loop Over # of Finite Elements on Processor
for( int ne = 0; ne < OverlapNumMyNodes-1; ++ne )
{
// Loop Over Gauss Points
for( int gp = 0; gp < 2; ++gp )
{
// Get the solution and coordinates at the nodes
xx[0]=xvec[ne];
xx[1]=xvec[ne+1];
uu[0] = u[ne];
uu[1] = u[ne+1];
uuold[0] = uold[ne];
uuold[1] = uold[ne+1];
for( int i = 0; i < numDep; ++i )
{
ddep[i][0] = (*dep[i])[ne];
ddep[i][1] = (*dep[i])[ne+1];
}
// Calculate the basis function and variables at the gauss points
basis.getBasis(gp, xx, uu, uuold, ddep);
// Loop over Nodes in Element
for( int i = 0; i < 2; ++i )
{
row = OverlapMap->GID(ne+i);
if( StandardMap->MyGID(row) )
{
(*rhs)[StandardMap->LID(OverlapMap->GID(ne+i))] +=
+ basis.wt * basis.dx
* ( peclet * (basis.duu / basis.dx) * basis.phi[i]
+ kappa * (1.0/(basis.dx*basis.dx)) * basis.duu * basis.dphide[i] );
}
}
}
}
//if( NOX::Epetra::Interface::Required::Residual == flag )
//{
// int lastDof = StandardMap->LID(StandardMap->MaxAllGID());
// std::cout << "\t\"" << myName << "\" u[0] = " << (*soln)[0]
// << "\tu[N] = " << (*soln)[lastDof] << std::endl;
// std::cout << "\t\"" << myName << "\" RHS[0] = " << (*rhs)[0]
// << "\tRHS[N] = " << (*rhs)[lastDof] << std::endl << std::endl;
//}
// Apply BCs
computeHeatFlux( soln );
double bcResidual = bcWeight * (myFlux - depProbPtr->getHeatFlux() ) -
(1.0 - bcWeight) * (u[interface_node] - depProbPtr->getInterfaceTemp() );
int lastDof = StandardMap->LID(StandardMap->MaxAllGID());
// "Left" boundary
if( LEFT == myInterface ) // this may break in parallel
{
(*rhs)[0] = bcResidual;
(*rhs)[lastDof] = (*soln)[lastDof] - Tright;
}
// "Right" boundary
else
{
(*rhs)[0] = (*soln)[0] - Tleft;
(*rhs)[lastDof] = bcResidual;
}
// Sync up processors to be safe
Comm->Barrier();
A->FillComplete();
#ifdef DEBUG
std::cout << "For residual fill :" << std::endl << *rhs << std::endl;
#endif
// Cleanup
for( int i = 0; i < numDep; ++i)
{
delete [] ddep[i];
delete dep[i];
}
delete [] xx ;
delete [] uu ;
delete [] uuold ;
return true;
}
void GridMapEditor::_duplicate_paste() {
if (!selection.active)
return;
int idx = options->get_popup()->get_item_index(MENU_OPTION_DUPLICATE_SELECTS);
bool reselect = options->get_popup()->is_item_checked( idx );
List< __Item > items;
Basis rot;
rot.set_orthogonal_index(selection.duplicate_rot);
for(int i=selection.begin.x;i<=selection.end.x;i++) {
for(int j=selection.begin.y;j<=selection.end.y;j++) {
for(int k=selection.begin.z;k<=selection.end.z;k++) {
int itm = node->get_cell_item(i,j,k);
if (itm==GridMap::INVALID_CELL_ITEM)
continue;
int orientation = node->get_cell_item_orientation(i,j,k);
__Item item;
Vector3 rel=Vector3(i,j,k)-selection.begin;
rel = rot.xform(rel);
Basis orm;
orm.set_orthogonal_index(orientation);
orm = rot * orm;
item.pos=selection.begin+rel;
item.item=itm;
item.rot=orm.get_orthogonal_index();
items.push_back(item);
}
}
}
Vector3 ofs=selection.current-selection.click;
if (items.size()) {
undo_redo->create_action("GridMap Duplicate Selection");
for(List< __Item >::Element *E=items.front();E;E=E->next()) {
__Item &it=E->get();
Vector3 pos = it.pos+ofs;
undo_redo->add_do_method(node,"set_cell_item",pos.x,pos.y,pos.z,it.item,it.rot);
undo_redo->add_undo_method(node,"set_cell_item",pos.x,pos.y,pos.z,node->get_cell_item(pos.x,pos.y,pos.z),node->get_cell_item_orientation(pos.x,pos.y,pos.z));
}
undo_redo->commit_action();
}
if (reselect) {
selection.begin+=ofs;
selection.end+=ofs;
selection.click=selection.begin;
selection.current=selection.end;
_validate_selection();
}
}
Basis Basis::scaled_local(const Vector3 &p_scale) const {
Basis b;
b.set_diagonal(p_scale);
return (*this) * b;
}
void GridMapEditor::_menu_option(int p_option) {
switch(p_option) {
case MENU_OPTION_CONFIGURE: {
} break;
case MENU_OPTION_LOCK_VIEW: {
int index=options->get_popup()->get_item_index(MENU_OPTION_LOCK_VIEW);
lock_view=!options->get_popup()->is_item_checked(index);
options->get_popup()->set_item_checked(index,lock_view);
} break;
case MENU_OPTION_CLIP_DISABLED:
case MENU_OPTION_CLIP_ABOVE:
case MENU_OPTION_CLIP_BELOW: {
clip_mode=ClipMode(p_option-MENU_OPTION_CLIP_DISABLED);
for(int i=0;i<3;i++) {
int index=options->get_popup()->get_item_index(MENU_OPTION_CLIP_DISABLED+i);
options->get_popup()->set_item_checked(index,i==clip_mode);
}
_update_clip();
} break;
case MENU_OPTION_X_AXIS:
case MENU_OPTION_Y_AXIS:
case MENU_OPTION_Z_AXIS: {
int new_axis = p_option-MENU_OPTION_X_AXIS;
for(int i=0;i<3;i++) {
int idx=options->get_popup()->get_item_index(MENU_OPTION_X_AXIS+i);
options->get_popup()->set_item_checked(idx,i==new_axis);
}
edit_axis=Vector3::Axis(new_axis);
update_grid();
_update_clip();
} break;
case MENU_OPTION_CURSOR_ROTATE_Y: {
Basis r;
if (input_action==INPUT_DUPLICATE) {
r.set_orthogonal_index(selection.duplicate_rot);
r.rotate(Vector3(0,1,0),-Math_PI/2.0);
selection.duplicate_rot=r.get_orthogonal_index();
_update_duplicate_indicator();
break;
}
r.set_orthogonal_index(cursor_rot);
r.rotate(Vector3(0,1,0),-Math_PI/2.0);
cursor_rot=r.get_orthogonal_index();
_update_cursor_transform();
} break;
case MENU_OPTION_CURSOR_ROTATE_X: {
Basis r;
if (input_action==INPUT_DUPLICATE) {
r.set_orthogonal_index(selection.duplicate_rot);
r.rotate(Vector3(1,0,0),-Math_PI/2.0);
selection.duplicate_rot=r.get_orthogonal_index();
_update_duplicate_indicator();
break;
}
r.set_orthogonal_index(cursor_rot);
r.rotate(Vector3(1,0,0),-Math_PI/2.0);
cursor_rot=r.get_orthogonal_index();
_update_cursor_transform();
} break;
case MENU_OPTION_CURSOR_ROTATE_Z: {
Basis r;
if (input_action==INPUT_DUPLICATE) {
r.set_orthogonal_index(selection.duplicate_rot);
r.rotate(Vector3(0,0,1),-Math_PI/2.0);
selection.duplicate_rot=r.get_orthogonal_index();
_update_duplicate_indicator();
break;
}
r.set_orthogonal_index(cursor_rot);
r.rotate(Vector3(0,0,1),-Math_PI/2.0);
cursor_rot=r.get_orthogonal_index();
_update_cursor_transform();
} break;
case MENU_OPTION_CURSOR_BACK_ROTATE_Y: {
Basis r;
r.set_orthogonal_index(cursor_rot);
r.rotate(Vector3(0,1,0),Math_PI/2.0);
cursor_rot=r.get_orthogonal_index();
_update_cursor_transform();
} break;
case MENU_OPTION_CURSOR_BACK_ROTATE_X: {
Basis r;
r.set_orthogonal_index(cursor_rot);
r.rotate(Vector3(1,0,0),Math_PI/2.0);
cursor_rot=r.get_orthogonal_index();
_update_cursor_transform();
} break;
case MENU_OPTION_CURSOR_BACK_ROTATE_Z: {
Basis r;
r.set_orthogonal_index(cursor_rot);
r.rotate(Vector3(0,0,1),Math_PI/2.0);
cursor_rot=r.get_orthogonal_index();
_update_cursor_transform();
} break;
case MENU_OPTION_CURSOR_CLEAR_ROTATION: {
if (input_action==INPUT_DUPLICATE) {
selection.duplicate_rot=0;
_update_duplicate_indicator();
break;
}
cursor_rot=0;
_update_cursor_transform();
} break;
case MENU_OPTION_DUPLICATE_SELECTS: {
int idx = options->get_popup()->get_item_index(MENU_OPTION_DUPLICATE_SELECTS);
options->get_popup()->set_item_checked( idx, !options->get_popup()->is_item_checked( idx ) );
} break;
case MENU_OPTION_SELECTION_MAKE_AREA:
case MENU_OPTION_SELECTION_MAKE_EXTERIOR_CONNECTOR: {
if (!selection.active)
break;
int area = node->get_unused_area_id();
Error err = node->create_area(area,Rect3(selection.begin,selection.end-selection.begin+Vector3(1,1,1)));
if (err!=OK) {
}
if (p_option==MENU_OPTION_SELECTION_MAKE_EXTERIOR_CONNECTOR) {
node->area_set_exterior_portal(area,true);
}
_update_areas_display();
update_areas();
} break;
case MENU_OPTION_REMOVE_AREA: {
if (selected_area<1)
return;
node->erase_area(selected_area);
_update_areas_display();
update_areas();
} break;
case MENU_OPTION_SELECTION_DUPLICATE:
if (!(selection.active && input_action==INPUT_NONE))
return;
if (last_mouseover==Vector3(-1,-1,-1)) //nono mouseovering anythin
break;
input_action=INPUT_DUPLICATE;
selection.click=last_mouseover;
selection.current=last_mouseover;
selection.duplicate_rot=0;
_update_duplicate_indicator();
break;
case MENU_OPTION_SELECTION_CLEAR: {
if (!selection.active)
return;
_delete_selection();
} break;
case MENU_OPTION_GRIDMAP_SETTINGS: {
settings_dialog->popup_centered(settings_vbc->get_combined_minimum_size() + Size2(50, 50));
} break;
}
}
void GDAPI godot_basis_set_quat_scale(godot_basis *p_self, const godot_quat *p_quat, const godot_vector3 *p_scale) {
Basis *self = (Basis *)p_self;
const Quat *quat = (const Quat *)p_quat;
const Vector3 *scale = (const Vector3 *)p_scale;
self->set_quat_scale(*quat, *scale);
}
// ---------------------------
// - Matrix and Residual Fills
// ---------------------------
bool evaluate(NOX::Epetra::Interface::Required::FillType flag,
const Epetra_Vector* soln,
Epetra_Vector* tmp_rhs,
Epetra_RowMatrix* tmp_matrix)
{
//Determine what to fill (F or Jacobian)
bool fillF = false;
bool fillMatrix = false;
if (tmp_rhs != 0) {
fillF = true;
rhs = tmp_rhs;
}
else {
fillMatrix = true;
}
// "flag" can be used to determine how accurate your fill of F should be
// depending on why we are calling evaluate (Could be using computeF to
// populate a Jacobian or Preconditioner).
if (flag == NOX::Epetra::Interface::Required::Residual) {
// Do nothing for now
}
else if (flag == NOX::Epetra::Interface::Required::Jac) {
// Do nothing for now
}
else if (flag == NOX::Epetra::Interface::Required::Prec) {
// Do nothing for now
}
else if (flag == NOX::Epetra::Interface::Required::User) {
// Do nothing for now
}
// Create the overlapped solution and position vectors
Epetra_Vector u(*OverlapMap);
Epetra_Vector uold(*OverlapMap);
Epetra_Vector xvec(*OverlapMap);
// Export Solution to Overlap vector
u.Import(*soln, *Importer, Insert);
uold.Import(*oldSolution, *Importer, Insert);
xvec.Import(*xptr, *Importer, Insert);
// Declare required variables
int OverlapNumMyElements = OverlapMap->NumMyElements();
int row, column;
double jac;
double xx[2];
double uu[2];
double uuold[2];
Basis basis;
// Zero out the objects that will be filled
if (fillF)
rhs->PutScalar(0.0);
if (fillMatrix)
jacobian->PutScalar(0.0);
// Loop Over # of Finite Elements on Processor
for (int ne=0; ne < OverlapNumMyElements-1; ne++) {
// Loop Over Gauss Points
for(int gp=0; gp < 2; gp++) {
// Get the solution and coordinates at the nodes
xx[0]=xvec[ne];
xx[1]=xvec[ne+1];
uu[0]=u[ne];
uu[1]=u[ne+1];
uuold[0]=uold[ne];
uuold[1]=uold[ne+1];
// Calculate the basis function at the gauss point
basis.computeBasis(gp, xx, uu, uuold);
// Loop over Nodes in Element
for (int i=0; i< 2; i++) {
row=OverlapMap->GID(ne+i);
//printf("Proc=%d GlobalRow=%d LocalRow=%d Owned=%d\n",
// MyPID, row, ne+i,StandardMap.MyGID(row));
if (StandardMap->MyGID(row)) {
if (fillF) {
(*rhs)[StandardMap->LID(OverlapMap->GID(ne+i))]+=
+basis.wt*basis.dx*(
(basis.uu-basis.uuold)/dt*basis.phi[i] +
(1.0/(basis.dx*basis.dx))*basis.duu*basis.dphide[i] -
8.0/factor/factor*basis.uu*basis.uu*
(1.0-basis.uu)*basis.phi[i]);
}
}
// Loop over Trial Functions
if (fillMatrix) {
for(int j=0;j < 2; j++) {
if (StandardMap->MyGID(row)) {
column=OverlapMap->GID(ne+j);
jac=basis.wt*basis.dx*(
basis.phi[j]/dt*basis.phi[i] +
(1.0/(basis.dx*basis.dx))*
basis.dphide[j]*basis.dphide[i] -
8.0/factor/factor*
(2.0*basis.uu-3.0*basis.uu*basis.uu)*
basis.phi[j]*basis.phi[i]);
jacobian->SumIntoGlobalValues(row, 1, &jac, &column);
}
}
}
}
}
}
// Insert Boundary Conditions and modify Jacobian and function (F)
// U(0)=1
if (MyPID==0) {
if (fillF)
(*rhs)[0]= (*soln)[0] - 1.0;
if (fillMatrix) {
column=0;
jac=1.0;
jacobian->ReplaceGlobalValues(0, 1, &jac, &column);
column=1;
jac=0.0;
jacobian->ReplaceGlobalValues(0, 1, &jac, &column);
}
}
// Insert Boundary Conditions and modify Jacobian and function (F)
// U(xmax)=0
if (MyPID==NumProc-1) {
if (fillF)
(*rhs)[NumMyElements-1]= (*soln)[NumMyElements-1] - 0.0;
if (fillMatrix) {
row=NumGlobalElements-1;
column=row;
jac=1.0;
jacobian->ReplaceGlobalValues(row, 1, &jac, &column);
column--;
jac=0.0;
jacobian->ReplaceGlobalValues(row, 1, &jac, &column);
}
}
// Sync up processors to be safe
Comm->Barrier();
jacobian->FillComplete();
return true;
}
int main(int argc, char * argv[])
{
srand(time(NULL));
// Let us define a 3 layer perceptron architecture
auto input = gaml::mlp::input<X>(INPUT_DIM, fillInput);
auto l1 = gaml::mlp::layer(input, HIDDEN_LAYER_SIZE, gaml::mlp::mlp_sigmoid(), gaml::mlp::mlp_dsigmoid());
auto l2 = gaml::mlp::layer(l1, HIDDEN_LAYER_SIZE, gaml::mlp::mlp_sigmoid(), gaml::mlp::mlp_dsigmoid());
auto output = gaml::mlp::layer(l2, OUTPUT_DIM, gaml::mlp::mlp_identity(), gaml::mlp::mlp_didentity());
auto mlp = gaml::mlp::perceptron(output, output_of);
// Create a training base
// Let us try to fit a noisy sinc function
Basis basis;
basis.resize(NB_SAMPLES);
for(auto& d: basis)
{
d.first = {{ -10.0 + 20.0 * gaml::random::uniform(0.0, 1.0) }} ;
d.second = noisy_oracle(d.first);
}
// Set up the parameters for learning the MLP with a gradient descent
gaml::mlp::learner::gradient::parameter gradient_params;
gradient_params.alpha = 1e-2;
gradient_params.dalpha = 1e-3;
gradient_params.verbose = true;
// The stopping criteria
gradient_params.max_iter = 10000;
gradient_params.min_dparams = 1e-7;
// Create the learner
auto learning_algorithm = gaml::mlp::learner::gradient::algorithm(mlp, gradient_params, gaml::mlp::loss::Quadratic(), fillOutput);
// Call the learner on the basis and get the learned predictor
auto predictor = learning_algorithm(basis.begin(),
basis.end(),
input_of_data,
output_of_data);
// Print out the structure of the perceptron we learned
std::cout << predictor << std::endl;
// Dump the results
std::ofstream outfile("example-005-samples.data");
for(auto& b: basis)
outfile << b.first[0] << " "
<< b.second[0] << " "
<< std::endl;
outfile.close();
outfile.open("example-005-regression.data");
X x;
for(x[0] = -10; x[0] < 10 ; x[0] += 0.1)
{
auto output = predictor(x);
outfile << x[0] << " "
<< oracle(x)[0] << " "
<< output[0] << std::endl;
}
outfile.close();
std::cout << "You can plot the results using gnuplot :" << std::endl;
std::cout << "gnuplot " << ML_MLP_SHAREDIR << "/plot-example-005.gplot" << std::endl;
std::cout << "This will produce example-005.ps" << std::endl;
// Let us compute the empirical risk.
auto evaluator = gaml::risk::empirical(gaml::mlp::loss::Quadratic());
double risk = evaluator(predictor,
basis.begin(),
basis.end(),
input_of_data,
output_of_data);
std::cout << "Empirical risk = " << risk << std::endl;
// We will use a 6-fold cross-validation to estimate the real risk.
auto kfold_evaluator = gaml::risk::cross_validation(gaml::mlp::loss::Quadratic(),
gaml::partition::kfold(6),
true);
double kfold_risk = kfold_evaluator(learning_algorithm,
basis.begin(),basis.end(),
input_of_data,output_of_data);
std::cout << "Estimation of the real risk (6-fold): "
<< kfold_risk << std::endl;
}
void GDAPI godot_basis_set_row(godot_basis *p_self, const godot_int p_row, const godot_vector3 *p_value) {
Basis *self = (Basis *)p_self;
const Vector3 *value = (const Vector3 *)p_value;
self->set_row(p_row, *value);
}
Basis Basis::scaled( const Vector3& p_scale ) const {
Basis m = *this;
m.scale(p_scale);
return m;
}
void GDAPI godot_basis_set_euler_scale(godot_basis *p_self, const godot_vector3 *p_euler, const godot_vector3 *p_scale) {
Basis *self = (Basis *)p_self;
const Vector3 *euler = (const Vector3 *)p_euler;
const Vector3 *scale = (const Vector3 *)p_scale;
self->set_euler_scale(*euler, *scale);
}
void basis_sort(Integer *basis) {
Basis *basisObj = Basis_find_object(*basis);
basisObj->sort();
}