void ImportSTL:: doImport
(
const std::string& name,
mesh::Mesh& mesh )
{
preciceTrace1("doImport()", name);
assertion1(mesh.getDimensions() == 3, mesh.getDimensions());
// TODO
}
double Physics::compute_mass(const mesh::Mesh& m, const_iterator u) {
double total_mass = 0.;
const double* source = reinterpret_cast<const double*>(&u[0]);
vdPackI(m.nodes(), &source[0], 2, &h_vec[0]);
process_volumes_psk( m );
for(int i=0; i<m.local_nodes(); i++)
//total_mass += m.volume(i).vol()*u[i].M;
total_mass += m.volume(i).vol()*theta_vec[i]*rho_vec[i];
return total_mass;
}
double Physics::mass_flux_per_time(const mesh::Mesh& m){
double flux_per_time = 0.;
for( int i=m.interior_cvfaces(); i<m.cvfaces(); i++ )
{
const mesh::CVFace& cvf = m.cvface(i);
int boundary_tag = cvf.boundary();
const BoundaryCondition& BC = boundary_condition_h( boundary_tag );
double t=0.;
if( BC.type()==3 )
flux_per_time -= BC.value(t) * m.cvface(i).area();
}
return flux_per_time*constants().rho_0();
}
void DriftRatchet:: createBodyWall
(
mesh::Mesh& mesh,
mesh::PropertyContainer* propertyContainer,
mesh::Vertex* cutVertices[],
mesh::Edge* cutEdges[] )
{
int sectionCount = getCutsAlongXAxis ( _discretizationWidth );
double currentXInImage = 0.0;
double currentXInPreImage = 0.0;
double xStepInImage = _length / (double)sectionCount;
double xStepInPreImage = (_pores * getCharacteristicLength(_maxRadius)) / (double)sectionCount;
int dimensions = mesh.getDimensions();
utils::DynVector currentCenter ( dimensions, 0.0 );
currentXInImage += xStepInImage;
currentXInPreImage += xStepInPreImage;
for ( int i=0; i < sectionCount; i++ ) {
currentCenter(0) = currentXInImage;
double radius = getRadius ( currentXInPreImage );
createBodyWallSection ( mesh, propertyContainer, cutVertices, cutEdges,
currentCenter, radius );
currentXInImage += xStepInImage;
currentXInPreImage += xStepInPreImage;
}
}
void DriftRatchet:: createRightWall
(
mesh::Mesh& mesh,
mesh::PropertyContainer* propertyContainer,
mesh::Vertex* cutVertices[],
mesh::Edge* cutEdges[] )
{
int dimensions = mesh.getDimensions();
if ( dimensions == 2 ){
utils::Vector2D center ( 0.0 );
center(0) += _length;
mesh::Vertex& centerVertex = mesh.createVertex ( center );
if ( propertyContainer != NULL ) {
centerVertex.addParent ( *propertyContainer );
}
mesh::Edge& e0 = mesh.createEdge ( centerVertex, *cutVertices[0] );
mesh::Edge& e1 = mesh.createEdge ( *cutVertices[1], centerVertex );
if ( propertyContainer != NULL ) {
e0.addParent ( *propertyContainer );
e1.addParent ( *propertyContainer );
}
}
else {
assertion1 ( dimensions == 3, dimensions );
utils::Vector3D center ( 0.0 );
center(0) += _length;
mesh::Vertex& centerVertex = mesh.createVertex ( center );
if ( propertyContainer != NULL ) {
centerVertex.addParent ( *propertyContainer );
}
int vertexCount = getNumberOfVerticesPerCut ( _discretizationWidth );
// Create edges and triangles
mesh::Edge& firstCenterEdge = mesh.createEdge ( centerVertex, *cutVertices[0] );
if ( propertyContainer != NULL ) {
firstCenterEdge.addParent ( *propertyContainer );
}
mesh::Edge* oldCenterEdge = & firstCenterEdge;
mesh::Edge* newCenterEdge = NULL;
for ( int i=0; i < vertexCount - 1; i++ ) {
newCenterEdge = & mesh.createEdge ( centerVertex, *cutVertices[i+1] );
mesh::Triangle& t = mesh.createTriangle (
*cutEdges[i], *oldCenterEdge, *newCenterEdge );
if ( propertyContainer != NULL ) {
newCenterEdge->addParent ( *propertyContainer );
t.addParent ( *propertyContainer );
}
oldCenterEdge = newCenterEdge;
}
mesh::Triangle& t = mesh.createTriangle ( *cutEdges[vertexCount-1],
*oldCenterEdge, firstCenterEdge );
if ( propertyContainer != NULL ) {
t.addParent ( *propertyContainer );
}
}
}
void ImportGeometry:: allocateDataValues
(
mesh::Mesh& mesh )
{
// Data values are already allocated during import when a checkpoint is read
// and should not be overwritten by reallocating them.
if ( not _importCheckpoint ){
mesh.allocateDataValues();
}
}
void run ()
{
Mesh::Mesh mesh;
if (get_options ("blocky").size()) {
auto input = Image<bool>::open (argument[0]);
Mesh::vox2mesh (input, mesh);
} else {
auto input = Image<float>::open (argument[0]);
float threshold = get_option_value ("threshold", Filter::estimate_optimal_threshold (input));
Mesh::vox2mesh_mc (input, threshold, mesh);
}
mesh.save (argument[1]);
}
void run ()
{
// Read in the mesh data
Mesh::Mesh mesh (argument[0]);
// If the .vtk files come from FIRST, they are defined in a native FSL space, and
// therefore the source image must be known in order to transform to real space
Options opt = get_options ("first");
if (opt.size()) {
Image::Header H_first (opt[0][0]);
mesh.transform_first_to_realspace (H_first);
}
// Get the template image
Image::Header template_image (argument[1]);
// Create the output image
mesh.output_pve_image (template_image, argument[2]);
}
void DriftRatchet:: specializedCreate
(
mesh::Mesh& seed )
{
using namespace mesh;
std::string nameSubID ( seed.getName() + "-side-" );
PropertyContainer* leftWall = NULL;
PropertyContainer* rightWall = NULL;
if ( seed.getNameIDPairs().count(nameSubID + "0") ) {
leftWall = & seed.getPropertyContainer ( nameSubID + "0" );
}
if ( seed.getNameIDPairs().count(nameSubID + "1") ) {
rightWall = & seed.getPropertyContainer ( nameSubID + "1" );
}
int count = getNumberOfVerticesPerCut ( _discretizationWidth );
mesh::Vertex** cutVertices = new mesh::Vertex* [count];
count = getOffset().size() == 3 ? count : 0; // Only used in 3D
mesh::Edge ** cutEdges = new mesh::Edge * [count];
createLeftWall ( seed, leftWall, cutVertices, cutEdges );
createBodyWall ( seed, NULL, cutVertices, cutEdges );
createRightWall ( seed, rightWall, cutVertices, cutEdges );
delete[] cutVertices;
delete[] cutEdges;
}
void Physics::preprocess_evaluation(double t, const mesh::Mesh& m,
const_iterator u, const_iterator udash)
{
++num_calls;
for (int i = 0; i < m.nodes(); ++i) {
assert(u[i].h == u[i].h &&
u[i].h != std::numeric_limits<double>::infinity() &&
u[i].h != -std::numeric_limits<double>::infinity()
);
assert(u[i].M == u[i].M &&
u[i].M != std::numeric_limits<double>::infinity() &&
u[i].M != -std::numeric_limits<double>::infinity()
);
}
// Copy h from solution vector to h_vec and c_vec
const double* source = reinterpret_cast<const double*>(&u[0]);
vdPackI(m.nodes(), &source[0], 2, &h_vec[0]);
// h and gradient at CV faces
shape_matrix.matvec( h_vec, h_faces );
shape_gradient_matrixX.matvec( h_vec, grad_h_faces_.x() );
shape_gradient_matrixY.matvec( h_vec, grad_h_faces_.y() );
if (dimension == 3)
shape_gradient_matrixZ.matvec( h_vec, grad_h_faces_.z() );
// determine the p-s-k values
process_volumes_psk( m );
// density at faces using shape functions
process_faces_shape( m );
// Compute psk values at faces using upwinding/limiting
process_faces_lim( m );
// compute fluxes
process_fluxes( t, m );
}
void CommunicateMesh:: receiveMesh
(
mesh::Mesh& mesh,
int rankSender )
{
preciceTrace2 ( "receiveMesh()", mesh.getName(), rankSender );
using tarch::la::raw;
int dim = mesh.getDimensions();
std::map<int, mesh::Vertex*> vertexMap;
int vertexCount;
_communication->startReceivePackage ( rankSender );
_communication->receive ( vertexCount, rankSender);
utils::DynVector coords(dim);
for ( int i=0; i < vertexCount; i++ ){
_communication->receive ( raw(coords), dim, rankSender );
mesh::Vertex& v = mesh.createVertex ( coords );
assertion1 ( v.getID() >= 0, v.getID() );
vertexMap[v.getID()] = &v;
}
std::map<int,mesh::Edge*> edgeMap; // only used in 3D
int edgeCount;
_communication->receive ( edgeCount, rankSender );
for ( int i=0; i < edgeCount; i++ ){
int vertexIndex1 = -1;
int vertexIndex2 = -1;
_communication->receive ( vertexIndex1, rankSender );
_communication->receive ( vertexIndex2, rankSender );
assertion ( vertexMap.find(vertexIndex1) != vertexMap.end() );
assertion ( vertexMap.find(vertexIndex2) != vertexMap.end() );
assertion1 ( vertexIndex1 != vertexIndex2, vertexIndex1 );
if ( dim == 2 ){
mesh.createEdge ( *vertexMap[vertexIndex1], *vertexMap[vertexIndex2] );
}
else {
assertion1 ( dim == 3, dim );
mesh::Edge & e = mesh.createEdge (
*vertexMap[vertexIndex1], *vertexMap[vertexIndex2] );
assertion1 ( e.getID() >= 0, e.getID() );
edgeMap[e.getID()] = &e;
}
}
if ( dim == 3 ){
int triangleCount = 0;
assertion ( (edgeMap.size() > 0) || (triangleCount == 0) );
_communication->receive ( triangleCount, rankSender );
for ( int i=0; i < triangleCount; i++ ) {
int index1 = -1;
int index2 = -1;
int index3 = -1;
_communication->receive ( index1, rankSender );
_communication->receive ( index2, rankSender );
_communication->receive ( index3, rankSender );
assertion ( edgeMap.find(index1) != edgeMap.end() );
assertion ( edgeMap.find(index2) != edgeMap.end() );
assertion ( edgeMap.find(index3) != edgeMap.end() );
assertion ( index1 != index2 );
assertion ( index2 != index3 );
assertion ( index3 != index1 );
mesh.createTriangle ( *edgeMap[index1], *edgeMap[index2], *edgeMap[index3] );
}
}
_communication->finishReceivePackage ();
}
void DriftRatchet:: createBodyWallSection
(
mesh::Mesh& mesh,
mesh::PropertyContainer* propertyContainer,
mesh::Vertex* cutVertices[],
mesh::Edge* cutEdges[],
const utils::DynVector& center,
double radius )
{
int dimensions = mesh.getDimensions();
if ( dimensions == 2 ){
utils::Vector2D upperPoint ( center[0], center[1] + radius );
utils::Vector2D lowerPoint ( center[0], center[1] - radius );
mesh::Vertex& upperVertex = mesh.createVertex ( upperPoint );
mesh::Vertex& lowerVertex = mesh.createVertex ( lowerPoint );
mesh::Edge& e0 = mesh.createEdge ( upperVertex, *cutVertices[0] );
mesh::Edge& e1 = mesh.createEdge ( *cutVertices[1], lowerVertex );
cutVertices[0] = & upperVertex;
cutVertices[1] = & lowerVertex;
if ( propertyContainer != NULL ) {
e0.addParent ( *propertyContainer );
e1.addParent ( *propertyContainer );
cutVertices[0]->addParent ( *propertyContainer );
cutVertices[1]->addParent ( *propertyContainer );
}
}
else {
assertion1 ( dimensions == 3, dimensions );
double currentAngle = 0.0;
int vertexCount = getNumberOfVerticesPerCut ( _discretizationWidth );
double angle = 2.0 * tarch::la::PI / static_cast<double>(vertexCount);
// Create vertices
mesh::Vertex ** newCutVertices = new mesh::Vertex * [vertexCount];
for ( int i=0; i < vertexCount; i++ ) {
utils::Vector3D currentCenter ( center );
double y = std::cos(currentAngle) * radius;
currentCenter(1) += y;
double z = std::sin(currentAngle) * radius;
currentCenter(2) += z;
currentAngle += angle;
newCutVertices[i] = & mesh.createVertex ( currentCenter );
if ( propertyContainer != NULL ) {
newCutVertices[i]->addParent ( *propertyContainer );
}
}
// Create edges and triangles
mesh::Edge** newCutEdges = new mesh::Edge * [vertexCount];
mesh::Edge* initialEdge = & mesh.createEdge ( *cutVertices[0],
*newCutVertices[0] );
if ( propertyContainer != NULL ) {
initialEdge->addParent ( *propertyContainer );
}
mesh::Edge* firstEdge = initialEdge;
mesh::Edge* crossingEdge = NULL;
mesh::Edge* secondEdge = NULL;
for ( int i=0; i < vertexCount - 1; i++ ) {
crossingEdge = & mesh.createEdge ( *cutVertices[i],
*newCutVertices[i+1] );
newCutEdges[i] = & mesh.createEdge ( *newCutVertices[i],
*newCutVertices[i+1] );
secondEdge = & mesh.createEdge ( *cutVertices[i+1],
*newCutVertices[i+1] );
mesh::Triangle& t0 = mesh.createTriangle ( *firstEdge, *newCutEdges[i], *crossingEdge );
mesh::Triangle& t1 = mesh.createTriangle ( *crossingEdge, *secondEdge, *cutEdges[i] );
if ( propertyContainer != NULL ) {
t0.addParent ( *propertyContainer );
t1.addParent ( *propertyContainer );
crossingEdge->addParent ( *propertyContainer );
secondEdge->addParent ( *propertyContainer );
}
firstEdge = secondEdge;
}
crossingEdge = & mesh.createEdge ( *cutVertices[vertexCount - 1],
*newCutVertices[0] );
newCutEdges[vertexCount - 1] =
& mesh.createEdge ( *newCutVertices[vertexCount - 1], *newCutVertices[0] );
secondEdge = initialEdge;
mesh::Triangle & t0 =
mesh.createTriangle ( *firstEdge, *newCutEdges[vertexCount -1], *crossingEdge );
mesh::Triangle & t1 =
mesh.createTriangle ( *crossingEdge, *secondEdge, *cutEdges[vertexCount - 1] );
if ( propertyContainer != NULL ) {
crossingEdge->addParent ( *propertyContainer );
newCutEdges[vertexCount - 1]->addParent ( *propertyContainer );
t0.addParent ( *propertyContainer );
t1.addParent ( *propertyContainer );
}
// Transfer cutting vertices and edges
for ( int i=0; i < vertexCount; i++ ) {
cutVertices[i] = newCutVertices[i];
cutEdges[i] = newCutEdges[i];
}
delete[] newCutVertices;
delete[] newCutEdges;
}
}
void DriftRatchet:: createLeftWall
(
mesh::Mesh& mesh,
mesh::PropertyContainer* propertyContainer,
mesh::Vertex* cutVertices[],
mesh::Edge* cutEdges[] )
{
int dimensions = mesh.getDimensions();
if ( dimensions == 2 ){
using utils::Vector2D;
double radius = getRadius ( 0.0 );
Vector2D center ( 0.0 );
mesh::Vertex& centerVertex = mesh.createVertex ( center );
if ( propertyContainer != NULL ) {
centerVertex.addParent ( *propertyContainer );
}
Vector2D upperPoint ( center(0), center(1) + radius );
cutVertices[0] = & mesh.createVertex ( upperPoint );
Vector2D lowerPoint ( center(0), center(1) - radius);
cutVertices[1] = & mesh.createVertex ( lowerPoint );
mesh::Edge& e0 = mesh.createEdge ( *cutVertices[0], centerVertex);
mesh::Edge& e1 = mesh.createEdge ( centerVertex, *cutVertices[1] );
if ( propertyContainer != NULL ) {
e0.addParent ( *propertyContainer );
e1.addParent ( *propertyContainer );
}
}
else {
assertion1 ( dimensions == 3, dimensions );
using utils::Vector3D;
double currentAngle = 0.0;
int vertexCount = getNumberOfVerticesPerCut ( _discretizationWidth );
double angle = 2.0 * tarch::la::PI / static_cast<double>(vertexCount);
double radius = getRadius ( 0.0 );
Vector3D center(0.0);
mesh::Vertex& centerVertex = mesh.createVertex ( center );
if ( propertyContainer != NULL ) {
centerVertex.addParent ( *propertyContainer );
}
// Create vertices
for ( int i=0; i < vertexCount; i++ ) {
Vector3D currentPoint ( center );
double y = std::cos(currentAngle) * radius;
currentPoint(1) += y;
double z = std::sin(currentAngle) * radius;
currentPoint(2) += z;
currentAngle += angle;
cutVertices[i] = & mesh.createVertex ( currentPoint );
if ( propertyContainer != NULL ) {
cutVertices[i]->addParent ( *propertyContainer );
}
}
// Create edges and triangles
mesh::Edge & firstCenterEdge = mesh.createEdge ( centerVertex,
*cutVertices[0] );
mesh::Edge * oldCenterEdge = & firstCenterEdge;
mesh::Edge * newCenterEdge = NULL;
for ( int i=0; i < vertexCount - 1; i++ ) {
newCenterEdge = & mesh.createEdge ( centerVertex, *cutVertices[i+1] );
cutEdges[i] = & mesh.createEdge ( *cutVertices[i], *cutVertices[i+1] );
mesh::Triangle & t = mesh.createTriangle ( *oldCenterEdge, *cutEdges[i], *newCenterEdge );
if ( propertyContainer != NULL ) {
cutEdges[i]->addParent ( *propertyContainer );
oldCenterEdge->addParent ( *propertyContainer );
t.addParent ( *propertyContainer );
}
oldCenterEdge = newCenterEdge;
}
cutEdges[vertexCount-1] = & mesh.createEdge ( *cutVertices[vertexCount-1],
*cutVertices[0] );
mesh::Triangle & t = mesh.createTriangle (
*oldCenterEdge, *cutEdges[vertexCount-1], firstCenterEdge );
if ( propertyContainer != NULL ) {
cutEdges[vertexCount-1]->addParent ( *propertyContainer );
t.addParent ( *propertyContainer );
}
}
}
void Physics::initialise(double& t, const mesh::Mesh& m,
iterator u, iterator udash, iterator temp,
Callback compute_residual)
{
// allocate storage
initialise_vectors( m );
// Set initial values
set_initial_conditions(t, m);
for( int i=0; i<m.local_nodes(); i++ ){
u[i].h = h_vec[i];
udash[i].M = 0;
}
// set M and C according to pressure and concentration
process_volumes_psk( m ); // find theta for each volume
for( int i=0; i<m.local_nodes(); i++ ){
u[i].M = rho_vec[i]*theta_vec[i];
//std::cout << u[i].M << " " << rho_vec[i] << " " << theta_vec[i] << std::endl;
}
// Compute residual
compute_residual(temp, true);
// determine the derivative coefficients
process_derivative_coefficients( m );
// Set initial derivatives
for( int f=0; f<m.interior_cvfaces(); f++ ){
int front_id = m.cvface(f).front().id();
double vol = m.volume(front_id).vol();
if (front_id < m.local_nodes()){
udash[front_id].M += M_flux_faces[f]/vol;
}
int back_id = m.cvface(f).back().id();
vol = m.volume(back_id).vol();
if (back_id < m.local_nodes()){
udash[back_id].M -= M_flux_faces[f]/vol;
}
}
for( int f=m.interior_cvfaces(); f<m.cvfaces(); f++){
int back_id = m.cvface(f).back().id();
double vol = m.volume(back_id).vol();
if (back_id < m.local_nodes()){
udash[back_id].M -= M_flux_faces[f]/vol;
}
}
/*
for(int i=0; i<m.local_nodes(); i++){
if(fabs(udash[i].M)>1e-10)
//std::cout << i << " " << u[i].h << " " << u[i].M << " " << udash[i].h << " " << udash[i].M << std::endl;
}
*/
}