------------------------------------------------------------------------------ Generate scale and position information for each atom sphere
| 353 | //------------------------------------------------------------------------------ |
| 354 | // Generate scale and position information for each atom sphere |
| 355 | void vtkMoleculeMapper::UpdateAtomGlyphPolyData() |
| 356 | { |
| 357 | this->AtomGlyphPolyData->Initialize(); |
| 358 | |
| 359 | vtkMolecule* molecule = this->GetInput(); |
| 360 | |
| 361 | vtkAbstractArray* inputColorArray = this->GetInputAbstractArrayToProcess(0, molecule); |
| 362 | vtkAbstractArray* colorArray = nullptr; |
| 363 | vtkUnsignedCharArray* singleColorArray = nullptr; |
| 364 | switch (this->AtomColorMode) |
| 365 | { |
| 366 | case SingleColor: |
| 367 | { |
| 368 | colorArray = vtkUnsignedCharArray::New(); |
| 369 | colorArray->SetNumberOfComponents(3); |
| 370 | vtkIdType size = 3 * molecule->GetNumberOfAtoms(); |
| 371 | colorArray->Allocate(size); |
| 372 | colorArray->SetName("Colors"); |
| 373 | singleColorArray = vtkArrayDownCast<vtkUnsignedCharArray>(colorArray); |
| 374 | this->AtomGlyphPolyData->GetPointData()->SetScalars(singleColorArray); |
| 375 | break; |
| 376 | } |
| 377 | case DiscreteByAtom: |
| 378 | default: |
| 379 | if (inputColorArray != nullptr) |
| 380 | { |
| 381 | colorArray = inputColorArray->NewInstance(); |
| 382 | colorArray->SetNumberOfComponents(inputColorArray->GetNumberOfComponents()); |
| 383 | colorArray->Allocate(colorArray->GetNumberOfComponents() * molecule->GetNumberOfAtoms()); |
| 384 | } |
| 385 | this->AtomGlyphMapper->SetLookupTable(this->LookupTable); |
| 386 | break; |
| 387 | } |
| 388 | |
| 389 | vtkNew<vtkUnsignedShortArray> atomicNbWithoutGhostArray; |
| 390 | vtkUnsignedShortArray* atomicNbFullArray = molecule->GetAtomicNumberArray(); |
| 391 | vtkNew<vtkPoints> points; |
| 392 | vtkPoints* allPoints = molecule->GetAtomicPositionArray(); |
| 393 | vtkUnsignedCharArray* ghosts = molecule->GetAtomGhostArray(); |
| 394 | for (vtkIdType i = 0; i < molecule->GetNumberOfAtoms(); i++) |
| 395 | { |
| 396 | /** |
| 397 | * Skip ghost atoms but not ghost bonds: |
| 398 | * - each atom is non-ghost for exactly one MPI node, that will handle it. |
| 399 | * - a ghost bond links an atom and a ghost atom. So there is exactly two MPI nodes |
| 400 | * that contain this ghost bond and no one that contains this bond as non-ghost. |
| 401 | * We let this two MPI nodes handle the ghost bond, as we cannot know if the bond |
| 402 | * was already handled. |
| 403 | */ |
| 404 | if (ghosts && ghosts->GetValue(i) == 1) |
| 405 | { |
| 406 | continue; |
| 407 | } |
| 408 | atomicNbWithoutGhostArray->InsertNextValue(atomicNbFullArray->GetValue(i)); |
| 409 | points->InsertNextPoint(allPoints->GetPoint(i)); |
| 410 | if (this->AtomColorMode == SingleColor) |
| 411 | { |
| 412 | singleColorArray->InsertNextTypedTuple(this->AtomColor); |
no test coverage detected