Fixed problem for nnz structure with PETSc global matrix solver.

AMDiS/src/parallel/ParallelDebug.cc

@@ -421,7 +421,7 @@ namespace AMDiS {
 	WorldVector<double> tmp = (it->second)[i];
 	tmp -=  recvCoords[it->first][i];
 
-	if (norm(tmp) > 1e-13) {
+	if (norm(tmp) > 1e-8) {
 	  // === Print error message if the coordinates are not the same. ===
 	  if (printCoords) {
 	    MSG("[DBG] i = %d\n", i);	  

AMDiS/src/parallel/PetscSolverGlobalMatrix.cc

@@ -48,7 +48,9 @@ namespace AMDiS {
     meshDistributor->getMpiComm().Allreduce(&sendValue, &recvAllValues, 
 					    1, MPI_INT, MPI_SUM);
 
-    if (!d_nnz || recvAllValues != 0) {
+    recvAllValues = 1;
+
+    if (!d_nnz || recvAllValues != 0 || alwaysCreateNnzStructure) {
       if (d_nnz) {
 	delete [] d_nnz;
 	d_nnz = NULL;

AMDiS/src/parallel/PetscSolverGlobalMatrix.h

@@ -39,9 +39,12 @@ namespace AMDiS {
 	d_nnz(NULL),
 	o_nnz(NULL),
 	lastMeshNnz(0),
-	zeroStartVector(false)
+	zeroStartVector(false),
+	alwaysCreateNnzStructure(false)
     {
       Parameters::get("parallel->use zero start vector", zeroStartVector);
+      Parameters::get("parallel->always create nnz structure", 
+		      alwaysCreateNnzStructure);
     }
 
     void fillPetscMatrix(Matrix<DOFMatrix*> *mat);
@@ -77,6 +80,14 @@ namespace AMDiS {
     int lastMeshNnz;
 
     bool zeroStartVector;
+
+    /// If this variable is set to true, the non-zero matrix structure is
+    /// created each time from scratch by calling \ref createPetscNnzStrcuture.
+    /// This can be necessary if the number of non-zeros in the matrix varies
+    /// though the mesh does not change. This may happen if there are many
+    /// operators using DOFVectors from old timestep containing many zeros due to
+    /// some phase fields.
+    bool alwaysCreateNnzStructure;
   };