clean up of some files

AMDiS/CMakeLists.txt

@@ -492,8 +492,7 @@ if(ENABLE_EXTENSIONS)
 		  ${EXTENSIONS_DIR}/base_problems/NavierStokes_TaylorHood_RB.cc
 		  ${EXTENSIONS_DIR}/base_problems/NavierStokes_TH_MultiPhase.cc
 		  ${EXTENSIONS_DIR}/base_problems/NavierStokes_TH_MultiPhase_RB.cc
-		  ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal_Base.cc
-    # 	      ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal.cc
+		  ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal.cc
 		  ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal_Phase.cc
 		  ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal_RB.cc)
 	list(APPEND COMPILEFLAGS "-DHAVE_BASE_PROBLEMS=1")

AMDiS/src/AbstractFunction.h

@@ -27,6 +27,10 @@
 
 #include "Global.h"
 
+#include <boost/preprocessor/arithmetic/inc.hpp>
+#include <boost/preprocessor/repetition/enum_params.hpp>
+#include <boost/preprocessor/repetition/repeat.hpp>
+
 namespace AMDiS {
 
   /** 
@@ -170,6 +174,53 @@ namespace AMDiS {
   };
 
 
+  ///////////////////////////////////////////////////////////////
+  // test of AbstractFunction with arbitrary number of arguments
+  
+  #define ABSTRACT_FUNCTION_MACRO(z, n, _) \
+   template< typename ReturnType, \
+      BOOST_PP_ENUM_PARAMS_Z(z, n, typename T) \
+   > class AbstractFunction ## n { \
+    AbstractFunction ## n (int degree = 0) : \
+      degree_(degree) \
+    {} \
+    virtual ~AbstractFunction ## n () {} \
+    inline int getDegree() const \
+    { \
+      return degree_; \
+    } \
+    virtual ReturnType operator()(BOOST_PP_ENUM_BINARY_PARAMS_Z(z, n, const T, &t)) const = 0; \
+    \
+  protected: \
+    int degree_; \
+   }; \
+   
+//   template< typename ReturnType,
+//     BOOST_PP_ENUM_PARAMS(N, typename T) // expands to typename T0, typename T1, typename T2...
+//     >
+//   class CONCAT_STR(AbstractFunction,N)
+//   {
+//   public:
+//     CONCAT_STR(AbstractFunction,N)(int degree = 0) : 
+//       degree_(degree) 
+//     {}
+// 
+//     virtual ~CONCAT_STR(AbstractFunction,N)() {}
+// 
+//     /// Returns \ref degree_.
+//     inline int getDegree() const 
+//     { 
+//       return degree_; 
+//     }
+// 
+//     /// function evaluation.
+//     virtual ReturnType operator()(BOOST_PP_ENUM_BINARY_PARAMS(N, const T, &t)) const = 0;
+// 
+//   protected:
+//     int degree_;
+//   };
+  
+  BOOST_PP_REPEAT_FROM_TO(1, 11, ABSTRACT_FUNCTION_MACRO, nil)
 
 
 }

AMDiS/src/AdaptInstationary.cc

@@ -192,7 +192,7 @@ namespace AMDiS {
       adaptInfo->setSpaceIteration(0);
 
 
-      // === Do only space iterations only if the maximum is higher than 0. === 
+      // === Do space iterations only if the maximum is higher than 0. === 
 
       if (adaptInfo->getMaxSpaceIteration() > 0) {
     

AMDiS/src/Global.h

@@ -65,6 +65,7 @@
 
 #include <boost/algorithm/string.hpp>
 #include <boost/algorithm/string/trim.hpp>
+#include <boost/math/special_functions/fpclassify.hpp>
 #include "boost/tuple/tuple.hpp"
 #include "AMDiS_fwd.h"
 #include "OpenMP.h"
@@ -148,6 +149,12 @@ namespace AMDiS {
 #endif
   }
   
+  /// check for inf and nan values
+  inline bool isNumber(double val)
+  {
+    return !boost::math::isnan(val) && !boost::math::isinf(val);
+  }
+
   
   /// trim std::string
   inline std::string trim(const std::string& oldStr)

AMDiS/src/ProblemStat.cc

@@ -514,6 +514,7 @@ namespace AMDiS {
   {
     FUNCNAME("ProblemStat::createSolver()");
     
+    // definition of standard-backends
 #if defined HAVE_PARALLEL_PETSC
     string backend("p_petsc");
 #elif defined HAVE_PARALLEL_MTL
@@ -576,7 +577,7 @@ namespace AMDiS {
 	for (int j = 0; j < nComponents; j++)
 	  estimator[i]->addSystem((*systemMatrix)[i][j], 
 				  solution->getDOFVector(j), 
-				  rhs->getDOFVector(j));      
+				  rhs->getDOFVector(j));      // TODO: hier eventuell (i) statt (j) ???
     }
   }
 
@@ -625,7 +626,7 @@ namespace AMDiS {
 					   solutionList));
     }
 
-    // Create own filewriters for each components of the problem
+    // Create own filewriters for each component of the problem
     for (int i = 0; i < nComponents; i++) {
       numberedName = name + "->output[" + boost::lexical_cast<string>(i) + "]";
       filename = "";
@@ -659,13 +660,12 @@ namespace AMDiS {
       return;
     }
 
-    clock_t first = clock();
-
+    Timer t;
     solver->solveSystem(solverMatrix, *solution, *rhs, 
 			createMatrixData, storeMatrixData);
 
     INFO(info, 8)("solution of discrete system needed %.5f seconds\n", 
-		  TIME_USED(first, clock()));
+		  t.elapsed());
 
     adaptInfo->setSolverIterations(solver->getIterations());
     adaptInfo->setMaxSolverIterations(solver->getMaxIterations());
@@ -678,11 +678,7 @@ namespace AMDiS {
   {
     FUNCNAME("ProblemStat::estimate()");
 
-#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
-    double first = MPI::Wtime();
-#else
-    clock_t first = clock();
-#endif
+    Timer t;
 
     if (computeExactError) {
       computeError(adaptInfo);
@@ -708,12 +704,9 @@ namespace AMDiS {
 
 #ifdef HAVE_PARALLEL_DOMAIN_AMDIS
     MPI::COMM_WORLD.Barrier();
-    INFO(info, 8)("estimation of the error needed %.5f seconds\n", 
-		  MPI::Wtime() - first);
-#else
-    INFO(info, 8)("estimation of the error needed %.5f seconds\n",
-		  TIME_USED(first, clock()));
 #endif
+    INFO(info, 8)("estimation of the error needed %.5f seconds\n", 
+		  t.elapsed());
   }
 
 
@@ -1506,8 +1499,7 @@ namespace AMDiS {
       if (matrix) {
 	matrix->assemble(1.0, elInfo, bound);
 	
-	// Take the matrix boundary manager from the public matrix,
-	// but assemble the boundary conditions on the thread private matrix.
+	// assemble the boundary conditions on the matrix.
 	if (matrix->getBoundaryManager())
 	  matrix->getBoundaryManager()->fillBoundaryConditions(elInfo, matrix);
       }
@@ -1518,9 +1510,6 @@ namespace AMDiS {
       elInfo = stack.traverseNext(elInfo);
     }
 
-    // == Finally, if we have assembled in parallel, we have to add the thread ==
-    // == private matrix and vector to the global one.                         ==
-
     if (matrix) {
       matrix->clearDirichletRows();
       matrix->finishAssembling();

AMDiS/src/solver/LinearSolver.h

@@ -95,7 +95,7 @@ namespace AMDiS {
 	print_cycle(100),
 	iterations(-1),
 	error(-1),
-	breakTolNotReached(false),
+	breakTolNotReached(true),
 	calculateResidual(false)
     {      
       Parameters::get(name + "->tolerance", tolerance);
@@ -136,7 +136,7 @@ namespace AMDiS {
 	
 	MSG("Residual norm: ||b-Ax|| = %e\n", residual);
 
-	TEST_EXIT(residual <= tolerance || !breakTolNotReached)
+	TEST_EXIT((isNumber(residual) && residual <= tolerance) || !breakTolNotReached)
 	  ("Tolerance tol = %e could not be reached!\n Set tolerance by '->solver->tolerance:' \n", tolerance);
       }
       return error_code;

AMDiS/src/solver/UmfPackSolver.h

@@ -67,13 +67,12 @@ namespace AMDiS {
 
       int code = (*solver)(x, b);
       
-      if (oem.getInfo() > 0) {
       VectorType r(b); 
       r -= A * x; 
       double residual = two_norm(r);
       oem.setResidual(residual);
       oem.setErrorCode(code);
-      }
+      
       return code;
     }