Initfile-parser extended

AMDiS/src/AMDiS.cc

@@ -41,7 +41,10 @@ namespace AMDiS {
     Zoltan_Initialize(argc, argv, &zoltanVersion);
 #endif
 #endif
-
+    
+    Parameters::clearData();
+    Parameters::readArgv(argc, argv);
+    
     if (initFileName == "") {
       TEST_EXIT(argc >= 2)("No init file!\n");
       Parameters::init(string(argv[1]));

AMDiS/src/DOFIndexed.h

@@ -92,20 +92,26 @@ namespace AMDiS {
   template<typename T>
   class DOFIndexed : public DOFIndexedBase
   {
+  public:
+    typedef T 			value_type;
+    typedef DegreeOfFreedom	size_type;
+    typedef value_type&		reference;
+    typedef value_type const&	const_reference;
+    
   public:
     virtual ~DOFIndexed() {}
 
     /// Returns iterator to the begin of container
-    virtual typename std::vector<T>::iterator begin() = 0;
+    virtual typename std::vector<value_type>::iterator begin() = 0;
 
     /// Returns iterator to the end of container
-    virtual typename std::vector<T>::iterator end() = 0;
+    virtual typename std::vector<value_type>::iterator end() = 0;
 
     /// Returns container element at index i
-    virtual T& operator[](DegreeOfFreedom i) = 0;
+    virtual reference operator[](size_type i) = 0;
 
     /// Returns container element at index i
-    virtual const T& operator[](DegreeOfFreedom i) const = 0;
+    virtual const_reference operator[](size_type i) const = 0;
   };
 
   void mv(MatrixTranspose transpose, 

AMDiS/src/Global.h

@@ -57,6 +57,7 @@
 #endif
 
 #include <boost/algorithm/string.hpp>
+#include <boost/algorithm/string/trim.hpp>
 #include "boost/tuple/tuple.hpp"
 #include "AMDiS_fwd.h"
 
@@ -123,6 +124,20 @@ namespace AMDiS {
     }
   };
 
+  /// check for file existence
+  inline bool file_exists(const std::string filename)
+  {
+    return access(filename.c_str(), F_OK) == 0;
+  };
+
+  /// trim std::string
+  inline std::string trim(const std::string& oldStr)
+  {
+    std::string swap(oldStr);
+    boost::algorithm::trim(swap);
+    return swap;
+  };
+
   // ===== some simple template functions ====================================== 
 
   template<typename T> inline T abs(T a) 

AMDiS/src/Initfile.cc

@@ -39,7 +39,6 @@ namespace AMDiS {
   void Initfile::init(std::string in)
   {
     initIntern();
-    singlett->clear();
     fn_include_list.clear();
     singlett->read(in);	
     singlett->getInternalParameters();
@@ -84,8 +83,8 @@ namespace AMDiS {
         Parser parser(sw);
         
         // add parameter to map after variable replacement
-        std::string paramName = variableReplacement(InitfileInternal::trim(parser.name));
-        std::string paramValue = variableReplacement(InitfileInternal::trim(parser.value));
+        std::string paramName = variableReplacement(trim(parser.name));
+        std::string paramValue = variableReplacement(trim(parser.value));
         paramValue = variableEvaluation(paramValue);
       
         operator[](paramName) = paramValue;
@@ -164,7 +163,7 @@ namespace AMDiS {
       std::string replaceName = inputSwap.substr(posVar , posVarEnd - posVar + (posVarBegin - posVar));
       inputSwap.replace(inputSwap.find(replaceName), replaceName.length(), varParam);
 
-      posVar = inputSwap.find_first_of('$',posVarEnd);
+      posVar = inputSwap.find_first_of('$',posVarBegin);
     }
 
     return inputSwap;
@@ -174,16 +173,11 @@ namespace AMDiS {
   {
     std::string whitespaces = " \t\r\f";
     std::string inputSwap = input;
-    size_t posVar = inputSwap.find_first_of('$');
+    size_t posVar = inputSwap.find("$(");
     while (posVar != string::npos) {
       size_t posVarBegin, posVarEnd;
-      if(inputSwap[posVar+1] == '(') {	// $(expr)
-        posVarEnd = inputSwap.find_first_of(')',posVar + 2);
-        posVarBegin = posVar + 1;
-      } else {
-	posVar = inputSwap.find_first_of('$',posVar+1);
-	continue;
-      }
+      posVarEnd = inputSwap.find_first_of(')',posVar + 2);
+      posVarBegin = posVar + 1;
       std::string varName = inputSwap.substr(posVarBegin + 1 , posVarEnd - posVarBegin - 1);
 
       double value = 0.0;
@@ -193,7 +187,7 @@ namespace AMDiS {
       std::string replaceName = inputSwap.substr(posVar , posVarEnd - posVar + (posVarBegin - posVar));
       inputSwap.replace(inputSwap.find(replaceName), replaceName.length(), varName);
 
-      posVar = inputSwap.find_first_of('$');
+      posVar = inputSwap.find("$(",posVarBegin);
     }
 
     return inputSwap;
@@ -201,11 +195,36 @@ namespace AMDiS {
 
   void Initfile::readArgv(int argc, char **argv)
   {
+    initIntern();
     for (int i = 0; i < argc; i++) {
       if (strcmp("-rs", argv[i]) == 0) {
         std::string input(argv[i + 1]);
         add("argv->rs", input, 0);
       }
+      else if (strcmp("-parameters", argv[i]) == 0) {
+        std::string input(argv[i + 1]);
+	int found = input.find_first_of(';');
+
+	std::vector<std::string> parameters;
+	while (found != static_cast<int>(std::string::npos)) {
+	  if (found > 2) {
+	    parameters.push_back(input.substr(0, found).c_str());
+	  }
+	  input = input.substr(found + 1);
+	  found = input.find_first_of(';');
+	}
+	if (input.length() > 2)
+	  parameters.push_back(input.c_str());
+
+	for (size_t i = 0; i < parameters.size(); i++) {
+	  int found = input.find_first_of(':');
+	  if (found != static_cast<int>(std::string::npos)) {
+	    std::string value = input.substr(found+1);
+	    set(input.substr(0, found), value, 0);
+	  }
+	}
+	
+      }
     }
   }
 

AMDiS/src/Initfile.h

@@ -24,7 +24,6 @@
 #include <typeinfo>
 #include "FixVec.h"
 
-#include <boost/algorithm/string/trim.hpp>
 #include <boost/lexical_cast.hpp>
 #include <boost/numeric/conversion/cast.hpp> 
 
@@ -132,16 +131,7 @@ namespace AMDiS {
         ">\nParser message: '" + m + "'") 
       {}
     };
-
-
-    /// trim std::string
-    inline std::string trim(const std::string& oldStr) 
-    {
-      std::string swap(oldStr);
-      boost::algorithm::trim(swap);
-      return swap;
-    }
-
+    
 
     /// return the delimiter or throw an exception if there is no known 
     /// delimiter in value

AMDiS/src/io/VtkWriter.cc

@@ -199,7 +199,7 @@ namespace AMDiS {
   {
     WorldVector<DOFVector<double>*> valuesWV;
     for (int i =0 ; i < valuesWV.getSize(); i++)
-      valuesWV[i] = new DOFVector<double>(values->getFeSpace(), "valuesWV_i");
+      valuesWV[i] = new DOFVector<double>(values->getFeSpace(), "values["+boost::lexical_cast<std::string>(i)+"]");
     transform(values, &valuesWV);
     writeFile(valuesWV, filename, writeParallel);
     for (int i = 0; i < valuesWV.getSize(); i++)