addBoundary*Operator, static updateAnimationFile and small changes in Initfile

AMDiS/src/Global.h

@@ -56,6 +56,7 @@
 #include <mpi.h>
 #endif
 
+#include <boost/algorithm/string.hpp>
 #include "boost/tuple/tuple.hpp"
 #include "AMDiS_fwd.h"
 
@@ -461,6 +462,7 @@ namespace AMDiS {
     GRD_PSI,
     GRD_PHI
   };
+
 }
 
 #endif // AMDIS_GLOBAL_H

AMDiS/src/Initfile.cc

@@ -8,25 +8,29 @@ using namespace std;
 
 namespace AMDiS {
 
-  /// the small parser for the initfile. see description of read(Initfile&, istream&)
+  /// the small parser for the initfile. see description of 
+  /// read(Initfile&,istream&)
   struct Parser {
     Parser(const string& line) 
     {
       size_t pos = line.find(':');
-      if (pos == string::npos)
-	throw runtime_error("cannot find the delimiter ':' in line '" + line + "'");
+      if (pos == string::npos) {
+        throw runtime_error("cannot find the delimiter ':' in line "
+            "'" + line + "'");
+      }
       name = line.substr(0, pos);
       value = line.substr(pos + 1, line.length() - (pos + 1));
 
       // remove everything after the %
       pos = value.find('%');
       if (pos != string::npos)
-	value = value.substr(0, pos);
+        value = value.substr(0, pos);
     }
     string name;
     string value;
   };
 
+
   Initfile* Initfile::singlett= NULL;
   std::set<std::string> Initfile::fn_include_list;
 
@@ -39,7 +43,7 @@ namespace AMDiS {
     fn_include_list.clear();
     singlett->read(in);	
     singlett->getInternalParameters();
-	
+
     // initialize global strcutures using parameters
     Global::init();
   }
@@ -53,8 +57,8 @@ namespace AMDiS {
       std::ifstream inputFile;
       inputFile.open(fn.c_str(), std::ios::in);
       if (!inputFile.is_open())
-	throw runtime_error("init-file cannot be opened for reading");
-		
+	      throw runtime_error("init-file cannot be opened for reading");
+
       fn_include_list.insert(fn);
       read(inputFile);
     }
@@ -71,34 +75,37 @@ namespace AMDiS {
       std::string whitespaces = " \t\r\f";
       std::string sw(swap);
       size_t pos0 = sw.find_first_not_of(whitespaces);
-		
-      if (pos0 != std::string::npos && sw[pos0] != '%' && sw[pos0] != '#' && sw[pos0] != 0) {
-	// parse line and extract map: tag->value
-	Parser parser(sw);
-	operator[](parser.name) = parser.value;
-      } else if (sw[pos0] == '#' && static_cast<size_t>(sw.find("#include")) == pos0) {
-	// include file by '#include "filename"' or '#include <filename>'
-	size_t pos = sw.find_first_not_of(whitespaces, std::string("#include").size() + 1);
-	size_t epos = 0;
-	std::string fn =  "";
-	std::stringstream errorMsg;
-	switch (char c= swap[pos++]) {
-	case '<':
-	  c= '>';
-	case '\"':
-	  whitespaces += c;
-	  epos = sw.find_first_of(whitespaces, pos);
-	  fn = sw.substr(pos, epos - pos);
-			
-	  if (sw[epos]!=c) {
-	    errorMsg << "filename in #include not terminated by " << c;
-	    throw std::runtime_error(errorMsg.str());
-	  }
-	  break;
-	default:
-	  throw std::runtime_error("no filename given for #include");
-	}
-	read(fn);
+
+      if (pos0 != std::string::npos && sw[pos0] != '%' 
+          && sw[pos0] != '#' && sw[pos0] != 0) {
+        // parse line and extract map: tag->value
+        Parser parser(sw);
+        operator[](parser.name) = parser.value;
+      } else if (sw[pos0] == '#' 
+          && static_cast<size_t>(sw.find("#include")) == pos0) {
+        // include file by '#include "filename"' or '#include <filename>'
+        size_t pos = sw.find_first_not_of(whitespaces, 
+          std::string("#include").size() + 1);
+        size_t epos = 0;
+        std::string fn =  "";
+        std::stringstream errorMsg;
+        switch (char c= swap[pos++]) {
+          case '<':
+            c= '>';
+          case '\"':
+            whitespaces += c;
+            epos = sw.find_first_of(whitespaces, pos);
+            fn = sw.substr(pos, epos - pos);
+
+            if (sw[epos]!=c) {
+              errorMsg << "filename in #include not terminated by " << c;
+              throw std::runtime_error(errorMsg.str());
+            }
+            break;
+          default:
+            throw std::runtime_error("no filename given for #include");
+        }
+        read(fn);
       }
       in.getline(swap, line_length);
     }
@@ -109,8 +116,8 @@ namespace AMDiS {
   {
     for (int i = 0; i < argc; i++) {
       if (strcmp("-rs", argv[i]) == 0) {
-	std::string input(argv[i + 1]);
-	add("argv->rs", input, 0);
+        std::string input(argv[i + 1]);
+        add("argv->rs", input, 0);
       }
     }
   }
@@ -122,15 +129,15 @@ namespace AMDiS {
     int val = 0;
     get("level of information", val, 0);
     msgInfo = val;
-	
+
     val = 1;
     get("WAIT", val, 0);
     msgWait = val;
-	
+
     val = 1;
     get("parameter information", val, 0);
     paramInfo = val;
-	
+
     val = 0;
     get("break on missing tag", val, 0);
     breakOnMissingTag = val;
@@ -145,7 +152,7 @@ namespace AMDiS {
   {
     initIntern();
     for (Initfile::iterator it = singlett->begin(); it != singlett->end(); it++)
-      std::cout << (*it).first << " => " << (*it).second << std::endl;
+    std::cout << (*it).first << " => " << (*it).second << std::endl;
   }
 
 
@@ -153,7 +160,7 @@ namespace AMDiS {
   void Initfile::write(ostream& out)
   {
     for (Initfile::iterator it = begin() ; it!=end(); it++)
-      out << (*it).first << ": " << (*it).second << std::endl;	
+    out << (*it).first << ": " << (*it).second << std::endl;	
   }
 
 
@@ -164,8 +171,7 @@ namespace AMDiS {
     outFile.open(fn.c_str(), std::ios::out);
     if (!outFile.is_open())
       throw runtime_error("init-file cannot be opened for writing");
-	
+
     write(outFile);
   }
-
-}
+} // end namespace AMDiS

AMDiS/src/Initfile.h

+//
+// Software License for AMDiS
+//
+// Copyright (c) 2010 Dresden University of Technology 
+// All rights reserved.
+// Authors: Simon Vey, Thomas Witkowski et al.
+//
+// This file is part of AMDiS
+//
+// See also license.opensource.txt in the distribution.
+
 #ifndef INITFILE_H
 #define INITFILE_H
 
@@ -25,23 +36,25 @@
 namespace AMDiS {
 
   namespace InitfileInternal {
-
+  
     /// Exceptions
     struct WrongVectorSize : std::runtime_error {
       WrongVectorSize(std::string m)
-	: std::runtime_error(m) 
+      : std::runtime_error(m) 
       {}
     };
 
+
     struct NoDelim : std::runtime_error {
       NoDelim(std::string m)
-	: std::runtime_error(m) 
+      : std::runtime_error(m) 
       {}
     };
 
+
     struct WrongVectorFormat : std::runtime_error {
       WrongVectorFormat(std::string m) 
-	: std::runtime_error(m) 
+      : std::runtime_error(m) 
       {}
     };
 
@@ -49,33 +62,33 @@ namespace AMDiS {
     struct WrongValueFormat : std::runtime_error {
       static std::string name(int) 
       { 
-	return "int"; 
+        return "int"; 
       }
-      
+
       static std::string name(bool) 
       { 
-	return "bool"; 
+        return "bool"; 
       }
-      
+
       static std::string name(double) 
       { 
-	return "double"; 
+        return "double"; 
       }
-      
+
       static std::string name(unsigned int) 
       { 
-	return "unsigned int";
+        return "unsigned int";
       }
 
       template<typename G>
       static std::string name(G) 
       { 
-	return std::string(typeid(G).name()); 
+        return std::string(typeid(G).name()); 
       }
-		
+
       WrongValueFormat(std::string value)
-	: std::runtime_error(std::string("cannot convert '") + 
-			     value + std::string("' into <") + name(T()) + ">")
+      : std::runtime_error(std::string("cannot convert '") + 
+        value + std::string("' into <") + name(T()) + ">")
       {}
     };
 
@@ -83,38 +96,38 @@ namespace AMDiS {
     struct BadArithmeticExpression : std::runtime_error {
       static std::string name(int) 
       {
-	return "int";
+        return "int";
       }
-      
+
       static std::string name(bool) 
       { 
-	return "bool";
+        return "bool";
       }
-      
+
       static std::string name(double) 
       { 
-	return "double";
+        return "double";
       }
-      
+
       static std::string name(unsigned int) 
       {
-	return "unsigned int";
+        return "unsigned int";
       }
-     
+
       template<typename G>
       static std::string name(G) 
       { 
-	return std::string(typeid(G).name());
+        return std::string(typeid(G).name());
       }
-		
+
       BadArithmeticExpression(std::string m, std::string value) 
-	: std::runtime_error(std::string("cannot evaluate expression '") + 
-			     value + std::string("' into <") + name(T()) + 
-			     ">\nParser message: '" + m + "'") 
+      : std::runtime_error(std::string("cannot evaluate expression '") + 
+        value + std::string("' into <") + name(T()) + 
+        ">\nParser message: '" + m + "'") 
       {}
     };
 
-	
+
     /// trim std::string
     inline std::string trim(const std::string& oldStr) 
     {
@@ -124,14 +137,15 @@ namespace AMDiS {
     }
 
 
-    /// return the delimiter or throw an exception if there is no known delimiter in value
+    /// return the delimiter or throw an exception if there is no known 
+    /// delimiter in value
     inline size_t checkDelim(const std::string& value, const std::string& delims)
     {
       size_t pos(std::string::npos);
       for (unsigned i = 0; i < delims.length(); i++) {
-	pos = value.find(delims[i]);
-	if (pos != std::string::npos)
-	  return i;
+        pos = value.find(delims[i]);
+        if (pos != std::string::npos)
+          return i;
       }
       throw NoDelim("cannot detect the delimiter in " + value);
       return 0; 
@@ -139,12 +153,12 @@ namespace AMDiS {
 
 
     /** parse an container from tag tag. The Container must have the properties:
-     * 	- type value_type
-     * 	- member function push_back
-     */
+    * 	- type value_type
+    * 	- member function push_back
+    */
     template< typename Container >
     inline void getContainer(const std::string val_, Container& c)
-    {		
+    {
       // accepted brackets and delimiters for vector input
       std::string begBrackets= "{[(";
       std::string endBrackets= "}])";
@@ -154,35 +168,37 @@ namespace AMDiS {
       std::string val = trim(val_); 
       size_t pos = begBrackets.find(val[0]);
       if (pos == std::string::npos)
-	throw WrongVectorFormat("cannot convert '" + val + "' into a list. No leading bracket found!");
+        throw WrongVectorFormat("cannot convert "
+            "'" + val + "' into a list. No leading bracket found!");
       if (val[val.length() - 1] != endBrackets[pos])
-	throw WrongVectorFormat("begin and end bracket are different in value '" + val + "'");
+        throw WrongVectorFormat("begin and end bracket are different in"
+            " value '" + val + "'");
       size_t oldPos = 1;
       size_t curDelim = 0;
       typedef typename Container::value_type ValueType;
       ValueType swap;
       try {
-	curDelim = checkDelim(val, delims);
-	pos = val.find(delims[curDelim], oldPos);
-	while (pos != std::string::npos) {
-	  std::string curWord = val.substr(oldPos, pos - oldPos);
-	  oldPos = pos + 1;
-	  convert(curWord, swap);
-	  c.push_back(swap);
-	  pos= val.find(delims[curDelim], oldPos);
-	}
-	//last entry
-	std::string curWord = val.substr(oldPos, val.length() - 1 - oldPos);
-	convert(curWord, swap);
-	c.push_back(swap);
+        curDelim = checkDelim(val, delims);
+        pos = val.find(delims[curDelim], oldPos);
+        while (pos != std::string::npos) {
+          std::string curWord = val.substr(oldPos, pos - oldPos);
+          oldPos = pos + 1;
+          convert(curWord, swap);
+          c.push_back(swap);
+          pos = val.find(delims[curDelim], oldPos);
+        }
+        //last entry
+        std::string curWord = val.substr(oldPos, val.length() - 1 - oldPos);
+        convert(curWord, swap);
+        c.push_back(swap);
       } catch (NoDelim nd) {
-	std::string curWord = val.substr(1, val.length() - 2);
-	curWord = trim(curWord);
-	if (curWord.length() > 0) {
-	  // container with one entry
-	  convert(curWord, swap);
-	  c.push_back(swap);
-	}
+        std::string curWord = val.substr(1, val.length() - 2);
+        curWord = trim(curWord);
+        if (curWord.length() > 0) {
+          // container with one entry
+          convert(curWord, swap);
+          c.push_back(swap);
+        }
       }
     }
 
@@ -197,43 +213,62 @@ namespace AMDiS {
     /// convert string to intrinsic type
     template<typename T>
     inline void convert(const std::string valStr, T& value , 
-			typename boost::enable_if<boost::is_pod<T> >::type* p = NULL , 
-			typename boost::disable_if<boost::is_enum<T> >::type* p2 = NULL)
+        typename boost::enable_if<boost::is_pod<T> >::type* p = NULL , 
+        typename boost::disable_if<boost::is_enum<T> >::type* p2 = NULL)
     {
       using boost::lexical_cast;
       using boost::numeric_cast;
 
       mu::Parser parser;
-
       parser.DefineConst(_T("M_PI"), m_pi);
       parser.DefineConst(_T("M_E"), m_e);
+
       try {
-	parser.SetExpr(valStr);
-	value = numeric_cast< T >(parser.Eval());
-      } catch(boost::bad_lexical_cast e) {
-	throw WrongValueFormat< T >(valStr);
-      } catch(boost::bad_numeric_cast e) {
-	throw WrongValueFormat< T >(valStr);
+        parser.SetExpr(valStr);
+        value = numeric_cast< T >(parser.Eval());
+      } catch (boost::bad_lexical_cast e) {
+        throw WrongValueFormat< T >(valStr);
+      } catch (boost::bad_numeric_cast e) {
+        throw WrongValueFormat< T >(valStr);
       } catch (mu::Parser::exception_type &e) {
-	throw BadArithmeticExpression<T>(e.GetMsg(), valStr);
+        throw BadArithmeticExpression<T>(e.GetMsg(), valStr);
       }
     }
 
 
     template<typename T>
     inline void convert(const std::string valStr, T& value, 
-			typename boost::enable_if< boost::is_enum< T > >::type* p = NULL) 
+        typename boost::enable_if< boost::is_enum< T > >::type* p = NULL)