Added init and finalize functions in AMDiS namespace. Removed Parameters class.

AMDiS/CMakeLists.txt

@@ -64,6 +64,7 @@ SET(AMDIS_SRC ${SOURCE_DIR}/AdaptBase.cc
 	      ${SOURCE_DIR}/AdaptInfo.cc
 	      ${SOURCE_DIR}/AdaptInstationary.cc
 	      ${SOURCE_DIR}/AdaptStationary.cc
+	      ${SOURCE_DIR}/AMDiS.cc
 	      ${SOURCE_DIR}/Assembler.cc
 	      ${SOURCE_DIR}/BasisFunction.cc
 	      ${SOURCE_DIR}/Boundary.cc

AMDiS/src/AMDiS.cc

+//
+// 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.
+
+
+#include "AMDiS.h"
+#include <string>
+#ifdef HAVE_ZOLTAN
+#include <zoltan_cpp.h>
+#endif
+
+namespace AMDiS {
+
+  using namespace std;
+
+  void init(int argc, char **argv)
+  {
+    FUNCNAME("AMDiS::init()");
+
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+    PetscInitialize(&argc, &argv, NULL, NULL);
+    mpi::startRand();
+
+#ifdef HAVE_ZOLTAN
+    float zoltanVersion = 0.0;
+    Zoltan_Initialize(argc, argv, &zoltanVersion);
+#endif
+#endif
+
+    TEST_EXIT(argc >= 2)("No init file!\n");
+
+    if (string(argv[0]) != "ddt")
+      Parameters::init(string(argv[1]));
+    else 
+      Parameters::init(string(argv[2]));
+
+    Parameters::readArgv(argc, argv);
+  }
+
+
+  void finalize()
+  {
+    FUNCNAME("AMDiS::finalize()");
+
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+    MeshDistributor::globalMeshDistributor->exitParallelization();
+    PetscFinalize();
+#endif
+  }
+
+}

AMDiS/src/AMDiS.h

@@ -144,4 +144,11 @@
 
 #endif
 
+namespace AMDiS {
+
+  void init(int argc, char **argv);
+  
+  void finalize();
+}
+
 #endif

AMDiS/src/CouplingTimeInterface.h

@@ -61,7 +61,7 @@ namespace AMDiS {
     /// Called at the end of each timestep.
     virtual void closeTimestep(AdaptInfo *adaptInfo) 
     {
-      int i, size = static_cast<int>(interfaces_.size());
+      int size = static_cast<int>(interfaces_.size());
       for (int i = 0; i < size; i++)
 	interfaces_[i]->closeTimestep(adaptInfo);
     }

AMDiS/src/CreatorMap.h

@@ -53,12 +53,14 @@ namespace AMDiS {
     }
 
     /// Creates a object of the type corresponding to key.
-    static CreatorInterface<BaseClass>* getCreator(std::string key) 
+    static CreatorInterface<BaseClass>* getCreator(std::string key,
+						   std::string initFileStr) 
     {
       FUNCNAME("CreatorMap::getCreator()");
       init();
       CreatorInterface<BaseClass> *creator = creatorMap[key];
-      TEST_EXIT(creator)("no creator for key %s\n", key.c_str());
+      TEST_EXIT(creator)("No creator for key \"%s\" defined in init file for parameter \"%s\"\n", 
+			 key.c_str(), initFileStr.c_str());
       return creator;
     }
 

AMDiS/src/Element.cc

@@ -561,7 +561,8 @@ namespace AMDiS {
     in.get();
 
     if (typeName != "NULL") {
-      elementData = CreatorMap<ElementData>::getCreator(typeName)->create();
+      elementData = 
+	CreatorMap<ElementData>::getCreator(typeName, "deserializetion from file")->create();
 
       if (elementData)
 	elementData->deserialize(in);

AMDiS/src/ElementData.cc

@@ -74,7 +74,8 @@ namespace AMDiS {
     in >> decoratedType; 
     in.get();
     if (decoratedType != "NULL") {
-      decorated = CreatorMap<ElementData>::getCreator(decoratedType)->create();
+      decorated = 
+	CreatorMap<ElementData>::getCreator(decoratedType, "deserialization from file")->create();
       decorated->deserialize(in);
     } else {
       decorated = NULL;

AMDiS/src/ITL_OEMSolver.hh

@@ -26,21 +26,24 @@ namespace AMDiS {
     void setPrecon(PreconPair< Vector >& pair, const Matrix& matrix)
     {
       /// Creator for the left preconditioner
-      CreatorInterface< ITL_BasePreconditioner< Vector > >* leftCreator(NULL);
+      CreatorInterface< ITL_BasePreconditioner<Vector> >* leftCreator(NULL);
 
       /// Creator for the right preconditioner
-      CreatorInterface< ITL_BasePreconditioner< Vector > >* rightCreator(NULL);
+      CreatorInterface< ITL_BasePreconditioner<Vector> >* rightCreator(NULL);
 
       std::string preconType("no");
-      Parameters::get(oem.getName() + "->left precon", preconType);
-
-      leftCreator = CreatorMap<ITL_BasePreconditioner< Vector > >::getCreator(preconType);
+      std::string initFileStr = oem.getName() + "->left precon";
+      Parameters::get(initFileStr, preconType);
+      leftCreator = 
+	CreatorMap<ITL_BasePreconditioner<Vector> >::getCreator(preconType, initFileStr);
       TEST_EXIT(leftCreator != NULL)
 	("there is no creator for the given left preconditioner");
 
       preconType = "no";
-      Parameters::get(oem.getName() + "->right precon", preconType);
-      rightCreator = CreatorMap<ITL_BasePreconditioner< Vector > >::getCreator(preconType);
+      initFileStr = oem.getName() + "->right precon";
+      Parameters::get(initFileStr, preconType);
+      rightCreator = 
+	CreatorMap<ITL_BasePreconditioner<Vector> >::getCreator(preconType, initFileStr);
       TEST_EXIT(rightCreator != NULL)
 	("there is no creator for the given right preconditioner");
 

AMDiS/src/Initfile.h

@@ -409,9 +409,8 @@ namespace AMDiS {
 
     static void init(int print, string filename, const char *flags = NULL) 
     {
-        WARNING("Parameters::init(int,std::string,const char*) is depreciated. "
-          "Use Parameters::init(std::string) instead!\n");
-        init(filename);
+      ERROR_EXIT("Parameters::init(int,std::string,const char*) is depreciated. "
+		 "Use Parameters::init(std::string) instead!\n");
     }
 
 

AMDiS/src/MTL4Types.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 MTL4TYPES_H
 #define MTL4TYPES_H
 #include <boost/numeric/mtl/mtl.hpp>
+
 namespace AMDiS {
+
   namespace MTLTypes {
-  typedef double value_type;
-  typedef mtl::matrix::compressed2D< value_type > MTLMatrix;
-  typedef mtl::vector::dense_vector< value_type > MTLVector;
+    typedef double value_type;
+    typedef mtl::matrix::compressed2D< value_type > MTLMatrix;
+    typedef mtl::vector::dense_vector< value_type > MTLVector;
   }
+
 }
+
 #endif
 

AMDiS/src/Parameters.cc

-//
-// 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.
-
-
-#include <fstream>
-#include <sstream>
-#include <algorithm>
-#include <stdarg.h>
-#include <time.h>
-#include <cstring>
-#include <sys/types.h>
-#include <sys/stat.h>
-
-#ifndef WIN32
-#include <unistd.h>
-#endif
-
-#include "Parameters.h"
-#include "Serializer.h"
-
-namespace AMDiS {
-
-  using namespace std;
-
-  const char Parameters::comment='%';
-  const string Parameters::separators=",; ";
-  Parameters* Parameters::singlett = NULL;
-
-
-  int Parameters::getGlobalParameter(int info, const string& key, 
-				     const char *format, ...)
-  {
-    FUNCNAME("Parameters::getGlobalParameter()");
-
-    vector<struct Parameters::param>::iterator i;
-    param tParam(key);
-    va_list arg;
-
-    Parameters::initIntern();
-
-    if (Parameters::singlett->paramInfo) {
-      if (Parameters::singlett->paramInfo > 1)
-	info = max(info, Parameters::singlett->paramInfo - 1);
-    } else {
-      info = 0;
-    }
-
-    if (0 == Parameters::singlett->allParam.size()) {
-      if (0 == Parameters::singlett->filename.size()) {
-	INFO(info, 1)("no parameters defined\n");
-	return 0;
-      } else {
-	Parameters::singlett->read(Parameters::singlett->filename,key);
-      }
-    }
-
-    i = find(Parameters::singlett->allParam.begin(),
-		  Parameters::singlett->allParam.end(), tParam);
-
-    if (i == Parameters::singlett->allParam.end()) {
-      INFO(info, 1)("initialization of parameter `%s' fails\n", key.data());     
-   
-      return 0;
-    }
-
-    va_start(arg, format);
-    int count = 0;
-  
-    INFO(info, 2)("parameter `%s' initialized with: ", key.data());
-
-    string s = (*i).parameters;
- 
-    for (const char *p = format; *p; p++) {
-      if (*p != '%')  
-	continue;
-
-      const char *word = Parameters::singlett->getNextWord(&s);
-      if (!*word) {
-	PRINT_INFO(info, 2)("\n");
-	va_end(arg);
-	return count;
-      }
-      count++;
-
-      switch(*++p) {
-      case 'S':
-	{
-	  char *Sval = va_arg(arg, char *);
-	  *Sval = static_cast<char>(atoi(word));
-	  INFO(info, 2)("%d ", *Sval);
-	}
-	break;
-      case 'U':
-	{
-	  unsigned char *Uval = va_arg(arg, unsigned char *);
-	  *Uval = static_cast<unsigned char>(atoi(word));
-	  INFO(info, 2)("%d ", *Uval);
-	}
-	break;
-      case 'c':
-	{
-	  char *cval = va_arg(arg, char *); 
-	  *cval = *word;
-	  INFO(info, 2)("%c ", *cval);
-	}
-	break;
-      case 's':
-	{
-	  char *sval = va_arg(arg, char *);
-	  strcpy(sval, word);
-	  INFO(info, 2)("%s ", sval);
-	}
-	break;
-      case 'd':
-	{
-	  int *ival = va_arg(arg, int *);
-	  *ival = atoi(word);
-	  INFO(info, 2)("%d ", *ival);
-	}
-	break;
-      case 'e':
-      case 'f':
-      case 'g':
-	{
-	  double *rval = va_arg(arg, double *);
-	  *rval = atof(word);
-	  INFO(info, 2)("%g ", *rval);
-	}
-	break;
-      case 'v':	
-	{
-	  WorldVector<double> *vecVal = va_arg(arg, WorldVector<double> *);
-	  string sstr = string(word);
-	  int ind = 0;
-	  int found = sstr.find_first_of(",; ");
-	  string seperator;
-	  seperator = sstr[found];
-	  
-	  while (found != static_cast<int>(string::npos) && 
-		 ind < static_cast<int>(vecVal->size())) {
-	    if (found > 0) {
-	      (*vecVal)[ind] = atof(sstr.substr(0, found).c_str());
-	      ind++;
-	    }
-	    sstr = sstr.substr(found + 1);
-	    found = sstr.find_first_of(seperator);
-	  }
-	  if (sstr.length() > 0 && ind < static_cast<int>(vecVal->size()))
-	    (*vecVal)[ind] = atof(sstr.c_str());	
-	}
-	break;
-      case 'E': // list of double values, example parameter: {a,b,c,d,e}
-      case 'F':
-      case 'G':
-	{
-	  vector<double> *vecVal = va_arg(arg, vector<double> *);
-	  string sstr = string(word);
-
-       string brackets1 = "[{(", brackets2 = "]})";
-	  int bracketIdx1 = sstr.find_first_of(brackets1);
-       int bracket = brackets1.find_first_of(sstr[bracketIdx1]);
-       int bracketIdx2 = sstr.find_first_of(brackets2[bracket]);
-       TEST_EXIT(bracket>=0 && bracketIdx1>=0 && bracketIdx2>=0 && bracketIdx1<bracketIdx2)
-		("no enclosing brackets found in '%s' \n",key.data());
-       sstr = sstr.substr(bracketIdx1+1, bracketIdx2-bracketIdx1);
-
-	  int found = sstr.find_first_of(separators);
-	  string seperator;
-	  seperator = sstr[found];
-	  
-	  while (found != static_cast<int>(string::npos)) {
-	    if (found > 0) {
-	      vecVal->push_back(atof(sstr.substr(0, found).c_str()));
-	    }
-	    sstr = sstr.substr(found + 1);
-	    found = sstr.find_first_of(seperator);
-	  }
-	  if (sstr.length() > 0)
-	    vecVal->push_back(atof(sstr.c_str()));
-	  if (vecVal->size() == 0)
-	    WARNING("no values in parameter vector!\n");
-	}
-	break;
-      case 'D': // list of int values, example parameter: {a,b,c,d,e}
-	{
-	  vector<int> *vecVal = va_arg(arg, vector<int> *);
-	  string sstr = string(word);
-
-       string brackets1 = "[{(", brackets2 = "]})";
-	  int bracketIdx1 = sstr.find_first_of(brackets1);
-       int bracket = brackets1.find_first_of(sstr[bracketIdx1]);
-       int bracketIdx2 = sstr.find_first_of(brackets2[bracket]);
-       TEST_EXIT(bracket>=0 && bracketIdx1>=0 && bracketIdx2>=0 && bracketIdx1<bracketIdx2)
-		("no enclosing brackets found in '%s' \n",key.data());
-       sstr = sstr.substr(bracketIdx1+1, bracketIdx2-bracketIdx1);
-
-	  int found = sstr.find_first_of(separators);
-	  string seperator;
-	  seperator = sstr[found];
-	  
-	  while (found != static_cast<int>(string::npos)) {
-	    if (found > 0) {
-	      vecVal->push_back(atoi(sstr.substr(0, found).c_str()));
-	    }
-	    sstr = sstr.substr(found + 1);
-	    found = sstr.find_first_of(seperator);
-	  }
-	  if (sstr.length() > 0)
-	    vecVal->push_back(atoi(sstr.c_str()));
-       if (vecVal->size() == 0)
-         WARNING("no values in parameter vector!\n");
-	}
-	break;
-      case '*':
-	break;
-      default: 
-	INFO(info, 2)("\n");
-	INFO(info, 2)
-	  ("unknow format specifier `%%%c', skipping initialization of %s\n",
-	   *p, key.data());
-      }
-    }
-
-    INFO(info, 2)("\n");
-
-    va_end(arg);
-
-    return count;
-  }
-
-
-  void Parameters::read(const string& aFilename, 
-			const string& maxKey)
-  {
-    FUNCNAME("Parameters::read()");
-
-    char line[256];
-    int nLine = 0;
-    string key, parameter;
-    string actfile;
-
-    if (aFilename.size() == 0)
-      return;
-
-    singlett->inputFile.open(aFilename.c_str(), ios::in);
-    if (!inputFile.is_open()) {
-      ERROR("init-file can't be opened\n");
-      return;
-    }
-
-    INFO(paramInfo, 2)("reading from file %s\n", aFilename.data());
-    actfile = getActFile(aFilename);
-    
-    while (!inputFile.eof()) {
-      inputFile.getline(line, 255);
-      nLine++;
-
-      key = getKey(line, nLine, aFilename);
-      
-      if (key == "")
-	continue;
-
-      parameter = getPar(key, line, &nLine, aFilename);
-      if (parameter == "")  
-	continue;
-      
-      addParam(key, parameter);
-    }
-
-    singlett->inputFile.close();
-  }
-
-
-  const string& Parameters::getActFile(const string& aFilename)
-  {
-    FUNCNAME("Parameters::getActFile()");
-
-    list< string >::iterator i;
-    for (i = filenames.begin(); i != filenames.end(); i++)
-      if (aFilename==*i) 
-	break;
-  
-    if (i != filenames.end()) {
-      return(const_cast<const string&>(*i));
-    } else {
-      filenames.push_back(aFilename);
-      return(const_cast<const string&>(aFilename));
-    }
-  }
-
-
-  void Parameters::swap(int i, int j)
-  {
-    param tmp(allParam[i]);
-    allParam[i] = allParam[j];
-    allParam[j] = tmp;
-  }
-
-
-  void Parameters::qsort(int left, int right)
-  {
-    if (left >= right) 
-      return;
-
-    swap(left, (left + right) / 2);
-    int last = left;
-    for (int i = left + 1; i <= right; i++)
-      if (allParam[i].key.compare(allParam[left].key) < 0)
-	swap(++last, i);
-
-    swap(left, last);
-    qsort(left, last - 1);
-    qsort(last + 1, right);
-  }
-
-
-  const string Parameters::getKey(const string& s, int nLine, 
-					 const string& aFilename)
-  {
-    FUNCNAME("Parameters::getKey()");
-
-    string fn, key = "";
-    char c;
-    int i, epos;
-    string h = " \t\r\f";
-    int pos = s.find_first_not_of(" \t\f\r"); //skip Blank
-  
-    if (pos < 0)
-      return key;
-
-    if (s[pos] == comment || s[pos] == '\0' || s[pos] == '\n')
-      return(key);
-
-    if (s[pos] == '#') {
-//       if (static_cast<int>(s.find("#include")) == pos) {
-// 	/****************************************************************************/
-// 	/*  another init file has to be included                                    */
-// 	/****************************************************************************/
-// 
-// 	pos += strlen("#include");
-// 	pos = s.find_first_not_of(" \t\f\r");
-// 
-// 	i = 0;
-// 	switch (c = s[pos++]) {
-// 	case '<':
-// 	  c = '>';
-// 	case '\"':
-// 	  h += c;
-// 	  epos = s.find_first_not_of(h, pos);
-// 	  fn = s.substr(pos,epos-1);
-//        
-// 	  if (s[epos] != c) {
-// 	    ERROR("aFilename of include not terminated by %c\n", c);
-// 	    ERROR("skipping line %d of file %s\n", nLine, aFilename.c_str());
-// 	    return("");
-// 	  }
-// 	  break;
-// 	default:
-// 	  ERROR("no aFilename of include file found\n");
-// 	  ERROR("skipping line %d of file %s\n", nLine, aFilename.c_str());
-// 	  return("");
-// 	}
-// 
-// 	read(fn);
-// 	return("");
-//       } else {
-// 	ERROR("# must not be the first character on a line; except #include\n");
-// 	return("");
-//       }
-    }
-
-    /****************************************************************************/
-    /*  now get the key                                                         */
-    /****************************************************************************/
-    i = 0;
-    epos=s.find_first_of(":#",pos+1);
-    if (s[epos] == '#') {
-      ERROR("key must not contain '%c'.\n", '#');
-      ERROR("Skipping line %d of file %s\n", nLine, aFilename.c_str());
-      return("");
-    }
-  
-    key = s.substr(pos,epos);
-
-    if (s[epos] != ':') {
-      ERROR("key was not terminated by ':'.\n");
-      ERROR("Skipping line %d of file %s\n", nLine, aFilename.c_str());
-      return("");
-    }
-    
-    if (key.size() == 0) {
-      ERROR("use of ':' without key.\n");