Changes in src/moleculelist.cpp [274d45:84c494]

File:

• src/moleculelist.cpp (modified) (14 diffs)

src/moleculelist.cpp

@@ -12 +12 @@
 #include "atom.hpp"
 #include "bond.hpp"
+#include "bondgraph.hpp"
 #include "boundary.hpp"
 #include "config.hpp"
@@ -23 +24 @@
 #include "periodentafel.hpp"
 #include "Helpers/Assert.hpp"
+#include "Matrix.hpp"
+#include "Box.hpp"
 
 #include "Helpers/Assert.hpp"
@@ -379 +382 @@
  * bonded to the same atom, then we add for this pair a correction term constructed from a Morse
  * potential function fit to QM calculations with respecting to the interatomic hydrogen distance.
- * \param *out output stream for debugging
- * \param *path path to file
- */
-bool MoleculeListClass::AddHydrogenCorrection(char *path)
+ * \param &path path to file
+ */
+bool MoleculeListClass::AddHydrogenCorrection(std::string &path)
 {
   bond *Binder = NULL;
@@ -400 +402 @@
   // 0a. find dimension of matrices with constants
   line = path;
-  line.append("/");
-  line += FRAGMENTPREFIX;
   line += "1";
   line += FITCONSTANTSUFFIX;
   input.open(line.c_str());
-  if (input == NULL) {
+  if (input.fail()) {
     DoLog(1) && (Log() << Verbose(1) << endl << "Unable to open " << line << ", is the directory correct?" << endl);
     return false;
@@ -569 +569 @@
 
 /** Store force indices, i.e. the connection between the nuclear index in the total molecule config and the respective atom in fragment config.
- * \param *out output stream for debugging
- * \param *path path to file
+ * \param &path path to file
  * \param *SortIndex Index to map from the BFS labeling to the sequence how of Ion_Type in the config
  * \return true - file written successfully, false - writing failed
  */
-bool MoleculeListClass::StoreForcesFile(char *path,
-    int *SortIndex)
+bool MoleculeListClass::StoreForcesFile(std::string &path, int *SortIndex)
 {
   bool status = true;
-  ofstream ForcesFile;
-  stringstream line;
+  string filename(path);
+  filename += FORCESFILE;
+  ofstream ForcesFile(filename.c_str());
   periodentafel *periode=World::getInstance().getPeriode();
 
   // open file for the force factors
   DoLog(1) && (Log() << Verbose(1) << "Saving  force factors ... ");
-  line << path << "/" << FRAGMENTPREFIX << FORCESFILE;
-  ForcesFile.open(line.str().c_str(), ios::out);
-  if (ForcesFile != NULL) {
+  if (!ForcesFile.fail()) {
     //Log() << Verbose(1) << "Final AtomicForcesList: ";
     //output << prefix << "Forces" << endl;
@@ -611 +608 @@
   } else {
     status = false;
-    DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl);
+    DoLog(1) && (Log() << Verbose(1) << "failed to open file " << filename << "." << endl);
   }
   ForcesFile.close();
@@ -620 +617 @@
 /** Writes a config file for each molecule in the given \a **FragmentList.
  * \param *out output stream for debugging
- * \param *configuration standard configuration to attach atoms in fragment molecule to.
+ * \param &prefix path and prefix to the fragment config files
  * \param *SortIndex Index to map from the BFS labeling to the sequence how of Ion_Type in the config
  * \return true - success (each file was written), false - something went wrong.
  */
-bool MoleculeListClass::OutputConfigForListOfFragments(config *configuration, int *SortIndex)
+bool MoleculeListClass::OutputConfigForListOfFragments(std::string &prefix, int *SortIndex)
 {
   ofstream outputFragment;
-  char FragmentName[MAXSTRINGSIZE];
+  std::string FragmentName;
   char PathBackup[MAXSTRINGSIZE];
   bool result = true;
@@ -636 +633 @@
   int FragmentCounter = 0;
   ofstream output;
-  double cell_size_backup[6];
-  double * const cell_size = World::getInstance().getDomain();
-
-  // backup cell_size
-  for (int i=0;i<6;i++)
-    cell_size_backup[i] = cell_size[i];
+  Matrix cell_size = World::getInstance().getDomain().getM();
+  Matrix cell_size_backup = cell_size;
+
   // store the fragments as config and as xyz
   for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
     // save default path as it is changed for each fragment
-    path = configuration->GetDefaultPath();
+    path = World::getInstance().getConfig()->GetDefaultPath();
     if (path != NULL)
       strcpy(PathBackup, path);
@@ -658 +652 @@
     // output xyz file
     FragmentNumber = FixedDigitNumber(ListOfMolecules.size(), FragmentCounter++);
-    sprintf(FragmentName, "%s/%s%s.conf.xyz", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
-    outputFragment.open(FragmentName, ios::out);
+    FragmentName = prefix + FragmentNumber + ".conf.xyz";
+    outputFragment.open(FragmentName.c_str(), ios::out);
     DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as XYZ ...");
     if ((intermediateResult = (*ListRunner)->OutputXYZ(&outputFragment)))
@@ -679 +673 @@
     (*ListRunner)->CenterEdge(&BoxDimension);
     (*ListRunner)->SetBoxDimension(&BoxDimension); // update Box of atoms by boundary
-    int j = -1;
     for (int k = 0; k < NDIM; k++) {
-      j += k + 1;
-      BoxDimension[k] = 2.5 * (configuration->GetIsAngstroem() ? 1. : 1. / AtomicLengthToAngstroem);
-      cell_size[j] = BoxDimension[k] * 2.;
-    }
+      BoxDimension[k] = 2.5 * (World::getInstance().getConfig()->GetIsAngstroem() ? 1. : 1. / AtomicLengthToAngstroem);
+      cell_size.at(k,k) = BoxDimension[k] * 2.;
+    }
+    World::getInstance().setDomain(cell_size);
     (*ListRunner)->Translate(&BoxDimension);
 
     // also calculate necessary orbitals
     (*ListRunner)->CountElements(); // this is a bugfix, atoms should shoulds actually be added correctly to this fragment
-    (*ListRunner)->CalculateOrbitals(*configuration);
+    //(*ListRunner)->CalculateOrbitals(*World::getInstance().getConfig);
 
     // change path in config
-    //strcpy(PathBackup, configuration->configpath);
-    sprintf(FragmentName, "%s/%s%s/", PathBackup, FRAGMENTPREFIX, FragmentNumber);
-    configuration->SetDefaultPath(FragmentName);
+    FragmentName = PathBackup;
+    FragmentName += "/";
+    FragmentName += FRAGMENTPREFIX;
+    FragmentName += FragmentNumber;
+    FragmentName += "/";
+    World::getInstance().getConfig()->SetDefaultPath(FragmentName.c_str());
 
     // and save as config
-    sprintf(FragmentName, "%s/%s%s.conf", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
+    FragmentName = prefix + FragmentNumber + ".conf";
     DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as config ...");
-    if ((intermediateResult = configuration->Save(FragmentName, (*ListRunner)->elemente, (*ListRunner))))
+    if ((intermediateResult = World::getInstance().getConfig()->Save(FragmentName.c_str(), (*ListRunner)->elemente, (*ListRunner))))
       DoLog(0) && (Log() << Verbose(0) << " done." << endl);
     else
@@ -706 +702 @@
 
     // restore old config
-    configuration->SetDefaultPath(PathBackup);
+    World::getInstance().getConfig()->SetDefaultPath(PathBackup);
 
     // and save as mpqc input file
-    sprintf(FragmentName, "%s/%s%s.conf", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
+    FragmentName = prefix + FragmentNumber + ".conf";
     DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as mpqc input ...");
-    if ((intermediateResult = configuration->SaveMPQC(FragmentName, (*ListRunner))))
+    if ((intermediateResult = World::getInstance().getConfig()->SaveMPQC(FragmentName.c_str(), (*ListRunner))))
       DoLog(2) && (Log() << Verbose(2) << " done." << endl);
     else
@@ -727 +723 @@
 
   // restore cell_size
-  for (int i=0;i<6;i++)
-    cell_size[i] = cell_size_backup[i];
+  World::getInstance().setDomain(cell_size_backup);
 
   return result;
@@ -767 +762 @@
 
   // 1. dissect the molecule into connected subgraphs
-  if (!configuration->BG->ConstructBondGraph(mol)) {
-    World::getInstance().destroyMolecule(mol);
-    DoeLog(1) && (eLog()<< Verbose(1) << "There are no bonds." << endl);
+  if (configuration->BG != NULL) {
+    if (!configuration->BG->ConstructBondGraph(mol)) {
+      World::getInstance().destroyMolecule(mol);
+      DoeLog(1) && (eLog()<< Verbose(1) << "There are no bonds." << endl);
+      return;
+    }
+  } else {
+    DoeLog(1) && (eLog()<< Verbose(1) << "There is no BondGraph class present to create bonds." << endl);
     return;
   }
@@ -884 +884 @@
   // center at set box dimensions
   mol->CenterEdge(&center);
-  World::getInstance().getDomain()[0] = center[0];
-  World::getInstance().getDomain()[1] = 0;
-  World::getInstance().getDomain()[2] = center[1];
-  World::getInstance().getDomain()[3] = 0;
-  World::getInstance().getDomain()[4] = 0;
-  World::getInstance().getDomain()[5] = center[2];
+  Matrix domain;
+  for(int i =0;i<NDIM;++i)
+    domain.at(i,i) = center[i];
+  World::getInstance().setDomain(domain);
   insert(mol);
 }