Changeset 41182a for molecuilder/src/config.cpp

Timestamp:

Jan 26, 2010, 12:45:41 PM (16 years ago)

Author:

Tillmann Crueger <crueger@…>

Children:

d34341

Parents:

931903 (diff), 16807e (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge commit 'heber/Analysis_PairCorrelation' into MenuRefactoring

Conflicts:

Makefile.am
molecuilder/src/Makefile.am
molecuilder/src/builder.cpp
molecuilder/src/unittests/Makefile.am

File:

• molecuilder/src/config.cpp (modified) (10 diffs)

molecuilder/src/config.cpp

@@ -140 +140 @@
 void ConfigFileBuffer::MapIonTypesInBuffer(const int NoAtoms)
 {
-  map<const char *, int, IonTypeCompare> LineList;
+  map<const char *, int, IonTypeCompare> IonTypeLineMap;
   if (LineMapping == NULL) {
     eLog() << Verbose(0) << "map pointer is NULL: " << LineMapping << endl;
@@ -149 +149 @@
   // put all into hashed map
   for (int i=0; i<NoAtoms; ++i) {
-    LineList.insert(pair<const char *, int> (buffer[CurrentLine+i], CurrentLine+i));
+    IonTypeLineMap.insert(pair<const char *, int> (buffer[CurrentLine+i], CurrentLine+i));
   }
 
   // fill map
   int nr=0;
-  for (map<const char *, int, IonTypeCompare>::iterator runner = LineList.begin(); runner != LineList.end(); ++runner) {
+  for (map<const char *, int, IonTypeCompare>::iterator runner = IonTypeLineMap.begin(); runner != IonTypeLineMap.end(); ++runner) {
     if (CurrentLine+nr < NoLines)
       LineMapping[CurrentLine+(nr++)] = runner->second;
@@ -1056 +1056 @@
 
   // 2. parse the bond graph file if given
-  BG = new BondGraph(IsAngstroem);
-  if (BG->LoadBondLengthTable(BondGraphFileName)) {
-    Log() << Verbose(0) << "Bond length table loaded successfully." << endl;
-  } else {
-    eLog() << Verbose(1) << "Bond length table loading failed." << endl;
+  if (BG == NULL) {
+    BG = new BondGraph(IsAngstroem);
+    if (BG->LoadBondLengthTable(BondGraphFileName)) {
+      Log() << Verbose(0) << "Bond length table loaded successfully." << endl;
+    } else {
+      eLog() << Verbose(1) << "Bond length table loading failed." << endl;
+    }
   }
 
   // 3. parse the molecule in
   LoadMolecule(mol, FileBuffer, periode, FastParsing);
+  mol->SetNameFromFilename(filename);
   mol->ActiveFlag = true;
+  MolList->insert(mol);
 
   // 4. dissect the molecule into connected subgraphs
-  MolList->DissectMoleculeIntoConnectedSubgraphs(mol,this);
-
-  delete(mol);
+  // don't do this here ...
+  //MolList->DissectMoleculeIntoConnectedSubgraphs(mol,this);
+  //delete(mol);
+
   delete(FileBuffer);
 };
@@ -1782 +1787 @@
   ofstream output;
   molecule *mol = new molecule(periode);
-
-  if (!strcmp(configpath, GetDefaultPath())) {
+  mol->SetNameFromFilename(ConfigFileName);
+
+  if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
     eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
   }
@@ -1791 +1797 @@
   if (ConfigFileName != NULL)
     strcpy(filename, ConfigFileName);
-  else
+  if (output == NULL)
     strcpy(filename,"main_pcp_linux");
   Log() << Verbose(0) << "Saving as pdb input ";
-  if (SavePDB(filename, molecules))
+  if (configuration->SavePDB(filename, molecules))
     Log() << Verbose(0) << "done." << endl;
   else
@@ -1802 +1808 @@
   if (ConfigFileName != NULL)
     strcpy(filename, ConfigFileName);
-  else
+  if (output == NULL)
     strcpy(filename,"main_pcp_linux");
   Log() << Verbose(0) << "Saving as tremolo data input ";
-  if (SaveTREMOLO(filename, molecules))
+  if (configuration->SaveTREMOLO(filename, molecules))
     Log() << Verbose(0) << "done." << endl;
   else
@@ -1830 +1836 @@
   Log() << Verbose(0) << "Storing configuration ... " << endl;
   // get correct valence orbitals
-  mol->CalculateOrbitals(*this);
-  InitMaxMinStopStep = MaxMinStopStep = MaxPsiDouble;
+  mol->CalculateOrbitals(*configuration);
+  configuration->InitMaxMinStopStep = configuration->MaxMinStopStep = configuration->MaxPsiDouble;
   if (ConfigFileName != NULL) { // test the file name
     strcpy(filename, ConfigFileName);
     output.open(filename, ios::trunc);
-  } else if (strlen(configname) != 0) {
-    strcpy(filename, configname);
-    output.open(configname, ios::trunc);
+  } else if (strlen(configuration->configname) != 0) {
+    strcpy(filename, configuration->configname);
+    output.open(configuration->configname, ios::trunc);
     } else {
       strcpy(filename, DEFAULTCONFIG);
@@ -1845 +1851 @@
   output.clear();
   Log() << Verbose(0) << "Saving of config file ";
-  if (Save(filename, periode, mol))
+  if (configuration->Save(filename, periode, mol))
     Log() << Verbose(0) << "successful." << endl;
   else
@@ -1856 +1862 @@
     output.open(filename, ios::trunc);
   }
-  else {
+  if (output == NULL) {
     strcpy(filename,"main_pcp_linux");
     strcat(filename, ".xyz");
@@ -1879 +1885 @@
   if (ConfigFileName != NULL)
     strcpy(filename, ConfigFileName);
-  else
+  if (output == NULL)
     strcpy(filename,"main_pcp_linux");
   Log() << Verbose(0) << "Saving as mpqc input ";
-  if (SaveMPQC(filename, mol))
+  if (configuration->SaveMPQC(filename, mol))
     Log() << Verbose(0) << "done." << endl;
   else
     Log() << Verbose(0) << "failed." << endl;
 
-  if (!strcmp(configpath, GetDefaultPath())) {
+  if (!strcmp(configuration->configpath, configuration->GetDefaultPath())) {
     eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
   }