Changes in src/config.cpp [235bed:49e1ae]

File:

• src/config.cpp (modified) (7 diffs)

src/config.cpp

@@ -6 +6 @@
 
 #include <stdio.h>
+#include <cstring>
 
 #include "atom.hpp"
@@ -27 +28 @@
     char number1[8];
     char number2[8];
-    char *dummy1, *dummy2;
+    const char *dummy1, *dummy2;
     //Log() << Verbose(0) << s1 << "  " << s2 << endl;
     dummy1 = strchr(s1, '_')+sizeof(char)*5;  // go just after "Ion_Type"
@@ -140 +141 @@
 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 +150 @@
   // 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 +1057 @@
 
   // 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);
 };
@@ -1771 +1777 @@
 };
 
-
-/** Tries given filename or standard on saving the config file.
- * \param *ConfigFileName name of file
- * \param *periode pointer to periodentafel structure with all the elements
- * \param *molecules list of molecules structure with all the atoms and coordinates
- */
-void config::SaveAll(char *ConfigFileName, periodentafel *periode, MoleculeListClass *molecules)
-{
-  char filename[MAXSTRINGSIZE];
-  ofstream output;
-  molecule *mol = new molecule(periode);
-
-  if (!strcmp(configpath, GetDefaultPath())) {
-    eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
-  }
-
-
-  // first save as PDB data
-  if (ConfigFileName != NULL)
-    strcpy(filename, ConfigFileName);
-  else
-    strcpy(filename,"main_pcp_linux");
-  Log() << Verbose(0) << "Saving as pdb input ";
-  if (SavePDB(filename, molecules))
-    Log() << Verbose(0) << "done." << endl;
-  else
-    Log() << Verbose(0) << "failed." << endl;
-
-  // then save as tremolo data file
-  if (ConfigFileName != NULL)
-    strcpy(filename, ConfigFileName);
-  else
-    strcpy(filename,"main_pcp_linux");
-  Log() << Verbose(0) << "Saving as tremolo data input ";
-  if (SaveTREMOLO(filename, molecules))
-    Log() << Verbose(0) << "done." << endl;
-  else
-    Log() << Verbose(0) << "failed." << endl;
-
-  // translate each to its center and merge all molecules in MoleculeListClass into this molecule
-  int N = molecules->ListOfMolecules.size();
-  int *src = new int[N];
-  N=0;
-  for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
-    src[N++] = (*ListRunner)->IndexNr;
-    (*ListRunner)->Translate(&(*ListRunner)->Center);
-  }
-  molecules->SimpleMultiAdd(mol, src, N);
-  delete[](src);
-
-  // ... and translate back
-  for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
-    (*ListRunner)->Center.Scale(-1.);
-    (*ListRunner)->Translate(&(*ListRunner)->Center);
-    (*ListRunner)->Center.Scale(-1.);
-  }
-
-  Log() << Verbose(0) << "Storing configuration ... " << endl;
-  // get correct valence orbitals
-  mol->CalculateOrbitals(*this);
-  InitMaxMinStopStep = MaxMinStopStep = 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 {
-      strcpy(filename, DEFAULTCONFIG);
-      output.open(DEFAULTCONFIG, ios::trunc);
-    }
-  output.close();
-  output.clear();
-  Log() << Verbose(0) << "Saving of config file ";
-  if (Save(filename, periode, mol))
-    Log() << Verbose(0) << "successful." << endl;
-  else
-    Log() << Verbose(0) << "failed." << endl;
-
-  // and save to xyz file
-  if (ConfigFileName != NULL) {
-    strcpy(filename, ConfigFileName);
-    strcat(filename, ".xyz");
-    output.open(filename, ios::trunc);
-  }
-  else {
-    strcpy(filename,"main_pcp_linux");
-    strcat(filename, ".xyz");
-    output.open(filename, ios::trunc);
-  }
-  Log() << Verbose(0) << "Saving of XYZ file ";
-  if (mol->MDSteps <= 1) {
-    if (mol->OutputXYZ(&output))
-      Log() << Verbose(0) << "successful." << endl;
-    else
-      Log() << Verbose(0) << "failed." << endl;
-  } else {
-    if (mol->OutputTrajectoriesXYZ(&output))
-      Log() << Verbose(0) << "successful." << endl;
-    else
-      Log() << Verbose(0) << "failed." << endl;
-  }
-  output.close();
-  output.clear();
-
-  // and save as MPQC configuration
-  if (ConfigFileName != NULL)
-    strcpy(filename, ConfigFileName);
-  else
-    strcpy(filename,"main_pcp_linux");
-  Log() << Verbose(0) << "Saving as mpqc input ";
-  if (SaveMPQC(filename, mol))
-    Log() << Verbose(0) << "done." << endl;
-  else
-    Log() << Verbose(0) << "failed." << endl;
-
-  if (!strcmp(configpath, GetDefaultPath())) {
-    eLog() << Verbose(2) << "config is found under different path then stated in config file::defaultpath!" << endl;
-  }
-
-  delete(mol);
-};
-
 /** Reads parameter from a parsed file.
  * The file is either parsed for a certain keyword or if null is given for
@@ -2241 +2124 @@
               }
               line++;
-            } while (dummy1 != NULL && (dummy1[0] == '#') || (dummy1[0] == '\n'));
+            } while ((dummy1 != NULL) && ((dummy1[0] == '#') || (dummy1[0] == '\n')));
             dummy = dummy1;
           } else { // simple int, strings or doubles start in the same line