Changes in src/config.cpp [97b825:83f176]

File:

• src/config.cpp (modified) (12 diffs)

src/config.cpp

@@ +1 @@
+/*
+ * Project: MoleCuilder
+ * Description: creates and alters molecular systems
+ * Copyright (C)  2010 University of Bonn. All rights reserved.
+ * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
+ */
+
 /** \file config.cpp
  *
@@ -5 +12 @@
  */
 
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
 #include "Helpers/MemDebug.hpp"
 
@@ -10 +22 @@
 #include <cstring>
 
+//#include "Actions/FragmentationAction/SubgraphDissectionAction.hpp"
 #include "atom.hpp"
 #include "bond.hpp"
@@ -471 +484 @@
       ParseForParameter(verbose,FileBuffer, name, 0, 2, 1, int_type, &Z, 1, critical);
       elementhash[i] = periode->FindElement(Z);
-      DoLog(1) && (Log() << Verbose(1) << i << ". Z = " << elementhash[i]->Z << " with " << No[i] << " ions." << endl);
+      DoLog(1) && (Log() << Verbose(1) << i << ". Z = " << elementhash[i]->getAtomicNumber() << " with " << No[i] << " ions." << endl);
       NoAtoms += No[i];
     }
@@ -851 +864 @@
   // 4. dissect the molecule into connected subgraphs
   // don't do this here ...
-  //MolList->DissectMoleculeIntoConnectedSubgraphs(mol,this);
+  //FragmentationSubgraphDissection();
   //delete(mol);
 
@@ -1339 +1352 @@
     AtomNo = 0;
     for (molecule::const_iterator iter = (*MolRunner)->begin(); iter != (*MolRunner)->end(); ++iter) {
-      sprintf(name, "%2s%2d",(*iter)->getType()->symbol, elementNo[(*iter)->getType()->Z]);
-      elementNo[(*iter)->getType()->Z] = (elementNo[(*iter)->getType()->Z]+1) % 100;   // confine to two digits
+      sprintf(name, "%2s%2d",(*iter)->getType()->getSymbol().c_str(), elementNo[(*iter)->getType()->getAtomicNumber()]);
+      elementNo[(*iter)->getType()->getAtomicNumber()] = (elementNo[(*iter)->getType()->getAtomicNumber()]+1) % 100;   // confine to two digits
       fprintf(f,
              "ATOM %6u %-4s %4s%c%4u    %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s%2s\n",
@@ -1351 +1364 @@
              (*iter)->at(1),                 /* position Y in Angstroem */
              (*iter)->at(2),                 /* position Z in Angstroem */
-             (double)(*iter)->getType()->Valence,         /* occupancy */
-             (double)(*iter)->getType()->NoValenceOrbitals,          /* temperature factor */
+             (double)(*iter)->getType()->getValence(),         /* occupancy */
+             (double)(*iter)->getType()->getNoValenceOrbitals(),          /* temperature factor */
              "0",            /* segment identifier */
-             (*iter)->getType()->symbol,    /* element symbol */
+             (*iter)->getType()->getSymbol().c_str(),    /* element symbol */
              "0");           /* charge */
       AtomNo++;
@@ -1392 +1405 @@
   AtomNo = 0;
   for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-    sprintf(name, "%2s%2d",(*iter)->getType()->symbol, elementNo[(*iter)->getType()->Z]);
-    elementNo[(*iter)->getType()->Z] = (elementNo[(*iter)->getType()->Z]+1) % 100;   // confine to two digits
+    sprintf(name, "%2s%2d",(*iter)->getType()->getSymbol().c_str(), elementNo[(*iter)->getType()->getAtomicNumber()]);
+    elementNo[(*iter)->getType()->getAtomicNumber()] = (elementNo[(*iter)->getType()->getAtomicNumber()]+1) % 100;   // confine to two digits
     fprintf(f,
            "ATOM %6u %-4s %4s%c%4u    %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s%2s\n",
@@ -1404 +1417 @@
            (*iter)->at(1),                 /* position Y in Angstroem */
            (*iter)->at(2),                 /* position Z in Angstroem */
-           (double)(*iter)->getType()->Valence,         /* occupancy */
-           (double)(*iter)->getType()->NoValenceOrbitals,          /* temperature factor */
+           (double)(*iter)->getType()->getValence(),         /* occupancy */
+           (double)(*iter)->getType()->getNoValenceOrbitals(),          /* temperature factor */
            "0",            /* segment identifier */
-           (*iter)->getType()->symbol,    /* element symbol */
+           (*iter)->getType()->getSymbol().c_str(),    /* element symbol */
            "0");           /* charge */
     AtomNo++;
@@ -1451 +1464 @@
     *output << 0 << "\t";
     *output << (*iter)->at(0) << "\t" << (*iter)->at(1) << "\t" << (*iter)->at(2) << "\t";
-    *output << static_cast<double>((*iter)->getType()->Valence) << "\t";
-    *output << (*iter)->getType()->symbol << "\t";
+    *output << static_cast<double>((*iter)->getType()->getValence()) << "\t";
+    *output << (*iter)->getType()->getSymbol() << "\t";
     for (BondList::iterator runner = (*iter)->ListOfBonds.begin(); runner != (*iter)->ListOfBonds.end(); runner++)
       *output << (*runner)->GetOtherAtom(*iter)->nr << "\t";
@@ -1523 +1536 @@
         *output << MolCounter+1 << "\t";
         *output << (*iter)->at(0) << "\t" << (*iter)->at(1) << "\t" << (*iter)->at(2) << "\t";
-        *output << (double)(*iter)->getType()->Valence << "\t";
-        *output << (*iter)->getType()->symbol << "\t";
+        *output << (double)(*iter)->getType()->getValence() << "\t";
+        *output << (*iter)->getType()->getSymbol() << "\t";
         for (BondList::iterator runner = (*iter)->ListOfBonds.begin(); runner != (*iter)->ListOfBonds.end(); runner++)
           *output << LocalNotoGlobalNoMap[ (*runner)->GetOtherAtom((*iter))->getId() ] << "\t";
@@ -1586 +1599 @@
     for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
       src[N++] = (*ListRunner)->IndexNr;
-      (*ListRunner)->Translate(&(*ListRunner)->Center);
     }
     mol = World::getInstance().createMolecule();
     mol->SetNameFromFilename(ConfigFileName);
-    molecules->SimpleMultiMerge(mol, src, N);
     //mol->CalculateOrbitals(*this);
     delete[](src);