Changes in src/config.cpp [952f38:2fe971]

File:

• src/config.cpp (modified) (8 diffs)

src/config.cpp

@@ -16 +16 @@
 #include "ConfigFileBuffer.hpp"
 #include "element.hpp"
-#include "Helpers/helpers.hpp"
-#include "Helpers/Info.hpp"
+#include "helpers.hpp"
+#include "info.hpp"
 #include "lists.hpp"
-#include "Helpers/Verbose.hpp"
-#include "Helpers/Log.hpp"
+#include "verbose.hpp"
+#include "log.hpp"
 #include "molecule.hpp"
 #include "molecule.hpp"
@@ -26 +26 @@
 #include "ThermoStatContainer.hpp"
 #include "World.hpp"
-#include "LinearAlgebra/Matrix.hpp"
+#include "Matrix.hpp"
 #include "Box.hpp"
 
@@ -1279 +1279 @@
     AtomNo = 0;
     for (molecule::const_iterator iter = (*MolRunner)->begin(); iter != (*MolRunner)->end(); ++iter) {
-      sprintf(name, "%2s%2d",(*iter)->type->symbol, elementNo[(*iter)->type->Z]);
+      sprintf(name, "%2s%2d",(*iter)->type->getSymbol().c_str(), elementNo[(*iter)->type->Z]);
       elementNo[(*iter)->type->Z] = (elementNo[(*iter)->type->Z]+1) % 100;   // confine to two digits
       fprintf(f,
@@ -1294 +1294 @@
              (double)(*iter)->type->NoValenceOrbitals,          /* temperature factor */
              "0",            /* segment identifier */
-             (*iter)->type->symbol,    /* element symbol */
+             (*iter)->type->getSymbol().c_str(),    /* element symbol */
              "0");           /* charge */
       AtomNo++;
@@ -1332 +1332 @@
   AtomNo = 0;
   for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-    sprintf(name, "%2s%2d",(*iter)->type->symbol, elementNo[(*iter)->type->Z]);
+    sprintf(name, "%2s%2d",(*iter)->type->getSymbol().c_str(), elementNo[(*iter)->type->Z]);
     elementNo[(*iter)->type->Z] = (elementNo[(*iter)->type->Z]+1) % 100;   // confine to two digits
     fprintf(f,
@@ -1347 +1347 @@
            (double)(*iter)->type->NoValenceOrbitals,          /* temperature factor */
            "0",            /* segment identifier */
-           (*iter)->type->symbol,    /* element symbol */
+           (*iter)->type->getSymbol().c_str(),    /* element symbol */
            "0");           /* charge */
     AtomNo++;
@@ -1392 +1392 @@
     *output << (*iter)->node->at(0) << "\t" << (*iter)->node->at(1) << "\t" << (*iter)->node->at(2) << "\t";
     *output << static_cast<double>((*iter)->type->Valence) << "\t";
-    *output << (*iter)->type->symbol << "\t";
+    *output << (*iter)->type->getSymbol() << "\t";
     for (BondList::iterator runner = (*iter)->ListOfBonds.begin(); runner != (*iter)->ListOfBonds.end(); runner++)
       *output << (*runner)->GetOtherAtom(*iter)->nr << "\t";
@@ -1464 +1464 @@
         *output << (*iter)->node->at(0) << "\t" << (*iter)->node->at(1) << "\t" << (*iter)->node->at(2) << "\t";
         *output << (double)(*iter)->type->Valence << "\t";
-        *output << (*iter)->type->symbol << "\t";
+        *output << (*iter)->type->getSymbol() << "\t";
         for (BondList::iterator runner = (*iter)->ListOfBonds.begin(); runner != (*iter)->ListOfBonds.end(); runner++)
           *output << LocalNotoGlobalNoMap[ (*runner)->GetOtherAtom((*iter))->getId() ] << "\t";