Changes in src/molecule.hpp [274d45:35b698]

File:

• src/molecule.hpp (modified) (5 diffs)

src/molecule.hpp

@@ -80 +80 @@
   double *PenaltyConstants;   //!<  penalty constant in front of each term
 };
-
-#define MaxThermostats 6      //!< maximum number of thermostat entries in Ions#ThermostatNames and Ions#ThermostatImplemented 
-enum thermostats { None, Woodcock, Gaussian, Langevin, Berendsen, NoseHoover };   //!< Thermostat names for output
-
 
 /** The complete molecule.
@@ -265 +261 @@
   /// Count and change present atoms' coordination.
   void CountElements();
-  void CalculateOrbitals(class config &configuration);
   bool CenterInBox();
   bool BoundInBox();
@@ -292 +287 @@
   double MinimiseConstrainedPotential(atom **&permutation, int startstep, int endstep, bool IsAngstroem);
   void EvaluateConstrainedForces(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
-  bool LinearInterpolationBetweenConfiguration(int startstep, int endstep, const char *prefix, config &configuration, bool MapByIdentity);
+  bool LinearInterpolationBetweenConfiguration(int startstep, int endstep, std::string &prefix, config &configuration, bool MapByIdentity);
         
   bool CheckBounds(const Vector *x) const;
@@ -324 +319 @@
 
   /// Fragment molecule by two different approaches:
-  int FragmentMolecule(int Order, config *configuration);
-  bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
-  bool StoreBondsToFile(char *path, char *filename);
-  bool StoreAdjacencyToFile(char *path, char *filename);
-  bool CheckAdjacencyFileAgainstMolecule(char *path, atom **ListOfAtoms);
-  bool ParseOrderAtSiteFromFile(char *path);
-  bool StoreOrderAtSiteFile(char *path);
-  bool StoreForcesFile(MoleculeListClass *BondFragments, char *path, int *SortIndex);
+  int FragmentMolecule(int Order, std::string &prefix);
+  bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, std::string path = "");
+  bool StoreBondsToFile(std::string &filename, std::string path = "");
+  bool StoreAdjacencyToFile(std::string &filename, std::string path = "");
+  bool CheckAdjacencyFileAgainstMolecule(std::string &path, atom **ListOfAtoms);
+  bool ParseOrderAtSiteFromFile(std::string &path);
+  bool StoreOrderAtSiteFile(std::string &path);
+  bool StoreForcesFile(MoleculeListClass *BondFragments, std::string &path, int *SortIndex);
   bool CreateMappingLabelsToConfigSequence(int *&SortIndex);
   bool CreateFatherLookupTable(atom **&LookupTable, int count = 0);
@@ -380 +375 @@
   ~MoleculeListClass();
 
-  bool AddHydrogenCorrection(char *path);
-  bool StoreForcesFile(char *path, int *SortIndex);
+  bool AddHydrogenCorrection(std::string &path);
+  bool StoreForcesFile(std::string &path, int *SortIndex);
   void insert(molecule *mol);
   void erase(molecule *mol);
   molecule * ReturnIndex(int index);
-  bool OutputConfigForListOfFragments(config *configuration, int *SortIndex);
+  bool OutputConfigForListOfFragments(std::string &prefix, int *SortIndex);
   int NumberOfActiveMolecules();
   void Enumerate(ostream *out);