Changes in src/molecule.hpp [a3fded:274d45]

File:

• src/molecule.hpp (modified) (4 diffs)

src/molecule.hpp

@@ -81 +81 @@
 };
 
+#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.
  * Class incorporates number of types
@@ -89 +93 @@
 
   public:
-    typedef std::set<atom*> atomSet;
+    typedef std::list<atom*> atomSet;
+    typedef std::set<atomId_t> atomIdSet;
     typedef ObservedIterator<atomSet> iterator;
     typedef atomSet::const_iterator const_iterator;
@@ -117 +122 @@
     Cacheable<int>    AtomCount;
     moleculeId_t id;
-    atomSet atoms; //<!set of atoms
+    atomSet atoms; //<!list of atoms
+    atomIdSet atomIds; //<!set of atomic ids to check uniqueness of atoms
   protected:
     //void CountAtoms();
@@ -149 +155 @@
   size_t size() const;
   const_iterator erase( const_iterator loc );
-  const_iterator erase( atom *& key );
-  const_iterator find (  atom *& key ) const;
+  const_iterator erase( atom * key );
+  const_iterator find (  atom * key ) const;
   pair<iterator,bool> insert ( atom * const key );
+  bool containsAtom(atom* key);