Changeset c830e8e for molecuilder/src/molecules.hpp

Timestamp:

Apr 2, 2009, 4:12:54 PM (17 years ago)

Author:

Frederik Heber <heber@…>

Children:

3021d93

Parents:

451d7a

Message:

Basic implementation of Multiple molecules.

builder.cpp:

• MoleculeListClass *molecules instead of molecule *mol
• in menu replaced list of elements and atoms by list of molecules
• new option: SetActiveMolecule
• new submenus/functions that all work on MoleculeListClass:
  • EditMolecule()
  • ManipulateMolecules() (global operations on all atoms in a molecule)
  • MergeMolecules()
  • ManipulateAtoms() (local operations on single atoms)
• SaveConfig(): SimpleMultiAdd() of all molecules into a single new one that is stored with the present configuration.

molecules.hpp:

• new STL list MoleculeList
• new variables in MoleculeListClass: list of molecules as STL list
• new variables in molecule: ActiveFlag, name of molecule, Center of molecule (used on merging)

moleculelist.cpp:

• replaced listofmolecules array by STL list everywhere (only smaller changes necessary)
• new merging function: SimpleMerge, SimpleAdd, SimpleMultiMerge, SimpleMultiAdd, (EmbedMerge, ScatterMerge ... both not finished). Add does not while merge does delete the src molecules.
• new function: Enumerate(). Output of all molecules with number of atoms and chemical formula
• new function: NumberOfActiveMolecules(). Counts the number of molecules in the list with ActiveFlag set.
• new function: insert(). Inserts a molecule into the list with a unique index

molecules.cpp:

• new function: SetNameFromFilename. Takes basename of a filename and sets name accordingly.
• new function: UnlinkAtom. Only removes atom from list, does not delete it from memory.

atom.cpp:

• Output() also accepts specific comment instead of "# molecule nr ..."

File:

• molecuilder/src/molecules.hpp (modified) (7 diffs)

molecuilder/src/molecules.hpp

@@ -68 +68 @@
 #define DistanceMultiMap multimap <double, pair < PointMap::iterator, PointMap::iterator> >
 #define DistanceMultiMapPair pair <double, pair < PointMap::iterator, PointMap::iterator> >
+
+#define MoleculeList list <molecule *>
+#define MoleculeListTest pair <MoleculeList::iterator, bool>
 
 /******************************** Some small functions and/or structures **********************************/
@@ -142 +145 @@
         ~atom();
 
-        bool Output(int ElementNo, int AtomNo, ofstream *out) const;
+        bool Output(int ElementNo, int AtomNo, ofstream *out, const char *comment = NULL) const;
         bool OutputXYZLine(ofstream *out) const;
         atom *GetTrueFather();
@@ -216 +219 @@
                 int NoCyclicBonds;      //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
                 double BondDistance;    //!< typical bond distance used in CreateAdjacencyList() and furtheron
+                bool ActiveFlag;    //!< in a MoleculeListClass used to discern active from inactive molecules
+                Vector Center;      //!< Center of molecule in a global box
+                char name[MAXSTRINGSIZE];         //!< arbitrary name
+                int IndexNr;        //!< index of molecule in a MoleculeListClass
 
         molecule(periodentafel *teil);
@@ -223 +230 @@
         bool AddAtom(atom *pointer);
         bool RemoveAtom(atom *pointer);
+        bool UnlinkAtom(atom *pointer);
         bool CleanupMolecule();
 
@@ -252 +260 @@
         Vector * DetermineCenterOfGravity(ofstream *out);
         Vector * DetermineCenterOfAll(ofstream *out);
+        void SetNameFromFilename(char *filename);
         void SetBoxDimension(Vector *dim);
         double * ReturnFullMatrixforSymmetric(double *cell_size);
@@ -326 +335 @@
 class MoleculeListClass {
         public:
-                molecule **ListOfMolecules;      //!< pointer list of fragment molecules to check for equality
-                int NumberOfMolecules;                          //!< Number of entries in \a **FragmentList and of to be returned one.
-                int NumberOfTopAtoms;                            //!< Number of atoms in the molecule from which all fragments originate
+          MoleculeList ListOfMolecules; //!< List of the contained molecules
+          int MaxIndex;
 
         MoleculeListClass();
-        MoleculeListClass(int Num, int NumAtoms);
         ~MoleculeListClass();
 
-        /// Output configs.
         bool AddHydrogenCorrection(ofstream *out, char *path);
         bool StoreForcesFile(ofstream *out, char *path, int *SortIndex);
+        bool insert(molecule *mol);
+        molecule * ReturnIndex(int index);
         bool OutputConfigForListOfFragments(ofstream *out, config *configuration, int *SortIndex);
+        int NumberOfActiveMolecules();
+        void Enumerate(ofstream *out);
         void Output(ofstream *out);
+
+        // merging of molecules
+  bool SimpleMerge(molecule *mol, molecule *srcmol);
+  bool SimpleAdd(molecule *mol, molecule *srcmol);
+  bool SimpleMultiMerge(molecule *mol, int *src, int N);
+  bool SimpleMultiAdd(molecule *mol, int *src, int N);
+  bool ScatterMerge(molecule *mol, int *src, int N);
+  bool EmbedMerge(molecule *mol, molecule *srcmol);
 
         private:
@@ -454 +472 @@
         bool Save(const char *filename, periodentafel *periode, molecule *mol) const;
         bool SaveMPQC(const char *filename, molecule *mol) const;
-        void Edit(molecule *mol);
+        void Edit();
         bool GetIsAngstroem() const;
         char *GetDefaultPath() const;