Changeset 32b6dc for molecuilder/src/molecules.hpp

Timestamp:

Jun 7, 2008, 1:21:53 PM (17 years ago)

Author:

Frederik Heber <heber@…>

Children:

d11f22

Parents:

a89a22

Message:

Working version of PAS transformation (tested on C-S-H cluster) and code scaffold of VolumeOfConvexEnvelope that's untested so far

PAS simply calculates inertia tensor, diagonalizes it via GSL and transforms molecule into eigenvector system such that z axis is eigenvector of biggest eigenvalue.

File:

• molecuilder/src/molecules.hpp (modified) (5 diffs)

molecuilder/src/molecules.hpp

@@ -13 +13 @@
 #include <gsl/gsl_vector.h>
 #include <gsl/gsl_matrix.h>
+#include <gsl/gsl_eigen.h>
 #include <gsl/gsl_heapsort.h>
 
@@ -43 +44 @@
 #define KeySetTestPair pair<KeySet::iterator, bool>
 #define GraphTestPair pair<Graph::iterator, bool>
+
+#define DistanceNrPair pair< double, atom* >
+#define Boundaries map <double, DistanceNrPair >
+#define BoundariesPair pair<double, DistanceNrPair >
+#define BoundariesTestPair pair<Boundaries::iterator, bool>
+#define LinetoAtomMap map < int, atom * > 
+#define LinetoAtomPair pair < int, atom * > 
+#define LinetoAtomTestPair pair < LinetoAtomMap::iterator, bool> 
 
 struct KeyCompare
@@ -265 +274 @@
   void CenterEdge(ofstream *out, vector *max); 
   void CenterOrigin(ofstream *out, vector *max); 
-  void CenterGravity(ofstream *out, vector *max); 
+  void CenterGravity(ofstream *out, vector *max);
   void Translate(const vector *x);
   void Mirror(const vector *x);
   void Align(vector *n);
   void Scale(double **factor);
-  void DetermineCenterOfGravity(vector &CenterOfGravity);
+  void DetermineCenter(vector &center);
+  vector * DetermineCenterOfGravity(ofstream *out);
   void SetBoxDimension(vector *dim);
   double * ReturnFullMatrixforSymmetric(double *cell_size);
   void ScanForPeriodicCorrection(ofstream *out);
-
+        void PrincipalAxisSystem(ofstream *out, bool DoRotate);
+        double VolumeOfConvexEnvelope(ofstream *out, bool IsAngstroem);
+        
   bool CheckBounds(const vector *x) const;
   void GetAlignVector(struct lsq_params * par) const;
@@ -283 +295 @@
   
   // Graph analysis
-  MoleculeLeafClass * DepthFirstSearchAnalysis(ofstream *out, bool ReturnStack, int *&MinimumRingSize);
+  MoleculeLeafClass * DepthFirstSearchAnalysis(ofstream *out, int *&MinimumRingSize);
   void CyclicStructureAnalysis(ofstream *out, class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize);
   bond * FindNextUnused(atom *vertex);
@@ -303 +315 @@
   bool ParseOrderAtSiteFromFile(ofstream *out, char *path);
   bool StoreOrderAtSiteFile(ofstream *out, char *path);
-  bool ParseKeySetFile(ofstream *out, char *filename, Graph *&FragmentList, bool IsAngstroem);
+  bool ParseKeySetFile(ofstream *out, char *filename, Graph *&FragmentList);
   bool StoreKeySetFile(ofstream *out, Graph &KeySetList, char *path);
   bool StoreForcesFile(ofstream *out, MoleculeListClass *BondFragments, char *path, int *SortIndex);