changes to structure class

removed push_back functionality, only setCoordinates publically available added third, optional boolean argument to class constructor, setting it to false only sets coordinates and does not calculate properties
Trombach · Oct 10, 2018 · 93d2dea · 93d2dea
1 parent 3794613
commit 93d2dea
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Showing 2 changed files with 17 additions and 23 deletions.
diff --git a/potential.cc b/potential.cc
@@ -22,12 +22,13 @@ pairPotential::pairPotential (void) {}
 
 double pairPotential::calcEnergy (const column_vector &v)
 {
-    structure S;
+    vector<coord3d> coordinates;
     for (long i = 0; i < v.size() / 3; ++i) 
     {
         coord3d sphere(v(3 * i), v(3 * i + 1), v(3 * i + 2));
-        S.push_back(sphere);
+        coordinates.push_back(sphere);
     }
+    structure S(0, coordinates, false);
     double f(0);
     for (int i = 0; i < S.nAtoms(); ++i) {
         for (int j = i + 1; j < S.nAtoms(); ++j) {
@@ -55,12 +56,13 @@ double pairPotential::calcEnergy (structure &S)
 
 const column_vector pairPotential::calcGradient (const column_vector &v)
 {
-    structure S;
+    vector<coord3d> coordinates;
     for (long i = 0; i < v.size() / 3; ++i) 
     {
         coord3d sphere(v(3 * i), v(3 * i + 1), v(3 * i + 2));
-        S.push_back(sphere);
+        coordinates.push_back(sphere);
     }
+    structure S(0, coordinates, false);
     vector<coord3d> gradients (S.nAtoms(), coord3d());
     for (int i = 0; i < S.nAtoms(); i++)
     {

diff --git a/structure.h b/structure.h
@@ -35,25 +35,17 @@ class structure {
     {}
 
     /* constructor calculates several properties based on coordinates on creation */    
-    structure (int number, std::vector<coord3d> coordinates) :  _energy(0),
-                                                                _number(number), 
-                                                                _coordinates(coordinates), 
-                                                                _hessian(0),
-                                                                _interPartDist(),
-                                                                _bondVector(),
-                                                                _adjMatrix_eigenvalues()
+    structure ( int number, 
+                std::vector<coord3d> coordinates, 
+                bool calcProp = true) : _energy(0),
+                                        _number(number), 
+                                        _hessian(0),
+                                        _interPartDist(),
+                                        _bondVector(),
+                                        _adjMatrix_eigenvalues()
     { 
-        this->shiftToCoM();
-
-        std::vector< std::vector<double> > inertiaTensor = this->momentOfInertia();
-        _momentOfInertia = diag(inertiaTensor);
-
-        matrix3d axis = this->m3d_principalAxis ();
-        this->rotateToPrincipalAxis(axis);
-
-        this->propertyInterPartDist();
-
-        this->propertyDistMatrix();
+        if (calcProp) this->setCoordinates(coordinates);
+        else _coordinates = coordinates;
     }
 
 
@@ -105,7 +97,7 @@ class structure {
 
     int nAtoms() { return (this->getCoordinates()).size(); }
 
-    void push_back(coord3d spheres) { _coordinates.push_back(spheres); }
+    //void push_back(coord3d spheres) { _coordinates.push_back(spheres); }
 
     structure &operator*= (const double &y) 
     {