Changes in / [ab1932:edb93c]

Location:

src

Files:

• atom.cpp (modified) (2 diffs)
• atom.hpp (modified) (1 diff)
• boundary.cpp (modified) (3 diffs)
• linkedcell.cpp (modified) (2 diffs)
• linkedcell.hpp (modified) (1 diff)
• molecules.hpp (modified) (2 diffs)
• parser.hpp (modified) (1 diff)
• tesselation.cpp (modified) (3 diffs)
• tesselation.hpp (modified) (3 diffs)
• vector.cpp (modified) (2 diffs)
• vector.hpp (modified) (2 diffs)

src/atom.cpp

@@ -113 +113 @@
 };
 
-ostream & operator << (ostream &ost, const atom &a)
+ostream & operator << (ostream &ost, const atom &a) 
 {
   ost << "[" << a.Name << "|" << &a << "]";
@@ -123 +123 @@
  * \return true - this one's is smaller, false - not
  */
-bool atom::Compare(const atom &ptr)
+bool atom::Compare(atom &ptr)
 {
   if (nr < ptr.nr)

src/atom.hpp

@@ -54 +54 @@
   bool OutputXYZLine(ofstream *out) const;
   atom *GetTrueFather();
-  bool Compare(const atom &ptr);
+  bool Compare(atom &ptr);
 
   private:

src/boundary.cpp

@@ -739 +739 @@
   FillerDistance.InverseMatrixMultiplication(M);
   for(int i=0;i<NDIM;i++)
-    N[i] = (int) ceil(1./FillerDistance.x[i]);
+    N[i] = ceil(1./FillerDistance.x[i]);
 
   // go over [0,1]^3 filler grid
@@ -813 +813 @@
   return Filling;
 };
-
 
 /** Tesselates the non convex boundary by rolling a virtual sphere along the surface of the molecule.
@@ -957 +956 @@
     cout << Verbose(2) << "None." << endl;
 
-  // Tests the IsInnerAtom() function.
-  Vector x (0, 0, 0);
-  cout << Verbose(0) << "Point to check: " << x << endl;
-  cout << Verbose(0) << "Check: IsInnerPoint() returns " << IsInnerPoint(x, Tess, LCList)
-    << "for vector " << x << "." << endl;
-  TesselPoint* a = Tess->PointsOnBoundary.begin()->second->node;
-  cout << Verbose(0) << "Point to check: " << *a << " (on boundary)." << endl;
-  cout << Verbose(0) << "Check: IsInnerAtom() returns " << IsInnerPoint(a, Tess, LCList)
-    << "for atom " << a << " (on boundary)." << endl;
-  LinkedNodes *List = NULL;
-  for (int i=0;i<NDIM;i++) { // each axis
-    LCList->n[i] = LCList->N[i]-1; // current axis is topmost cell
-    for (LCList->n[(i+1)%NDIM]=0;LCList->n[(i+1)%NDIM]<LCList->N[(i+1)%NDIM];LCList->n[(i+1)%NDIM]++)
-      for (LCList->n[(i+2)%NDIM]=0;LCList->n[(i+2)%NDIM]<LCList->N[(i+2)%NDIM];LCList->n[(i+2)%NDIM]++) {
-        List = LCList->GetCurrentCell();
-        //cout << Verbose(2) << "Current cell is " << LC->n[0] << ", " << LC->n[1] << ", " << LC->n[2] << " with No. " << LC->index << "." << endl;
-        if (List != NULL) {
-          for (LinkedNodes::iterator Runner = List->begin();Runner != List->end();Runner++) {
-            if (Tess->PointsOnBoundary.find((*Runner)->nr) == Tess->PointsOnBoundary.end()) {
-              a = *Runner;
-              i=3;
-              for (int j=0;j<NDIM;j++)
-                LCList->n[j] = LCList->N[j];
-              break;
-            }
-          }
-        }
-      }
-  }
-  cout << Verbose(0) << "Check: IsInnerPoint() returns " << IsInnerPoint(a, Tess, LCList)
-    << "for atom " << a << " (inside)." << endl;
-
-
   if (freeTess)
     delete(Tess);

src/linkedcell.cpp

@@ -147 +147 @@
  * \return if the atom is also found in this cell - true, else - false
  */
-bool LinkedCell::SetIndexToNode(const TesselPoint *Walker)
+bool LinkedCell::SetIndexToNode(TesselPoint *Walker)
 {
   bool status = false;
@@ -164 +164 @@
 };
 
-/** Calculates the interval bounds of the linked cell grid.
- * \param *lower lower bounds
- * \param *upper upper bounds
- */
-void LinkedCell::GetNeighbourBounds(int lower[NDIM], int upper[NDIM])
-{
-  for (int i=0;i<NDIM;i++) {
-    lower[i] = ((n[i]-1) >= 0) ? n[i]-1 : 0;
-    upper[i] = ((n[i]+1) < N[i]) ? n[i]+1 : N[i]-1;
-    //cout << " [" << Nlower[i] << "," << Nupper[i] << "] ";
-    // check for this axis whether the point is outside of our grid
-    if (n[i] < 0)
-      upper[i] = lower[i];
-    if (n[i] > N[i])
-      lower[i] = upper[i];
-
-    //cout << "axis " << i << " has bounds [" << lower[i] << "," << upper[i] << "]" << endl;
-  }
-};
-
 /** Calculates the index for a given Vector *x.
  * \param *x Vector with coordinates
  * \return Vector is inside bounding box - true, else - false
  */
-bool LinkedCell::SetIndexToVector(const Vector *x)
+bool LinkedCell::SetIndexToVector(Vector *x)
 {
   bool status = true;

src/linkedcell.hpp

@@ -46 +46 @@
     ~LinkedCell();
     LinkedNodes* GetCurrentCell();
-    bool SetIndexToNode(const TesselPoint *Walker);
-    bool SetIndexToVector(const Vector *x);
+    bool SetIndexToNode(TesselPoint *Walker);
+    bool SetIndexToVector(Vector *x);
     bool CheckBounds();
-    void GetNeighbourBounds(int lower[NDIM], int upper[NDIM]);
 
     // not implemented yet

src/molecules.hpp

@@ -104 +104 @@
   element *type;
 };
+
 
 #define MaxThermostats 6      //!< maximum number of thermostat entries in Ions#ThermostatNames and Ions#ThermostatImplemented 
@@ -139 +140 @@
 
   molecule(periodentafel *teil);
-  virtual ~molecule();
+  ~molecule();
 
   // re-definition of virtual functions from PointCloud

src/parser.hpp

@@ -55 +55 @@
   
   MatrixContainer();
-  virtual ~MatrixContainer();
+  ~MatrixContainer();
   
   bool InitialiseIndices(class MatrixContainer *Matrix = NULL);

src/tesselation.cpp

@@ -1693 +1693 @@
   CirclePlaneNormal.SubtractVector(BaseLine->endpoints[1]->node->node);
 
-  // calculate squared radius TesselPoint *ThirdNode,f circle
+  // calculate squared radius atom *ThirdNode,f circle
   radius = CirclePlaneNormal.ScalarProduct(&CirclePlaneNormal);
   if (radius/4. < RADIUS*RADIUS) {
@@ -1914 +1914 @@
 /** Sort function for the candidate list.
  */
-bool sortCandidates(CandidateForTesselation* candidate1, CandidateForTesselation* candidate2) 
-{
+bool sortCandidates(CandidateForTesselation* candidate1, CandidateForTesselation* candidate2) {
   Vector BaseLineVector, OrthogonalVector, helper;
   if (candidate1->BaseLine != candidate2->BaseLine) {  // sanity check
@@ -1955 +1954 @@
   return phi < psi;
 };
-
-
-/**
- * Checks whether the provided atom is within the tesselation structure.
- *
- * @param *Atom of which to check the position
- * @param tesselation structure
- *
- * @return true if the atom is inside the tesselation structure, false otherwise
- */
-bool IsInnerPoint(TesselPoint *Atom, class Tesselation *Tess, LinkedCell* LC) 
-{
-  if (Tess->LinesOnBoundary.begin() == Tess->LinesOnBoundary.end()) {
-    cout << Verbose(0) << "Error: There is no tesselation structure to compare the point with, "
-        << "please create one first.";
-    exit(1);
-  }
-
-  class TesselPoint *trianglePoints[3];
-  trianglePoints[0] = findClosestAtom(Atom, LC);
-  // check whether closest atom is "too close" :), then it's inside
-  if (trianglePoints[0]->node->DistanceSquared(Atom->node) < MYEPSILON)
-    return true;
-  list<TesselPoint*> *connectedClosestPoints = Tess->getClosestConnectedAtoms(trianglePoints[0], Atom);
-  trianglePoints[1] = connectedClosestPoints->front();
-  trianglePoints[2] = connectedClosestPoints->back();
-  for (int i=0;i<3;i++) {
-    if (trianglePoints[i] == NULL) {
-      cout << Verbose(1) << "IsInnerPoint encounters serious error, point " << i << " not found." << endl;
-    }
-
-    cout << Verbose(1) << "List of possible atoms:" << endl;
-    cout << *trianglePoints[i] << endl;
-
-//    for(list<TesselPoint*>::iterator runner = connectedClosestPoints->begin(); runner != connectedClosestPoints->end(); runner++)
-//      cout << Verbose(2) << *(*runner) << endl;
-  }
-  delete(connectedClosestPoints);
-
-  list<BoundaryTriangleSet*> *triangles = Tess->FindTriangles(trianglePoints);
-
-  if (triangles->empty()) {
-    cout << Verbose(0) << "Error: There is no nearest triangle. Please check the tesselation structure.";
-    exit(1);
-  }
-
-  Vector helper;
-  helper.CopyVector(Atom->node);
-
-  // Only in case of degeneration, there will be two different scalar products.
-  // If at least one scalar product is positive, the point is considered to be outside.
-  bool status = (helper.ScalarProduct(&triangles->front()->NormalVector) < 0)
-      && (helper.ScalarProduct(&triangles->back()->NormalVector) < 0);
-  delete(triangles);
-  return status;
-}
-
-/**
- * Finds the atom which is closest to the provided one.
- *
- * @param atom to which to find the closest other atom
- * @param linked cell structure
- *
- * @return atom which is closest to the provided one
- */
-TesselPoint* findClosestAtom(const TesselPoint* Atom, LinkedCell* LC) 
-{
-  LinkedNodes *List = NULL;
-  TesselPoint* closestAtom = NULL;
-  double distance = 1e16;
-  Vector helper;
-  int N[NDIM], Nlower[NDIM], Nupper[NDIM];
-
-  LC->SetIndexToVector(Atom->node); // ignore status as we calculate bounds below sensibly
-  for(int i=0;i<NDIM;i++) // store indices of this cell
-    N[i] = LC->n[i];
-  //cout << Verbose(2) << "INFO: Center cell is " << N[0] << ", " << N[1] << ", " << N[2] << " with No. " << LC->index << "." << endl;
-
-  LC->GetNeighbourBounds(Nlower, Nupper);
-  //cout << endl;
-  for (LC->n[0] = Nlower[0]; LC->n[0] <= Nupper[0]; LC->n[0]++)
-    for (LC->n[1] = Nlower[1]; LC->n[1] <= Nupper[1]; LC->n[1]++)
-      for (LC->n[2] = Nlower[2]; LC->n[2] <= Nupper[2]; LC->n[2]++) {
-        List = LC->GetCurrentCell();
-        //cout << "The current cell " << LC->n[0] << "," << LC->n[1] << "," << LC->n[2] << endl;
-        if (List != NULL) {
-          for (LinkedNodes::iterator Runner = List->begin(); Runner != List->end(); Runner++) {
-            helper.CopyVector(Atom->node);
-            helper.SubtractVector((*Runner)->node);
-            double currentNorm = helper. Norm();
-            if (currentNorm < distance) {
-              distance = currentNorm;
-              closestAtom = (*Runner);
-            }
-          }
-        } else {
-          cerr << "ERROR: The current cell " << LC->n[0] << "," << LC->n[1] << ","
-            << LC->n[2] << " is invalid!" << endl;
-        }
-      }
-
-  return closestAtom;
-}
-
-/**
- * Gets all atoms connected to the provided atom by triangulation lines.
- *
- * @param atom of which get all connected atoms
- * @param atom to be checked whether it is an inner atom
- *
- * @return list of the two atoms linked to the provided one and closest to the atom to be checked,
- */
-list<TesselPoint*> * Tesselation::getClosestConnectedAtoms(TesselPoint* Atom, TesselPoint* AtomToCheck) 
-{
-  list<TesselPoint*> connectedAtoms;
-  map<double, TesselPoint*> anglesOfAtoms;
-  map<double, TesselPoint*>::iterator runner;
-  LineMap::iterator findLines = LinesOnBoundary.begin();
-  list<TesselPoint*>::iterator listRunner;
-  Vector center, planeNorm, currentPoint, OrthogonalVector, helper;
-  TesselPoint* current;
-  bool takeAtom = false;
-
-  planeNorm.CopyVector(Atom->node);
-  planeNorm.SubtractVector(AtomToCheck->node);
-  planeNorm.Normalize();
-
-  while (findLines != LinesOnBoundary.end()) {
-    takeAtom = false;
-
-    if (findLines->second->endpoints[0]->Nr == Atom->nr) {
-      takeAtom = true;
-      current = findLines->second->endpoints[1]->node;
-    } else if (findLines->second->endpoints[1]->Nr == Atom->nr) {
-      takeAtom = true;
-      current = findLines->second->endpoints[0]->node;
-    }
-
-    if (takeAtom) {
-      connectedAtoms.push_back(current);
-      currentPoint.CopyVector(current->node);
-      currentPoint.ProjectOntoPlane(&planeNorm);
-      center.AddVector(&currentPoint);
-    }
-
-    findLines++;
-  }
-
-  cout << "Summed vectors " << center << "; number of atoms " << connectedAtoms.size()
-    << "; scale factor " << 1.0/connectedAtoms.size();
-
-  center.Scale(1.0/connectedAtoms.size());
-  listRunner = connectedAtoms.begin();
-
-  cout << " calculated center " << center <<  endl;
-
-  // construct one orthogonal vector
-  helper.CopyVector(AtomToCheck->node);
-  helper.ProjectOntoPlane(&planeNorm);
-  OrthogonalVector.MakeNormalVector(&center, &helper, (*listRunner)->node);
-  while (listRunner != connectedAtoms.end()) {
-    double angle = getAngle(*((*listRunner)->node), *(AtomToCheck->node), center, OrthogonalVector);
-    cout << "Calculated angle " << angle << " for atom " << **listRunner << endl;
-    anglesOfAtoms.insert(pair<double, TesselPoint*>(angle, (*listRunner)));
-    listRunner++;
-  }
-
-  list<TesselPoint*> *result = new list<TesselPoint*>;
-  runner = anglesOfAtoms.begin();
-  cout << "First value is " << *runner->second << endl;
-  result->push_back(runner->second);
-  runner = anglesOfAtoms.end();
-  runner--;
-  cout << "Second value is " << *runner->second << endl;
-  result->push_back(runner->second);
-
-  cout << "List of closest atoms has " << result->size() << " elements, which are "
-    << *(result->front()) << " and " << *(result->back()) << endl;
-
-  return result;
-}
-
-/**
- * Finds triangles belonging to the three provided atoms.
- *
- * @param atom list, is expected to contain three atoms
- *
- * @return triangles which belong to the provided atoms, will be empty if there are none,
- *         will usually be one, in case of degeneration, there will be two
- */
-list<BoundaryTriangleSet*> *Tesselation::FindTriangles(TesselPoint* Points[3]) 
-{
-  list<BoundaryTriangleSet*> *result = new list<BoundaryTriangleSet*>;
-  LineMap::iterator FindLine;
-  PointMap::iterator FindPoint;
-  TriangleMap::iterator FindTriangle;
-  class BoundaryPointSet *TrianglePoints[3];
-
-  for (int i = 0; i < 3; i++) {
-    FindPoint = PointsOnBoundary.find(Points[i]->nr);
-    if (FindPoint != PointsOnBoundary.end()) {
-      TrianglePoints[i] = FindPoint->second;
-    } else {
-      TrianglePoints[i] = NULL;
-    }
-  }
-
-  // checks lines between the points in the Points for their adjacent triangles
-  for (int i = 0; i < 3; i++) {
-    if (TrianglePoints[i] != NULL) {
-      for (int j = i; j < 3; j++) {
-        if (TrianglePoints[j] != NULL) {
-          FindLine = TrianglePoints[i]->lines.find(TrianglePoints[j]->node->nr);
-          if (FindLine != TrianglePoints[i]->lines.end()) {
-            for (; FindLine->first == TrianglePoints[j]->node->nr; FindLine++) {
-              FindTriangle = FindLine->second->triangles.begin();
-              for (; FindTriangle != FindLine->second->triangles.end(); FindTriangle++) {
-                if ((
-                  (FindTriangle->second->endpoints[0] == TrianglePoints[0])
-                    || (FindTriangle->second->endpoints[0] == TrianglePoints[1])
-                    || (FindTriangle->second->endpoints[0] == TrianglePoints[2])
-                  ) && (
-                    (FindTriangle->second->endpoints[1] == TrianglePoints[0])
-                    || (FindTriangle->second->endpoints[1] == TrianglePoints[1])
-                    || (FindTriangle->second->endpoints[1] == TrianglePoints[2])
-                  ) && (
-                    (FindTriangle->second->endpoints[2] == TrianglePoints[0])
-                    || (FindTriangle->second->endpoints[2] == TrianglePoints[1])
-                    || (FindTriangle->second->endpoints[2] == TrianglePoints[2])
-                  )
-                ) {
-                  result->push_back(FindTriangle->second);
-                }
-              }
-            }
-            // Is it sufficient to consider one of the triangle lines for this.
-            return result;
-
-          }
-        }
-      }
-    }
-  }
-
-  return result;
-}
-
-/**
- * Gets the angle between a point and a reference relative to the provided center.
- *
- * @param point to calculate the angle for
- * @param reference to which to calculate the angle
- * @param center for which to calculate the angle between the vectors
- * @param OrthogonalVector helps discern between [0,pi] and [pi,2pi] in acos()
- *
- * @return angle between point and reference
- */
-double getAngle(Vector point, Vector reference, Vector center, Vector OrthogonalVector) 
-{
-  Vector ReferenceVector, helper;
-  cout << Verbose(2) << reference << " is our reference " << endl;
-  cout << Verbose(2) << center << " is our center " << endl;
-  // create baseline vector
-  ReferenceVector.CopyVector(&reference);
-  ReferenceVector.SubtractVector(&center);
-  if (ReferenceVector.IsNull())
-    return M_PI;
-
-  // calculate both angles and correct with in-plane vector
-  helper.CopyVector(&point);
-  helper.SubtractVector(&center);
-  if (helper.IsNull())
-    return M_PI;
-  double phi = ReferenceVector.Angle(&helper);
-  if (OrthogonalVector.ScalarProduct(&helper) > 0) {
-    phi = 2.*M_PI - phi;
-  }
-
-  cout << Verbose(2) << point << " has angle " << phi << endl;
-
-  return phi;
-}
-
-/**
- * Checks whether the provided point is within the tesselation structure.
- *
- * This is a wrapper function for IsInnerAtom, so it can be used with a simple
- * vector, too.
- *
- * @param point of which to check the position
- * @param tesselation structure
- *
- * @return true if the point is inside the tesselation structure, false otherwise
- */
-bool IsInnerPoint(Vector Point, class Tesselation *Tess, LinkedCell* LC) 
-{
-  TesselPoint *temp_atom = new TesselPoint;
-  bool status = false;
-  temp_atom->node->CopyVector(&Point);
-
-  status = IsInnerPoint(temp_atom, Tess, LC);
-  delete(temp_atom);
-
-  return status;
-}
-

src/tesselation.hpp

@@ -150 +150 @@
 public:
   PointCloud();
-  virtual ~PointCloud();
+  ~PointCloud();
 
   virtual Vector *GetCenter(ofstream *out) { return NULL; };
@@ -208 +208 @@
     bool CorrectConcaveBaselines(ofstream *out);
 
-    list<TesselPoint*> * getClosestConnectedAtoms(TesselPoint* Atom, TesselPoint* AtomToCheck);
-    list<BoundaryTriangleSet*> *FindTriangles(TesselPoint* Points[3]);
-
     PointMap PointsOnBoundary;
     LineMap LinesOnBoundary;
@@ -227 +224 @@
 bool CheckLineCriteriaforDegeneratedTriangle(class BoundaryPointSet *nodes[3]);
 bool sortCandidates(class CandidateForTesselation* candidate1, class CandidateForTesselation* candidate2);
-TesselPoint* findClosestAtom(const TesselPoint* Atom, LinkedCell* LC);
-double getAngle(Vector point, Vector reference, Vector center, Vector OrthogonalVector);
-bool IsInnerPoint(Vector Point, class Tesselation *Tess, LinkedCell* LC) ;
-bool IsInnerPoint(TesselPoint *Atom, class Tesselation *Tess, LinkedCell* LC);
+
 
 #endif /* TESSELATION_HPP_ */

src/vector.cpp

@@ -349 +349 @@
 };
 
-/** Checks whether vector has all components zero.
- * @return true - vector is zero, false - vector is not
- */
-bool Vector::IsNull()
-{
-  return (fabs(x[0]+x[1]+x[2]) < MYEPSILON);
-};
-
 /** Calculates the angle between this and another vector.
  * \param *y array to second vector
@@ -465 +457 @@
 };
 
-ostream& operator<<(ostream& ost, const Vector& m)
+ostream& operator<<(ostream& ost,Vector& m)
 {
   ost << "(";

src/vector.hpp

@@ -28 +28 @@
   double NormSquared() const;
   double Angle(const Vector *y) const;
-  bool IsNull();
 
   void AddVector(const Vector *y);
@@ -63 +62 @@
 };
 
-ostream & operator << (ostream& ost, const Vector &m);
+ostream & operator << (ostream& ost, Vector &m);
 //Vector& operator+=(Vector& a, const Vector& b);
 //Vector& operator*=(Vector& a, const double m);