Changes in / [edb93c:ab1932]

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(atom &ptr)
+bool atom::Compare(const atom &ptr)
 {
   if (nr < ptr.nr)

src/atom.hpp

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

src/boundary.cpp

@@ -739 +739 @@
   FillerDistance.InverseMatrixMultiplication(M);
   for(int i=0;i<NDIM;i++)
-    N[i] = ceil(1./FillerDistance.x[i]);
+    N[i] = (int) 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.
@@ -956 +957 @@
     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(TesselPoint *Walker)
+bool LinkedCell::SetIndexToNode(const 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(Vector *x)
+bool LinkedCell::SetIndexToVector(const Vector *x)
 {
   bool status = true;

src/linkedcell.hpp

@@ -46 +46 @@
     ~LinkedCell();
     LinkedNodes* GetCurrentCell();
-    bool SetIndexToNode(TesselPoint *Walker);
-    bool SetIndexToVector(Vector *x);
+    bool SetIndexToNode(const TesselPoint *Walker);
+    bool SetIndexToVector(const 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 
@@ -140 +139 @@
 
   molecule(periodentafel *teil);
-  ~molecule();
+  virtual ~molecule();
 
   // re-definition of virtual functions from PointCloud

src/parser.hpp

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

src/tesselation.cpp

@@ -1693 +1693 @@
   CirclePlaneNormal.SubtractVector(BaseLine->endpoints[1]->node->node);
 
-  // calculate squared radius atom *ThirdNode,f circle
+  // calculate squared radius TesselPoint *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
@@ -1954 +1955 @@
   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();
-  ~PointCloud();
+  virtual ~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;
@@ -224 +227 @@
 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
@@ -457 +465 @@
 };
 
-ostream& operator<<(ostream& ost,Vector& m)
+ostream& operator<<(ostream& ost, const Vector& m)
 {
   ost << "(";

src/vector.hpp

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