Changeset 0dbddc for src

Timestamp:

Aug 3, 2009, 6:58:46 PM (15 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

ab1932

Parents:

2319ed (diff), 8c54a3 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'ConcaveHull' of ​ssh://heber@192.168.194.2/home/metzler/workspace/espack into ConcaveHull

Conflicts:

molecuilder/src/atom.cpp
molecuilder/src/boundary.cpp
molecuilder/src/boundary.hpp
molecuilder/src/linkedcell.cpp
molecuilder/src/linkedcell.hpp
molecuilder/src/molecules.hpp
molecuilder/src/vector.hpp

• added Saskia Metzler's code that finds whether a point is in- or outside.
• The code is not yet incorporated, but I rather want to continue with merging TesselationRefactoring first.

Location:

src

Files:

• atom.cpp (modified) (2 diffs)
• boundary.cpp (modified) (6 diffs)
• boundary.hpp (modified) (2 diffs)
• linkedcell.cpp (modified) (2 diffs)
• linkedcell.hpp (modified) (1 diff)
• molecules.hpp (modified) (1 diff)
• vector.cpp (modified) (2 diffs)
• vector.hpp (modified) (2 diffs)

src/atom.cpp

@@ -108 +108 @@
 };
 
-ostream & operator << (ostream &ost, const atom &a) 
+ostream & operator << (ostream &ost, const atom &a)
 {
   ost << "[" << a.Name << "|" << &a << "]";
@@ -118 +118 @@
  * \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/boundary.cpp

@@ -1152 +1152 @@
   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
@@ -1164 +1164 @@
         FillIt = true;
         for (MoleculeList::iterator ListRunner = List->ListOfMolecules.begin(); ListRunner != List->ListOfMolecules.end(); ListRunner++) {
-          FillIt = FillIt && (!(*ListRunner)->TesselStruct->IsInside(&CurrentPosition));
+          //FillIt = FillIt && (!(*ListRunner)->TesselStruct->IsInside(&CurrentPosition));
         }
 
@@ -2181 +2181 @@
  */
 int Tesselation::CheckPresenceOfTriangle(ofstream *out, atom *Candidates[3]) {
+// TODO: use findTriangles here and return result.size();
   LineMap::iterator FindLine;
   PointMap::iterator FindPoint;
@@ -3123 +3124 @@
  */
 bool sortCandidates(CandidateForTesselation* candidate1, CandidateForTesselation* candidate2) {
+  // TODO: use get angle and remove duplicate code
   Vector BaseLineVector, OrthogonalVector, helper;
-  if (candidate1->BaseLine != candidate2->BaseLine) {  // sanity check
-    cout << Verbose(0) << "ERROR: sortCandidates was called for two different baselines: " << candidate1->BaseLine << " and " << candidate2->BaseLine << "." << endl;
-    //return false;
-    exit(1);
-  }
-  // create baseline vector
-  BaseLineVector.CopyVector(&(candidate1->BaseLine->endpoints[1]->node->x));
-  BaseLineVector.SubtractVector(&(candidate1->BaseLine->endpoints[0]->node->x));
-  BaseLineVector.Normalize();
+        if (candidate1->BaseLine != candidate2->BaseLine) {  // sanity check
+          cout << Verbose(0) << "ERROR: sortCandidates was called for two different baselines: " << candidate1->BaseLine << " and " << candidate2->BaseLine << "." << endl;
+          //return false;
+          exit(1);
+        }
+        // create baseline vector
+        BaseLineVector.CopyVector(&(candidate1->BaseLine->endpoints[1]->node->x));
+        BaseLineVector.SubtractVector(&(candidate1->BaseLine->endpoints[0]->node->x));
+        BaseLineVector.Normalize();
 
   // create normal in-plane vector to cope with acos() non-uniqueness on [0,2pi] (note that is pointing in the "right" direction already, hence ">0" test!)
@@ -3161 +3163 @@
   // return comparison
   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 IsInnerAtom(atom *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 atom with, "
+        << "please create one first.";
+    exit(1);
+  }
+
+  class atom *trianglePoints[3];
+  trianglePoints[0] = findClosestAtom(Atom, LC);
+  // check whether closest atom is "too close" :), then it's inside
+  if (trianglePoints[0]->x.DistanceSquared(&Atom->x) < MYEPSILON)
+    return true;
+  list<atom*> *connectedClosestAtoms = Tess->getClosestConnectedAtoms(trianglePoints[0], Atom);
+  trianglePoints[1] = connectedClosestAtoms->front();
+  trianglePoints[2] = connectedClosestAtoms->back();
+  for (int i=0;i<3;i++) {
+    if (trianglePoints[i] == NULL) {
+      cout << Verbose(1) << "IsInnerAtom encounters serious error, point " << i << " not found." << endl;
+    }
+
+    cout << Verbose(1) << "List of possible atoms:" << endl;
+    cout << *trianglePoints[i] << endl;
+
+//    for(list<atom*>::iterator runner = connectedClosestAtoms->begin(); runner != connectedClosestAtoms->end(); runner++)
+//      cout << Verbose(2) << *(*runner) << endl;
+  }
+  delete(connectedClosestAtoms);
+
+  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->x);
+
+  // 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
+ */
+atom* findClosestAtom(const atom* Atom, LinkedCell* LC) {
+  LinkedAtoms *List = NULL;
+  atom* closestAtom = NULL;
+  double distance = 1e16;
+  Vector helper;
+  int N[NDIM], Nlower[NDIM], Nupper[NDIM];
+
+  LC->SetIndexToVector(&Atom->x); // 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 (LinkedAtoms::iterator Runner = List->begin(); Runner != List->end(); Runner++) {
+            helper.CopyVector(&Atom->x);
+            helper.SubtractVector(&(*Runner)->x);
+            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<atom*> * Tesselation::getClosestConnectedAtoms(atom* Atom, atom* AtomToCheck) {
+  list<atom*> connectedAtoms;
+  map<double, atom*> anglesOfAtoms;
+  map<double, atom*>::iterator runner;
+  LineMap::iterator findLines = LinesOnBoundary.begin();
+  list<atom*>::iterator listRunner;
+  Vector center, planeNorm, currentPoint, OrthogonalVector, helper;
+  atom* current;
+  bool takeAtom = false;
+
+  planeNorm.CopyVector(&Atom->x);
+  planeNorm.SubtractVector(&AtomToCheck->x);
+  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->x);
+      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->x);
+  helper.ProjectOntoPlane(&planeNorm);
+  OrthogonalVector.MakeNormalVector(&center, &helper, &(*listRunner)->x);
+  while (listRunner != connectedAtoms.end()) {
+    double angle = getAngle((*listRunner)->x, AtomToCheck->x, center, OrthogonalVector);
+    cout << "Calculated angle " << angle << " for atom " << **listRunner << endl;
+    anglesOfAtoms.insert(pair<double, atom*>(angle, (*listRunner)));
+    listRunner++;
+  }
+
+  list<atom*> *result = new list<atom*>;
+  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(atom* 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) {
+  atom *temp_atom = new atom;
+  bool status = false;
+  temp_atom->x.CopyVector(&Point);
+
+  status = IsInnerAtom(temp_atom, Tess, LC);
+  delete(temp_atom);
+
+  return status;
 }
 
@@ -3248 +3548 @@
     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;
+  atom* a = Tess->PointsOnBoundary.begin()->second->node;
+  cout << Verbose(0) << "Point to check: " << *a << " (on boundary)." << endl;
+  cout << Verbose(0) << "Check: IsInnerAtom() returns " << IsInnerAtom(a, Tess, LCList)
+    << "for atom " << a << " (on boundary)." << endl;
+  LinkedAtoms *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 (LinkedAtoms::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: IsInnerAtom() returns " << IsInnerAtom(a, Tess, LCList)
+    << "for atom " << a << " (inside)." << endl;
+
+
   if (freeTess)
     delete(Tess);

src/boundary.hpp

@@ -114 +114 @@
     bool InsertStraddlingPoints(ofstream *out, molecule *mol);
     bool CorrectConcaveBaselines(ofstream *out);
+    list<atom*> *getClosestConnectedAtoms(atom* Atom, atom* AtomToCheck);
+    list<BoundaryTriangleSet*> *FindTriangles(atom* TrianglePoints[3]);
 
     PointMap PointsOnBoundary;
@@ -144 +146 @@
 bool existsIntersection(Vector point1, Vector point2, Vector point3, Vector point4);
 bool sortCandidates(CandidateForTesselation* candidate1, CandidateForTesselation* candidate2);
+bool IsInnerPoint(Vector Point, class Tesselation *Tess, LinkedCell* LC);
+bool IsInnerAtom(atom *Atom, class Tesselation *Tess, LinkedCell* LC);
+atom* findClosestAtom(const atom* Atom, LinkedCell* LC);
+double getAngle(Vector point, Vector reference, Vector center, Vector OrthogonalVector);
 
 #endif /*BOUNDARY_HPP_*/

src/linkedcell.cpp

@@ -129 +129 @@
 
 /** Calculates the index for a given atom *Walker.
- * \param *Walker atom to set index to
+ * \param Walker atom to set index to
  * \return if the atom is also found in this cell - true, else - false
  */
-bool LinkedCell::SetIndexToAtom(atom *Walker)
+bool LinkedCell::SetIndexToAtom(const atom &Walker)
 {
   bool status = false;
   for (int i=0;i<NDIM;i++) {
-    n[i] = (int)floor((Walker->x.x[i] - min.x[i])/RADIUS);
+    n[i] = (int)floor((Walker.x.x[i] - min.x[i])/RADIUS);
   }
   index = n[0] * N[1] * N[2] + n[1] * N[2] + n[2];
   if (CheckBounds()) {
     for (LinkedAtoms::iterator Runner = LC[index].begin(); Runner != LC[index].end(); Runner++)
-      status = status || ((*Runner) == Walker);
+      status = status || ((*Runner) == &Walker);
     return status;
   } else {
-    cerr << Verbose(1) << "ERROR: Atom "<< *Walker << " at " << Walker->x << " is out of bounds." << endl;
+    cerr << Verbose(1) << "ERROR: Atom "<< Walker << " at " << Walker.x << " is out of bounds." << endl;
     return false;
+  }
+};
+
+/** 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;
   }
 };
@@ -153 +173 @@
  * \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

@@ -25 +25 @@
     ~LinkedCell();
     LinkedAtoms* GetCurrentCell();
-    bool SetIndexToAtom(atom *Walker);
-    bool SetIndexToVector(Vector *x);
+    bool SetIndexToAtom(const atom &Walker);
+    bool SetIndexToVector(const Vector *x);
     bool CheckBounds();
+    void GetNeighbourBounds(int lower[NDIM], int upper[NDIM]);
 
     // not implemented yet

src/molecules.hpp

@@ -156 +156 @@
   bool OutputXYZLine(ofstream *out) const;
   atom *GetTrueFather();
-  bool Compare(atom &ptr);
+  bool Compare(const atom &ptr);
 
   private:

src/vector.cpp

@@ -348 +348 @@
 };
 
+/** 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
@@ -456 +464 @@
 };
 
-ostream& operator<<(ostream& ost,Vector& m)
+ostream& operator<<(ostream& ost, const Vector& m)
 {
   ost << "(";

src/vector.hpp

@@ -24 +24 @@
   double NormSquared() const;
   double Angle(const Vector *y) const;
+  bool IsNull();
 
   void AddVector(const Vector *y);
@@ -58 +59 @@
 };
 
-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);