Changeset e9b8bb

Timestamp:

Aug 6, 2008, 9:02:01 AM (16 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:

5e0d1f

Parents:

d7e30c

Message:

Rename of class vector to Vector to avoid conflict with vector from STL.

Location:

src

Files:

• boundary.cpp (modified) (8 diffs)
• boundary.hpp (modified) (1 diff)
• builder.cpp (modified) (27 diffs)
• moleculelist.cpp (modified) (1 diff)
• molecules.cpp (modified) (22 diffs)
• molecules.hpp (modified) (4 diffs)
• vector.cpp (modified) (39 diffs)
• vector.hpp (modified) (3 diffs)

src/boundary.cpp

@@ -151 +151 @@
 };
 
-void BoundaryTriangleSet::GetNormalVector(vector &NormalVector)
+void BoundaryTriangleSet::GetNormalVector(Vector &NormalVector)
 {
   // get normal vector
@@ -211 +211 @@
   Boundaries *BoundaryPoints = new Boundaries [NDIM];  // first is alpha, second is (r, nr)
   BoundariesTestPair BoundaryTestPair;
-  vector AxisVector, AngleReferenceVector, AngleReferenceNormalVector;
+  Vector AxisVector, AngleReferenceVector, AngleReferenceNormalVector;
   double radius, angle;
   // 3a. Go through every axis
@@ -233 +233 @@
     while (Walker->next != mol->end) {
       Walker = Walker->next;
-      vector ProjectedVector;
+      Vector ProjectedVector;
       ProjectedVector.CopyVector(&Walker->x);
       ProjectedVector.ProjectOntoPlane(&AxisVector);
@@ -316 +316 @@
         // construct the vector of each side of the triangle on the projected plane (defined by normal vector AxisVector)
         {
-          vector SideA, SideB, SideC, SideH;
+          Vector SideA, SideB, SideC, SideH;
           SideA.CopyVector(&left->second.second->x);
           SideA.ProjectOntoPlane(&AxisVector);
@@ -394 +394 @@
     GreatestDiameter[i] = 0.;
   double OldComponent, tmp, w1, w2;
-  vector DistanceVector, OtherVector;
+  Vector DistanceVector, OtherVector;
   int component, Othercomponent;
   for(int axis=0;axis<NDIM;axis++) { // regard each projected plane
@@ -470 +470 @@
   double PyramidVolume = 0.;
   double G,h;
-  vector x,y;
+  Vector x,y;
   double a,b,c;
 
   // 1. calculate center of gravity
   *out << endl;
-  vector *CenterOfGravity = mol->DetermineCenterOfGravity(out);
+  Vector *CenterOfGravity = mol->DetermineCenterOfGravity(out);
   
   // 2. translate all points into CoG
@@ -578 +578 @@
     clustervolume = ClusterVolume;
   double *GreatestDiameter = GetDiametersOfCluster(out, BoundaryPoints, mol, IsAngstroem);
-  vector BoxLengths;
+  Vector BoxLengths;
   int repetition[NDIM] = {1, 1, 1};
   int TotalNoClusters = 1;
@@ -755 +755 @@
   class BoundaryPointSet *peak = NULL;
   double SmallestAngle, TempAngle;
-  vector NormalVector, VirtualNormalVector, CenterVector, TempVector, PropagationVector;
+  Vector NormalVector, VirtualNormalVector, CenterVector, TempVector, PropagationVector;
   LineMap::iterator LineChecker[2];
   do {

src/boundary.hpp

@@ -88 +88 @@
     ~BoundaryTriangleSet();
     
-    void GetNormalVector(vector &NormalVector);
+    void GetNormalVector(Vector &NormalVector);
     
     class BoundaryPointSet *endpoints[3];

src/builder.cpp

@@ -63 +63 @@
 {
   atom *first, *second, *third, *fourth;
-  vector **atoms;
-  vector x,y,z,n;  // coordinates for absolute point in cell volume
+  Vector **atoms;
+  Vector x,y,z,n;  // coordinates for absolute point in cell volume
   double a,b,c;
   char choice;  // menu choice char
@@ -99 +99 @@
           cout << Verbose(0) << "Enter relative coordinates." << endl;
           first->x.AskPosition(mol->cell_size, false);
-          first->x.AddVector((const vector *)&x);
+          first->x.AddVector((const Vector *)&x);
           cout << Verbose(0) << "\n";
-        } while (!(valid = mol->CheckBounds((const vector *)&first->x)));
+        } while (!(valid = mol->CheckBounds((const Vector *)&first->x)));
         first->type = periode->AskElement();  // give type
         mol->AddAtom(first);  // add to molecule
@@ -117 +117 @@
             first->x.x[i] += second->x.x[i];
           }
-        } while (!(valid = mol->CheckBounds((const vector *)&first->x)));
+        } while (!(valid = mol->CheckBounds((const Vector *)&first->x)));
         first->type = periode->AskElement();  // give type
         mol->AddAtom(first);  // add to molecule
@@ -219 +219 @@
           first->x.Output((ofstream *)&cout);
           cout << Verbose(0) << endl;
-        } while (!(valid = mol->CheckBounds((const vector *)&first->x)));
+        } while (!(valid = mol->CheckBounds((const Vector *)&first->x)));
         first->type = periode->AskElement();  // give type
         mol->AddAtom(first);  // add to molecule
@@ -226 +226 @@
       case 'e': // least square distance position to a set of atoms
         first = new atom;
-        atoms = new (vector*[128]);
+        atoms = new (Vector*[128]);
         valid = true;
         for(int i=128;i--;)
@@ -259 +259 @@
 static void CenterAtoms(molecule *mol)
 {
-  vector x, y;
+  Vector x, y;
   char choice;  // menu choice char
   
@@ -315 +315 @@
 {
   atom *first, *second, *third;
-  vector x,n;
+  Vector x,n;
   char choice;  // menu choice char
 
@@ -335 +335 @@
       third = mol->AskAtom("Enter third atom: ");
 
-      n.MakeNormalVector((const vector *)&first->x,(const vector *)&second->x,(const vector *)&third->x);
+      n.MakeNormalVector((const Vector *)&first->x,(const Vector *)&second->x,(const Vector *)&third->x);
       break;
     case 'b': // normal vector of mirror plane
@@ -346 +346 @@
       second = mol->AskAtom("Enter second atom: ");
 
-      n.CopyVector((const vector *)&first->x);  
-      n.SubtractVector((const vector *)&second->x);  
+      n.CopyVector((const Vector *)&first->x);  
+      n.SubtractVector((const Vector *)&second->x);  
       n.Normalize();
       break;        
     case 'd':
       char shorthand[4];
-      vector a;
+      Vector a;
       struct lsq_params param;
       do {
@@ -383 +383 @@
 {
   atom *first, *second, *third;
-  vector n;
+  Vector n;
   char choice;  // menu choice char
   
@@ -402 +402 @@
       third = mol->AskAtom("Enter third atom: ");
 
-      n.MakeNormalVector((const vector *)&first->x,(const vector *)&second->x,(const vector *)&third->x);
+      n.MakeNormalVector((const Vector *)&first->x,(const Vector *)&second->x,(const Vector *)&third->x);
       break;
     case 'b': // normal vector of mirror plane
@@ -413 +413 @@
       second = mol->AskAtom("Enter second atom: ");
 
-      n.CopyVector((const vector *)&first->x);  
-      n.SubtractVector((const vector *)&second->x);  
+      n.CopyVector((const Vector *)&first->x);  
+      n.SubtractVector((const Vector *)&second->x);  
       n.Normalize();
       break;          
@@ -421 +421 @@
   n.Output((ofstream *)&cout);
   cout << Verbose(0) << endl;
-  mol->Mirror((const vector *)&n);
+  mol->Mirror((const Vector *)&n);
 };
 
@@ -458 +458 @@
       while(first->next != mol->end) {
         first = first->next;
-        if (first->x.Distance((const vector *)&second->x) > tmp1*tmp1) // distance to first above radius ...
+        if (first->x.Distance((const Vector *)&second->x) > tmp1*tmp1) // distance to first above radius ...
           mol->RemoveAtom(first);
       }
@@ -488 +488 @@
 {
   atom *first, *second, *third;
-  vector x,y;
+  Vector x,y;
   double min[256], tmp1, tmp2, tmp3;
   int Z;
@@ -519 +519 @@
         tmp1 = 0.;
         if (first != second) {
-          x.CopyVector((const vector *)&first->x);
-          x.SubtractVector((const vector *)&second->x);
+          x.CopyVector((const Vector *)&first->x);
+          x.SubtractVector((const Vector *)&second->x);
           tmp1 = x.Norm();
         }
@@ -535 +535 @@
       for (int i=NDIM;i--;)
         min[i] = 0.;
-      x.CopyVector((const vector *)&first->x);
-      x.SubtractVector((const vector *)&second->x);
+      x.CopyVector((const Vector *)&first->x);
+      x.SubtractVector((const Vector *)&second->x);
       tmp1 = x.Norm();
       cout << Verbose(1) << "Distance vector is ";
@@ -549 +549 @@
       third  = mol->AskAtom("Enter last atom: ");
       tmp1 = tmp2 = tmp3 = 0.;
-      x.CopyVector((const vector *)&first->x);
-      x.SubtractVector((const vector *)&second->x);
-      y.CopyVector((const vector *)&third->x);
-      y.SubtractVector((const vector *)&second->x);
+      x.CopyVector((const Vector *)&first->x);
+      x.SubtractVector((const Vector *)&second->x);
+      y.CopyVector((const Vector *)&third->x);
+      y.SubtractVector((const Vector *)&second->x);
       cout << Verbose(0) << "Bond angle between first atom Nr." << first->nr << ", central atom Nr." << second->nr << " and last atom Nr." << third->nr << ": ";
-      cout << Verbose(0) << (acos(x.ScalarProduct((const vector *)&y)/(y.Norm()*x.Norm()))/M_PI*180.) << " degrees" << endl;         
+      cout << Verbose(0) << (acos(x.ScalarProduct((const Vector *)&y)/(y.Norm()*x.Norm()))/M_PI*180.) << " degrees" << endl;         
       break;
     case 'd':
@@ -727 +727 @@
 static int ParseCommandLineOptions(int argc, char **argv, molecule *&mol, periodentafel *&periode, config& configuration, char *&ConfigFileName, char *&PathToDatabases)
 {
-  vector x,y,z,n;  // coordinates for absolute point in cell volume
+  Vector x,y,z,n;  // coordinates for absolute point in cell volume
   double *factor; // unit factor if desired
   ifstream test;
@@ -889 +889 @@
               for (int i=NDIM;i--;)
                 x.x[i] = atof(argv[argptr+i]);
-              mol->Translate((const vector *)&x);
+              mol->Translate((const Vector *)&x);
               argptr+=3;
               break;
@@ -958 +958 @@
                 mol->cell_size[j] += x.x[i]*2.;
               }
-              mol->Translate((const vector *)&x);
+              mol->Translate((const Vector *)&x);
               break;
             case 'O':
@@ -1034 +1034 @@
                 int count;
                 element ** Elements;
-                vector ** vectors;
+                Vector ** vectors;
                 if (faktor < 1) {
                   cerr << Verbose(0) << "ERROR: Repetition faktor mus be greater than 1!" << endl;
@@ -1043 +1043 @@
                   count = mol->AtomCount;   // is changed becausing of adding, thus has to be stored away beforehand
                   Elements = new element *[count];
-                  vectors = new vector *[count];
+                  vectors = new Vector *[count];
                   j = 0;
                   first = mol->start;
@@ -1117 +1117 @@
   atom *first, *second;
   char choice;  // menu choice char
-  vector x,y,z,n;  // coordinates for absolute point in cell volume
+  Vector x,y,z,n;  // coordinates for absolute point in cell volume
         double *factor; // unit factor if desired
   bool valid; // flag if input was valid or not
@@ -1132 +1132 @@
   clock_t start,end;
   element **Elements;
-  vector **vectors;
+  Vector **vectors;
 
   // =========================== PARSE COMMAND LINE OPTIONS ====================================
@@ -1231 +1231 @@
           count = mol->AtomCount;   // is changed becausing of adding, thus has to be stored away beforehand
           Elements = new element *[count];
-          vectors = new vector *[count];
+          vectors = new Vector *[count];
           j = 0;
           first = mol->start;
@@ -1335 +1335 @@
        cout << Verbose(0) << "Enter translation vector." << endl;       
        x.AskPosition(mol->cell_size,0);
-       mol->Translate((const vector *)&x);
+       mol->Translate((const Vector *)&x);
        break;
   

src/moleculelist.cpp

@@ -388 +388 @@
   bool intermediateResult = true;
   atom *Walker = NULL;
-  vector BoxDimension;
+  Vector BoxDimension;
   char *FragmentNumber = NULL;
   char *path = NULL;

src/molecules.cpp

@@ -18 +18 @@
   double sum = 0.;
   struct LSQ_params *par = (struct LSQ_params *)params;
-  vector **vectors = par->vectors;
+  Vector **vectors = par->vectors;
   int num = par->num;
 
@@ -180 +180 @@
   atom *FirstOtherAtom = NULL, *SecondOtherAtom = NULL, *ThirdOtherAtom = NULL; // pointer to hydrogen atoms to be added
   double b,l,d,f,g, alpha, factors[NDIM];    // hold temporary values in triple bond case for coordination determination
-  vector Orthovector1, Orthovector2;  // temporary vectors in coordination construction
-  vector InBondvector;    // vector in direction of *Bond
+  Vector Orthovector1, Orthovector2;  // temporary vectors in coordination construction
+  Vector InBondvector;    // vector in direction of *Bond
   bond *Binder = NULL;
   double *matrix;
@@ -587 +587 @@
  * \param *dim vector class
  */
-void molecule::SetBoxDimension(vector *dim)
+void molecule::SetBoxDimension(Vector *dim)
 {
   cell_size[0] = dim->x[0];
@@ -601 +601 @@
  * \param *BoxLengths box lengths
  */
-bool molecule::CenterInBox(ofstream *out, vector *BoxLengths)
+bool molecule::CenterInBox(ofstream *out, Vector *BoxLengths)
 {
   bool status = true;
   atom *ptr = NULL;
-  vector *min = new vector;
-  vector *max = new vector;
+  Vector *min = new Vector;
+  Vector *max = new Vector;
   
   // gather min and max for each axis
@@ -651 +651 @@
  * \param *max coordinates of other edge, specifying box dimensions.
  */
-void molecule::CenterEdge(ofstream *out, vector *max)
-{
-  vector *min = new vector;
+void molecule::CenterEdge(ofstream *out, Vector *max)
+{
+  Vector *min = new Vector;
   
 //  *out << Verbose(3) << "Begin of CenterEdge." << endl;
@@ -690 +690 @@
  * \param *center return vector for translation vector
  */
-void molecule::CenterOrigin(ofstream *out, vector *center)
+void molecule::CenterOrigin(ofstream *out, Vector *center)
 {
   int Num = 0;
@@ -713 +713 @@
  * \return pointer to center of gravity vector
  */
-vector * molecule::DetermineCenterOfGravity(ofstream *out)
+Vector * molecule::DetermineCenterOfGravity(ofstream *out)
 {
         atom *ptr = start->next;  // start at first in list
-        vector *a = new vector();
-        vector tmp;
+        Vector *a = new Vector();
+        Vector tmp;
   double Num = 0;
         
@@ -742 +742 @@
  * \param *center return vector for translation vector
  */
-void molecule::CenterGravity(ofstream *out, vector *center)
+void molecule::CenterGravity(ofstream *out, Vector *center)
 {
   if (center == NULL) {
@@ -769 +769 @@
  * \param trans[] translation vector.
  */
-void molecule::Translate(const vector *trans)
+void molecule::Translate(const Vector *trans)
 {
   atom *ptr = start;
@@ -782 +782 @@
  * \param n[] normal vector of mirror plane.
  */
-void molecule::Mirror(const vector *n)
+void molecule::Mirror(const Vector *n)
 {
   atom *ptr = start;
@@ -795 +795 @@
  * \param Center reference to return vector
  */
-void molecule::DetermineCenter(vector &Center)
+void molecule::DetermineCenter(Vector &Center)
 {
   atom *Walker = start;
@@ -802 +802 @@
   double tmp;
   bool flag;
-  vector Testvector, Translationvector;
+  Vector Testvector, Translationvector;
   
   do {
@@ -867 +867 @@
         atom *ptr = start;  // start at first in list
         double InertiaTensor[NDIM*NDIM];
-        vector *CenterOfGravity = DetermineCenterOfGravity(out);
+        Vector *CenterOfGravity = DetermineCenterOfGravity(out);
 
         CenterGravity(out, CenterOfGravity);
@@ -878 +878 @@
         while (ptr->next != end) {
                 ptr = ptr->next;
-                vector x;
+                Vector x;
                 x.CopyVector(&ptr->x);
                 //x.SubtractVector(CenterOfGravity);
@@ -934 +934 @@
     while (ptr->next != end) {
       ptr = ptr->next;
-      vector x;
+      Vector x;
       x.CopyVector(&ptr->x);
       //x.SubtractVector(CenterOfGravity);
@@ -1060 +1060 @@
  * \param n[] alignment vector.
  */
-void molecule::Align(vector *n)
+void molecule::Align(Vector *n)
 {
   atom *ptr = start;
   double alpha, tmp;
-  vector z_axis;
+  Vector z_axis;
   z_axis.x[0] = 0.;
   z_axis.x[1] = 0.;
@@ -1168 +1168 @@
  * \return true - is within, false - out of cell
  */
-bool molecule::CheckBounds(const vector *x) const
+bool molecule::CheckBounds(const Vector *x) const
 {
   bool result = true;
@@ -1188 +1188 @@
 {
   double res = 0, t;
-  vector a,b,c,d;
+  Vector a,b,c,d;
   struct lsq_params *par = (struct lsq_params *)params;
   atom *ptr = par->mol->start;
@@ -1209 +1209 @@
       d.Scale(&t);
       c.SubtractVector(&d);   // ... yielding distance vector
-      res += d.ScalarProduct((const vector *)&d);        // add squared distance
+      res += d.ScalarProduct((const Vector *)&d);        // add squared distance
     }
   }
@@ -1542 +1542 @@
   double distance, MinDistance, MaxDistance;
   double *matrix = ReturnFullMatrixforSymmetric(cell_size);
-  vector x;
+  Vector x;
  
   BondDistance = bonddistance; // * ((IsAngstroem) ? 1. : 1./AtomicLengthToAngstroem);
@@ -3925 +3925 @@
   enum Shading *ColorList = NULL;
   double tmp;
-  vector Translationvector;
+  Vector Translationvector;
   //class StackClass<atom *> *CompStack = NULL;
   class StackClass<atom *> *AtomStack = new StackClass<atom *>(AtomCount);
@@ -4326 +4326 @@
   int flag;
   double *Distances = NULL, *OtherDistances = NULL;
-  vector CenterOfGravity, OtherCenterOfGravity;
+  Vector CenterOfGravity, OtherCenterOfGravity;
   size_t *PermMap = NULL, *OtherPermMap = NULL;
   int *PermutationMap = NULL;

src/molecules.hpp

@@ -73 +73 @@
  */
 struct LSQ_params {
-  vector **vectors;
+  Vector **vectors;
   int num;
 };
@@ -94 +94 @@
 class atom {
   public:
-    vector x;       //!< coordinate array of atom, giving position within cell
-    vector v;       //!< velocity array of atom
+    Vector x;       //!< coordinate array of atom, giving position within cell
+    Vector v;       //!< velocity array of atom
     element *type;  //!< pointing to element
     atom *previous; //!< previous atom in molecule list
@@ -212 +212 @@
   void CountElements();
   void CalculateOrbitals(class config &configuration);
-  bool CenterInBox(ofstream *out, vector *BoxLengths);
-  void CenterEdge(ofstream *out, vector *max); 
-  void CenterOrigin(ofstream *out, vector *max); 
-  void CenterGravity(ofstream *out, vector *max);
-  void Translate(const vector *x);
-  void Mirror(const vector *x);
-  void Align(vector *n);
+  bool CenterInBox(ofstream *out, Vector *BoxLengths);
+  void CenterEdge(ofstream *out, Vector *max); 
+  void CenterOrigin(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 DetermineCenter(vector &center);
-  vector * DetermineCenterOfGravity(ofstream *out);
-  void SetBoxDimension(vector *dim);
+  void DetermineCenter(Vector &center);
+  Vector * DetermineCenterOfGravity(ofstream *out);
+  void SetBoxDimension(Vector *dim);
   double * ReturnFullMatrixforSymmetric(double *cell_size);
   void ScanForPeriodicCorrection(ofstream *out);
@@ -229 +229 @@
         bool VerletForceIntegration(char *file, double delta_t);
         
-  bool CheckBounds(const vector *x) const;
+  bool CheckBounds(const Vector *x) const;
   void GetAlignvector(struct lsq_params * par) const;
 

src/vector.cpp

@@ -12 +12 @@
 /** Constructor of class vector.
  */
-vector::vector() { x[0] = x[1] = x[2] = 0.; };
+Vector::Vector() { x[0] = x[1] = x[2] = 0.; };
 
 /** Constructor of class vector.
  */
-vector::vector(double x1, double x2, double x3) { x[0] = x1; x[1] = x2; x[2] = x3; };
+Vector::Vector(double x1, double x2, double x3) { x[0] = x1; x[1] = x2; x[2] = x3; };
 
 /** Desctructor of class vector.
  */
-vector::~vector() {};
+Vector::~Vector() {};
 
 /** Calculates distance between this and another vector.
@@ -26 +26 @@
  * \return \f$| x - y |^2\f$
  */
-double vector::Distance(const vector *y) const
+double Vector::Distance(const Vector *y) const
 {
   double res = 0.;
@@ -39 +39 @@
  * \return \f$| x - y |^2\f$
  */
-double vector::PeriodicDistance(const vector *y, const double *cell_size) const
+double Vector::PeriodicDistance(const Vector *y, const double *cell_size) const
 {
   double res = Distance(y), tmp, matrix[NDIM*NDIM];
-  vector Shiftedy, TranslationVector;
+  Vector Shiftedy, TranslationVector;
   int N[NDIM];
   matrix[0] = cell_size[0];
@@ -76 +76 @@
  * Tries to translate a vector into each adjacent neighbouring cell.
  */
-void vector::KeepPeriodic(ofstream *out, double *matrix)
+void Vector::KeepPeriodic(ofstream *out, double *matrix)
 {
 //  int N[NDIM];
 //  bool flag = false;
   //vector Shifted, TranslationVector;
-  vector TestVector;
+  Vector TestVector;
 //  *out << Verbose(1) << "Begin of KeepPeriodic." << endl;
 //  *out << Verbose(2) << "Vector is: ";
@@ -107 +107 @@
  * \return \f$\langle x, y \rangle\f$
  */
-double vector::ScalarProduct(const vector *y) const
+double Vector::ScalarProduct(const Vector *y) const
 {
   double res = 0.;
@@ -119 +119 @@
  * \return \f$\langle x, y \rangle\f$
  */
-void vector::ProjectOntoPlane(const vector *y)
-{
-  vector tmp;
+void Vector::ProjectOntoPlane(const Vector *y)
+{
+  Vector tmp;
   tmp.CopyVector(y);
   tmp.Scale(Projection(y));
@@ -131 +131 @@
  * \return \f$\langle x, y \rangle\f$
  */
-double vector::Projection(const vector *y) const
+double Vector::Projection(const Vector *y) const
 {
   return (ScalarProduct(y));
@@ -139 +139 @@
  * \return \f$|x|\f$
  */
-double vector::Norm() const
+double Vector::Norm() const
 {
   double res = 0.;
@@ -149 +149 @@
 /** Normalizes this vector.
  */
-void vector::Normalize()
+void Vector::Normalize()
 {
   double res = 0.;
@@ -160 +160 @@
 /** Zeros all components of this vector.
  */
-void vector::Zero()
+void Vector::Zero()
 {
   for (int i=NDIM;i--;)
@@ -168 +168 @@
 /** Zeros all components of this vector.
  */
-void vector::One(double one)
+void Vector::One(double one)
 {
   for (int i=NDIM;i--;)
@@ -176 +176 @@
 /** Initialises all components of this vector.
  */
-void vector::Init(double x1, double x2, double x3)
+void Vector::Init(double x1, double x2, double x3)
 { 
   x[0] = x1;
@@ -187 +187 @@
  * \return \f$\acos\bigl(frac{\langle x, y \rangle}{|x||y|}\bigr)\f$
  */
-double vector::Angle(vector *y) const
+double Vector::Angle(Vector *y) const
 {
   return acos(this->ScalarProduct(y)/Norm()/y->Norm()); 
@@ -196 +196 @@
  * \param alpha rotation angle in radian
  */
-void vector::RotateVector(const vector *axis, const double alpha)
-{
-  vector a,y;
+void Vector::RotateVector(const Vector *axis, const double alpha)
+{
+  Vector a,y;
   // normalise this vector with respect to axis
   a.CopyVector(this);
@@ -220 +220 @@
  * \return lhs + a
  */
-vector& operator+=(vector& a, const vector& b)
+Vector& operator+=(Vector& a, const Vector& b)
 {
   a.AddVector(&b);
@@ -230 +230 @@
  * \return lhs.x[i] * m
  */
-vector& operator*=(vector& a, const double m)
+Vector& operator*=(Vector& a, const double m)
 {
   a.Scale(m);
@@ -241 +241 @@
  * \return a + b
  */
-vector& operator+(const vector& a, const vector& b)
-{
-  vector *x = new vector;
+Vector& operator+(const Vector& a, const Vector& b)
+{
+  Vector *x = new Vector;
   x->CopyVector(&a);
   x->AddVector(&b);
@@ -254 +254 @@
  * \return a + b
  */
-vector& operator*(const vector& a, const double m)
-{
-  vector *x = new vector;
+Vector& operator*(const Vector& a, const double m)
+{
+  Vector *x = new Vector;
   x->CopyVector(&a);
   x->Scale(m);
@@ -266 +266 @@
  * \param *out output stream
  */
-bool vector::Output(ofstream *out) const
+bool Vector::Output(ofstream *out) const
 {
   if (out != NULL) {
@@ -281 +281 @@
 };
 
-ofstream& operator<<(ofstream& ost,vector& m)
+ofstream& operator<<(ofstream& ost,Vector& m)
 {
         m.Output(&ost);
@@ -290 +290 @@
  * \param *factor pointer to scaling factor
  */
-void vector::Scale(double **factor)
+void Vector::Scale(double **factor)
 {
   for (int i=NDIM;i--;)
@@ -296 +296 @@
 };
 
-void vector::Scale(double *factor)
+void Vector::Scale(double *factor)
 {
   for (int i=NDIM;i--;)
@@ -302 +302 @@
 };
 
-void vector::Scale(double factor)
+void Vector::Scale(double factor)
 {
   for (int i=NDIM;i--;)
@@ -311 +311 @@
  * \param trans[] translation vector.
  */
-void vector::Translate(const vector *trans)
+void Vector::Translate(const Vector *trans)
 {
   for (int i=NDIM;i--;)
@@ -320 +320 @@
  * \param *matrix NDIM_NDIM array
  */
-void vector::MatrixMultiplication(double *M)
-{
-  vector C;
+void Vector::MatrixMultiplication(double *M)
+{
+  Vector C;
   // do the matrix multiplication
   C.x[0] = M[0]*x[0]+M[3]*x[1]+M[6]*x[2];
@@ -335 +335 @@
  * \param *matrix NDIM_NDIM array
  */
-void vector::InverseMatrixMultiplication(double *A)
-{
-  vector C;
+void Vector::InverseMatrixMultiplication(double *A)
+{
+  Vector C;
   double B[NDIM*NDIM];
   double detA = RDET3(A);
@@ -375 +375 @@
  * \param *factors three-component vector with the factor for each given vector
  */
-void vector::LinearCombinationOfVectors(const vector *x1, const vector *x2, const vector *x3, double *factors)
+void Vector::LinearCombinationOfVectors(const Vector *x1, const Vector *x2, const Vector *x3, double *factors)
 {
   for(int i=NDIM;i--;)
@@ -384 +384 @@
  * \param n[] normal vector of mirror plane.
  */
-void vector::Mirror(const vector *n)
+void Vector::Mirror(const Vector *n)
 {
   double projection;
@@ -406 +406 @@
  * \return true - success, vectors are linear independent, false - failure due to linear dependency
  */
-bool vector::MakeNormalVector(const vector *y1, const vector *y2, const vector *y3)
-{
-  vector x1, x2;
+bool Vector::MakeNormalVector(const Vector *y1, const Vector *y2, const Vector *y3)
+{
+  Vector x1, x2;
 
   x1.CopyVector(y1);
@@ -442 +442 @@
  * \return true - success, vectors are linear independent, false - failure due to linear dependency
  */
-bool vector::MakeNormalVector(const vector *y1, const vector *y2)
-{
-  vector x1,x2;
+bool Vector::MakeNormalVector(const Vector *y1, const Vector *y2)
+{
+  Vector x1,x2;
   x1.CopyVector(y1);
   x2.CopyVector(y2);
@@ -472 +472 @@
  * \return true - success, false - vector is zero
  */
-bool vector::MakeNormalVector(const vector *y1)
+bool Vector::MakeNormalVector(const Vector *y1)
 {
         bool result = false;
-  vector x1;
+  Vector x1;
   x1.CopyVector(y1);
   x1.Scale(x1.Projection(this));
@@ -491 +491 @@
  * \return true - success, false - failure (null vector given)
  */
-bool vector::GetOneNormalVector(const vector *GivenVector)
+bool Vector::GetOneNormalVector(const Vector *GivenVector)
 {
   int Components[NDIM]; // contains indices of non-zero components
@@ -537 +537 @@
  * \return scaling parameter for this vector
  */
-double vector::CutsPlaneAt(vector *A, vector *B, vector *C)
+double Vector::CutsPlaneAt(Vector *A, Vector *B, Vector *C)
 {
 //  cout << Verbose(3) << "For comparison: ";
@@ -552 +552 @@
  * \return true if success, false if failed due to linear dependency
  */
-bool vector::LSQdistance(vector **vectors, int num) 
+bool Vector::LSQdistance(Vector **vectors, int num) 
 {
         int j;
@@ -634 +634 @@
  * \param *y vector
  */
-void vector::AddVector(const vector *y)
+void Vector::AddVector(const Vector *y)
 {
   for (int i=NDIM;i--;)
@@ -643 +643 @@
  * \param *y vector
  */
-void vector::SubtractVector(const vector *y)
+void Vector::SubtractVector(const Vector *y)
 {
   for (int i=NDIM;i--;)
@@ -652 +652 @@
  * \param *y vector
  */
-void vector::CopyVector(const vector *y)
+void Vector::CopyVector(const Vector *y)
 {
   for (int i=NDIM;i--;)
@@ -663 +663 @@
  * \param check whether bounds shall be checked (true) or not (false)
  */
-void vector::AskPosition(double *cell_size, bool check)
+void Vector::AskPosition(double *cell_size, bool check)
 {
   char coords[3] = {'x','y','z'};
@@ -691 +691 @@
  * \bug this is not yet working properly 
  */
-bool vector::SolveSystem(vector *x1, vector *x2, vector *y, double alpha, double beta, double c)
+bool Vector::SolveSystem(Vector *x1, Vector *x2, Vector *y, double alpha, double beta, double c)
 {
   double D1,D2,D3,E1,E2,F1,F2,F3,p,q=0., A, B1, B2, C;

src/vector.hpp

@@ -2 +2 @@
 #define VECTOR_HPP_
 
-class vector;
+class Vector;
 
 /** Single vector.
  * basically, just a x[3] but with helpful functions
  */
-class vector {   
+class Vector {   
   public:
     double x[NDIM];
 
-  vector();
-  vector(double x1, double x2, double x3);
-  ~vector();
+  Vector();
+  Vector(double x1, double x2, double x3);
+  ~Vector();
 
-  double Distance(const vector *y) const;
-  double PeriodicDistance(const vector *y, const double *cell_size) const;
-  double ScalarProduct(const vector *y) const;
-  double Projection(const vector *y) const;
+  double Distance(const Vector *y) const;
+  double PeriodicDistance(const Vector *y, const double *cell_size) const;
+  double ScalarProduct(const Vector *y) const;
+  double Projection(const Vector *y) const;
   double Norm() const ;
-  double Angle(vector *y) const;
+  double Angle(Vector *y) const;
 
-  void AddVector(const vector *y);
-  void SubtractVector(const vector *y);
-  void CopyVector(const vector *y);
-  void RotateVector(const vector *y, const double alpha);
-  void ProjectOntoPlane(const vector *y);
+  void AddVector(const Vector *y);
+  void SubtractVector(const Vector *y);
+  void CopyVector(const Vector *y);
+  void RotateVector(const Vector *y, const double alpha);
+  void ProjectOntoPlane(const Vector *y);
   void Zero(); 
   void One(double one);
   void Init(double x1, double x2, double x3);
   void Normalize();
-  void Translate(const vector *x);
-  void Mirror(const vector *x);
+  void Translate(const Vector *x);
+  void Mirror(const Vector *x);
   void Scale(double **factor);
   void Scale(double *factor);
@@ -39 +39 @@
   void InverseMatrixMultiplication(double *M);
   void KeepPeriodic(ofstream *out, double *matrix);
-  void LinearCombinationOfVectors(const vector *x1, const vector *x2, const vector *x3, double *factors);
+  void LinearCombinationOfVectors(const Vector *x1, const Vector *x2, const Vector *x3, double *factors);
   
-  double CutsPlaneAt(vector *A, vector *B, vector *C);
-  bool GetOneNormalVector(const vector *x1);
-  bool MakeNormalVector(const vector *y1);
-  bool MakeNormalVector(const vector *y1, const vector *y2);
-  bool MakeNormalVector(const vector *x1, const vector *x2, const vector *x3);
-  bool SolveSystem(vector *x1, vector *x2, vector *y, double alpha, double beta, double c);
-  bool LSQdistance(vector **vectors, int dim);
+  double CutsPlaneAt(Vector *A, Vector *B, Vector *C);
+  bool GetOneNormalVector(const Vector *x1);
+  bool MakeNormalVector(const Vector *y1);
+  bool MakeNormalVector(const Vector *y1, const Vector *y2);
+  bool MakeNormalVector(const Vector *x1, const Vector *x2, const Vector *x3);
+  bool SolveSystem(Vector *x1, Vector *x2, Vector *y, double alpha, double beta, double c);
+  bool LSQdistance(Vector **vectors, int dim);
 
   void AskPosition(double *cell_size, bool check);
@@ -53 +53 @@
 };
 
-ofstream& operator<<(ofstream& ost, vector& m);
-vector& operator+=(vector& a, const vector& b);
-vector& operator*=(vector& a, const double m);
-vector& operator*(const vector& a, const double m);
-vector& operator+(const vector& a, const vector& b);
+ofstream& operator<<(ofstream& ost, Vector& m);
+Vector& operator+=(Vector& a, const Vector& b);
+Vector& operator*=(Vector& a, const double m);
+Vector& operator*(const Vector& a, const double m);
+Vector& operator+(const Vector& a, const Vector& b);
 
 #endif /*VECTOR_HPP_*/