Changeset e9b8bb for src/molecules.cpp

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.

File:

• src/molecules.cpp (modified) (22 diffs)

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;