Changeset 833b15 for src/molecule_geometry.cpp

Timestamp:

Sep 9, 2014, 7:42:32 PM (10 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:

a090e3

Parents:

2d701e

git-author:

Frederik Heber <heber@…> (09/01/14 15:54:02)

git-committer:

Frederik Heber <heber@…> (09/09/14 19:42:32)

Message:

FIX: Changes to function signatures in molecule_geometry.

• no more returning allocated pointer (Vector *)
• no more Pointers as parameters.
• removed functions that are only convenience and have nothing to do with the molecule.
• changes elsewhere due to signature changes.

File:

• src/molecule_geometry.cpp (modified) (24 diffs)

src/molecule_geometry.cpp

@@ -58 +58 @@
 /************************************* Functions for class molecule *********************************/
 
+/** Returns vector pointing to center of the domain.
+ * \return pointer to center of the domain
+ */
+#ifdef HAVE_INLINE
+inline
+#else
+static
+#endif
+const Vector DetermineCenterOfBox()
+{
+  Vector a(0.5,0.5,0.5);
+  const RealSpaceMatrix &M = World::getInstance().getDomain().getM();
+  a *= M;
+  return a;
+}
 
 /** Centers the molecule in the box whose lengths are defined by vector \a *BoxLengths.
@@ -65 +80 @@
 {
   bool status = true;
-  const Vector *Center = DetermineCenterOfAll();
-  const Vector *CenterBox = DetermineCenterOfBox();
+  const Vector Center = DetermineCenterOfAll();
+  const Vector CenterBox = DetermineCenterOfBox();
   Box &domain = World::getInstance().getDomain();
 
   // go through all atoms
-  const Vector difference = *CenterBox - *Center;
-  Translate(&difference);
+  Translate(CenterBox - Center);
   getAtomSet().transformNodes(boost::bind(&Box::enforceBoundaryConditions,domain,_1));
 
-  delete(Center);
-  delete(CenterBox);
   return status;
-};
+}
 
 
@@ -92 +104 @@
 
   return status;
-};
+}
 
 /** Centers the edge of the atoms at (0,0,0).
- * \param *out output stream for debugging
- * \param *max coordinates of other edge, specifying box dimensions.
- */
-void molecule::CenterEdge(Vector *max)
+ */
+void molecule::CenterEdge()
 {
   const_iterator iter = begin();
   if (iter != end()) {   //list not empty?
     Vector min = (*begin())->getPosition();
-    *max = min;
     for (;iter != end(); ++iter) { // continue with second if present
       const Vector &currentPos = (*iter)->getPosition();
-      for (size_t i=0;i<NDIM;++i) {
+      for (size_t i=0;i<NDIM;++i)
         if (min[i] > currentPos[i])
           min[i] = currentPos[i];
-        if ((*max)[i] < currentPos[i])
-          (*max)[i] = currentPos[i];
-      }
-    }
-    LOG(1, "INFO: Maximum is " << *max << ", Minimum is " << min << ".");
-    const Vector temp = -1.*min;
-    Translate(&temp);
-  }
-};
+    }
+    Translate(-1.*min);
+  }
+}
 
 /** Centers the center of the atoms at (0,0,0).
@@ -136 +140 @@
     }
     Center.Scale(-1./(double)Num); // divide through total number (and sign for direction)
-    Translate(&Center);
-  }
-};
+    Translate(Center);
+  }
+}
 
 /** Returns vector pointing to center of all atoms.
  * \return pointer to center of all vector
  */
-Vector * molecule::DetermineCenterOfAll() const
+const Vector molecule::DetermineCenterOfAll() const
 {
   const_iterator iter = begin();  // start at first in list
-  Vector *a = new Vector();
+  Vector a;
   double Num = 0;
 
-  a->Zero();
+  a.Zero();
 
   if (iter != end()) {   //list not empty?
     for (; iter != end(); ++iter) {  // continue with second if present
       Num++;
-      (*a) += (*iter)->getPosition();
-    }
-    a->Scale(1./(double)Num); // divide through total mass (and sign for direction)
+      a += (*iter)->getPosition();
+    }
+    a.Scale(1./(double)Num); // divide through total mass (and sign for direction)
   }
   return a;
-};
-
-/** Returns vector pointing to center of the domain.
- * \return pointer to center of the domain
- */
-Vector * molecule::DetermineCenterOfBox() const
-{
-  Vector *a = new Vector(0.5,0.5,0.5);
-  const RealSpaceMatrix &M = World::getInstance().getDomain().getM();
-  (*a) *= M;
-  return a;
-};
+}
+
 
 /** Returns vector pointing to center of gravity.
@@ -176 +170 @@
  * \return pointer to center of gravity vector
  */
-Vector * molecule::DetermineCenterOfGravity() const
+const Vector molecule::DetermineCenterOfGravity() const
 {
   const_iterator iter = begin();  // start at first in list
-  Vector *a = new Vector();
+  Vector a;
   Vector tmp;
   double Num = 0;
 
-  a->Zero();
+  a.Zero();
 
   if (iter != end()) {   //list not empty?
@@ -189 +183 @@
       Num += (*iter)->getType()->getMass();
       tmp = (*iter)->getType()->getMass() * (*iter)->getPosition();
-      (*a) += tmp;
-    }
-    a->Scale(1./Num); // divide through total mass
-  }
-  LOG(1, "INFO: Resulting center of gravity: " << *a << ".");
+      a += tmp;
+    }
+    a.Scale(1./Num); // divide through total mass
+  }
+  LOG(1, "INFO: Resulting center of gravity: " << a << ".");
   return a;
-};
+}
 
 /** Centers the center of gravity of the atoms at (0,0,0).
@@ -205 +199 @@
   Vector NewCenter;
   DeterminePeriodicCenter(NewCenter);
-  NewCenter *= -1.;
-  Translate(&NewCenter);
-};
+  Translate(-1.*NewCenter);
+}
 
 
@@ -214 +207 @@
  * \param *center return vector for translation vector
  */
-void molecule::CenterAtVector(Vector *newcenter)
-{
-  const Vector temp = -1.**newcenter;
-  Translate(&temp);
-};
+void molecule::CenterAtVector(const Vector &newcenter)
+{
+  Translate(-1.*newcenter);
+}
 
 /** Calculate the inertia tensor of a the molecule.
@@ -227 +219 @@
 {
   RealSpaceMatrix InertiaTensor;
-  Vector *CenterOfGravity = DetermineCenterOfGravity();
+  const Vector CenterOfGravity = DetermineCenterOfGravity();
 
   // reset inertia tensor
@@ -235 +227 @@
   for (const_iterator iter = begin(); iter != end(); ++iter) {
     Vector x = (*iter)->getPosition();
-    x -= *CenterOfGravity;
+    x -= CenterOfGravity;
     const double mass = (*iter)->getType()->getMass();
     InertiaTensor.at(0,0) += mass*(x[1]*x[1] + x[2]*x[2]);
@@ -250 +242 @@
   LOG(1, "INFO: The inertia tensor of molecule " << getName() <<  " is:" << InertiaTensor);
 
-  delete CenterOfGravity;
   return InertiaTensor;
 }
@@ -261 +252 @@
 void molecule::RotateToPrincipalAxisSystem(const Vector &Axis)
 {
-  Vector *CenterOfGravity = DetermineCenterOfGravity();
+  const Vector CenterOfGravity = DetermineCenterOfGravity();
   RealSpaceMatrix InertiaTensor = getInertiaTensor();
 
@@ -273 +264 @@
 
   // obtain first column, eigenvector to biggest eigenvalue
-  Vector BiggestEigenvector(InertiaTensor.column(Eigenvalues.SmallestComponent()));
+  const Vector BiggestEigenvector(InertiaTensor.column(Eigenvalues.SmallestComponent()));
   Vector DesiredAxis(Axis.getNormalized());
 
@@ -287 +278 @@
   // and rotate
   for (iterator iter = begin(); iter != end(); ++iter) {
-    *(*iter) -= *CenterOfGravity;
+    *(*iter) -= CenterOfGravity;
     (*iter)->setPosition(RotationAxis.rotateVector((*iter)->getPosition(), alpha));
-    *(*iter) += *CenterOfGravity;
+    *(*iter) += CenterOfGravity;
   }
   LOG(0, "STATUS: done.");
-
-  delete CenterOfGravity;
 }
 
@@ -304 +293 @@
  * x=(**factor) * x (as suggested by comment)
  */
-void molecule::Scale(const double ** const factor)
+void molecule::Scale(const double *factor)
 {
   for (iterator iter = begin(); iter != end(); ++iter) {
     for (size_t j=0;j<(*iter)->getTrajectorySize();j++) {
       Vector temp = (*iter)->getPositionAtStep(j);
-      temp.ScaleAll(*factor);
+      temp.ScaleAll(factor);
       (*iter)->setPositionAtStep(j,temp);
     }
@@ -318 +307 @@
  * \param trans[] translation vector.
  */
-void molecule::Translate(const Vector *trans)
-{
-  getAtomSet().translate(*trans);
+void molecule::Translate(const Vector &trans)
+{
+  getAtomSet().translate(trans);
 };
 
@@ -327 +316 @@
  * TODO treatment of trajectories missing
  */
-void molecule::TranslatePeriodically(const Vector *trans)
+void molecule::TranslatePeriodically(const Vector &trans)
 {
   Translate(trans);
@@ -338 +327 @@
  * \param n[] normal vector of mirror plane.
  */
-void molecule::Mirror(const Vector *n)
-{
-  Plane p(*n,0);
+void molecule::Mirror(const Vector &n)
+{
+  Plane p(n,0);
   getAtomSet().transformNodes(boost::bind(&Plane::mirrorVector,p,_1));
 };
@@ -356 +345 @@
   Vector Testvector, Translationvector;
   Vector Center;
-  BondGraph *BG = World::getInstance().getBondGraph();
+  const BondGraph * const BG = World::getInstance().getBondGraph();
 
   do {
@@ -407 +396 @@
 
   Center.Scale(1./static_cast<double>(getAtomCount()));
-  CenterAtVector(&Center);
+  CenterAtVector(Center);
 };
 
@@ -413 +402 @@
  * \param n[] alignment vector.
  */
-void molecule::Align(Vector *n)
+void molecule::Align(const Vector &n)
 {
   double alpha, tmp;
   Vector z_axis;
+  Vector alignment(n);
   z_axis[0] = 0.;
   z_axis[1] = 0.;
@@ -423 +413 @@
   // rotate on z-x plane
   LOG(0, "Begin of Aligning all atoms.");
-  alpha = atan(-n->at(0)/n->at(2));
+  alpha = atan(-alignment.at(0)/alignment.at(2));
   LOG(1, "INFO: Z-X-angle: " << alpha << " ... ");
   for (iterator iter = begin(); iter != end(); ++iter) {
@@ -437 +427 @@
   }
   // rotate n vector
-  tmp = n->at(0);
-  n->at(0) =  cos(alpha) * tmp +  sin(alpha) * n->at(2);
-  n->at(2) = -sin(alpha) * tmp +  cos(alpha) * n->at(2);
-  LOG(1, "alignment vector after first rotation: " << n);
+  tmp = alignment.at(0);
+  alignment.at(0) =  cos(alpha) * tmp +  sin(alpha) * alignment.at(2);
+  alignment.at(2) = -sin(alpha) * tmp +  cos(alpha) * alignment.at(2);
+  LOG(1, "alignment vector after first rotation: " << alignment);
 
   // rotate on z-y plane
-  alpha = atan(-n->at(1)/n->at(2));
+  alpha = atan(-alignment.at(1)/alignment.at(2));
   LOG(1, "INFO: Z-Y-angle: " << alpha << " ... ");
   for (iterator iter = begin(); iter != end(); ++iter) {
@@ -457 +447 @@
   }
   // rotate n vector (for consistency check)
-  tmp = n->at(1);
-  n->at(1) =  cos(alpha) * tmp +  sin(alpha) * n->at(2);
-  n->at(2) = -sin(alpha) * tmp +  cos(alpha) * n->at(2);
-
-
-  LOG(1, "alignment vector after second rotation: " << n);
+  tmp = alignment.at(1);
+  alignment.at(1) =  cos(alpha) * tmp +  sin(alpha) * alignment.at(2);
+  alignment.at(2) = -sin(alpha) * tmp +  cos(alpha) * alignment.at(2);
+
+  LOG(1, "alignment vector after second rotation: " << alignment);
   LOG(0, "End of Aligning all atoms.");
 };