Changeset f429d7

Timestamp:

Jun 30, 2010, 3:39:55 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

89e820

Parents:

3dcb1f

Message:

Move Vector::WrapPeriodically to Box class

Location:

src

Files:

• Box.cpp (modified) (2 diffs)
• Box.hpp (modified) (1 diff)
• molecule_geometry.cpp (modified) (4 diffs)
• vector.cpp (modified) (1 diff)
• vector.hpp (modified) (1 diff)

src/Box.cpp

@@ -9 +9 @@
 
 #include "Box.hpp"
+
+#include <cmath>
 
 #include "Matrix.hpp"
@@ -57 +59 @@
 }
 
+Vector Box::WrapPeriodically(const Vector &point){
+  Vector helper = translateOut(point);
+  for(int i=NDIM;i--;){
+    double intpart,fracpart;
+    fracpart = modf(helper.at(i),&intpart);
+    if(fracpart<0.)
+      fracpart+=1.;
+    helper.at(i)=fracpart;
+  }
+  return translateIn(helper);
+}
+
 Box &Box::operator=(const Box &src){
   if(&src!=this){

src/Box.hpp

@@ -29 +29 @@
   Vector translateOut(const Vector &point);
 
+  Vector WrapPeriodically(const Vector &point);
+
 private:
   Matrix *M;    //!< Defines the layout of the box

src/molecule_geometry.cpp

@@ -35 +35 @@
   const Vector *Center = DetermineCenterOfAll();
   const Vector *CenterBox = DetermineCenterOfBox();
-  const Matrix &M = World::getInstance().getDomain().getM();
-  const Matrix &Minv = World::getInstance().getDomain().getMinv();
+  Box &domain = World::getInstance().getDomain();
 
   // go through all atoms
@@ -42 +41 @@
   ActOnAllVectors( &Vector::SubtractVector, *CenterBox);
   BOOST_FOREACH(atom* iter, atoms){
-    iter->node->WrapPeriodically(M, Minv);
+    *iter->node = domain.WrapPeriodically(*iter->node);
   }
 
@@ -56 +55 @@
 {
   bool status = true;
-  const Matrix &M = World::getInstance().getDomain().getM();
-  const Matrix &Minv = World::getInstance().getDomain().getMinv();
+  Box &domain = World::getInstance().getDomain();
 
   // go through all atoms
   BOOST_FOREACH(atom* iter, atoms){
-    iter->node->WrapPeriodically(M, Minv);
+    *iter->node = domain.WrapPeriodically(*iter->node);
   }
 
@@ -239 +237 @@
 void molecule::TranslatePeriodically(const Vector *trans)
 {
-  const Matrix &M = World::getInstance().getDomain().getM();
-  const Matrix &Minv = World::getInstance().getDomain().getMinv();
+  Box &domain = World::getInstance().getDomain();
 
   // go through all atoms
   ActOnAllVectors( &Vector::AddVector, *trans);
   BOOST_FOREACH(atom* iter, atoms){
-    iter->node->WrapPeriodically(M, Minv);
+    *iter->node = domain.WrapPeriodically(*iter->node);
   }
 

src/vector.cpp

@@ -458 +458 @@
 {
   gsl_vector_scale(content,factor);
-};
-
-/** Given a box by its matrix \a *M and its inverse *Minv the vector is made to point within that box.
- * \param *M matrix of box
- * \param *Minv inverse matrix
- */
-void Vector::WrapPeriodically(const Matrix &M, const Matrix &Minv)
-{
-  *this *= Minv;
-  // truncate to [0,1] for each axis
-  for (int i=0;i<NDIM;i++) {
-    //at(i) += 0.5;  // set to center of box
-    while (at(i) >= 1.)
-      at(i) -= 1.;
-    while (at(i) < 0.)
-      at(i) += 1.;
-  }
-  *this *= M;
 };
 

src/vector.hpp

@@ -62 +62 @@
   bool MakeNormalTo(const Vector &y1);
   bool IsInParallelepiped(const Vector &offset, const Matrix& _parallelepiped) const;
-  void WrapPeriodically(const Matrix &M, const Matrix &Minv);
   std::pair<Vector,Vector> partition(const Vector&) const;
   std::pair<pointset,Vector> partition(const pointset&) const;