Changeset 1dc9ec for src

Timestamp:

Jun 17, 2010, 3:09:22 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:

d386e8

Parents:

5f5a7b (diff), 0c7ed8 (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 'VectorRefactoring' into stable

Conflicts:

molecuilder/src/vector.cpp

Location:

src

Files:

• gslvector.cpp (modified) (2 diffs)
• gslvector.hpp (modified) (2 diffs)
• linearsystemofequations.cpp (modified) (1 diff)
• vector.cpp (modified) (20 diffs)
• vector.hpp (modified) (3 diffs)

src/gslvector.cpp

@@ -13 +13 @@
 #include "gslvector.hpp"
 #include "defs.hpp"
+#include "vector.hpp"
 
 /** Constructor of class GSLVector.
@@ -61 +62 @@
   gsl_vector_memcpy (vector, &m.vector);
 };
+
+/**
+ * This function sets the GSLvector from an ordinary vector.
+ *
+ * Takes access to the internal gsl_vector and copies it
+ */
+void GSLVector::SetFromVector(Vector &v){
+  gsl_vector_memcpy (vector, v.get());
+}
 
 /** This function returns the i-th element of a vector.

src/gslvector.hpp

@@ -24 +24 @@
 
 class GSLVector;
+class Vector;
 
 /********************************************** declarations *******************************/
@@ -38 +39 @@
   // Accessing
   void SetFromDoubleArray(double *x);
+  void SetFromVector(Vector &v);
   double Get(size_t m) const;
   void Set(size_t m, double x);

src/linearsystemofequations.cpp

@@ -56 +56 @@
 {
   assert ( columns == NDIM && "Vector class is always three-dimensional, unlike this LEqS!");
-  b->SetFromDoubleArray(x->get());
+  b->SetFromVector(*x);
 };
 

src/vector.cpp

@@ -24 +24 @@
 Vector::Vector()
 {
-  x[0] = x[1] = x[2] = 0.;
+  content = gsl_vector_calloc (NDIM);
 };
 
@@ -33 +33 @@
 Vector::Vector(const Vector& src)
 {
-  x[0] = src[0];
-  x[1] = src[1];
-  x[2] = src[2];
+  content = gsl_vector_alloc(NDIM);
+  gsl_vector_set(content,0,src[0]);
+  gsl_vector_set(content,1,src[1]);
+  gsl_vector_set(content,2,src[2]);
 }
 
@@ -42 +43 @@
 Vector::Vector(const double x1, const double x2, const double x3)
 {
-  x[0] = x1;
-  x[1] = x2;
-  x[2] = x3;
+  content = gsl_vector_alloc(NDIM);
+  gsl_vector_set(content,0,x1);
+  gsl_vector_set(content,1,x2);
+  gsl_vector_set(content,2,x3);
 };
 
@@ -53 +55 @@
   // check for self assignment
   if(&src!=this){
-    x[0] = src[0];
-    x[1] = src[1];
-    x[2] = src[2];
+    gsl_vector_set(content,0,src[0]);
+    gsl_vector_set(content,1,src[1]);
+    gsl_vector_set(content,2,src[2]);
   }
   return *this;
@@ -62 +64 @@
 /** Desctructor of class vector.
  */
-Vector::~Vector() {};
+Vector::~Vector() {
+  gsl_vector_free(content);
+};
 
 /** Calculates square of distance between this and another vector.
@@ -72 +76 @@
   double res = 0.;
   for (int i=NDIM;i--;)
-    res += (x[i]-y[i])*(x[i]-y[i]);
+    res += (at(i)-y[i])*(at(i)-y[i]);
   return (res);
 };
@@ -200 +204 @@
   double res = 0.;
   for (int i=NDIM;i--;)
-    res += x[i]*y[i];
+    res += at(i)*y[i];
   return (res);
 };
@@ -214 +218 @@
 {
   Vector tmp;
-  tmp[0] = x[1]* y[2] - x[2]* y[1];
-  tmp[1] = x[2]* y[0] - x[0]* y[2];
-  tmp[2] = x[0]* y[1] - x[1]* y[0];
+  for(int i=NDIM;i--;)
+    tmp[i] = at((i+1)%NDIM)*y[(i+2)%NDIM] - at((i+2)%NDIM)*y[(i+1)%NDIM];
   (*this) = tmp;
 };
@@ -309 +312 @@
 bool Vector::IsZero() const
 {
-  return (fabs(x[0])+fabs(x[1])+fabs(x[2]) < MYEPSILON);
+  return (fabs(at(0))+fabs(at(1))+fabs(at(2)) < MYEPSILON);
 };
 
@@ -338 +341 @@
   bool status = true;
   for (int i=0;i<NDIM;i++) {
-    if (fabs(x[i] - a[i]) > MYEPSILON)
+    if (fabs(at(i) - a[i]) > MYEPSILON)
       status = false;
   }
@@ -366 +369 @@
 double& Vector::operator[](size_t i){
   ASSERT(i<=NDIM && i>=0,"Vector Index out of Range");
-  return x[i];
+  return *gsl_vector_ptr (content, i);
 }
 
 const double& Vector::operator[](size_t i) const{
   ASSERT(i<=NDIM && i>=0,"Vector Index out of Range");
-  return x[i];
+  return *gsl_vector_ptr (content, i);
 }
 
@@ -382 +385 @@
 }
 
-double* Vector::get(){
-  return x;
+gsl_vector* Vector::get(){
+  return content;
 }
 
@@ -498 +501 @@
 {
   for (int i=NDIM;i--;)
-    x[i] *= factor[i];
+    at(i) *= factor[i];
 };
 
@@ -506 +509 @@
 {
   for (int i=NDIM;i--;)
-    x[i] *= factor;
+    at(i) *= factor;
 };
 
@@ -518 +521 @@
   // truncate to [0,1] for each axis
   for (int i=0;i<NDIM;i++) {
-    //x[i] += 0.5;  // set to center of box
-    while (x[i] >= 1.)
-      x[i] -= 1.;
-    while (x[i] < 0.)
-      x[i] += 1.;
+    //at(i) += 0.5;  // set to center of box
+    while (at(i) >= 1.)
+      at(i) -= 1.;
+    while (at(i) < 0.)
+      at(i) += 1.;
   }
   MatrixMultiplication(M);
@@ -549 +552 @@
 void Vector::MatrixMultiplication(const double * const M)
 {
+  Vector tmp;
   // do the matrix multiplication
-  at(0) = M[0]*x[0]+M[3]*x[1]+M[6]*x[2];
-  at(1) = M[1]*x[0]+M[4]*x[1]+M[7]*x[2];
-  at(2) = M[2]*x[0]+M[5]*x[1]+M[8]*x[2];
+  for(int i=NDIM;i--;)
+    tmp[i] = M[i]*at(0)+M[i+3]*at(1)+M[i+6]*at(2);
+
+  (*this) = tmp;
 };
 
@@ -577 +582 @@
     B[8] =  detAReci*RDET2(A[0],A[1],A[3],A[4]);    // A_33
 
-    // do the matrix multiplication
-    at(0) = B[0]*x[0]+B[3]*x[1]+B[6]*x[2];
-    at(1) = B[1]*x[0]+B[4]*x[1]+B[7]*x[2];
-    at(2) = B[2]*x[0]+B[5]*x[1]+B[8]*x[2];
+    MatrixMultiplication(B);
 
     return true;
@@ -616 +618 @@
   SubtractVector(x1);
   for (int i=NDIM;i--;)
-    result = result || (fabs(x[i]) > MYEPSILON);
+    result = result || (fabs(at(i)) > MYEPSILON);
 
   return result;
@@ -678 +680 @@
 {
   for(int i=NDIM;i--;)
-    x[i] += y[i];
+    at(i) += y[i];
 }
 
@@ -687 +689 @@
 {
   for(int i=NDIM;i--;)
-    x[i] -= y[i];
+    at(i) -= y[i];
 }
 

src/vector.hpp

@@ -31 +31 @@
  */
 class Vector : public Space{
-protected:
-  // this struct is used to indicate calls to the Baseconstructor from inside vectors.
-  struct Baseconstructor{};
 public:
 
@@ -82 +79 @@
 
   // Access to internal structure
-  double* get();
+  gsl_vector* get();
 
   // Methods that are derived directly from other methods
@@ -107 +104 @@
 
 private:
-  double x[NDIM];
+  gsl_vector *content;
 
 };