Changeset 436f04

Timestamp:

Jun 26, 2010, 12:21:48 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:

a679d1

Parents:

e3ffd3

Message:

Added a method that allows faster setting of matrix elements using direct access to the gsl_matrix_set() function

Location:

src

Files:

• Matrix.cpp (modified) (4 diffs)
• Matrix.hpp (modified) (1 diff)

src/Matrix.cpp

@@ -22 +22 @@
 Matrix::Matrix(const double* src){
   content = gsl_matrix_alloc(NDIM, NDIM);
-  this->at(0,0) = src[0];
-  this->at(1,0) = src[1];
-  this->at(2,0) = src[2];
+  set(0,0, src[0]);
+  set(1,0, src[1]);
+  set(2,0, src[2]);
 
-  this->at(0,1) = src[3];
-  this->at(1,1) = src[4];
-  this->at(2,1) = src[5];
+  set(0,1, src[3]);
+  set(1,1, src[4]);
+  set(2,1, src[5]);
 
-  this->at(0,2) = src[6];
-  this->at(1,2) = src[7];
-  this->at(2,2) = src[8];
+  set(0,2, src[6]);
+  set(1,2, src[7]);
+  set(2,2, src[8]);
 }
 
@@ -95 +95 @@
 }
 
-const double &Matrix::at(size_t i, size_t j) const{
+const double Matrix::at(size_t i, size_t j) const{
   ASSERT(i>=0&&i<NDIM,"Index i for Matrix access out of range");
   ASSERT(j>=0&&j<NDIM,"Index j for Matrix access out of range");
-  return *gsl_matrix_ptr (content, i, j);
+  return gsl_matrix_get(content, i, j);
+}
+
+void Matrix::set(size_t i, size_t j, const double value){
+  ASSERT(i>=0&&i<NDIM,"Index i for Matrix access out of range");
+  ASSERT(j>=0&&j<NDIM,"Index j for Matrix access out of range");
+  gsl_matrix_set(content,i,j,value);
 }
 
@@ -118 +124 @@
   double detReci = 1./det;
   Matrix res;
-  res.at(0,0) =  detReci*RDET2(at(1,1),at(2,1),at(1,2),at(2,2));    // A_11
-  res.at(1,0) = -detReci*RDET2(at(1,0),at(2,0),at(1,2),at(2,2));    // A_21
-  res.at(2,0) =  detReci*RDET2(at(1,0),at(2,0),at(1,1),at(2,1));    // A_31
-  res.at(0,1) = -detReci*RDET2(at(0,1),at(2,1),at(0,2),at(2,2));    // A_12
-  res.at(1,1) =  detReci*RDET2(at(0,0),at(2,0),at(0,2),at(2,2));    // A_22
-  res.at(2,1) = -detReci*RDET2(at(0,0),at(2,0),at(0,1),at(2,1));    // A_32
-  res.at(0,2) =  detReci*RDET2(at(0,1),at(1,1),at(0,2),at(1,2));    // A_13
-  res.at(1,2) = -detReci*RDET2(at(0,0),at(1,0),at(0,2),at(1,2));    // A_23
-  res.at(2,2) =  detReci*RDET2(at(0,0),at(1,0),at(0,1),at(1,1));    // A_33
+  res.set(0,0,  detReci*RDET2(at(1,1),at(2,1),at(1,2),at(2,2)));    // A_11
+  res.set(1,0, -detReci*RDET2(at(1,0),at(2,0),at(1,2),at(2,2)));    // A_21
+  res.set(2,0,  detReci*RDET2(at(1,0),at(2,0),at(1,1),at(2,1)));    // A_31
+  res.set(0,1, -detReci*RDET2(at(0,1),at(2,1),at(0,2),at(2,2)));    // A_12
+  res.set(1,1,  detReci*RDET2(at(0,0),at(2,0),at(0,2),at(2,2)));    // A_22
+  res.set(2,1, -detReci*RDET2(at(0,0),at(2,0),at(0,1),at(2,1)));    // A_32
+  res.set(0,2,  detReci*RDET2(at(0,1),at(1,1),at(0,2),at(1,2)));    // A_13
+  res.set(1,2, -detReci*RDET2(at(0,0),at(1,0),at(0,2),at(1,2)));    // A_23
+  res.set(2,2,  detReci*RDET2(at(0,0),at(1,0),at(0,1),at(1,1)));    // A_33
   return res;
 }
@@ -152 +158 @@
 {
   Matrix matrix;
-  matrix.at(0,0) = symm[0];
-  matrix.at(1,0) = symm[1];
-  matrix.at(2,0) = symm[3];
-  matrix.at(0,1) = symm[1];
-  matrix.at(1,1) = symm[2];
-  matrix.at(2,1) = symm[4];
-  matrix.at(0,2) = symm[3];
-  matrix.at(1,2) = symm[4];
-  matrix.at(2,2) = symm[5];
+  matrix.set(0,0, symm[0]);
+  matrix.set(1,0, symm[1]);
+  matrix.set(2,0, symm[3]);
+  matrix.set(0,1, symm[1]);
+  matrix.set(1,1, symm[2]);
+  matrix.set(2,1, symm[4]);
+  matrix.set(0,2, symm[3]);
+  matrix.set(1,2, symm[4]);
+  matrix.set(2,2, symm[5]);
   return matrix;
 };

src/Matrix.hpp

@@ -24 +24 @@
 
   double &at(size_t i, size_t j);
-  const double &at(size_t i, size_t j) const;
+  const double at(size_t i, size_t j) const;
+
+  void set(size_t i, size_t j, const double value);
 
   double determinant() const;