Changeset a679d1 for src/vector.cpp

Timestamp:

Jun 26, 2010, 12:35:18 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:

4d206f

Parents:

436f04

Message:

Replaced Matrix access with direct access at several places

File:

• src/vector.cpp (modified) (1 diff)

src/vector.cpp

@@ -105 +105 @@
 double Vector::PeriodicDistance(const Vector &y, const double * const cell_size) const
 {
-  double res = distance(y), tmp;
-  Matrix matrix;
+  return sqrt(PeriodicDistanceSquared);
+};
+
+/** Calculates distance between this and another vector in a periodic cell.
+ * \param *y array to second vector
+ * \param *cell_size 6-dimensional array with (xx, xy, yy, xz, yz, zz) entries specifying the periodic cell
+ * \return \f$| x - y |^2\f$
+ */
+double Vector::PeriodicDistanceSquared(const Vector &y, const double * const cell_size) const
+{
+  double res = DistanceSquared(y), tmp;
+  Matrix matrix = ReturnFullMatrixforSymmetric(cell_size);
     Vector Shiftedy, TranslationVector;
     int N[NDIM];
-    matrix.at(0,0) = cell_size[0];
-    matrix.at(1,0) = cell_size[1];
-    matrix.at(2,0) = cell_size[3];
-    matrix.at(0,1) = cell_size[1];
-    matrix.at(1,1) = cell_size[2];
-    matrix.at(2,1) = cell_size[4];
-    matrix.at(0,2) = cell_size[3];
-    matrix.at(1,2) = cell_size[4];
-    matrix.at(2,2) = cell_size[5];
-    // in order to check the periodic distance, translate one of the vectors into each of the 27 neighbouring cells
-    for (N[0]=-1;N[0]<=1;N[0]++)
-      for (N[1]=-1;N[1]<=1;N[1]++)
-        for (N[2]=-1;N[2]<=1;N[2]++) {
-          // create the translation vector
-          TranslationVector.Zero();
-          for (int i=NDIM;i--;)
-            TranslationVector[i] = (double)N[i];
-          TranslationVector.MatrixMultiplication(matrix);
-          // add onto the original vector to compare with
-          Shiftedy = y + TranslationVector;
-          // get distance and compare with minimum so far
-          tmp = distance(Shiftedy);
-          if (tmp < res) res = tmp;
-        }
-    return (res);
-};
-
-/** Calculates distance between this and another vector in a periodic cell.
- * \param *y array to second vector
- * \param *cell_size 6-dimensional array with (xx, xy, yy, xz, yz, zz) entries specifying the periodic cell
- * \return \f$| x - y |^2\f$
- */
-double Vector::PeriodicDistanceSquared(const Vector &y, const double * const cell_size) const
-{
-  double res = DistanceSquared(y), tmp;
-  Matrix matrix;
-    Vector Shiftedy, TranslationVector;
-    int N[NDIM];
-    matrix.at(0,0) = cell_size[0];
-    matrix.at(1,0) = cell_size[1];
-    matrix.at(2,0) = cell_size[3];
-    matrix.at(0,1) = cell_size[1];
-    matrix.at(1,1) = cell_size[2];
-    matrix.at(2,1) = cell_size[4];
-    matrix.at(0,2) = cell_size[3];
-    matrix.at(1,2) = cell_size[4];
-    matrix.at(2,2) = cell_size[5];
+
     // in order to check the periodic distance, translate one of the vectors into each of the 27 neighbouring cells
     for (N[0]=-1;N[0]<=1;N[0]++)