Changeset 273382 for src/molecule.cpp

Timestamp:

Apr 13, 2010, 1:22:42 PM (16 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, Candidate_v1.7.0, 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:

1bd79e

Parents:

72e7fa

Message:

Prepared interface of Vector Class for transition to VectorComposites

File:

• src/molecule.cpp (modified) (11 diffs)

src/molecule.cpp

@@ -220 +220 @@
 //  Log() << Verbose(3) << "Begin of AddHydrogenReplacementAtom." << endl;
   // create vector in direction of bond
-  InBondvector.CopyVector(&TopReplacement->x);
-  InBondvector.SubtractVector(&TopOrigin->x);
+  InBondvector = TopReplacement->x - TopOrigin->x;
   bondlength = InBondvector.Norm();
 
@@ -240 +239 @@
     matrix = ReturnFullMatrixforSymmetric(cell_size);
     Orthovector1.MatrixMultiplication(matrix);
-    InBondvector.SubtractVector(&Orthovector1); // subtract just the additional translation
+    InBondvector.SubtractVector(Orthovector1); // subtract just the additional translation
     Free(&matrix);
     bondlength = InBondvector.Norm();
@@ -265 +264 @@
       FirstOtherAtom = World::getInstance().createAtom();    // new atom
       FirstOtherAtom->type = elemente->FindElement(1);  // element is Hydrogen
-      FirstOtherAtom->v.CopyVector(&TopReplacement->v); // copy velocity
+      FirstOtherAtom->v = TopReplacement->v; // copy velocity
       FirstOtherAtom->FixedIon = TopReplacement->FixedIon;
       if (TopReplacement->type->Z == 1) { // neither rescale nor replace if it's already hydrogen
@@ -274 +273 @@
       }
       InBondvector.Scale(&BondRescale);   // rescale the distance vector to Hydrogen bond length
-      FirstOtherAtom->x.CopyVector(&TopOrigin->x); // set coordination to origin ...
-      FirstOtherAtom->x.AddVector(&InBondvector);  // ... and add distance vector to replacement atom
+      FirstOtherAtom->x = TopOrigin->x; // set coordination to origin ...
+      FirstOtherAtom->x = InBondvector;  // ... and add distance vector to replacement atom
       AllWentWell = AllWentWell && AddAtom(FirstOtherAtom);
 //      Log() << Verbose(4) << "Added " << *FirstOtherAtom << " at: ";
@@ -316 +315 @@
         }
       } else {
-        Orthovector1.GetOneNormalVector(&InBondvector);
+        Orthovector1.GetOneNormalVector(InBondvector);
       }
       //Log() << Verbose(3)<< "Orthovector1: ";
@@ -331 +330 @@
       FirstOtherAtom->type = elemente->FindElement(1);
       SecondOtherAtom->type = elemente->FindElement(1);
-      FirstOtherAtom->v.CopyVector(&TopReplacement->v); // copy velocity
+      FirstOtherAtom->v = TopReplacement->v; // copy velocity
       FirstOtherAtom->FixedIon = TopReplacement->FixedIon;
-      SecondOtherAtom->v.CopyVector(&TopReplacement->v); // copy velocity
+      SecondOtherAtom->v = TopReplacement->v; // copy velocity
       SecondOtherAtom->FixedIon = TopReplacement->FixedIon;
       FirstOtherAtom->father = NULL;  // we are just an added hydrogen with no father
@@ -388 +387 @@
       SecondOtherAtom->type = elemente->FindElement(1);
       ThirdOtherAtom->type = elemente->FindElement(1);
-      FirstOtherAtom->v.CopyVector(&TopReplacement->v); // copy velocity
+      FirstOtherAtom->v = TopReplacement->v; // copy velocity
       FirstOtherAtom->FixedIon = TopReplacement->FixedIon;
-      SecondOtherAtom->v.CopyVector(&TopReplacement->v); // copy velocity
+      SecondOtherAtom->v = TopReplacement->v; // copy velocity
       SecondOtherAtom->FixedIon = TopReplacement->FixedIon;
-      ThirdOtherAtom->v.CopyVector(&TopReplacement->v); // copy velocity
+      ThirdOtherAtom->v = TopReplacement->v; // copy velocity
       ThirdOtherAtom->FixedIon = TopReplacement->FixedIon;
       FirstOtherAtom->father = NULL;  //  we are just an added hydrogen with no father
@@ -399 +398 @@
 
       // we need to vectors orthonormal the InBondvector
-      AllWentWell = AllWentWell && Orthovector1.GetOneNormalVector(&InBondvector);
+      AllWentWell = AllWentWell && Orthovector1.GetOneNormalVector(InBondvector);
 //      Log() << Verbose(3) << "Orthovector1: ";
 //      Orthovector1.Output(out);
@@ -426 +425 @@
       factors[1] = f;
       factors[2] = 0.;
-      FirstOtherAtom->x.LinearCombinationOfVectors(&InBondvector, &Orthovector1, &Orthovector2, factors);
+      FirstOtherAtom->x.LinearCombinationOfVectors(InBondvector, Orthovector1, Orthovector2, factors);
       factors[1] = -0.5*f;
       factors[2] = g;
-      SecondOtherAtom->x.LinearCombinationOfVectors(&InBondvector, &Orthovector1, &Orthovector2, factors);
+      SecondOtherAtom->x.LinearCombinationOfVectors(InBondvector, Orthovector1, Orthovector2, factors);
       factors[2] = -g;
-      ThirdOtherAtom->x.LinearCombinationOfVectors(&InBondvector, &Orthovector1, &Orthovector2, factors);
+      ThirdOtherAtom->x.LinearCombinationOfVectors(InBondvector, Orthovector1, Orthovector2, factors);
 
       // rescale each to correct BondDistance
@@ -439 +438 @@
 
       // and relative to *origin atom
-      FirstOtherAtom->x.AddVector(&TopOrigin->x);
-      SecondOtherAtom->x.AddVector(&TopOrigin->x);
-      ThirdOtherAtom->x.AddVector(&TopOrigin->x);
+      FirstOtherAtom->x += TopOrigin->x;
+      SecondOtherAtom->x += TopOrigin->x;
+      ThirdOtherAtom->x += TopOrigin->x;
 
       // ... and add to molecule
@@ -1022 +1021 @@
     Log() << Verbose(5) << "Center of Gravity: " << CenterOfGravity << endl;
     Log() << Verbose(5) << "Other Center of Gravity: " << OtherCenterOfGravity << endl;
-    if (CenterOfGravity.DistanceSquared(&OtherCenterOfGravity) > threshold*threshold) {
+    if (CenterOfGravity.DistanceSquared(OtherCenterOfGravity) > threshold*threshold) {
       Log() << Verbose(4) << "Centers of gravity don't match." << endl;
       result = false;