Changeset 273382 for src/analysis_correlation.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/analysis_correlation.cpp (modified) (10 diffs)

src/analysis_correlation.cpp

@@ -55 +55 @@
                 if (Walker->nr < OtherWalker->nr)
                   if ((type2 == NULL) || (OtherWalker->type == type2)) {
-                    distance = Walker->node->PeriodicDistance(OtherWalker->node, (*MolWalker)->cell_size);
+                    distance = Walker->node->PeriodicDistance(*(OtherWalker->node), (*MolWalker)->cell_size);
                     //Log() << Verbose(1) <<"Inserting " << *Walker << " and " << *OtherWalker << endl;
                     outmap->insert ( pair<double, pair <atom *, atom*> > (distance, pair<atom *, atom*> (Walker, OtherWalker) ) );
@@ -104 +104 @@
         Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl;
         if ((type1 == NULL) || (Walker->type == type1)) {
-          periodicX.CopyVector(Walker->node);
+          periodicX = *(Walker->node);
           periodicX.MatrixMultiplication(FullInverseMatrix);  // x now in [0,1)^3
           // go through every range in xyz and get distance
@@ -110 +110 @@
             for (n[1]=-ranges[1]; n[1] <= ranges[1]; n[1]++)
               for (n[2]=-ranges[2]; n[2] <= ranges[2]; n[2]++) {
-                checkX.Init(n[0], n[1], n[2]);
-                checkX.AddVector(&periodicX);
+                checkX = Vector(n[0], n[1], n[2]) + periodicX;
                 checkX.MatrixMultiplication(FullMatrix);
                 for (MoleculeList::const_iterator MolOtherWalker = MolWalker; MolOtherWalker != molecules->ListOfMolecules.end(); MolOtherWalker++)
@@ -122 +121 @@
                       if (Walker->nr < OtherWalker->nr)
                         if ((type2 == NULL) || (OtherWalker->type == type2)) {
-                          periodicOtherX.CopyVector(OtherWalker->node);
+                          periodicOtherX = *(OtherWalker->node);
                           periodicOtherX.MatrixMultiplication(FullInverseMatrix);  // x now in [0,1)^3
                           // go through every range in xyz and get distance
@@ -128 +127 @@
                             for (Othern[1]=-ranges[1]; Othern[1] <= ranges[1]; Othern[1]++)
                               for (Othern[2]=-ranges[2]; Othern[2] <= ranges[2]; Othern[2]++) {
-                                checkOtherX.Init(Othern[0], Othern[1], Othern[2]);
-                                checkOtherX.AddVector(&periodicOtherX);
+                                checkOtherX = Vector(Othern[0], Othern[1], Othern[2]) + periodicOtherX;
                                 checkOtherX.MatrixMultiplication(FullMatrix);
-                                distance = checkX.Distance(&checkOtherX);
+                                distance = checkX.Distance(checkOtherX);
                                 //Log() << Verbose(1) <<"Inserting " << *Walker << " and " << *OtherWalker << endl;
                                 outmap->insert ( pair<double, pair <atom *, atom*> > (distance, pair<atom *, atom*> (Walker, OtherWalker) ) );
@@ -174 +172 @@
         Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl;
         if ((type == NULL) || (Walker->type == type)) {
-          distance = Walker->node->PeriodicDistance(point, (*MolWalker)->cell_size);
+          distance = Walker->node->PeriodicDistance(*point, (*MolWalker)->cell_size);
           Log() << Verbose(4) << "Current distance is " << distance << "." << endl;
           outmap->insert ( pair<double, pair<atom *, const Vector*> >(distance, pair<atom *, const Vector*> (Walker, point) ) );
@@ -216 +214 @@
         Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl;
         if ((type == NULL) || (Walker->type == type)) {
-          periodicX.CopyVector(Walker->node);
+          periodicX = *(Walker->node);
           periodicX.MatrixMultiplication(FullInverseMatrix);  // x now in [0,1)^3
           // go through every range in xyz and get distance
@@ -222 +220 @@
             for (n[1]=-ranges[1]; n[1] <= ranges[1]; n[1]++)
               for (n[2]=-ranges[2]; n[2] <= ranges[2]; n[2]++) {
-                checkX.Init(n[0], n[1], n[2]);
-                checkX.AddVector(&periodicX);
+                checkX = Vector(n[0], n[1], n[2]) + periodicX;
                 checkX.MatrixMultiplication(FullMatrix);
-                distance = checkX.Distance(point);
+                distance = checkX.Distance(*point);
                 Log() << Verbose(4) << "Current distance is " << distance << "." << endl;
                 outmap->insert ( pair<double, pair<atom *, const Vector*> >(distance, pair<atom *, const Vector*> (Walker, point) ) );
@@ -320 +317 @@
         Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl;
         if ((type == NULL) || (Walker->type == type)) {
-          periodicX.CopyVector(Walker->node);
+          periodicX = *(Walker->node);
           periodicX.MatrixMultiplication(FullInverseMatrix);  // x now in [0,1)^3
           // go through every range in xyz and get distance
@@ -327 +324 @@
             for (n[1]=-ranges[1]; n[1] <= ranges[1]; n[1]++)
               for (n[2]=-ranges[2]; n[2] <= ranges[2]; n[2]++) {
-                checkX.Init(n[0], n[1], n[2]);
-                checkX.AddVector(&periodicX);
+                checkX = Vector(n[0], n[1], n[2]) + periodicX;
                 checkX.MatrixMultiplication(FullMatrix);
                 triangle = Surface->FindClosestTriangleToVector(&checkX, LC);