Changeset 244a84 for src/builder.cpp

Timestamp:

Jan 26, 2010, 12:52:31 PM (15 years ago)

Author:

Frederik Heber <heber@…>

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:

04b6f9, 481601

Parents:

315164

Message:

GetDistanceToSurface() separated, filling now with water instead of boron, DissectMoleculeIntoConnectedSubgraphs() now working on list of molecules instead of single one.

• MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs() so far was working on a single molecule (given by parameter) instead of the list already contained in the list of its class.
• Tesselation::GetDistanceSquaredToSurface() is split up into function of same name, which calls finds the closest triangle and calls Tesselation::GetDistanceSquaredToTriangle() which contains the former code.
• PeriodicCorrelationToSurface() was adapted to the above split.
• in tesselation.cpp lots of list<> and set<>s were replaced by the already present and appropriate define's.

• small verbosity changes in: MatrixContainer::ParseMatrix(), TesselPoint::TesselPoint(), TesselPoint::~TesselPoint(), PointCloud::PointCloud(), PointCloud::~PointCloud(), Tesselation::GuessStartingTriangle(), BondGraph::LoadBondLengthTable() (status of parsing gives appropriate message).

Signed-off-by: Frederik Heber <heber@…>

File:

• src/builder.cpp (modified) (4 diffs)

src/builder.cpp

@@ -1551 +1551 @@
      if (configuration.BG == NULL) {
        configuration.BG = new BondGraph(configuration.GetIsAngstroem());
-       if ((BondGraphFileName.empty()) && (configuration.BG->LoadBondLengthTable(BondGraphFileName))) {
+       if ((!BondGraphFileName.empty()) && (configuration.BG->LoadBondLengthTable(BondGraphFileName))) {
          Log() << Verbose(0) << "Bond length table loaded successfully." << endl;
        } else {
@@ -1660 +1660 @@
               Log() << Verbose(1) << "Dissecting molecular system into a set of disconnected subgraphs ... " << endl;
               // @TODO rather do the dissection afterwards
-              molecules->DissectMoleculeIntoConnectedSubgraphs(mol,&configuration);
+              molecules->DissectMoleculeIntoConnectedSubgraphs(periode, &configuration);
               mol = NULL;
               if (molecules->ListOfMolecules.size() != 0) {
@@ -1708 +1708 @@
                 int ranges[NDIM] = {1,1,1};
                 CorrelationToSurfaceMap *surfacemap = PeriodicCorrelationToSurface( molecules, elemental, TesselStruct, LCList, ranges );
+                //OutputCorrelationToSurface(&output, surfacemap);
                 BinPairMap *binmap = BinData( surfacemap, 0.5, 0., 0. );
                 OutputCorrelation ( &binoutput, binmap );
@@ -1744 +1745 @@
                 Log() << Verbose(1) << "Filling Box with water molecules." << endl;
                 // construct water molecule
-                molecule *filler = new molecule(periode);;
+                molecule *filler = new molecule(periode);
                 molecule *Filling = NULL;
-//                atom *second = NULL, *third = NULL;
+                atom *second = NULL, *third = NULL;
+//                first = new atom();
+//                first->type = periode->FindElement(5);
+//                first->x.Zero();
+//                filler->AddAtom(first);
                 first = new atom();
-                first->type = periode->FindElement(5);
-                first->x.Zero();
+                first->type = periode->FindElement(1);
+                first->x.Init(0.441, -0.143, 0.);
                 filler->AddAtom(first);
-//                first = new atom();
-//                first->type = periode->FindElement(1);
-//                first->x.Init(0.441, -0.143, 0.);
-//                filler->AddAtom(first);
-//                second = new atom();
-//                second->type = periode->FindElement(1);
-//                second->x.Init(-0.464, 1.137, 0.0);
-//                filler->AddAtom(second);
-//                third = new atom();
-//                third->type = periode->FindElement(8);
-//                third->x.Init(-0.464, 0.177, 0.);
-//                filler->AddAtom(third);
-//                filler->AddBond(first, third, 1);
-//                filler->AddBond(second, third, 1);
+                second = new atom();
+                second->type = periode->FindElement(1);
+                second->x.Init(-0.464, 1.137, 0.0);
+                filler->AddAtom(second);
+                third = new atom();
+                third->type = periode->FindElement(8);
+                third->x.Init(-0.464, 0.177, 0.);
+                filler->AddAtom(third);
+                filler->AddBond(first, third, 1);
+                filler->AddBond(second, third, 1);
                 // call routine
                 double distance[NDIM];