Changeset 53d6b2 for src


Ignore:
Timestamp:
Mar 2, 2011, 9:53:07 PM (14 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:
766ba5
Parents:
99752a
git-author:
Frederik Heber <heber@…> (02/25/11 15:44:44)
git-committer:
Frederik Heber <heber@…> (03/02/11 21:53:07)
Message:

Moved unused function BreadthFirstSearchAdd and subfunctions into functor in Graph/

  • new commodity library libMolecuilderGraph and new subfolder Graph with own Makefile.am.
Location:
src
Files:
3 added
3 edited

Legend:

Unmodified
Added
Removed

  • src/Makefile.am

    r99752a r53d6b2  
    88        LinearAlgebra \
    99        Shapes \
     10        Graph \
    1011        Actions \
    1112        UIElements
    … …  
    319320        UIElements/libMolecuilderUI.la \
    320321        Actions/libMolecuilderActions.la \
     322        Graph/libMolecuilderGraph.la \
    321323        libMolecuilder.la \
    322324        Parser/libMolecuilderParser.la \
    … …  
    340342        UIElements/libMolecuilderQtUI.la \
    341343        Actions/libMolecuilderActions.la \
     344        Graph/libMolecuilderGraph.la \
    342345        libMolecuilder.la \
    343346        Parser/libMolecuilderParser.la \
    … …  
    354357        UIElements/libMolecuilderUI.la \
    355358        Actions/libMolecuilderActions.la \
     359        Graph/libMolecuilderGraph.la \
    356360        libMolecuilder.la \
    357361        Parser/libMolecuilderParser.la \
    … …  
    367371        UIElements/libMolecuilderUI.la \
    368372        Actions/libMolecuilderActions.la \
     373        Graph/libMolecuilderGraph.la \
    369374        libMolecuilder.la \
    370375        Parser/libMolecuilderParser.la \

  • src/molecule.hpp

    r99752a r53d6b2  
    214214  bool CreateMappingLabelsToConfigSequence(int *&SortIndex);
    215215  bool CreateFatherLookupTable(atom **&LookupTable, int count = 0);
    216   void BreadthFirstSearchAdd(molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);
    217216
    218217  /// -# BOSSANOVA

  • src/molecule_graph.cpp

    r99752a r53d6b2  
    11381138;
    11391139
    1140 void BreadthFirstSearchAdd_Init(struct BFSAccounting &BFS, atom *&Root, int AtomCount, int BondOrder, atom **AddedAtomList = NULL)
    1141 {
    1142   BFS.AtomCount = AtomCount;
    1143   BFS.BondOrder = BondOrder;
    1144   BFS.PredecessorList = new atom*[AtomCount];
    1145   BFS.ShortestPathList = new int[AtomCount];
    1146   BFS.ColorList = new enum bond::Shading[AtomCount];
    1147   BFS.BFSStack = new std::deque<atom *> (AtomCount);
    1148 
    1149   BFS.Root = Root;
    1150   BFS.BFSStack->clear();
    1151   BFS.BFSStack->push_front(Root);
    1152 
    1153   // initialise each vertex as white with no predecessor, empty queue, color Root lightgray
    1154   for (int i = AtomCount; i--;) {
    1155     BFS.PredecessorList[i] = NULL;
    1156     BFS.ShortestPathList[i] = -1;
    1157     if ((AddedAtomList != NULL) && (AddedAtomList[i] != NULL)) // mark already present atoms (i.e. Root and maybe others) as visited
    1158       BFS.ColorList[i] = bond::lightgray;
    1159     else
    1160       BFS.ColorList[i] = bond::white;
    1161   }
    1162   //BFS.ShortestPathList[Root->getNr()] = 0; // done by Calloc
    1163 }
    1164 ;
    1165 
    1166 void BreadthFirstSearchAdd_Free(struct BFSAccounting &BFS)
    1167 {
    1168   delete[](BFS.PredecessorList);
    1169   delete[](BFS.ShortestPathList);
    1170   delete[](BFS.ColorList);
    1171   delete (BFS.BFSStack);
    1172   BFS.AtomCount = 0;
    1173 }
    1174 ;
    1175 
    1176 void BreadthFirstSearchAdd_UnvisitedNode(molecule *Mol, struct BFSAccounting &BFS, atom *&Walker, atom *&OtherAtom, bond *&Binder, bond *&Bond, atom **&AddedAtomList, bond **&AddedBondList, bool IsAngstroem)
    1177 {
    1178   if (Binder != Bond) // let other atom white if it's via Root bond. In case it's cyclic it has to be reached again (yet Root is from OtherAtom already black, thus no problem)
    1179     BFS.ColorList[OtherAtom->getNr()] = bond::lightgray;
    1180   BFS.PredecessorList[OtherAtom->getNr()] = Walker; // Walker is the predecessor
    1181   BFS.ShortestPathList[OtherAtom->getNr()] = BFS.ShortestPathList[Walker->getNr()] + 1;
    1182   DoLog(2) && (Log() << Verbose(2) << "Coloring OtherAtom " << OtherAtom->getName() << " " << ((BFS.ColorList[OtherAtom->getNr()] == bond::white) ? "white" : "lightgray") << ", its predecessor is " << Walker->getName() << " and its Shortest Path is " << BFS.ShortestPathList[OtherAtom->getNr()] << " egde(s) long." << endl);
    1183   if ((((BFS.ShortestPathList[OtherAtom->getNr()] < BFS.BondOrder) && (Binder != Bond)))) { // Check for maximum distance
    1184     DoLog(3) && (Log() << Verbose(3));
    1185     if (AddedAtomList[OtherAtom->getNr()] == NULL) { // add if it's not been so far
    1186       AddedAtomList[OtherAtom->getNr()] = Mol->AddCopyAtom(OtherAtom);
    1187       DoLog(0) && (Log() << Verbose(0) << "Added OtherAtom " << OtherAtom->getName());
    1188       AddedBondList[Binder->nr] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
    1189       DoLog(0) && (Log() << Verbose(0) << " and bond " << *(AddedBondList[Binder->nr]) << ", ");
    1190     } else { // this code should actually never come into play (all white atoms are not yet present in BondMolecule, that's why they are white in the first place)
    1191       DoLog(0) && (Log() << Verbose(0) << "Not adding OtherAtom " << OtherAtom->getName());
    1192       if (AddedBondList[Binder->nr] == NULL) {
    1193         AddedBondList[Binder->nr] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
    1194         DoLog(0) && (Log() << Verbose(0) << ", added Bond " << *(AddedBondList[Binder->nr]));
    1195       } else
    1196         DoLog(0) && (Log() << Verbose(0) << ", not added Bond ");
    1197     }
    1198     DoLog(0) && (Log() << Verbose(0) << ", putting OtherAtom into queue." << endl);
    1199     BFS.BFSStack->push_front(OtherAtom);
    1200   } else { // out of bond order, then replace
    1201     if ((AddedAtomList[OtherAtom->getNr()] == NULL) && (Binder->Cyclic))
    1202       BFS.ColorList[OtherAtom->getNr()] = bond::white; // unmark if it has not been queued/added, to make it available via its other bonds (cyclic)
    1203     if (Binder == Bond)
    1204       DoLog(3) && (Log() << Verbose(3) << "Not Queueing, is the Root bond");
    1205     else if (BFS.ShortestPathList[OtherAtom->getNr()] >= BFS.BondOrder)
    1206       DoLog(3) && (Log() << Verbose(3) << "Not Queueing, is out of Bond Count of " << BFS.BondOrder);
    1207     if (!Binder->Cyclic)
    1208       DoLog(0) && (Log() << Verbose(0) << ", is not part of a cyclic bond, saturating bond with Hydrogen." << endl);
    1209     if (AddedBondList[Binder->nr] == NULL) {
    1210       if ((AddedAtomList[OtherAtom->getNr()] != NULL)) { // .. whether we add or saturate
    1211         AddedBondList[Binder->nr] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
    1212       } else {
    1213 #ifdef ADDHYDROGEN
    1214         if (!Mol->AddHydrogenReplacementAtom(Binder, AddedAtomList[Walker->getNr()], Walker, OtherAtom, IsAngstroem))
    1215         exit(1);
    1216 #endif
    1217       }
    1218     }
    1219   }
    1220 }
    1221 ;
    1222 
    1223 void BreadthFirstSearchAdd_VisitedNode(molecule *Mol, struct BFSAccounting &BFS, atom *&Walker, atom *&OtherAtom, bond *&Binder, bond *&Bond, atom **&AddedAtomList, bond **&AddedBondList, bool IsAngstroem)
    1224 {
    1225   DoLog(3) && (Log() << Verbose(3) << "Not Adding, has already been visited." << endl);
    1226   // This has to be a cyclic bond, check whether it's present ...
    1227   if (AddedBondList[Binder->nr] == NULL) {
    1228     if ((Binder != Bond) && (Binder->Cyclic) && (((BFS.ShortestPathList[Walker->getNr()] + 1) < BFS.BondOrder))) {
    1229       AddedBondList[Binder->nr] = Mol->CopyBond(AddedAtomList[Walker->getNr()], AddedAtomList[OtherAtom->getNr()], Binder);
    1230     } else { // if it's root bond it has to broken (otherwise we would not create the fragments)
    1231 #ifdef ADDHYDROGEN
    1232       if(!Mol->AddHydrogenReplacementAtom(Binder, AddedAtomList[Walker->getNr()], Walker, OtherAtom, IsAngstroem))
    1233       exit(1);
    1234 #endif
    1235     }
    1236   }
    1237 }
    1238 ;
    1239 
    1240 /** Adds atoms up to \a BondCount distance from \a *Root and notes them down in \a **AddedAtomList.
    1241  * Gray vertices are always enqueued in an std::deque<atom *> FIFO queue, the rest is usual BFS with adding vertices found was
    1242  * white and putting into queue.
    1243  * \param *Mol Molecule class to add atoms to
    1244  * \param **AddedAtomList list with added atom pointers, index is atom father's number
    1245  * \param **AddedBondList list with added bond pointers, index is bond father's number
    1246  * \param *Root root vertex for BFS
    1247  * \param *Bond bond not to look beyond
    1248  * \param BondOrder maximum distance for vertices to add
    1249  * \param IsAngstroem lengths are in angstroem or bohrradii
    1250  */
    1251 void molecule::BreadthFirstSearchAdd(molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem)
    1252 {
    1253   struct BFSAccounting BFS;
    1254   atom *Walker = NULL, *OtherAtom = NULL;
    1255   bond *Binder = NULL;
    1256 
    1257   // add Root if not done yet
    1258   if (AddedAtomList[Root->getNr()] == NULL) // add Root if not yet present
    1259     AddedAtomList[Root->getNr()] = Mol->AddCopyAtom(Root);
    1260 
    1261   BreadthFirstSearchAdd_Init(BFS, Root, BondOrder, getAtomCount(), AddedAtomList);
    1262 
    1263   // and go on ... Queue always contains all lightgray vertices
    1264   while (!BFS.BFSStack->empty()) {
    1265     // we have to pop the oldest atom from stack. This keeps the atoms on the stack always of the same ShortestPath distance.
    1266     // e.g. if current atom is 2, push to end of stack are of length 3, but first all of length 2 would be popped. They again
    1267     // append length of 3 (their neighbours). Thus on stack we have always atoms of a certain length n at bottom of stack and
    1268     // followed by n+1 till top of stack.
    1269     Walker = BFS.BFSStack->front(); // pop oldest added
    1270     BFS.BFSStack->pop_front();
    1271     const BondList& ListOfBonds = Walker->getListOfBonds();
    1272     DoLog(1) && (Log() << Verbose(1) << "Current Walker is: " << Walker->getName() << ", and has " << ListOfBonds.size() << " bonds." << endl);
    1273     for (BondList::const_iterator Runner = ListOfBonds.begin();
    1274         Runner != ListOfBonds.end();
    1275         ++Runner) {
    1276       if ((*Runner) != NULL) { // don't look at bond equal NULL
    1277         Binder = (*Runner);
    1278         OtherAtom = (*Runner)->GetOtherAtom(Walker);
    1279         DoLog(2) && (Log() << Verbose(2) << "Current OtherAtom is: " << OtherAtom->getName() << " for bond " << *(*Runner) << "." << endl);
    1280         if (BFS.ColorList[OtherAtom->getNr()] == bond::white) {
    1281           BreadthFirstSearchAdd_UnvisitedNode(Mol, BFS, Walker, OtherAtom, Binder, Bond, AddedAtomList, AddedBondList, IsAngstroem);
    1282         } else {
    1283           BreadthFirstSearchAdd_VisitedNode(Mol, BFS, Walker, OtherAtom, Binder, Bond, AddedAtomList, AddedBondList, IsAngstroem);
    1284         }
    1285       }
    1286     }
    1287     BFS.ColorList[Walker->getNr()] = bond::black;
    1288     DoLog(1) && (Log() << Verbose(1) << "Coloring Walker " << Walker->getName() << " black." << endl);
    1289   }
    1290   BreadthFirstSearchAdd_Free(BFS);
    1291 }
    1292 ;
    1293 
    12941140/** Adds a bond as a copy to a given one
    12951141 * \param *left leftatom of new bond
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