Changeset 07a47e for src/Fragmentation

Timestamp:

Oct 26, 2011, 3:02:53 PM (13 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:

41d023

Parents:

99b0dc

Message:

Replaced enable/disable-hydrogen by internal switch.

• changes in Fragmentation, Graph and molecule structures.
• switch is now enum HydrogenSaturation that is constant everywhere except in the Actions. FragmentMoleculeAction and DepthFirstSearchAction have new parameter DoSaturation with default value of true.

Location:

src/Fragmentation

Files:

• BondsPerShortestPath.cpp (modified) (2 diffs)
• BondsPerShortestPath.hpp (modified) (2 diffs)
• Fragmentation.cpp (modified) (9 diffs)
• Fragmentation.hpp (modified) (3 diffs)
• HydrogenSaturation_enum.hpp (added)
• PowerSetGenerator.cpp (modified) (2 diffs)
• PowerSetGenerator.hpp (modified) (2 diffs)

src/Fragmentation/BondsPerShortestPath.cpp

@@ -101 +101 @@
  * \param _RootKeyNr index of root node
  * \param RestrictedKeySet Restricted vertex set to use in context of molecule
- */
-void BondsPerShortestPath::FillSPListandLabelVertices(int _RootKeyNr, KeySet &RestrictedKeySet)
+ * \param saturation this tells whether to treat hydrogen special or not.
+ */
+void BondsPerShortestPath::FillSPListandLabelVertices(int _RootKeyNr, KeySet &RestrictedKeySet, const enum HydrogenSaturation saturation)
 {
   // Actually, we should construct a spanning tree vom the root atom and select all edges therefrom and put them into
@@ -146 +147 @@
         OtherWalker = (*Runner)->GetOtherAtom(Walker);
         if ((RestrictedKeySet.find(OtherWalker->getNr()) != RestrictedKeySet.end())
-  #ifdef ADDHYDROGEN
-         && (OtherWalker->getType()->getAtomicNumber() != 1)
-  #endif
-                                                              ) {  // skip hydrogens and restrict to fragment
+            // skip hydrogens if desired and restrict to fragment
+            && ((saturation == DontSaturate) || (OtherWalker->getType()->getAtomicNumber() != 1))) {
           DoLog(2) && (Log() << Verbose(2) << "Current partner is " << *OtherWalker << " with nr " << OtherWalker->getNr() << " in bond " << *(*Runner) << "." << endl);
           // set the label if not set (and push on root stack as well)

src/Fragmentation/BondsPerShortestPath.hpp

@@ -13 +13 @@
 #include <config.h>
 #endif
+
+#include "Fragmentation/HydrogenSaturation_enum.hpp"
 
 #include <list>
@@ -31 +33 @@
   void SetSPList(atom *_Root);
   void ResetSPList();
-  void FillSPListandLabelVertices(int _RootKeyNr, KeySet &RestrictedKeySet);
+  void FillSPListandLabelVertices(int _RootKeyNr, KeySet &RestrictedKeySet, const enum HydrogenSaturation saturation);
   void OutputSPList();
   int CountNumbersInBondsList();

src/Fragmentation/Fragmentation.cpp

@@ -45 +45 @@
 /** Constructor of class Fragmentation.
  *
- */
-Fragmentation::Fragmentation(molecule *_mol) :
-  mol(_mol)
+ * \param _mol molecule for internal use (looking up atoms)
+ * \param _saturation whether to treat hydrogen special and saturate dangling bonds or not
+ */
+Fragmentation::Fragmentation(molecule *_mol, const enum HydrogenSaturation _saturation) :
+  mol(_mol),
+  saturation(_saturation)
 {}
 
@@ -90 +93 @@
 
   DoLog(0) && (Log() << Verbose(0) << endl);
-#ifdef ADDHYDROGEN
-  DoLog(0) && (Log() << Verbose(0) << "I will treat hydrogen special and saturate dangling bonds with it." << endl);
-#else
-  DoLog(0) && (Log() << Verbose(0) << "Hydrogen is treated just like the rest of the lot." << endl);
-#endif
+  switch (saturation) {
+    case DoSaturate:
+      DoLog(0) && (Log() << Verbose(0) << "I will treat hydrogen special and saturate dangling bonds with it." << endl);
+      break;
+    case DontSaturate:
+      DoLog(0) && (Log() << Verbose(0) << "Hydrogen is treated just like the rest of the lot." << endl);
+      break;
+    default:
+      ASSERT(0, "Fragmentation::FragmentMolecule() - there is a saturation setting which I have no idea about.");
+      break;
+  }
 
   // ++++++++++++++++++++++++++++ INITIAL STUFF: Bond structure analysis, file parsing, ... ++++++++++++++++++++++++++++++++++++++++++
@@ -151 +160 @@
     AtomMask[mol->getAtomCount()] = true;   // last plus one entry is used as marker that we have been through this loop once already in CheckOrderAtSite()
     // ===== 6b. fill RootStack for each subgraph (second adaptivity check) =====
-    Subgraphs->next->FillRootStackForSubgraphs(RootStack, AtomMask, (FragmentCounter = 0));
+    Subgraphs->next->FillRootStackForSubgraphs(RootStack, AtomMask, (FragmentCounter = 0), saturation);
 
     // ===== 7. fill the bond fragment list =====
@@ -359 +368 @@
       FragmentLowerOrdersList[RootNr][0] = new Graph;
       FragmentSearch.PrepareForPowersetGeneration(1., FragmentLowerOrdersList[RootNr][0], Walker);
-      NumMoleculesOfOrder[RootNr] = PSG(CompleteMolecule);
+      NumMoleculesOfOrder[RootNr] = PSG(CompleteMolecule, saturation);
 
       // output resulting number
@@ -487 +496 @@
       DoeLog(2) && (eLog()<< Verbose(2) << "Unable to parse file, incrementing all." << endl);
       for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-    #ifdef ADDHYDROGEN
-        if ((*iter)->getType()->getAtomicNumber() != 1) // skip hydrogen
-    #endif
+        if ((saturation == DontSaturate) || ((*iter)->getType()->getAtomicNumber() != 1)) // skip hydrogen
         {
           AtomMask[(*iter)->getNr()] = true;  // include all (non-hydrogen) atoms
@@ -502 +509 @@
   } else { // global increase of Bond Order
     for(molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-  #ifdef ADDHYDROGEN
-      if ((*iter)->getType()->getAtomicNumber() != 1) // skip hydrogen
-  #endif
+      if ((saturation == DontSaturate) || ((*iter)->getType()->getAtomicNumber() != 1)) // skip hydrogen
       {
         AtomMask[(*iter)->getNr()] = true;  // include all (non-hydrogen) atoms
@@ -670 +675 @@
   atom *FatherOfRunner = NULL;
 
-#ifdef ADDHYDROGEN
-  molecule::const_iterator runner;
-#endif
   // we increment the iter just before skipping the hydrogen
   for (molecule::const_iterator iter = Leaf->begin(); iter != Leaf->end();) {
@@ -700 +702 @@
         } else {
 //          Log() << Verbose(0) << ", who has no son in this fragment molecule." << endl;
-#ifdef ADDHYDROGEN
           //Log() << Verbose(3) << "Adding Hydrogen to " << (*iter)->Name << " and a bond in between." << endl;
-          if(!Leaf->AddHydrogenReplacementAtom((*BondRunner), (*iter), FatherOfRunner, OtherFather, IsAngstroem))
-            exit(1);
-#endif
+          if (saturation == DoSaturate)
+            if (!Leaf->AddHydrogenReplacementAtom((*BondRunner), (*iter), FatherOfRunner, OtherFather, IsAngstroem))
+              exit(1);
           //NumBonds[(*iter)->getNr()] += Binder->BondDegree;
         }
@@ -715 +716 @@
     }
     ++iter;
-#ifdef ADDHYDROGEN
-    while ((iter != Leaf->end()) && ((*iter)->getType()->getAtomicNumber() == 1)){ // skip added hydrogen
-      iter++;
-    }
-#endif
+    if (saturation == DoSaturate) {
+      while ((iter != Leaf->end()) && ((*iter)->getType()->getAtomicNumber() == 1)){ // skip added hydrogen
+        iter++;
+      }
+    }
   }
 };

src/Fragmentation/Fragmentation.hpp

@@ -18 +18 @@
 #include "Graph/DepthFirstSearchAnalysis.hpp"
 
+#include "Fragmentation/HydrogenSaturation_enum.hpp"
 #include "Fragmentation/fragmentation_helpers.hpp"
 
@@ -31 +32 @@
 {
 public:
-  Fragmentation(molecule *_mol);
+  Fragmentation(molecule *_mol, const enum HydrogenSaturation _saturation);
   ~Fragmentation();
 
@@ -58 +59 @@
   //!> pointer to molecule that is fragmented
   molecule *mol;
+  //!> whether to saturate dangling bonds with hydrogen and hence treat hydrogen special
+  const enum HydrogenSaturation saturation;
   //!> list of parser types for which a configuration file per fragment is stored
   std::vector<std::string> typelist;

src/Fragmentation/PowerSetGenerator.cpp

@@ -172 +172 @@
  * with SP of 2, then those with SP of 3, then those with SP of 4 and so on.
  * \param RestrictedKeySet Restricted vertex set to use in context of molecule
+ * \param saturation whether to treat hydrogen special or not
  * \return number of inserted fragments
  * \note ShortestPathList in FragmentSearch structure is probably due to NumberOfAtomsSPLevel and SP not needed anymore
  */
-int PowerSetGenerator::operator()(KeySet &RestrictedKeySet)
+int PowerSetGenerator::operator()(KeySet &RestrictedKeySet, const enum HydrogenSaturation saturation)
 {
   int Counter = FragmentSearch->FragmentCounter; // mark current value of counter
@@ -185 +186 @@
 
   // do a BFS search to fill the SP lists and label the found vertices
-  BondsPerSPList.FillSPListandLabelVertices(FragmentSearch->getRoot()->GetTrueFather()->getNr(), RestrictedKeySet);
+  BondsPerSPList.FillSPListandLabelVertices(FragmentSearch->getRoot()->GetTrueFather()->getNr(), RestrictedKeySet, saturation);
 
   // outputting all list for debugging

src/Fragmentation/PowerSetGenerator.hpp

@@ -18 +18 @@
 
 #include "Fragmentation/BondsPerShortestPath.hpp"
+#include "Fragmentation/HydrogenSaturation_enum.hpp"
 
 class bond;
@@ -29 +30 @@
 
   void SPFragmentGenerator(int RootDistance, std::vector<bond *> &BondsSet, int SetDimension, int SubOrder);
-  int operator()(KeySet &RestrictedKeySet);
+  int operator()(KeySet &RestrictedKeySet, const enum HydrogenSaturation saturation);
   void RemoveAllTouchedFromSnakeStack(int verbosity, KeySet *FragmentSet, int *&TouchedList, int &TouchedIndex);
   int FillBondsList(std::vector<bond *> &BondsList, std::list<bond *>::const_iterator SetFirst, std::list<bond *>::const_iterator SetLast, int *&TouchedList, int TouchedIndex);