Changeset 9291d04

Timestamp:

Feb 27, 2013, 12:42:36 PM (12 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:

39a07a

Parents:

c7c615

git-author:

Frederik Heber <heber@…> (12/11/12 10:39:30)

git-committer:

Frederik Heber <heber@…> (02/27/13 12:42:36)

Message:

Split saturation with hydrogen of treatment of hydrogen.

• now saturation means dangling bonds are saturated, and treatment means that in a bond graph hydrogen is skipped.
• FragmentationAction and DepthFirstSearchAction adapted in options.

Files:

• src/Actions/FragmentationAction/FragmentationAction.cpp (modified) (3 diffs)
• src/Actions/FragmentationAction/FragmentationAction.def (modified) (1 diff)
• src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (1 diff)
• src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) (1 diff)
• src/Actions/GraphAction/DepthFirstSearchAction.def (modified) (1 diff)
• src/Fragmentation/BondsPerShortestPath.cpp (modified) (2 diffs)
• src/Fragmentation/BondsPerShortestPath.hpp (modified) (1 diff)
• src/Fragmentation/Fragmentation.cpp (modified) (6 diffs)
• src/Fragmentation/Fragmentation.hpp (modified) (2 diffs)
• src/Fragmentation/HydrogenSaturation_enum.hpp (modified) (1 diff)
• src/Fragmentation/PowerSetGenerator.cpp (modified) (2 diffs)
• src/Fragmentation/PowerSetGenerator.hpp (modified) (1 diff)
• src/Graph/CyclicStructureAnalysis.cpp (modified) (2 diffs)
• src/Graph/CyclicStructureAnalysis.hpp (modified) (2 diffs)
• src/molecule.hpp (modified) (1 diff)
• src/molecule_geometry.cpp (modified) (3 diffs)
• tests/Python/AllActions/options.dat (modified) (1 diff)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -100 +100 @@
   }
 
-  // get whether to saturate or not
-  const enum HydrogenSaturation saturation =  params.DoSaturation.get() ? DoSaturate : DontSaturate;
-
   // parse in Adjacency file
   boost::shared_ptr<AdjacencyList> FileChecker;
@@ -143 +140 @@
     LOG(2, "INFO: Fragmenting in molecule " << mol->getName() << " in " << clusters.count(mol) 
         << " atoms, out of " << mol->getAtomCount() << ".");
-    Fragmentation Fragmenter(mol, *FileChecker, saturation);
+    const enum HydrogenTreatment treatment =  params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen;
+    Fragmentation Fragmenter(mol, *FileChecker, treatment);
 
     // perform fragmentation
@@ -167 +165 @@
   // store molecule's fragment to file
   {
+    const enum HydrogenSaturation saturation =  params.DoSaturation.get() ? DoSaturate : DontSaturate;
     ExportGraph_ToFiles exporter(TotalGraph, saturation);
     exporter.setPrefix(params.prefix.get());

src/Actions/FragmentationAction/FragmentationAction.def

@@ -20 +20 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
-#define paramtypes (std::string)(double)(unsigned int)(bool)(std::vector<std::string>)
-#define paramtokens ("fragment-molecule")("distance")("order")("DoSaturate")("output-types")
-#define paramdescriptions ("prefix of each fragment file")("distance in space")("order of a discretization, dissection, ...")("do saturate dangling bonds with hydrogen")("type(s) of parsers that output fragment config files")
-#define paramdefaults (NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT(true)) (PARAM_DEFAULT(std::vector<std::string>(1, std::string("pcp"))))
-#define paramreferences (prefix)(distance)(order)(DoSaturation)(types)
+#define paramtypes (std::string)(double)(unsigned int)(bool)(bool)(std::vector<std::string>)
+#define paramtokens ("fragment-molecule")("distance")("order")("DoSaturate")("ExcludeHydrogen")("output-types")
+#define paramdescriptions ("prefix of each fragment file")("distance in space")("order of a discretization, dissection, ...")("do saturate dangling bonds with hydrogen")("whether to exclude hydrogen in the bond graph dissection or not")("type(s) of parsers that output fragment config files")
+#define paramdefaults (NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT(true))(PARAM_DEFAULT(true))(PARAM_DEFAULT(std::vector<std::string>(1, std::string("pcp"))))
+#define paramreferences (prefix)(distance)(order)(DoSaturation)(HowtoTreatHydrogen)(types)
 #define paramvalids \
 (DummyValidator< std::string >()) \
 (BoxLengthValidator()) \
 (DummyValidator< unsigned int >()) \
+(DummyValidator< bool >()) \
 (DummyValidator< bool >()) \
 (STLVectorValidator< std::vector<std::string> >(1, 10, ParserTypeValidator()))

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -65 +65 @@
 #include "Fragmentation/ForceMatrix.hpp"
 #include "Fragmentation/Fragmentation.hpp"
-#include "Fragmentation/HydrogenSaturation_enum.hpp"
 #include "Fragmentation/Homology/HomologyContainer.hpp"
 #include "Fragmentation/Homology/HomologyGraph.hpp"

src/Actions/GraphAction/DepthFirstSearchAction.cpp

@@ -71 +71 @@
       LocalBackEdgeStack = new std::deque<bond::ptr >; // no need to have it Subgraphs->Leaf->BondCount size
       DFS.PickLocalBackEdges(ListOfAtoms, LocalBackEdgeStack);
-      CyclicStructureAnalysis CycleAnalysis(params.DoSaturation.get() ? DoSaturate : DontSaturate);
+      CyclicStructureAnalysis CycleAnalysis(params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen);
       CycleAnalysis(LocalBackEdgeStack);
       delete(LocalBackEdgeStack);

src/Actions/GraphAction/DepthFirstSearchAction.def

@@ -15 +15 @@
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
 #define paramtypes (bool)
-#define paramtokens ("DoSaturate")
+#define paramtokens ("ExcludeHydrogen")
 #define paramdescriptions ("whether to treat hydrogen special or not")
 #define paramdefaults (PARAM_DEFAULT(true))
-#define paramreferences (DoSaturation)
+#define paramreferences (HowtoTreatHydrogen)
 #define paramvalids \
 (DummyValidator< bool >())

src/Fragmentation/BondsPerShortestPath.cpp

@@ -122 +122 @@
  * \param _RootKeyNr index of root node
  * \param RestrictedKeySet Restricted vertex set to use in context of molecule
- * \param saturation this tells whether to treat hydrogen special or not.
- */
-void BondsPerShortestPath::FillSPListandLabelVertices(int _RootKeyNr, KeySet &RestrictedKeySet, const enum HydrogenSaturation saturation)
+ * \param treatment this tells whether to treat hydrogen special or not.
+ */
+void BondsPerShortestPath::FillSPListandLabelVertices(int _RootKeyNr, KeySet &RestrictedKeySet, const enum HydrogenTreatment treatment)
 {
   // Actually, we should construct a spanning tree vom the root atom and select all edges therefrom and put them into
@@ -173 +173 @@
         if ((RestrictedKeySet.find(OtherWalker->getNr()) != RestrictedKeySet.end())
             // skip hydrogens if desired and restrict to fragment
-            && ((saturation == DontSaturate) || (OtherWalker->getType()->getAtomicNumber() != 1))) {
+            && ((treatment == IncludeHydrogen) || (OtherWalker->getType()->getAtomicNumber() != 1))) {
           LOG(2, "Current partner is " << *OtherWalker << " with nr " << OtherWalker->getNr() << " in bond " << *(*Runner) << ".");
           // set the label if not set (and push on root stack as well)

src/Fragmentation/BondsPerShortestPath.hpp

@@ -33 +33 @@
   void SetSPList(atom *_Root);
   void ResetSPList();
-  void FillSPListandLabelVertices(int _RootKeyNr, KeySet &RestrictedKeySet, const enum HydrogenSaturation saturation);
+  void FillSPListandLabelVertices(int _RootKeyNr, KeySet &RestrictedKeySet, const enum HydrogenTreatment treatment);
   void OutputSPList();
   int CountNumbersInBondsList();

src/Fragmentation/Fragmentation.cpp

@@ -64 +64 @@
  * \param _mol molecule for internal use (looking up atoms)
  * \param _FileChecker instance contains adjacency parsed from elsewhere
- * \param _saturation whether to treat hydrogen special and saturate dangling bonds or not
- */
-Fragmentation::Fragmentation(molecule *_mol, AdjacencyList &_FileChecker, const enum HydrogenSaturation _saturation) :
+ * \param _treatment whether to treat hydrogen special and saturate dangling bonds or not
+ */
+Fragmentation::Fragmentation(molecule *_mol, AdjacencyList &_FileChecker, const enum HydrogenTreatment _treatment) :
   mol(_mol),
-  saturation(_saturation),
+  treatment(_treatment),
   FileChecker(_FileChecker)
 {}
@@ -109 +109 @@
 
   LOG(0, std::endl);
-  switch (saturation) {
-    case DoSaturate:
-      LOG(0, "I will treat hydrogen special and saturate dangling bonds with it.");
+  switch (treatment) {
+    case ExcludeHydrogen:
+      LOG(0, "I will treat hydrogen special.");
       break;
-    case DontSaturate:
+    case IncludeHydrogen:
       LOG(0, "Hydrogen is treated just like the rest of the lot.");
       break;
     default:
-      ASSERT(0, "Fragmentation::FragmentMolecule() - there is a saturation setting which I have no idea about.");
+      ASSERT(0, "Fragmentation::FragmentMolecule() - there is a HydrogenTreatment setting which I have no idea about.");
       break;
   }
@@ -137 +137 @@
   for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
     // remove in hydrogen and we do saturate
-    if ((saturation == DoSaturate) && ((*iter)->getType()->getAtomicNumber() == 1)) // skip hydrogen
+    if ((treatment == ExcludeHydrogen) && ((*iter)->getType()->getAtomicNumber() == 1)) // skip hydrogen
       AtomMask.setFalse((*iter)->getNr());
   }
@@ -258 +258 @@
 
       // Create list of Graphs of current Bond Order (i.e. F_{ij})
-      NumMoleculesOfOrder[RootNr] = PSG(CompleteMolecule, saturation);
+      NumMoleculesOfOrder[RootNr] = PSG(CompleteMolecule, treatment);
 
       // output resulting number
@@ -309 +309 @@
     c = (ListOfBonds.size() > c) ? ListOfBonds.size() : c;
   }
-  FragmentCount = (saturation == DoSaturate ? mol->getNoNonHydrogen() : mol->getAtomCount()) *(1 << (c*order));
+  FragmentCount = (treatment == ExcludeHydrogen ? mol->getNoNonHydrogen() : mol->getAtomCount()) *(1 << (c*order));
   LOG(1, "Upper limit for this subgraph is " << FragmentCount << " for "
       << mol->getNoNonHydrogen() << " non-H atoms with maximum bond degree of " << c << ".");
@@ -466 +466 @@
     const atom * const Father = (*iter)->GetTrueFather();
     if (AtomMask.isTrue(Father->getNr())) // apply mask
-      if ((saturation == DontSaturate) || ((*iter)->getType()->getAtomicNumber() != 1)) // skip hydrogen
+      if ((treatment == IncludeHydrogen) || ((*iter)->getType()->getAtomicNumber() != 1)) // skip hydrogen
         RootStack.push_front((*iter)->getNr());
   }

src/Fragmentation/Fragmentation.hpp

@@ -34 +34 @@
 {
 public:
-  Fragmentation(molecule *_mol, AdjacencyList &_FileChecker, const enum HydrogenSaturation _saturation);
+  Fragmentation(
+      molecule *_mol,
+      AdjacencyList &_FileChecker,
+      const enum HydrogenTreatment _treatment);
   ~Fragmentation();
 
@@ -61 +64 @@
   //!> pointer to molecule that is fragmented
   molecule *mol;
-  //!> whether to saturate dangling bonds with hydrogen and hence treat hydrogen special
-  const enum HydrogenSaturation saturation;
+  //!> whether to treat hydrogen special
+  const enum HydrogenTreatment treatment;
   //!> reference to an external adjacency for comparison
   AdjacencyList &FileChecker;

src/Fragmentation/HydrogenSaturation_enum.hpp

@@ -19 +19 @@
 };
 
+enum HydrogenTreatment {
+  ExcludeHydrogen, //!< exclude hydrogen from the bond graph, i.e. fragmentation treats hydrogen special
+  IncludeHydrogen,   //!< include hydrogen from the bond graph, i.e. fragmentation treats hydrogen just as the rest
+};
+
 
 #endif /* HYDROGENSATURATION_ENUM_HPP_ */

src/Fragmentation/PowerSetGenerator.cpp

@@ -191 +191 @@
  * 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
+ * \param treatment 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, const enum HydrogenSaturation saturation)
+int PowerSetGenerator::operator()(KeySet &RestrictedKeySet, const enum HydrogenTreatment treatment)
 {
   int Counter = FragmentSearch->FragmentCounter; // mark current value of counter
@@ -205 +205 @@
 
   // do a BFS search to fill the SP lists and label the found vertices
-  BondsPerSPList.FillSPListandLabelVertices(FragmentSearch->getRoot()->GetTrueFather()->getNr(), RestrictedKeySet, saturation);
+  BondsPerSPList.FillSPListandLabelVertices(FragmentSearch->getRoot()->GetTrueFather()->getNr(), RestrictedKeySet, treatment);
 
   // outputting all list for debugging

src/Fragmentation/PowerSetGenerator.hpp

@@ -30 +30 @@
 
   void SPFragmentGenerator(int RootDistance, std::vector<bond::ptr > &BondsSet, int SetDimension, int SubOrder);
-  int operator()(KeySet &RestrictedKeySet, const enum HydrogenSaturation saturation);
+  int operator()(KeySet &RestrictedKeySet, const enum HydrogenTreatment treatment);
   void RemoveAllTouchedFromSnakeStack(int verbosity, KeySet *FragmentSet, int *&TouchedList, int &TouchedIndex);
   int FillBondsList(std::vector<bond::ptr > &BondsList, std::list<bond::ptr >::const_iterator SetFirst, std::list<bond::ptr >::const_iterator SetLast, int *&TouchedList, int TouchedIndex);

src/Graph/CyclicStructureAnalysis.cpp

@@ -46 +46 @@
 #include "molecule.hpp"
 
-CyclicStructureAnalysis::CyclicStructureAnalysis(const enum HydrogenSaturation _saturation) :
-  saturation(_saturation)
+CyclicStructureAnalysis::CyclicStructureAnalysis(const enum HydrogenTreatment _treatment) :
+  treatment(_treatment)
 {}
 
@@ -117 +117 @@
       if ((*Runner) != BackEdge) { // only walk along DFS spanning tree (otherwise we always find SP of one being backedge Binder)
         OtherAtom = (*Runner)->GetOtherAtom(Walker);
-        if ((saturation == DontSaturate) || (OtherAtom->getType()->getAtomicNumber() != 1)) {
+        if ((treatment == IncludeHydrogen) || (OtherAtom->getType()->getAtomicNumber() != 1)) {
           LOG(2, "INFO: Current OtherAtom is: " << OtherAtom->getName() << " for bond " << *(*Runner) << "." << endl);
           if (ColorList[OtherAtom->getNr()] == GraphEdge::white) {

src/Graph/CyclicStructureAnalysis.hpp

@@ -29 +29 @@
 {
 public:
-  explicit CyclicStructureAnalysis(const enum HydrogenSaturation _saturation);
+  explicit CyclicStructureAnalysis(const enum HydrogenTreatment _treatment);
   ~CyclicStructureAnalysis();
 
@@ -60 +60 @@
 
   //!> whether to treat hydrogen special or not
-  const enum HydrogenSaturation saturation;
+  const enum HydrogenTreatment treatment;
 
   bool BackStepping;

src/molecule.hpp

@@ -268 +268 @@
   void Align(Vector *n);
   void Scale(const double ** const factor);
-  void DeterminePeriodicCenter(Vector &center, const enum HydrogenSaturation _saturation = DoSaturate);
+  void DeterminePeriodicCenter(Vector &center, const enum HydrogenTreatment _treatment = ExcludeHydrogen);
   Vector * DetermineCenterOfGravity() const;
   Vector * DetermineCenterOfAll() const;

src/molecule_geometry.cpp

@@ -371 +371 @@
 /** Determines center of molecule (yet not considering atom masses).
  * \param center reference to return vector
- * \param saturation whether to treat hydrogen special or not
- */
-void molecule::DeterminePeriodicCenter(Vector &center, const enum HydrogenSaturation saturation)
+ * \param treatment whether to treat hydrogen special or not
+ */
+void molecule::DeterminePeriodicCenter(Vector &center, const enum HydrogenTreatment treatment)
 {
   const RealSpaceMatrix &matrix = World::getInstance().getDomain().getM();
@@ -387 +387 @@
     flag = true;
     for (const_iterator iter = begin(); iter != end(); ++iter) {
-      if ((saturation == DontSaturate) || ((*iter)->getType()->getAtomicNumber() != 1)) {
+      if ((treatment == IncludeHydrogen) || ((*iter)->getType()->getAtomicNumber() != 1)) {
         Testvector = inversematrix * (*iter)->getPosition();
         Translationvector.Zero();
@@ -413 +413 @@
         Center += Testvector;
         LOG(1, "vector is: " << Testvector);
-        if (saturation == DoSaturate) {
+        if (treatment == ExcludeHydrogen) {
           // now also change all hydrogens
           for (BondList::const_iterator Runner = ListOfBonds.begin();

tests/Python/AllActions/options.dat

@@ -66 +66 @@
 elements        "1 8"
 end-step        "1"
+ExcludeHydrogen "1"
 fastparsing     "1"
 filename        "test.exttypes"