Changeset f96874 for src/Fragmentation

Timestamp:

Oct 26, 2012, 1:24:01 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:

f7307f

Parents:

6d551c

git-author:

Frederik Heber <heber@…> (09/07/12 09:14:32)

git-committer:

Frederik Heber <heber@…> (10/26/12 13:24:01)

Message:

AtomMask is now a set, inherited into own class.

• this is preparatory for multiple molecules fragmentation. Otherwise AtomMask would always have size of total system.
• introduced template Mask class and added MoleculeMask for masking molecules.

Location:

src/Fragmentation

Files:

• AdaptivityMap.cpp (modified) (3 diffs)
• AdaptivityMap.hpp (modified) (2 diffs)
• AtomMask.hpp (added)
• Fragmentation.cpp (modified) (7 diffs)
• Fragmentation.hpp (modified) (2 diffs)
• Makefile.am (modified) (2 diffs)
• Mask.hpp (added)
• MoleculeMask.hpp (added)
• fragmentation_helpers.cpp (modified) (3 diffs)
• fragmentation_helpers.hpp (modified) (1 diff)

src/Fragmentation/AdaptivityMap.cpp

@@ -42 +42 @@
 
 #include "Atom/atom.hpp"
+#include "Fragmentation/AtomMask.hpp"
 #include "Helpers/defs.hpp"
 #include "Helpers/helpers.hpp"
@@ -191 +192 @@
 /** Marks all candidate sites for update if below adaptive threshold.
  * Picks a given number of highest values and set *AtomMask to true.
- * \param *AtomMask defines true/false per global Atom::Nr to mask in/out each nuclear site, used to activate given number of site to increment order adaptively
+ * \param AtomMask defines true/false per global Atom::Nr to mask in/out each nuclear site, used to activate given number of site to increment order adaptively
  * \param Order desired order
  * \param *mol molecule with atoms
  * \return true - if update is necessary, false - not
  */
-bool AdaptivityMap::MarkUpdateCandidates(bool *AtomMask, int Order, molecule *mol) const
+bool AdaptivityMap::MarkUpdateCandidates(AtomMask_t &AtomMask, int Order, molecule *mol) const
 {
   atom *Walker = NULL;
@@ -208 +209 @@
     //if (Walker->AdaptiveOrder < MinimumRingSize[Walker->getNr()]) {
       LOG(2, "Root " << No << " is still above threshold (10^{" << Order <<"}: " << runner->first << ", setting entry " << No << " of Atom mask to true.");
-      AtomMask[No] = true;
+      AtomMask.setTrue(No);
       status = true;
     //} else

src/Fragmentation/AdaptivityMap.hpp

@@ -21 +21 @@
 #include "Fragmentation/KeySet.hpp"
 
+class AtomMask_t;
 class molecule;
 
@@ -33 +34 @@
   void ReMapAdaptiveCriteriaListToValue(molecule *mol);
   int CountLinesinFile(std::ifstream &InputFile) const;
-  bool MarkUpdateCandidates(bool *AtomMask, int Order, molecule *mol) const ;
+  bool MarkUpdateCandidates(AtomMask_t &AtomMask, int Order, molecule *mol) const ;
 
   bool IsAdaptiveCriteriaListEmpty() const;

src/Fragmentation/Fragmentation.cpp

@@ -46 +46 @@
 #include "Element/periodentafel.hpp"
 #include "Fragmentation/AdaptivityMap.hpp"
+#include "Fragmentation/AtomMask.hpp"
 #include "Fragmentation/fragmentation_helpers.hpp"
 #include "Fragmentation/Graph.hpp"
@@ -107 +108 @@
   Graph TotalGraph;     // graph with all keysets however local numbers
   int TotalNumberOfKeySets = 0;
-  bool *AtomMask = NULL;
+  AtomMask_t AtomMask;
 
   LOG(0, endl);
@@ -170 +171 @@
   // ===== 6b. prepare and go into the adaptive (Order<0), single-step (Order==0) or incremental (Order>0) cycle
   KeyStack *RootStack = new KeyStack[Subgraphs->next->Count()];
-  AtomMask = new bool[mol->getAtomCount()+1];
-  AtomMask[mol->getAtomCount()] = false;
   FragmentationToDo = false;  // if CheckOrderAtSite just ones recommends fragmentation, we will save fragments afterwards
-  while ((CheckOrder = CheckOrderAtSite(AtomMask, &ParsedFragmentList, Order, prefix))) {
+  bool LoopDoneAlready = false;
+  while ((CheckOrder = CheckOrderAtSite(AtomMask, &ParsedFragmentList, Order, prefix, LoopDoneAlready))) {
     FragmentationToDo = FragmentationToDo || CheckOrder;
-    AtomMask[mol->getAtomCount()] = true;   // last plus one entry is used as marker that we have been through this loop once already in CheckOrderAtSite()
+    LoopDoneAlready = 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), saturation);
@@ -197 +197 @@
   LOG(2, "CheckOrder is " << CheckOrder << ".");
   delete[](RootStack);
-  delete[](AtomMask);
 
   // ==================================== End of FRAGMENTATION ============================================
@@ -479 +478 @@
 
 /** Checks whether the OrderAtSite is still below \a Order at some site.
- * \param *AtomMask defines true/false per global Atom::Nr to mask in/out each nuclear site, used to activate given number of site to increment order adaptively
+ * \param AtomMask defines true/false per global Atom::Nr to mask in/out each nuclear site, used to activate given number of site to increment order adaptively
  * \param *GlobalKeySetList list of keysets with global ids (valid in "this" molecule) needed for adaptive increase
  * \param Order desired Order if positive, desired exponent in threshold criteria if negative (0 is single-step)
  * \param path path to ENERGYPERFRAGMENT file (may be NULL if Order is non-negative)
+ * \param LoopDoneAlready indicate whether we have done a fragmentation loop already
  * \return true - needs further fragmentation, false - does not need fragmentation
  */
-bool Fragmentation::CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, std::string path)
+bool Fragmentation::CheckOrderAtSite(AtomMask_t &AtomMask, Graph *GlobalKeySetList, int Order, std::string path, bool LoopDoneAlready)
 {
   bool status = false;
 
   // initialize mask list
-  for(int i=mol->getAtomCount();i--;)
-    AtomMask[i] = false;
+  AtomMask.clear();
 
   if (Order < 0) { // adaptive increase of BondOrder per site
-    if (AtomMask[mol->getAtomCount()] == true)  // break after one step
+    if (LoopDoneAlready)  // break after one step
       return false;
 
@@ -515 +514 @@
         if ((saturation == DontSaturate) || ((*iter)->getType()->getAtomicNumber() != 1)) // skip hydrogen
         {
-          AtomMask[(*iter)->getNr()] = true;  // include all (non-hydrogen) atoms
+          AtomMask.setTrue((*iter)->getNr());  // include all (non-hydrogen) atoms
           status = true;
         }
@@ -528 +527 @@
       if ((saturation == DontSaturate) || ((*iter)->getType()->getAtomicNumber() != 1)) // skip hydrogen
       {
-        AtomMask[(*iter)->getNr()] = true;  // include all (non-hydrogen) atoms
+        AtomMask.setTrue((*iter)->getNr());  // include all (non-hydrogen) atoms
         if ((Order != 0) && ((*iter)->AdaptiveOrder < Order)) // && ((*iter)->AdaptiveOrder < MinimumRingSize[(*iter)->getNr()]))
           status = true;
       }
     }
-    if ((!Order) && (!AtomMask[mol->getAtomCount()]))  // single stepping, just check
+    if ((!Order) && (!LoopDoneAlready))  // single stepping, just check
       status = true;
 

src/Fragmentation/Fragmentation.hpp

@@ -25 +25 @@
 
 class atom;
+class AtomMask_t;
 class Graph;
 class KeySet;
@@ -47 +48 @@
 
   // order at site
-  bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, std::string path);
+  bool CheckOrderAtSite(AtomMask_t &AtomMask, Graph *GlobalKeySetList, int Order, std::string path, bool LoopDoneAlready);
   bool StoreOrderAtSiteFile(std::string &path);
   bool ParseOrderAtSiteFromFile(std::string &path);

src/Fragmentation/Makefile.am

@@ -20 +20 @@
 FRAGMENTATIONHEADER = \
         Fragmentation/AdaptivityMap.hpp \
+        Fragmentation/AtomMask.hpp \
         Fragmentation/BondsPerShortestPath.hpp \
         Fragmentation/defs.hpp \
@@ -34 +35 @@
         Fragmentation/KeySetsContainer.hpp \
         Fragmentation/MatrixContainer.hpp \
+        Fragmentation/Mask.hpp \
+        Fragmentation/MoleculeMask.hpp \
         Fragmentation/PowerSetGenerator.hpp \
         Fragmentation/UniqueFragments.hpp

src/Fragmentation/fragmentation_helpers.cpp

@@ -45 +45 @@
 #include "Element/element.hpp"
 #include "Fragmentation/AdaptivityMap.hpp"
+#include "Fragmentation/AtomMask.hpp"
 #include "Fragmentation/Graph.hpp"
 #include "Fragmentation/KeySet.hpp"
@@ -54 +55 @@
 
 /** print atom mask for debugging.
- * \param *out output stream for debugging
- * \param *AtomMask defines true/false per global Atom::Nr to mask in/out each nuclear site, used to activate given number of site to increment order adaptively
+ * \param AtomMask defines true/false per global Atom::Nr to mask in/out each nuclear site, used to activate given number of site to increment order adaptively
  * \param AtomCount number of entries in \a *AtomMask
  */
-void PrintAtomMask(bool *AtomMask, int AtomCount)
+void PrintAtomMask(const AtomMask_t &AtomMask, int AtomCount)
 {
   {
@@ -71 +71 @@
     output << "Atom mask is: ";
     for(int i=0;i<AtomCount;i++)
-      output << (AtomMask[i] ? "t" : "f");
+      output << AtomMask.printBit(i);
     LOG(2, output.str());
   }

src/Fragmentation/fragmentation_helpers.hpp

@@ -22 +22 @@
 typedef std::deque<int> KeyStack;
 
+class AtomMask_t;
 class Graph;
 class KeySet;
 class molecule;
 
-void PrintAtomMask(bool *AtomMask, int AtomCount);
+void PrintAtomMask(const AtomMask_t &AtomMask, int AtomCount);
 
 int CombineAllOrderListIntoOne(Graph *&FragmentList, Graph ***FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol);