Changeset 461e93 for molecuilder

Timestamp:

May 8, 2008, 4:18:07 PM (17 years ago)

Author:

Frederik Heber <heber@…>

Children:

a3ff7b2

Parents:

d88597

Message:

molecule::CheckOrderAtSite() returns bool and used as threshold criterium to break while in molecule::FragmentMolecule()

As we are now near the end of the switch to adaptive increase of the bond order, the first step was to increment the OrderAtSite on all sites equally. This is now implemented. CheckOrderAtSite() checks whether the order is still below the desired value at one site and if so continues. In this while-loop we fill the RootStack and call BOSSANOVA. The sequence of AssignKeySets.. and FillRootStack... was flipped for this.

Location:

molecuilder/src

Files:

• molecules.cpp (modified) (5 diffs)
• molecules.hpp (modified) (1 diff)

molecuilder/src/molecules.cpp

@@ -2139 +2139 @@
  * \param &FragmentationToDo return boolean
  * \param Order desired Order
- */
-void molecule::CheckOrderAtSite(ofstream *out, bool &FragmentationToDo, int Order)
-{
-  atom *Walker = NULL; 
-  
-  if (FragmentationToDo) { // check whether OrderAtSite is above Order everywhere
-    FragmentationToDo = false;
-    Walker = start;
-    while (Walker->next != end) {
-      Walker = Walker->next;
+ * \return true - needs further fragmentation, false - does not need fragmentation
+ */
+bool molecule::CheckOrderAtSite(ofstream *out, int Order)
+{
+  atom *Walker = NULL;
+  bool status = false;
+  
+  Walker = start;
+  while (Walker->next != end) {
+    Walker = Walker->next;
 #ifdef ADDHYDROGEN
-      if (Walker->type->Z != 1) // skip hydrogen
+    if (Walker->type->Z != 1) // skip hydrogen
 #endif
-        if (Walker->AdaptiveOrder < Order)
-          FragmentationToDo = true;
-    }
-    if (!FragmentationToDo)
-      *out << Verbose(1) << "Order at every site is already equal or above desired order " << Order << "." << endl;
-  } else
-    *out << Verbose(1) << "Parsing order at site file failed" << endl;
+      if (Walker->AdaptiveOrder < Order)
+        status = true;
+  }
+  if (!status)
+    *out << Verbose(1) << "Order at every site is already equal or above desired order " << Order << "." << endl;
+ 
+  return status;
 };
 
@@ -2234 +2234 @@
 #endif
 
-  // ++++++++++++++++++++++++++++ INITIAL STUFF: Bond structure analysis, ... ++++++++++++++++++++++++++++++++++++++++++
+  // ++++++++++++++++++++++++++++ INITIAL STUFF: Bond structure analysis, file parsing, ... ++++++++++++++++++++++++++++++++++++++++++
   
   // ===== 1. Check whether bond structure is same as stored in files ====
@@ -2258 +2258 @@
   // ===== 4. check globally whether there's something to do actually (first adaptivity check)
   FragmentationToDo = FragmentationToDo && ParseOrderAtSiteFromFile(out, configuration->configpath);
-  CheckOrderAtSite(out, FragmentationToDo, Order);
   
   // =================================== Begin of FRAGMENTATION =============================== 
@@ -2265 +2264 @@
     *out << Verbose(0) << "Bond order " << Order << " greater than or equal to Minimum Ring size of " << MinimumRingSize << " found is not allowed." << endl;
   } else {
-    // ===== 6a. fill RootStack for each subgraph (second adaptivity check) ===== 
-    // NOTE: (keep this extern of following while loop, as lateron we may here look for which site to add to which subgraph)
-    // fill the root stack
+    // ===== 6a. assign each keyset to its respective subgraph ===== 
+    Subgraphs->next->AssignKeySetsToFragment(out, this, ParsedFragmentList, ListOfLocalAtoms, FragmentList, (FragmentCounter = 0), false);
+    delete(ParsedFragmentList);
+
     KeyStack *RootStack = new KeyStack[Subgraphs->next->Count()];
-    Subgraphs->next->FillRootStackForSubgraphs(out, RootStack, Order, (FragmentCounter = 0));
-
-   // ===== 6b. assign each keyset to its respective subgraph ===== 
-    Subgraphs->next->AssignKeySetsToFragment(out, this, ParsedFragmentList, ListOfLocalAtoms, FragmentList, (FragmentCounter = 0), false);
-
-   // ===== 7. fill the bond fragment list =====
-    FragmentCounter = 0;
-    MolecularWalker = Subgraphs;
-    while (MolecularWalker->next != NULL) {
-      MolecularWalker = MolecularWalker->next;
-      *out << Verbose(1) << "Fragmenting subgraph " << MolecularWalker << "." << endl;
-      // output ListOfBondsPerAtom for debugging
-      MolecularWalker->Leaf->OutputListOfBonds(out);
-      if (MolecularWalker->Leaf->first->next != MolecularWalker->Leaf->last) {
-      
-        // call BOSSANOVA method
-        *out << Verbose(0) << endl << " ========== BOND ENERGY of subgraph " << FragmentCounter << " ========================= " << endl;
-        MolecularWalker->Leaf->FragmentBOSSANOVA(out, FragmentList[FragmentCounter], RootStack[FragmentCounter]);
-      } else {
-        cerr << "Subgraph " << MolecularWalker << " has no atoms!" << endl;
-      }
-      FragmentCounter++;  // next fragment list
-    }
+    while (CheckOrderAtSite(out, Order)) {
+      // ===== 6b. fill RootStack for each subgraph (second adaptivity check) ===== 
+      Subgraphs->next->FillRootStackForSubgraphs(out, RootStack, Order, (FragmentCounter = 0));
+
+      // ===== 7. fill the bond fragment list =====
+      FragmentCounter = 0;
+      MolecularWalker = Subgraphs;
+      while (MolecularWalker->next != NULL) {
+        MolecularWalker = MolecularWalker->next;
+        *out << Verbose(1) << "Fragmenting subgraph " << MolecularWalker << "." << endl;
+        // output ListOfBondsPerAtom for debugging
+        MolecularWalker->Leaf->OutputListOfBonds(out);
+        if (MolecularWalker->Leaf->first->next != MolecularWalker->Leaf->last) {
+        
+          // call BOSSANOVA method
+          *out << Verbose(0) << endl << " ========== BOND ENERGY of subgraph " << FragmentCounter << " ========================= " << endl;
+          MolecularWalker->Leaf->FragmentBOSSANOVA(out, FragmentList[FragmentCounter], RootStack[FragmentCounter]);
+        } else {
+          cerr << "Subgraph " << MolecularWalker << " has no atoms!" << endl;
+        }
+        FragmentCounter++;  // next fragment list
+      }
+    }
+    delete[](RootStack);
   }
   
@@ -2305 +2306 @@
   
   // free subgraph memory again
-  delete(ParsedFragmentList);
   FragmentCounter = 0;
   if (Subgraphs != NULL) {

molecuilder/src/molecules.hpp

@@ -340 +340 @@
   /// Fragment molecule by two different approaches:
   void FragmentMolecule(ofstream *out, int Order, config *configuration);
-  void CheckOrderAtSite(ofstream *out, bool &FragmentationToDo, int Order);
+  bool CheckOrderAtSite(ofstream *out, int Order);
   bool StoreAdjacencyToFile(ofstream *out, char *path);
   bool CheckAdjacencyFileAgainstMolecule(ofstream *out, char *path, atom **ListOfAtoms);