Changeset 2e7888 for src/Graph/BondGraph.hpp

Timestamp:

Dec 26, 2025, 9:39:01 PM (2 days ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.7.1, stable

Children:

47ebb2

Parents:

802a9d

git-author:

Frederik Heber <frederik.heber@…> (11/24/25 11:45:10)

git-committer:

Frederik Heber <frederik.heber@…> (12/26/25 21:39:01)

Message:

Adds computed bond table.

• The bond table is complete for all elements up to Calcium with exception of the noble gases.
• Bromium included because it's needed for Fragmentation test cases.
• NOTE: bondtable needs to include all elements consecutively without gaps. Hence, added a log of "-1" where no bond length is known.
• calculated at theory level CLHF, STO-3G basis set, excluding noble gases up until element "Br".
• adds README.me to explain how they have been created.

File:

• src/Graph/BondGraph.hpp (modified) (1 diff)

src/Graph/BondGraph.hpp

@@ -194 +194 @@
     // get all elements
     const std::set< const element *> PresentElements = getElementSetFromNumbers(elements);
+    LOG(2, "INFO: Present elememts are " << PresentElements << ".");
 
     // count atoms in molecule = dimension of matrix (also give each unique name and continuous numbering)
     const unsigned int counter = Set.size();
     if (counter > 1) {
-      LOG(1, "STATUS: Setting max bond distance.");
-      LOG(1, "STATUS: Creating LinkedCell structure for given " << counter << " atoms.");
-      LinkedCell::LinkedCell_View LC = getLinkedCell(getMaxPossibleBondDistance(PresentElements));
+      const double linkedCellLength = getMaxPossibleBondDistance(PresentElements) + BondThreshold;
+      LOG(1, "STATUS: Using max bond distance plus threshold as linked cell edge length of " << linkedCellLength << ".");
+      LOG(1, "STATUS: Creating LinkedCell structure for givenlinkedCellLength" << counter << " atoms.");
+      LinkedCell::LinkedCell_View LC = getLinkedCell(linkedCellLength);
+
 
       LOG(1, "STATUS: Evaluating distance criterion for each atom.");