Changeset 38bcbe

Timestamp:

Apr 23, 2021, 8:43:27 PM (5 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.7.0, stable

Children:

ea30e6

Parents:

4de4f6

git-author:

Frederik Heber <frederik.heber@…> (10/04/20 21:45:25)

git-committer:

Frederik Heber <frederik.heber@…> (04/23/21 20:43:27)

Message:

StretchBondAction will used tabled distances when given distance is less or equal zero.

Files:

• doc/userguide/userguide.xml (modified) (1 diff)
• src/Actions/MoleculeAction/StretchBondAction.cpp (modified) (1 diff)
• src/Bond/StretchBond.cpp (modified) (2 diffs)
• src/Graph/BondGraph.hpp (modified) (2 diffs)

doc/userguide/userguide.xml

@@ -1277 +1277 @@
             undo).</para>
           </warning>
+          <note>The action will uses typical bond distances, taken from
+          <link linkend='bond.create-adjacency'>bond-table</link> to scale
+          the bond length if the desired bond length is non-positive.</note>
         </section>
         <section xml:id="bond.change-bond-angle">

src/Actions/MoleculeAction/StretchBondAction.cpp

@@ -62 +62 @@
   const std::vector< atom *> atoms = World::getInstance().getSelectedAtoms();
   StretchBondUtil stretcher(atoms);
-  bool status = stretcher(params.bonddistance.get());
+
+  const double bonddistance = params.bonddistance.get();
+  bool status = stretcher(bonddistance);
 
   if (status) {

src/Bond/StretchBond.cpp

@@ -51 +51 @@
 #include "Descriptors/AtomIdDescriptor.hpp"
 #include "Descriptors/MoleculeIdDescriptor.hpp"
+#include "Element/element.hpp"
+#include "Graph/BondGraph.hpp"
 #include "Graph/BoostGraphCreator.hpp"
 #include "Graph/BreadthFirstSearchGatherer.hpp"
@@ -93 +95 @@
 }
 
-bool StretchBondUtil::operator()(const double newdistance)
+bool StretchBondUtil::operator()(double newdistance)
 {
+  if (newdistance <= 0.) {
+    // get typical distance from table
+    BondGraph *&BG = World::getInstance().getBondGraph();
+    newdistance = BG->GetBondLength(
+        atoms[0]->getElementNo(),
+        atoms[1]->getElementNo());
+    LOG(1, "INFO: Using typical bond distance of " << newdistance
+        << " between " << atoms[0]->getElement().getSymbol() << " and "
+        << atoms[1]->getElement().getSymbol() << ".");
+  }
+
   const Vector NormalVector = (atoms[0]->getPosition() - atoms[1]->getPosition())* (1./olddistance);
   const double shift = 0.5*(newdistance - olddistance);

src/Graph/BondGraph.hpp

@@ -414 +414 @@
   }
 
-private:
-  /** Convenience function to place access to World::getLinkedCell() into source module.
-   *
-   * @return ref to LinkedCell_View
-   */
-  LinkedCell::LinkedCell_View getLinkedCell(const double max_distance) const;
-
-  /** Convenience function to place access to World::getDomain() into source module.
-   *
-   * @return ref to Box
-   */
-  Box &getDomain() const;
-
-  /** Convenience function to place access to WorldTime::getTime() into source module.
-   *
-   * @return current time step
-   */
-  unsigned int getTime() const;
-
   /** Returns the BondLengthMatrix entry for a given index pair.
    * \param firstelement index/atom number of first element (row index)
@@ -441 +422 @@
       int firstelement,
       int secondelement) const;
+
+private:
+  /** Convenience function to place access to World::getLinkedCell() into source module.
+   *
+   * @return ref to LinkedCell_View
+   */
+  LinkedCell::LinkedCell_View getLinkedCell(const double max_distance) const;
+
+  /** Convenience function to place access to World::getDomain() into source module.
+   *
+   * @return ref to Box
+   */
+  Box &getDomain() const;
+
+  /** Convenience function to place access to WorldTime::getTime() into source module.
+   *
+   * @return current time step
+   */
+  unsigned int getTime() const;
 
   /** Returns bond criterion for given pair based on a bond length matrix.