Changeset 9f55b9

Timestamp:

Apr 23, 2021, 8:34:22 PM (5 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.7.0, stable

Children:

4de4f6

Parents:

f3eb6a

git-author:

Frederik Heber <frederik.heber@…> (10/04/20 20:13:46)

git-committer:

Frederik Heber <frederik.heber@…> (04/23/21 20:34:22)

Message:

Extracted functor StretchBondUtil from StretchBondAction.

Location:

src

Files:

• Actions/MoleculeAction/StretchBondAction.cpp (modified) (3 diffs)
• Bond/StretchBond.cpp (added)
• Bond/StretchBond.hpp (added)
• Graph/BoostGraphHelpers.hpp (modified) (1 diff)
• Makefile.am (modified) (2 diffs)

src/Actions/MoleculeAction/StretchBondAction.cpp

@@ -39 +39 @@
 #include <boost/bind.hpp>
 
-#include "CodePatterns/Assert.hpp"
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
@@ -47 +46 @@
 #include "Atom/atom.hpp"
 #include "Bond/bond.hpp"
-#include "Descriptors/AtomIdDescriptor.hpp"
-#include "Graph/BoostGraphCreator.hpp"
+#include "Bond/StretchBond.hpp"
 #include "Graph/BoostGraphHelpers.hpp"
-#include "Graph/BreadthFirstSearchGatherer.hpp"
-#include "molecule.hpp"
 #include "World.hpp"
 
@@ -61 +57 @@
 
 
-static bool addEdgePredicate(
-    const bond &_bond,
-    const std::vector<atomId_t> &_atomids)
-{
-  ASSERT(_atomids.size() == (size_t)2,
-      "addEdgePredicate() - atomids must contain exactly two ids.");
-  // do not add selected edge
-  return ((_bond.leftatom->getId() != _atomids[0])
-      || (_bond.rightatom->getId() != _atomids[1]));
-}
-
 /** =========== define the function ====================== */
 ActionState::ptr MoleculeStretchBondAction::performCall()
 {
-  // check preconditions
   const std::vector< atom *> atoms = World::getInstance().getSelectedAtoms();
-  if (atoms.size() != 2) {
-    STATUS("Exactly two atoms must be selected.");
+  StretchBondUtil stretcher(atoms);
+  bool status = stretcher(params.bonddistance.get());
+
+  if (status) {
+    MoleculeStretchBondState *UndoState =
+        new MoleculeStretchBondState(
+            stretcher.getShift(),
+            stretcher.getBondSides(),
+            &stretcher.getMolecule(),
+            params);
+    return ActionState::ptr(UndoState);
+  } else {
+    STATUS("Failed, exactly two atoms must be selected.");
     return Action::failure;
   }
-  molecule *mol = World::getInstance().
-      getMolecule(MoleculeById(atoms[0]->getMolecule()->getId()));
-  if (mol != atoms[1]->getMolecule()) {
-    STATUS("The two selected atoms must belong to the same molecule.");
-    return Action::failure;
-  }
-
-  // gather undo information
-  const double olddistance = atoms[0]->getPosition().distance(atoms[1]->getPosition());
-  const double newdistance = params.bonddistance.get();
-  LOG(1, "INFO: Old bond distance is " << olddistance << ", stretching to " << newdistance << ".");
-
-  // gather sorted ids
-  std::vector<atomId_t> atomids(2);
-  atomids[0] = atoms[0]->getId();
-  atomids[1] = atoms[1]->getId();
-  std::sort(atomids.begin(), atomids.end());
-  LOG(1, "DEBUG: Selected nodes are " << atomids);
-
-  const Vector NormalVector = (atoms[0]->getPosition() - atoms[1]->getPosition())* (1./olddistance);
-  const double shift = 0.5*(newdistance - olddistance);
-  std::vector<Vector> Shift(2);
-  Shift[0] = shift * NormalVector;
-  Shift[1] = -shift * NormalVector;
-  Box &domain = World::getInstance().getDomain();
-
-  // Assume the selected bond splits the molecule into two parts, each one on
-  // either side of the bond. We need to perform a BFS from each bond partner
-  // not using the selected bond. Therefrom, we obtain two sets of atoms/nodes.
-  // If both are disjoint, the bond is not contained in a cycle and we simply
-  // shift either set as desired. If not, then we simply shift each atom,
-  // leaving the other positions untouched.
-
-  // get nodes on either side of selected bond via BFS discovery
-  BoostGraphCreator BGcreator;
-  BGcreator.createFromMolecule(*mol,
-      boost::bind(addEdgePredicate, _1, boost::ref(atomids)));
-  BreadthFirstSearchGatherer NodeGatherer(BGcreator);
-  std::vector< BoostGraphHelpers::Nodeset_t > bondside_sets(2);
-  for(size_t j=0;j<2;++j) {
-    bondside_sets[j] = NodeGatherer(atoms[j]->getId());
-    std::sort(bondside_sets[j].begin(), bondside_sets[j].end());
-  }
-
-  // simple test whether bond has split the system in two disjoint sets or not
-  bool isCyclic = false;
-  if ((bondside_sets[0].size() + bondside_sets[1].size()) > BGcreator.getNumVertices()) {
-      // Check whether there are common nodes in each set of distances
-    if (BoostGraphHelpers::isCommonNodeInVector(bondside_sets[0], bondside_sets[1])) {
-      ELOG(2, "Sets contain common node, hence bond must have been by cyclic."
-          << " Shifting only bond partners.");
-      for(size_t j=0;j<2;++j) {
-        bondside_sets[j].clear();
-        bondside_sets[j].push_back( atomids[j] );
-        const Vector &position = atoms[j]->getPosition();
-        atoms[j]->setPosition( domain.enforceBoundaryConditions(position+Shift[j]) );
-      }
-      isCyclic = true;
-    }
-  }
-
-  // go through the molecule and stretch each atom in either set of nodes
-  if (!isCyclic) {
-    for (molecule::iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-      const Vector &position = (*iter)->getPosition();
-      // for each atom determine in which set of nodes it is and shift accordingly
-      const atomId_t &atomid = (*iter)->getId();
-      if (std::binary_search(bondside_sets[0].begin(), bondside_sets[0].end(), atomid)) {
-        (*iter)->setPosition( domain.enforceBoundaryConditions(position+Shift[0]) );
-      } else if (std::binary_search(bondside_sets[1].begin(), bondside_sets[1].end(), atomid)) {
-        (*iter)->setPosition( domain.enforceBoundaryConditions(position+Shift[1]) );
-      } else {
-        ELOG(1, "Atom " << *iter << " is not contained on either side of bond? Undoing done shifts");
-        // Have to undo shifts
-        for (size_t i=0;i<2;++i) {
-          for (BoostGraphHelpers::Nodeset_t::const_iterator iter = bondside_sets[i].begin();
-              iter != bondside_sets[i].end(); ++iter) {
-            atom &walker = *World::getInstance().getAtom(AtomById(*iter));
-            const Vector &position = walker.getPosition();
-            walker.setPosition( domain.enforceBoundaryConditions(position-Shift[i]) );
-          }
-        }
-        return Action::failure;
-      }
-    }
-  }
-
-  MoleculeStretchBondState *UndoState = new MoleculeStretchBondState(Shift, bondside_sets, mol, params);
-  return ActionState::ptr(UndoState);
 }
 

src/Graph/BoostGraphHelpers.hpp

@@ -16 +16 @@
 
 #include <vector>
+
+#include "types.hpp"
 
 namespace BoostGraphHelpers {

src/Makefile.am

@@ -33 +33 @@
         Bond/bond_observable.cpp \
         Bond/BondInfo.cpp \
-        Bond/GraphEdge.cpp
+        Bond/GraphEdge.cpp \
+        Bond/StretchBond.cpp
 
 BONDHEADER = \
@@ -39 +40 @@
         Bond/bond_observable.hpp \
         Bond/BondInfo.hpp \
-        Bond/GraphEdge.hpp
+        Bond/GraphEdge.hpp \
+        Bond/StretchBond.hpp
 
 DESCRIPTORSOURCE = \