Piece wise remove topology item

include/votca/csg/basebead.h

@@ -14,11 +14,10 @@
  * limitations under the License.
  *
  */
-#pragma once
 #ifndef VOTCA_CSG_BASEBEAD_H
 #define VOTCA_CSG_BASEBEAD_H
+#pragma once
 
-#include "topologyitem.h"
 #include <assert.h>
 #include <memory>
 #include <votca/tools/constants.h>
@@ -74,9 +73,6 @@ class BaseBead {
    */
   Index getMoleculeId() const noexcept { return molecule_id_; }
 
-  /// Gets the topology pointer the bead is attached too
-  Topology *getParent() const { return topology_item_.getParent(); }
-
   /**
    * get the bead type
    * \return const string
@@ -141,8 +137,6 @@ class BaseBead {
  protected:
   BaseBead(){};
 
-  TopologyItem topology_item_ = nullptr;
-
   std::string type_ = tools::topology_constants::unassigned_bead_type;
   Index id_ = tools::topology_constants::unassigned_residue_id;
   Index molecule_id_ = tools::topology_constants::unassigned_molecule_id;

include/votca/csg/bead.h

@@ -15,8 +15,9 @@
  *
  */
 
-#ifndef _VOTCA_CSG_BEAD_H
-#define _VOTCA_CSG_BEAD_H
+#ifndef VOTCA_CSG_BEAD_H
+#define VOTCA_CSG_BEAD_H
+#pragma once
 
 #include <assert.h>
 #include <cassert>
@@ -289,10 +290,9 @@ class Bead : public BaseBead {
   bool bead_force_set_;
 
   /// constructor
-  Bead(Topology *owner, Index id, std::string type, Symmetry symmetry,
-       std::string name, Index resnr, double m, double q)
+  Bead(Index id, std::string type, Symmetry symmetry, std::string name,
+       Index resnr, double m, double q)
       : symmetry_(symmetry), charge_(q), residue_number_(resnr) {
-    topology_item_._parent = owner;
     setId(id);
     setType(type);
     setName(name);
@@ -372,4 +372,4 @@ inline void Bead::HasW(bool b) { bW_ = b; }
 }  // namespace csg
 }  // namespace votca
 
-#endif  // _VOTCA_CSG_BEAD_H
+#endif  // VOTCA_CSG_BEAD_H

include/votca/csg/boundarycondition.h

@@ -14,9 +14,9 @@
  * limitations under the License.
  *
  */
-#pragma once
 #ifndef VOTCA_CSG_BOUNDARYCONDITION_H
 #define VOTCA_CSG_BOUNDARYCONDITION_H
+#pragma once
 
 #include <memory>
 #include <votca/tools/eigen.h>
@@ -62,6 +62,14 @@ class BoundaryCondition {
    */
   const Eigen::Matrix3d &getBox() const noexcept { return _box; };
 
+  /**
+   * @brief Self explanatory gets the shortest dimension of the boundary
+   * conditions
+   *
+   * @return
+   */
+  double getShortestBoxDimension() const;
+
   /**
    * get the volume of the box
    * \return box volume as double

include/votca/csg/interaction.h

@@ -15,8 +15,9 @@
  *
  */
 
-#ifndef _VOTCA_CSG_INTERACTION_H
-#define _VOTCA_CSG_INTERACTION_H
+#pragma once
+#ifndef VOTCA_CSG_INTERACTION_H
+#define VOTCA_CSG_INTERACTION_H
 
 #include "bead.h"
 #include "topology.h"
@@ -79,8 +80,8 @@ class Interaction {
   }
 
   virtual Eigen::Vector3d Grad(const Topology &top, Index bead) = 0;
-  Index BeadCount() { return _beads.size(); }
-  Index getBeadId(Index bead) {
+  Index BeadCount() const { return _beads.size(); }
+  Index getBeadId(Index bead) const {
     assert(bead > -1 && boost::lexical_cast<size_t>(bead) < _beads.size());
     return _beads[bead];
   }
@@ -321,4 +322,4 @@ inline Eigen::Vector3d IDihedral::Grad(const Topology &top, Index bead) {
 }  // namespace csg
 }  // namespace votca
 
-#endif  // _VOTCA_CSG_INTERACTION_H
+#endif  // VOTCA_CSG_INTERACTION_H

include/votca/csg/map.h

@@ -15,9 +15,11 @@
  *
  */
 
-#ifndef _VOTCA_CSG_MAP_H
-#define _VOTCA_CSG_MAP_H
+#ifndef VOTCA_CSG_MAP_H
+#define VOTCA_CSG_MAP_H
+#pragma once
 
+#include "boundarycondition.h"
 #include "molecule.h"
 #include <vector>
 #include <votca/tools/eigen.h>
@@ -37,7 +39,7 @@ class Map {
 
   void AddBeadMap(BeadMap *bmap) { _maps.push_back(bmap); }
 
-  void Apply();
+  void Apply(const BoundaryCondition &bc);
 
  protected:
   Molecule _in, _out;
@@ -50,7 +52,7 @@ class Map {
 class BeadMap {
  public:
   virtual ~BeadMap() = default;
-  virtual void Apply() = 0;
+  virtual void Apply(const BoundaryCondition &) = 0;
   virtual void Initialize(Molecule *in, Bead *out, tools::Property *opts_map,
                           tools::Property *opts_bead);
 
@@ -76,7 +78,7 @@ inline void BeadMap::Initialize(Molecule *in, Bead *out,
 class Map_Sphere : public BeadMap {
  public:
   Map_Sphere() = default;
-  void Apply() override;
+  void Apply(const BoundaryCondition &) override;
 
   void Initialize(Molecule *in, Bead *out, tools::Property *opts_bead,
                   tools::Property *opts_map) override;
@@ -106,12 +108,12 @@ inline void Map_Sphere::AddElem(Bead *in, double weight, double force_weight) {
 class Map_Ellipsoid : public Map_Sphere {
  public:
   Map_Ellipsoid() = default;
-  void Apply() override;
+  void Apply(const BoundaryCondition &) override;
 
  protected:
 };
 
 }  // namespace csg
 }  // namespace votca
 
-#endif /* _VOTCA_CSG_MAP_H */
+#endif  // VOTCA_CSG_MAP_H

include/votca/csg/molecule.h

@@ -15,11 +15,11 @@
  *
  */
 
-#ifndef _VOTCA_CSG_MOLECULE_H
-#define _VOTCA_CSG_MOLECULE_H
+#pragma once
+#ifndef VOTCA_CSG_MOLECULE_H
+#define VOTCA_CSG_MOLECULE_H
 
 #include "bead.h"
-#include "topologyitem.h"
 #include <assert.h>
 #include <map>
 #include <string>
@@ -39,7 +39,7 @@ class Interaction;
     \todo sort atoms in molecule
 
 */
-class Molecule : public TopologyItem {
+class Molecule {
  public:
   /// get the molecule ID
   Index getId() const { return _id; }
@@ -98,8 +98,7 @@ class Molecule : public TopologyItem {
   void *_userdata;
 
   /// constructor
-  Molecule(Topology *parent, Index id, std::string name)
-      : TopologyItem(parent), _id(id), _name(name) {}
+  Molecule(Index id, std::string name) : _id(id), _name(name) {}
 
   friend class Topology;
 };
@@ -117,4 +116,4 @@ inline Index Molecule::getBeadIdByName(const std::string &name) {
 }  // namespace csg
 }  // namespace votca
 
-#endif /* _VOTCA_CSG_MOLECULE_H */
+#endif  // VOTCA_CSG_MOLECULE_H

include/votca/csg/residue.h

@@ -14,11 +14,10 @@
  * limitations under the License.
  *
  */
+#pragma once
+#ifndef VOTCA_CSG_RESIDUE_H
+#define VOTCA_CSG_RESIDUE_H
 
-#ifndef _VOTCA_CSG_RESIDUE_H
-#define _VOTCA_CSG_RESIDUE_H
-
-#include "topologyitem.h"
 #include <string>
 
 namespace votca {
@@ -32,7 +31,7 @@ namespace csg {
    based on their residue.
 
 */
-class Residue : public TopologyItem {
+class Residue {
  public:
   /// get the name of the residue
   const std::string &getName();
@@ -46,8 +45,7 @@ class Residue : public TopologyItem {
 
  private:
   /// constructor
-  Residue(Topology *parent, Index id, const std::string &name)
-      : TopologyItem(parent), _id(id), _name(name) {}
+  Residue(Index id, const std::string &name) : _id(id), _name(name) {}
   friend class Topology;
 };
 
@@ -56,4 +54,4 @@ inline const std::string &Residue::getName() { return _name; }
 }  // namespace csg
 }  // namespace votca
 
-#endif /* _VOTCA_CSG_RESIDUE_H */
+#endif  // VOTCA_CSG_RESIDUE_H

include/votca/csg/topology.h

@@ -15,8 +15,9 @@
  *
  */
 
-#ifndef _VOTCA_CSG_TOPOLOGY_H
-#define _VOTCA_CSG_TOPOLOGY_H
+#ifndef VOTCA_CSG_TOPOLOGY_H
+#define VOTCA_CSG_TOPOLOGY_H
+#pragma once
 
 #include <cassert>
 #include <list>
@@ -25,7 +26,6 @@
 #include <vector>
 
 #include "bead.h"
-#include "beadtype.h"
 #include "boundarycondition.h"
 #include "exclusionlist.h"
 #include "molecule.h"
@@ -176,6 +176,9 @@ class Topology {
    * @return bonded interaction container
    */
   InteractionContainer &BondedInteractions() { return _interactions; }
+  const InteractionContainer &BondedInteractions() const {
+    return _interactions;
+  }
 
   void AddBondedInteraction(Interaction *ic);
   std::list<Interaction *> InteractionsInGroup(const std::string &group);
@@ -289,6 +292,13 @@ class Topology {
    */
   const Eigen::Matrix3d &getBox() const { return _bc->getBox(); };
 
+  /**
+   * @brief Return the boundary condition object
+   */
+  const BoundaryCondition &getBoundary() const {
+    assert(_bc != nullptr && "Cannot return boundary condition is null");
+    return *_bc;
+  };
   /**
    * set the time of current frame
    * \param t simulation time in ns
@@ -427,25 +437,25 @@ inline Bead *Topology::CreateBead(Bead::Symmetry symmetry, std::string name,
                                   std::string type, Index resnr, double m,
                                   double q) {
 
-  Bead *b = new Bead(this, _beads.size(), type, symmetry, name, resnr, m, q);
+  Bead *b = new Bead(_beads.size(), type, symmetry, name, resnr, m, q);
   _beads.push_back(b);
   return b;
 }
 
 inline Molecule *Topology::CreateMolecule(std::string name) {
-  Molecule *mol = new Molecule(this, _molecules.size(), name);
+  Molecule *mol = new Molecule(_molecules.size(), name);
   _molecules.push_back(mol);
   return mol;
 }
 
 inline Residue *Topology::CreateResidue(std::string name, Index id) {
-  Residue *res = new Residue(this, id, name);
+  Residue *res = new Residue(id, name);
   _residues.push_back(res);
   return res;
 }
 
 inline Residue *Topology::CreateResidue(std::string name) {
-  Residue *res = new Residue(this, _residues.size(), name);
+  Residue *res = new Residue(_residues.size(), name);
   _residues.push_back(res);
   return res;
 }
@@ -464,4 +474,4 @@ inline void Topology::InsertExclusion(Bead *bead1, iteratable &l) {
 
 #include "interaction.h"
 
-#endif /* _VOTCA_CSG_TOPOLOGY_H */
+#endif  // VOTCA_CSG_TOPOLOGY_H