Piece wize basebead

include/votca/csg/basebead.h

@@ -14,16 +14,15 @@
  * limitations under the License.
  *
  */
-
-#ifndef _VOTCA_CSG_BASEBEAD_H
-#define _VOTCA_CSG_BASEBEAD_H
+#pragma once
+#ifndef VOTCA_CSG_BASEBEAD_H
+#define VOTCA_CSG_BASEBEAD_H
 
 #include <assert.h>
 #include <memory>
-#include <votca/csg/moleculeitem.h>
 #include <votca/csg/topologyitem.h>
+#include <votca/tools/constants.h>
 #include <votca/tools/eigen.h>
-#include <votca/tools/identity.h>
 #include <votca/tools/name.h>
 #include <votca/tools/types.h>
 namespace TOOLS = votca::tools;
@@ -47,22 +46,33 @@ class BaseBead {
   virtual ~BaseBead() = default;
 
   /// Gets the id of the bead
-  Index getId() const { return id_.getId(); }
+  Index getId() const noexcept { return id_; }
 
   /// Sets the id of the bead
-  void setId(Index id) { id_.setId(id); }
+  void setId(const Index &id) noexcept { id_ = id; }
 
   /// Gets the name of the bead
   std::string getName() const { return name_.getName(); }
 
   /// Sets the name of the bead
   void setName(std::string name) { return name_.setName(name); }
 
-  /// Sets the molecule the bead is attached too
-  void setMolecule(Molecule *molecule) { molecule_item_.setMolecule(molecule); }
+  /**
+   * @brief assign the bead to a molecule with the provided id
+   *
+   * @param molecule_id
+   */
+  void setMoleculeId(const Index &molecule_id) noexcept {
+    molecule_id_ = molecule_id;
+  }
 
-  /// Gets the molecule pointer the bead is attached too
-  Molecule *getMolecule() const { return molecule_item_.getMolecule(); }
+  /**
+   * @brief Get the id of the molecule the bead is a part of, if the molecule
+   * id has not been set return topology_constants::unassigned_molecule_id
+   *
+   * @return
+   */
+  Index getMoleculeId() const noexcept { return molecule_id_; }
 
   /// Gets the topology pointer the bead is attached too
   Topology *getParent() const { return topology_item_.getParent(); }
@@ -71,25 +81,33 @@ class BaseBead {
    * get the bead type
    * \return const string
    */
-  virtual const std::string getType() const { return type_.getName(); }
+  virtual const std::string getType() const noexcept { return type_; }
 
   /**
    * set the bead type
    * \param bead type object
    */
-  virtual void setType(std::string type) { type_.setName(type); }
+  virtual void setType(const std::string &type) noexcept { type_ = type; }
+
+  /**
+   * @brief Returns the element type of the bead
+   *
+   * @return either the element symbol i.e. "Si" for silcon or unassigned if it
+   * has not been specified.
+   */
+  std::string getElement() const noexcept { return element_symbol_; }
 
   /**
    * get the mass of the base bead
    * \return - base bead mass
    */
-  virtual const double &getMass() const { return mass_; }
+  virtual const double &getMass() const noexcept { return mass_; }
 
   /**
    * set the mass of the base bead
    * \param - base bead mass
    */
-  virtual void setMass(const double &m) { mass_ = m; }
+  virtual void setMass(const double &m) noexcept { mass_ = m; }
 
   /**
    * set the position of the base bead
@@ -113,24 +131,23 @@ class BaseBead {
   }
 
   /** does this configuration store positions? */
-  bool HasPos() const { return bead_position_set_; }
+  bool HasPos() const noexcept { return bead_position_set_; }
 
   /** set has position to true */
-  void HasPos(bool true_or_false) { bead_position_set_ = true_or_false; }
+  void HasPos(const bool &true_or_false) noexcept {
+    bead_position_set_ = true_or_false;
+  }
 
  protected:
-  BaseBead()
-      : topology_item_(nullptr),
-        molecule_item_(nullptr),
-        mass_(0.0),
-        bead_position_set_(false){};
+  BaseBead() : topology_item_(nullptr), mass_(0.0), bead_position_set_(false){};
 
   TopologyItem topology_item_;
-  MoleculeItem molecule_item_;
 
-  TOOLS::Identity<Index> id_;
+  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;
+  std::string element_symbol_ = tools::topology_constants::unassigned_element;
   TOOLS::Name name_;
-  TOOLS::Name type_;
 
   double mass_;
   Eigen::Vector3d bead_position_;
@@ -151,4 +168,4 @@ inline const Eigen::Vector3d &BaseBead::getPos() const {
 }  // namespace csg
 }  // namespace votca
 
-#endif  // _VOTCA_CSG_BASEBEAD_H
+#endif  // VOTCA_CSG_BASEBEAD_H

src/libcsg/exclusionlist.cc

@@ -49,7 +49,7 @@ void ExclusionList::CreateExclusions(Topology *top) {
 
 bool ExclusionList::IsExcluded(Bead *bead1, Bead *bead2) {
   exclusion_t *excl;
-  if (bead1->getMolecule() != bead2->getMolecule()) {
+  if (bead1->getMoleculeId() != bead2->getMoleculeId()) {
     return false;
   }
   if (bead2->getId() < bead1->getId()) {

src/libcsg/map.cc

@@ -168,8 +168,7 @@ void Map_Sphere::Apply() {
             ", " + bead->getName() + " (id " +
             boost::lexical_cast<string>(bead->getId() + 1) + ")" +
             +" , molecule " +
-            boost::lexical_cast<string>(bead->getMolecule()->getId() + 1) +
-            ")");
+            boost::lexical_cast<string>(bead->getMoleculeId() + 1) + ")");
       }
       cg += iter._weight * (r + r0);
       bPos = true;

src/libcsg/modules/io/lammpsdatareader.cc

@@ -480,7 +480,7 @@ void LAMMPSDataReader::ReadAtoms_(Topology &top) {
                          residue_index, mass, charge);
 
       mol->AddBead(b, bead_type_name);
-      b->setMolecule(mol);
+      b->setMoleculeId(mol->getId());
 
     } else {
       b = top.getBead(atomIndex - startingIndex);
@@ -533,7 +533,7 @@ void LAMMPSDataReader::ReadBonds_(Topology &top) {
       ic->setGroup("BONDS");
       ic->setIndex(bondId);
       auto b = top.getBead(atom1Index);
-      auto mi = b->getMolecule();
+      auto mi = top.getMolecule(b->getMoleculeId());
       ic->setMolecule(atomIdToMoleculeId_[atom1Index]);
       top.AddBondedInteraction(ic);
       mi->AddInteraction(ic);
@@ -591,7 +591,7 @@ void LAMMPSDataReader::ReadAngles_(Topology &top) {
       ic->setGroup("ANGLES");
       ic->setIndex(angleId);
       auto b = top.getBead(atom1Index);
-      auto mi = b->getMolecule();
+      auto mi = top.getMolecule(b->getMoleculeId());
       ic->setMolecule(atomIdToMoleculeId_[atom1Index]);
       top.AddBondedInteraction(ic);
       mi->AddInteraction(ic);
@@ -662,7 +662,7 @@ void LAMMPSDataReader::ReadDihedrals_(Topology &top) {
       ic->setGroup("DIHEDRALS");
       ic->setIndex(dihedralId);
       auto b = top.getBead(atom1Index);
-      auto mi = b->getMolecule();
+      auto mi = top.getMolecule(b->getMoleculeId());
       ic->setMolecule(atomIdToMoleculeId_[atom1Index]);
       top.AddBondedInteraction(ic);
       mi->AddInteraction(ic);

src/libcsg/molecule.cc

@@ -28,7 +28,7 @@ void Molecule::AddBead(Bead *bead, const string &name) {
   _bead_names.push_back(name);
   _beadmap[name] = _beads.size() - 1;
 
-  bead->setMolecule(this);
+  bead->setMoleculeId(_id);
 }
 
 long Molecule::getBeadByName(const string &name) {

src/tests/test_basebead.cc

@@ -68,10 +68,7 @@ BOOST_AUTO_TEST_CASE(test_basebead_getters_setters) {
   BOOST_CHECK_EQUAL(xyz3.isApprox(xyz_ref, 1e-5), true);
 
   Topology top;
-  auto mol = top.CreateMolecule("Molecule1");
-  basebead.setMolecule(mol);
-  auto mol2 = basebead.getMolecule();
-  bool molecules_equal = mol2->getName() == "Molecule1";
-  BOOST_CHECK(molecules_equal);
+  basebead.setMoleculeId(0);
+  BOOST_CHECK_EQUAL(basebead.getMoleculeId(), 0);
 }
 BOOST_AUTO_TEST_SUITE_END()

src/tests/test_bead.cc

@@ -94,7 +94,7 @@ BOOST_AUTO_TEST_CASE(test_bead_setters) {
   string molecule_name = "TestMol";
   Molecule *mol = top.CreateMolecule(molecule_name);
 
-  b->setMolecule(mol);
+  b->setMoleculeId(mol->getId());
 
   BOOST_CHECK_CLOSE(b->getMass(), newMass, 1e-5);
   BOOST_CHECK_CLOSE(b->getQ(), newCharge, 1e-5);
@@ -104,9 +104,7 @@ BOOST_AUTO_TEST_CASE(test_bead_setters) {
   auto new_xyz_vel = b->getVel();
   BOOST_CHECK(new_xyz_vel.isApprox(xyz_vel, 1e-7));
 
-  auto mol_new = b->getMolecule();
-  bool same = !(molecule_name.compare(mol_new->getName()));
-  BOOST_CHECK(same);
+  BOOST_CHECK_EQUAL(b->getMoleculeId(), mol->getId());
 }
 
 BOOST_AUTO_TEST_SUITE_END()

src/tests/test_nblist_3body.cc

@@ -64,7 +64,6 @@ BOOST_AUTO_TEST_CASE(test_nblist_3body_generate_list) {
                      charge);
   b->setPos(pos);
   mol->AddBead(b, bead_type_name);
-  b->setMolecule(mol);
 
   name = "dummy2";
   resnr = 0;
@@ -73,7 +72,6 @@ BOOST_AUTO_TEST_CASE(test_nblist_3body_generate_list) {
   b = top.CreateBead(Bead::spherical, name, bead_type_name, resnr, mass,
                      charge);
   mol->AddBead(b, bead_type_name);
-  b->setMolecule(mol);
   pos = Eigen::Vector3d::UnitX();
   b->setPos(pos);
 
@@ -84,7 +82,6 @@ BOOST_AUTO_TEST_CASE(test_nblist_3body_generate_list) {
   b = top.CreateBead(Bead::spherical, name, bead_type_name, resnr, mass,
                      charge);
   mol->AddBead(b, bead_type_name);
-  b->setMolecule(mol);
   pos[0] = 1.0;
   pos[1] = 1.0;
   pos[2] = 0.0;

src/tests/test_nblistgrid_3body.cc

@@ -66,7 +66,6 @@ BOOST_AUTO_TEST_CASE(test_nblist_3body_generate_list) {
   pos[2] = 0.0;
   b->setPos(pos);
   mol->AddBead(b, bead_type_name);
-  b->setMolecule(mol);
 
   name = "dummy2";
   resnr = 0;
@@ -75,7 +74,6 @@ BOOST_AUTO_TEST_CASE(test_nblist_3body_generate_list) {
   b = top.CreateBead(Bead::spherical, name, bead_type_name, resnr, mass,
                      charge);
   mol->AddBead(b, bead_type_name);
-  b->setMolecule(mol);
   pos[0] = 1.0;
   pos[1] = 0.0;
   pos[2] = 0.0;
@@ -88,7 +86,6 @@ BOOST_AUTO_TEST_CASE(test_nblist_3body_generate_list) {
   b = top.CreateBead(Bead::spherical, name, bead_type_name, resnr, mass,
                      charge);
   mol->AddBead(b, bead_type_name);
-  b->setMolecule(mol);
   pos[0] = 1.0;
   pos[1] = 1.0;
   pos[2] = 0.0;