MoleculeStamp.hpp

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 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the following paper when you publish your work:
 *
 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
 *
 * Good starting points for code and simulation methodology are:
 *
 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
 */
 
#ifndef TYPES_MOLECULESTAMP_HPP
#define TYPES_MOLECULESTAMP_HPP
 
#include <utility>
#include <vector>
 
#include "types/AtomStamp.hpp"
#include "types/BendStamp.hpp"
#include "types/BondStamp.hpp"
#include "types/ConstraintStamp.hpp"
#include "types/CutoffGroupStamp.hpp"
#include "types/FragmentStamp.hpp"
#include "types/InversionStamp.hpp"
#include "types/RigidBodyStamp.hpp"
#include "types/TorsionStamp.hpp"
 
namespace OpenMD {
  class MoleculeStamp : public DataHolder {
    DeclareParameter(Name, std::string);
    DeclareParameter(ConstrainTotalCharge, bool);
 
  public:
    MoleculeStamp();
    virtual ~MoleculeStamp();
 
    bool addAtomStamp(AtomStamp* atom);
    bool addBondStamp(BondStamp* bond);
    bool addBendStamp(BendStamp* bend);
    bool addTorsionStamp(TorsionStamp* torsion);
    bool addInversionStamp(InversionStamp* inversion);
    bool addRigidBodyStamp(RigidBodyStamp* rigidbody);
    bool addCutoffGroupStamp(CutoffGroupStamp* cutoffgroup);
    bool addFragmentStamp(FragmentStamp* fragment);
    bool addConstraintStamp(ConstraintStamp* constraint);
 
    void setIdent(int id) { ident_ = id; }
    int getIdent() { return ident_; }
 
    void setRegion(int r) { region_ = r; }
    int getRegion() { return region_; }
 
    std::size_t getNAtoms() { return atomStamps_.size(); }
    std::size_t getNBonds() { return bondStamps_.size(); }
    std::size_t getNBends() { return bendStamps_.size(); }
    std::size_t getNTorsions() { return torsionStamps_.size(); }
    std::size_t getNInversions() { return inversionStamps_.size(); }
    std::size_t getNRigidBodies() { return rigidBodyStamps_.size(); }
    std::size_t getNCutoffGroups() { return cutoffGroupStamps_.size(); }
    std::size_t getNConstraints() { return constraintStamps_.size(); }
    int getNIntegrable() { return nintegrable_; }
    std::size_t getNFreeAtoms() { return freeAtoms_.size(); }
    virtual void validate();
 
    AtomStamp* getAtomStamp(int index) { return atomStamps_[index]; }
    BondStamp* getBondStamp(int index) { return bondStamps_[index]; }
    BendStamp* getBendStamp(int index) { return bendStamps_[index]; }
    TorsionStamp* getTorsionStamp(int index) { return torsionStamps_[index]; }
    InversionStamp* getInversionStamp(int index) {
      return inversionStamps_[index];
    }
    RigidBodyStamp* getRigidBodyStamp(int index) {
      return rigidBodyStamps_[index];
    }
    CutoffGroupStamp* getCutoffGroupStamp(int index) {
      return cutoffGroupStamps_[index];
    }
    FragmentStamp* getFragmentStamp(int index) {
      return fragmentStamps_[index];
    }
    ConstraintStamp* getConstraintStamp(int index) {
      return constraintStamps_[index];
    }
 
    bool isBondInSameRigidBody(BondStamp* bond);
    bool isAtomInRigidBody(int atomIndex);
    bool isAtomInRigidBody(int atomIndex, int& whichRigidBody,
                           int& consAtomIndex);
    std::vector<std::pair<int, int>> getJointAtoms(int rb1, int rb2);
 
  private:
    void fillBondInfo();
    void checkAtoms();
    void checkBonds();
    void checkBends();
    void checkTorsions();
    void checkInversions();
    void checkRigidBodies();
    void checkCutoffGroups();
    void checkFragments();
    void checkConstraints();
 
    template<class Cont, class T>
    bool addIndexSensitiveStamp(Cont& cont, T* stamp) {
      // typename Cont::iterator i;
      unsigned int index = stamp->getIndex();
      bool ret           = false;
      size_t size        = cont.size();
 
      if (size >= index + 1) {
        if (cont[index] != NULL) {
          ret = false;
        } else {
          cont[index] = stamp;
          ret         = true;
        }
      } else {
        cont.insert(cont.end(), index - cont.size() + 1, NULL);
        cont[index] = stamp;
        ret         = true;
      }
 
      return ret;
    }
 
    std::vector<AtomStamp*> atomStamps_;
    std::vector<int> freeAtoms_;
    std::vector<BondStamp*> bondStamps_;
    std::vector<BendStamp*> bendStamps_;
    std::vector<TorsionStamp*> torsionStamps_;
    std::vector<InversionStamp*> inversionStamps_;
    std::vector<RigidBodyStamp*> rigidBodyStamps_;
    std::vector<CutoffGroupStamp*> cutoffGroupStamps_;
    std::vector<FragmentStamp*> fragmentStamps_;
    std::vector<ConstraintStamp*> constraintStamps_;
    std::vector<int> atom2Rigidbody;
    int nintegrable_;
    int region_;
    int ident_;
  };
 
  class MoleculeStampCompare {
  public:
    bool operator()(MoleculeStamp* lhs, MoleculeStamp* rhs) const {
      return lhs->getIdent() < rhs->getIdent();
    }
  };
 
  using MoleculeStampSet = std::set<MoleculeStamp*, MoleculeStampCompare>;
}  // namespace OpenMD
 
#endif