ReplacementVisitor.hpp

/*
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 * POSSIBILITY OF SUCH DAMAGE.
 *
 * 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 VISITORS_REPLACEMENTVISITOR_HPP
#define VISITORS_REPLACEMENTVISITOR_HPP
 
#include <memory>
#include <set>
 
#include "visitors/AtomVisitor.hpp"
 
namespace OpenMD {
 
  /**
   * @class ReplacementVisitor
   *
   * Replaces an atomic object with a collection atomic sites.  These
   * sites are specified with reference location to the object, as well as
   * a name.
   */
  class ReplacementVisitor : public BaseAtomVisitor {
  public:
    using BaseVisitor::visit;
    ReplacementVisitor(SimInfo* info) : BaseAtomVisitor(info) {
      visitorName = "ReplacementVisitor";
      sites_      = std::make_shared<AtomData>();
    }
 
    void visit(Atom*) {}
    void visit(DirectionalAtom* datom);
    void visit(RigidBody*) {}
 
    const std::string toString();
 
    void addReplacedAtomName(const std::string& repName);
    void addSite(const std::string& name, const Vector3d& refPos);
    void addSite(const std::string& name, const Vector3d& refPos,
                 const Vector3d& refVec);
 
  private:
    inline bool isReplacedAtom(const std::string& atomType);
    std::set<std::string> myTypes_;
    std::shared_ptr<AtomData> sites_;
  };
 
  class SSDAtomVisitor : public ReplacementVisitor {
  public:
    using BaseVisitor::visit;
    SSDAtomVisitor(SimInfo* info) : ReplacementVisitor(info) {
      visitorName = "SSDAtomVisitor";
 
      /// these are the atom names we can replace with a fixed structure
      addReplacedAtomName("SSD");
      addReplacedAtomName("SSD_E");
      addReplacedAtomName("SSD_RF");
      addReplacedAtomName("SSD1");
      addReplacedAtomName("SSDQ");
      addReplacedAtomName("SSDQO");
      addReplacedAtomName("TAP");
      addReplacedAtomName("TRED");
 
      // this is the reference structure we'll use for the replacement:
      addSite("H", Vector3d(0.0, -0.75695, 0.5206));
      addSite("H", Vector3d(0.0, 0.75695, 0.5206));
      addSite("O", Vector3d(0.0, 0.0, -0.0654));
      addSite("X", Vector3d(0.0, 0.0, 0.0), Vector3d(0, 0, 1));
    }
  };
 
  class GBtailVisitor : public ReplacementVisitor {
  public:
    using BaseVisitor::visit;
    GBtailVisitor(SimInfo* info) : ReplacementVisitor(info) {
      visitorName = "GBtailVisitor";
 
      /// these are the atom names we can replace with a fixed structure
      addReplacedAtomName("GBtail");
 
      // this is the reference structure we'll use for the replacement:
      addSite("C", Vector3d(0.0, 0.0, 9.0));
      addSite("C", Vector3d(0.0, 0.0, 0.0));
      addSite("C", Vector3d(0.0, 0.0, -9.0));
    }
  };
 
  class GBheadVisitor : public ReplacementVisitor {
  public:
    using BaseVisitor::visit;
    GBheadVisitor(SimInfo* info) : ReplacementVisitor(info) {
      visitorName = "GBheadVisitor";
 
      /// these are the atom names we can replace with a fixed structure
      addReplacedAtomName("GBhead");
 
      // this is the reference structure we'll use for the replacement:
      addSite("N", Vector3d(0.0, 0.0, 3.5));
      addSite("C", Vector3d(0.0, 0.0, 0.0));
      addSite("P", Vector3d(0.0, 0.0, -3.5));
    }
  };
}  // namespace OpenMD
 
#endif