SPFForceManager.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 OPENMD_RNEMD_SPFFORCEMANAGER_HPP
#define OPENMD_RNEMD_SPFFORCEMANAGER_HPP
 
#include <config.h>
 
#include <cmath>
#include <memory>
 
#include "brains/ForceManager.hpp"
#include "brains/SimInfo.hpp"
#include "brains/Snapshot.hpp"
#include "brains/Thermo.hpp"
#include "math/Vector3.hpp"
#include "primitives/Molecule.hpp"
 
namespace OpenMD::RNEMD {
 
  class SPFMethod;
 
  class SPFForceManager : public ForceManager {
  public:
    SPFForceManager(SimInfo* info);
    ~SPFForceManager();
 
    void setSelectedMolecule(Molecule* selectedMolecule);
    void setDeltaLambda(RealType spfTarget);
    RealType getScaledDeltaU();
 
    bool getHasSelectedMolecule() const { return hasSelectedMolecule_; }
 
    void setHasSelectedMolecule(bool hasSelectedMolecule) {
      hasSelectedMolecule_ = hasSelectedMolecule;
    }
 
    Molecule* getSelectedMolecule() { return selectedMolecule_; }
    Snapshot getTemporarySourceSnapshot() { return *temporarySourceSnapshot_; }
    Snapshot getTemporarySinkSnapshot() { return *temporarySinkSnapshot_; }
 
    void updateSPFState() {
      combineForcesAndTorques();
      updatePotentials();
      updateVirialTensor();
    }
 
    SPFMethod* spfRNEMD_;
 
  private:
    void calcForces() override;
 
    void combineForcesAndTorques();
    void updatePotentials();
    void updateLongRangePotentials();
    void updateShortRangePotentials();
    void updateSelfPotentials();
    void updateExcludedPotentials();
    void updateRestraintPotentials();
    void updateSelectionPotentials();
    void updateVirialTensor();
 
    RealType f_lambda(RealType lambda) const {
      RealType result = std::pow(lambda, k_);
 
      return std::clamp(result, 0.0, 1.0);
    }
 
    template<typename T>
    T linearCombination(T quantityA, T quantityB) {
      RealType result = f_lambda(currentSnapshot_->getSPFData()->lambda);
 
      return T {(1.0 - result) * quantityA + result * quantityB};
    }
 
    std::unique_ptr<Thermo> thermo_ {nullptr};
 
    Snapshot* currentSnapshot_ {nullptr};
    Snapshot* temporarySourceSnapshot_ {nullptr};
    Snapshot* temporarySinkSnapshot_ {nullptr};
 
    // to preserve the Verlet Neighbor lists in source and sink snapshots:
    std::vector<int> sourceNeighborList_;
    std::vector<int> sourcePoint_;
    std::vector<Vector3d> sourceSavedPositions_;
 
    std::vector<int> sinkNeighborList_;
    std::vector<int> sinkPoint_;
    std::vector<Vector3d> sinkSavedPositions_;
 
    bool hasSelectedMolecule_ {};
 
    Molecule* selectedMolecule_ {nullptr};
    int k_ {};
 
    RealType deltaLambda_ {};
 
    RealType potentialSource_ {};
    RealType potentialSink_ {};
  };
}  // namespace OpenMD::RNEMD
 
#endif  // OPENMD_RNEMD_SPFFORCEMANAGER_HPP